diff --git a/Core/Code/Algorithms/mitkCompareImageDataFilter.cpp b/Core/Code/Algorithms/mitkCompareImageDataFilter.cpp
index 7c209d2d4a..809186c2ca 100644
--- a/Core/Code/Algorithms/mitkCompareImageDataFilter.cpp
+++ b/Core/Code/Algorithms/mitkCompareImageDataFilter.cpp
@@ -1,137 +1,140 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
// mitk includes
#include "mitkCompareImageDataFilter.h"
#include "mitkImageAccessByItk.h"
#include "mitkITKImageImport.h"
#include "mitkImageCaster.h"
#include "mitkMultiComponentImageDataComparisonFilter.h"
// itk includes
#include <itkTestingComparisonImageFilter.h>
mitk::CompareImageDataFilter::CompareImageDataFilter()
+ : m_Tolerance(0.0)
{
this->SetNumberOfRequiredInputs(2);
this->ResetCompareResultsToInitial();
}
void mitk::CompareImageDataFilter::ResetCompareResultsToInitial()
{
m_CompareDetails.m_MaximumDifference = 0.0f;
m_CompareDetails.m_MinimumDifference = itk::NumericTraits< double >::max();
m_CompareDetails.m_MeanDifference = 0.0f;
m_CompareDetails.m_TotalDifference = 0.0f;
m_CompareDetails.m_PixelsWithDifference = 0;
m_CompareDetails.m_FilterCompleted = false;
m_CompareDetails.m_ExceptionMessage = "";
}
void mitk::CompareImageDataFilter::GenerateData()
{
// check inputs
const mitk::Image* input1 = this->GetInput(0);
const mitk::Image* input2 = this->GetInput(1);
// Generally this filter is part of the mitk::Image::Equal() method and only checks the equality of the image data
// so no further image type comparison is performed!
// CAVE: If the images differ in a parameter other then the image data, the filter may fail!!
// check what number of components the inputs have
if(input1->GetPixelType().GetNumberOfComponents() == 1 &&
input2->GetPixelType().GetNumberOfComponents() == 1)
{
AccessByItk_1( input1, EstimateValueDifference, input2);
}
else if(input1->GetPixelType().GetNumberOfComponents() > 1 &&
input2->GetPixelType().GetNumberOfComponents() > 1 )
{
this->ResetCompareResultsToInitial();
MultiComponentImageDataComparisonFilter::Pointer mcComparator = MultiComponentImageDataComparisonFilter::New();
mcComparator->SetTestImage(input1);
mcComparator->SetValidImage(input2);
mcComparator->SetCompareFilterResult( &m_CompareDetails);
+ mcComparator->SetTolerance(m_Tolerance);
mcComparator->Update();
m_CompareResult = mcComparator->GetResult();
}
}
bool mitk::CompareImageDataFilter::GetResult(size_t threshold)
{
if (! m_CompareResult)
{
return false;
}
if( m_CompareDetails.m_PixelsWithDifference > threshold )
{
return false;
}
return true;
}
template< typename TPixel, unsigned int VImageDimension>
void mitk::CompareImageDataFilter::EstimateValueDifference(itk::Image< TPixel, VImageDimension>* itkImage1,
const mitk::Image* referenceImage)
{
typedef itk::Image< TPixel, VImageDimension> InputImageType;
typedef itk::Image< double, VImageDimension > OutputImageType;
typename InputImageType::Pointer itk_reference = InputImageType::New();
mitk::CastToItkImage( referenceImage,
itk_reference );
typedef itk::Testing::ComparisonImageFilter< InputImageType, OutputImageType > CompareFilterType;
typename CompareFilterType::Pointer compare_filter = CompareFilterType::New();
compare_filter->SetTestInput( itkImage1 );
compare_filter->SetValidInput( itk_reference );
+ compare_filter->SetDifferenceThreshold( m_Tolerance );
try
{
compare_filter->Update();
}
catch( const itk::ExceptionObject& e)
{
m_CompareDetails.m_FilterCompleted = false;
m_CompareDetails.m_ExceptionMessage = e.what();
MITK_WARN << e.what();
m_CompareResult = false;
return;
}
// the filter has completed the calculation
m_CompareResult = true;
m_CompareDetails.m_FilterCompleted = true;
m_CompareDetails.m_MaximumDifference = compare_filter->GetMaximumDifference();
m_CompareDetails.m_MinimumDifference = compare_filter->GetMinimumDifference();
m_CompareDetails.m_MeanDifference = compare_filter->GetMeanDifference();
m_CompareDetails.m_TotalDifference = compare_filter->GetTotalDifference();
m_CompareDetails.m_PixelsWithDifference = compare_filter->GetNumberOfPixelsWithDifferences();
mitk::Image::Pointer output = mitk::GrabItkImageMemory( compare_filter->GetOutput() );
this->SetOutput( MakeNameFromOutputIndex(0), output.GetPointer() );
}
diff --git a/Core/Code/Algorithms/mitkCompareImageDataFilter.h b/Core/Code/Algorithms/mitkCompareImageDataFilter.h
index 67fd799288..7f912e34ae 100644
--- a/Core/Code/Algorithms/mitkCompareImageDataFilter.h
+++ b/Core/Code/Algorithms/mitkCompareImageDataFilter.h
@@ -1,120 +1,123 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef MITKCOMPAREIMAGEDATAFILTER_H
#define MITKCOMPAREIMAGEDATAFILTER_H
//MITK
#include "mitkImageToImageFilter.h"
#include "mitkImage.h"
//ITK
#include <itkImage.h>
namespace mitk
{
/**
* @brief A simple struct to hold the result of the comparison filter.
*/
struct CompareFilterResults
{
void PrintSelf()
{
if( !m_FilterCompleted )
{
MITK_INFO << "Comparison filter terminated due to an exception: \n "
<< m_ExceptionMessage;
return;
}
MITK_INFO << "Min. difference: " << m_MinimumDifference <<"\n"
<< "Max. difference: " << m_MaximumDifference <<"\n"
<< "Total difference: " << m_TotalDifference <<"\n"
<< "Mean difference: " << m_MeanDifference <<"\n"
<< "Number of pixels with differences: " << m_PixelsWithDifference;
}
double m_MinimumDifference;
double m_MaximumDifference;
double m_TotalDifference;
double m_MeanDifference;
size_t m_PixelsWithDifference;
bool m_FilterCompleted;
std::string m_ExceptionMessage;
};
/**
* @brief Filter for comparing two mitk::Image objects by pixel values
*
* The comparison is pixel-wise, the filter uses the itk::Testing::ComparisonImageFilter
* to find differences. The filter expects two images as input, provide them by using the SetInput( int, mitk::Image)
* method.
*/
class MITK_CORE_EXPORT CompareImageDataFilter
: public ImageToImageFilter
{
public:
mitkClassMacro(CompareImageDataFilter,
ImageToImageFilter)
itkSimpleNewMacro(Self)
/**
* @brief Get the result of the comparison
*
* The method compares only the number of pixels with differences. It returns true if the amount
* is under the specified threshold. To get the complete results, use the GetCompareResults method.
*
* Returns false also if the itk ComparisionImageFilter raises an exception during update.
*
* @param threshold Allowed amount of pixels with differences
*/
bool GetResult(size_t threshold = 0);
/**
* @brief Get the detailed results of the comparision run
*
* @sa CompareFilterResults
*/
CompareFilterResults GetCompareResults()
{
return m_CompareDetails;
}
+ void SetTolerance(double eps){ m_Tolerance=eps; }
+
protected:
CompareImageDataFilter();
virtual ~CompareImageDataFilter() {}
virtual void GenerateData();
/*! \brief Method resets the compare detail memeber struct to its initial state */
void ResetCompareResultsToInitial();
/** ITK-like method which calls the ComparisionFilter on the two inputs of the filter */
template< typename TPixel, unsigned int VImageDimension>
void EstimateValueDifference( itk::Image< TPixel, VImageDimension>* itkImage1,
const mitk::Image* referenceImage);
bool m_CompareResult;
CompareFilterResults m_CompareDetails;
+ double m_Tolerance;
};
} // end namespace mitk
#endif // MITKCompareImageDataFilter_H
diff --git a/Core/Code/Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp b/Core/Code/Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp
index 2227af2015..56f128b04d 100644
--- a/Core/Code/Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp
+++ b/Core/Code/Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp
@@ -1,190 +1,190 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
// mitk includes
#include "mitkMultiComponentImageDataComparisonFilter.h"
#include "mitkImageReadAccessor.h"
#include "mitkImagePixelReadAccessor.h"
// other includes
// #include <omp.h>
namespace mitk
{
MultiComponentImageDataComparisonFilter::MultiComponentImageDataComparisonFilter(): ImageToImageFilter(),
m_Tolerance(0.0f), m_CompareResult(false), m_CompareDetails(NULL)
{
this->SetNumberOfRequiredInputs(2);
}
MultiComponentImageDataComparisonFilter::~MultiComponentImageDataComparisonFilter()
{
}
bool MultiComponentImageDataComparisonFilter::GetResult(double threshold)
{
if ( !m_CompareResult )
{
return false;
}
if( m_CompareDetails->m_PixelsWithDifference > threshold )
{
return false;
}
return true;
}
void MultiComponentImageDataComparisonFilter::SetValidImage( const Image *_arg )
{
this->SetInput(0, _arg);
}
void MultiComponentImageDataComparisonFilter::SetTestImage( const Image *_arg )
{
this->SetInput(1, _arg);
}
const Image* MultiComponentImageDataComparisonFilter::GetValidImage()
{
return this->GetInput(0);
}
const Image* MultiComponentImageDataComparisonFilter::GetTestImage()
{
return this->GetInput(1);
}
void MultiComponentImageDataComparisonFilter::SetCompareFilterResult( CompareFilterResults* results )
{
m_CompareDetails = results;
}
CompareFilterResults* MultiComponentImageDataComparisonFilter::GetCompareFilterResult()
{
return m_CompareDetails;
}
void MultiComponentImageDataComparisonFilter::GenerateData()
{
// check inputs
const Image* testInput = this->GetTestImage();
const Image* validInput = this->GetValidImage();
// Generally this filter is part of the mitk::Image::Equal() method and only checks the equality of the image data
// so no further image type comparison is performed!
// CAVE: If the images differ in a parameter other then the image data, the filter may fail!!
PixelType type = validInput->GetPixelType();
if(type.GetComponentType() == itk::ImageIOBase::CHAR)
{
CompareMultiComponentImage<char>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::UCHAR)
{
CompareMultiComponentImage<unsigned char>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::INT)
{
CompareMultiComponentImage<int>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::UINT)
{
CompareMultiComponentImage<unsigned int>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::SHORT)
{
CompareMultiComponentImage<short>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::USHORT)
{
CompareMultiComponentImage<unsigned short>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::LONG)
{
CompareMultiComponentImage<long>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::ULONG)
{
CompareMultiComponentImage<unsigned long>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::FLOAT)
{
CompareMultiComponentImage<float>( testInput, validInput);
}
else if (type.GetComponentType() == itk::ImageIOBase::DOUBLE)
{
CompareMultiComponentImage<double>( testInput, validInput);
}
else
{
mitkThrow() << "Pixel component type not supported!";
}
}
template <typename TPixel >
void mitk::MultiComponentImageDataComparisonFilter::CompareMultiComponentImage( const Image* testImage, const Image* validImage )
{
unsigned int noOfTimes = validImage->GetDimension(3);
unsigned int noOfPixels = validImage->GetDimension(0)*validImage->GetDimension(1)*validImage->GetDimension(2);
unsigned int noOfComponents = validImage->GetPixelType().GetNumberOfComponents();
for( unsigned int t = 0; t < noOfTimes; ++t)
{
ImageReadAccessor readAccTImage(const_cast<Image*>(testImage), const_cast<Image*>(testImage)->GetVolumeData(t));
ImageReadAccessor readAccVImage(const_cast<Image*>(validImage), const_cast<Image*>(validImage)->GetVolumeData(t));
for( unsigned int p = 0; p < noOfPixels*noOfComponents; ++p )
{
TPixel vDataItem = static_cast<TPixel*>(const_cast<void*>(readAccVImage.GetData()))[p];
TPixel tDataItem = static_cast<TPixel*>(const_cast<void*>(readAccTImage.GetData()))[p];
- if( tDataItem != vDataItem )
+ if( std::abs( static_cast<double>(tDataItem - vDataItem) )>m_Tolerance )
{
++m_CompareDetails->m_PixelsWithDifference;
m_CompareDetails->m_MaximumDifference = std::max(m_CompareDetails->m_MaximumDifference,
std::abs( static_cast<double>(tDataItem - vDataItem) ) );
double min = std::min(m_CompareDetails->m_MinimumDifference,
std::abs( static_cast<double>(tDataItem - vDataItem) ));
if(min != 0.0f) // a difference of zero is not a difference!
m_CompareDetails->m_MinimumDifference = min;
m_CompareDetails->m_TotalDifference += std::abs(static_cast<double>(tDataItem - vDataItem) );
}
}
}
if(m_CompareDetails->m_PixelsWithDifference > 0)
{
m_CompareDetails->m_MeanDifference = m_CompareDetails->m_TotalDifference / m_CompareDetails->m_PixelsWithDifference;
m_CompareResult = false;
}
else
{
m_CompareResult = true;
}
m_CompareDetails->m_FilterCompleted = true;
}
-} // end namespace mitk
\ No newline at end of file
+} // end namespace mitk
diff --git a/Core/Code/DataManagement/mitkImage.cpp b/Core/Code/DataManagement/mitkImage.cpp
index 609f527f60..ebc3148837 100644
--- a/Core/Code/DataManagement/mitkImage.cpp
+++ b/Core/Code/DataManagement/mitkImage.cpp
@@ -1,1383 +1,1384 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
//MITK
#include "mitkImage.h"
#include "mitkImageStatisticsHolder.h"
#include "mitkPixelTypeMultiplex.h"
#include <mitkProportionalTimeGeometry.h>
#include "mitkCompareImageDataFilter.h"
//VTK
#include <vtkImageData.h>
//Other
#include <cmath>
#define FILL_C_ARRAY( _arr, _size, _value) for(unsigned int i=0u; i<_size; i++) \
{ _arr[i] = _value; }
mitk::Image::Image() :
m_Dimension(0), m_Dimensions(NULL), m_ImageDescriptor(NULL), m_OffsetTable(NULL), m_CompleteData(NULL),
m_ImageStatistics(NULL)
{
m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];
FILL_C_ARRAY( m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u);
m_Initialized = false;
}
mitk::Image::Image(const Image &other) : SlicedData(other), m_Dimension(0), m_Dimensions(NULL),
m_ImageDescriptor(NULL), m_OffsetTable(NULL), m_CompleteData(NULL), m_ImageStatistics(NULL)
{
m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];
FILL_C_ARRAY( m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u);
this->Initialize( other.GetPixelType(), other.GetDimension(), other.GetDimensions());
//Since the above called "Initialize" method doesn't take the geometry into account we need to set it
//here manually
TimeGeometry::Pointer cloned = other.GetTimeGeometry()->Clone();
this->SetTimeGeometry(cloned.GetPointer());
if (this->GetDimension() > 3)
{
const unsigned int time_steps = this->GetDimension(3);
for (unsigned int i = 0u; i < time_steps; ++i)
{
ImageDataItemPointer volume = const_cast<Image&>(other).GetVolumeData(i);
this->SetVolume(volume->GetData(), i);
}
}
else
{
ImageDataItemPointer volume = const_cast<Image&>(other).GetVolumeData(0);
this->SetVolume(volume->GetData(), 0);
}
}
mitk::Image::~Image()
{
Clear();
m_ReferenceCountLock.Lock();
m_ReferenceCount = 3;
m_ReferenceCountLock.Unlock();
m_ReferenceCountLock.Lock();
m_ReferenceCount = 0;
m_ReferenceCountLock.Unlock();
if(m_OffsetTable != NULL)
delete [] m_OffsetTable;
if(m_ImageStatistics != NULL)
delete m_ImageStatistics;
}
const mitk::PixelType mitk::Image::GetPixelType(int n) const
{
return this->m_ImageDescriptor->GetChannelTypeById(n);
}
unsigned int mitk::Image::GetDimension() const
{
return m_Dimension;
}
unsigned int mitk::Image::GetDimension(int i) const
{
if((i>=0) && (i<(int)m_Dimension))
return m_Dimensions[i];
return 1;
}
void* mitk::Image::GetData()
{
if(m_Initialized==false)
{
if(GetSource().IsNull())
return NULL;
if(GetSource()->Updating()==false)
GetSource()->UpdateOutputInformation();
}
m_CompleteData=GetChannelData();
// update channel's data
// if data was not available at creation point, the m_Data of channel descriptor is NULL
// if data present, it won't be overwritten
m_ImageDescriptor->GetChannelDescriptor(0).SetData(m_CompleteData->GetData());
return m_CompleteData->GetData();
}
template <class T>
void AccessPixel( const mitk::PixelType ptype, void* data, const unsigned int offset, double& value )
{
value = 0.0;
if( data == NULL ) return;
if(ptype.GetBpe() != 24)
{
value = (double) (((T*) data)[ offset ]);
}
else
{
const unsigned int rgboffset = 3 * offset;
double returnvalue = (((T*) data)[rgboffset ]);
returnvalue += (((T*) data)[rgboffset + 1]);
returnvalue += (((T*) data)[rgboffset + 2]);
value = returnvalue;
}
}
double mitk::Image::GetPixelValueByIndex(const mitk::Index3D &position, unsigned int timestep)
{
double value = 0;
if (this->GetTimeSteps() < timestep)
{
timestep = this->GetTimeSteps();
}
value = 0.0;
const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions();
const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0);
// Comparison ?>=0 not needed since all position[i] and timestep are unsigned int
// (position[0]>=0 && position[1] >=0 && position[2]>=0 && timestep>=0)
// bug-11978 : we still need to catch index with negative values
if ( position[0] < 0 ||
position[1] < 0 ||
position[2] < 0 )
{
MITK_WARN << "Given position ("<< position << ") is out of image range, returning 0." ;
}
// check if the given position is inside the index range of the image, the 3rd dimension needs to be compared only if the dimension is not 0
else if ( (unsigned int)position[0] >= imageDims[0] ||
(unsigned int)position[1] >= imageDims[1] ||
( imageDims[2] && (unsigned int)position[2] >= imageDims[2] ))
{
MITK_WARN << "Given position ("<< position << ") is out of image range, returning 0." ;
}
else
{
const unsigned int offset = position[0] + position[1]*imageDims[0] + position[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2];
mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value );
}
return value;
}
double mitk::Image::GetPixelValueByWorldCoordinate(const mitk::Point3D& position, unsigned int timestep)
{
double value = 0.0;
if (this->GetTimeSteps() < timestep)
{
timestep = this->GetTimeSteps();
}
Index3D itkIndex;
this->GetGeometry()->WorldToIndex(position, itkIndex);
value = this->GetPixelValueByIndex( itkIndex, timestep);
return value;
}
mitk::ImageVtkAccessor* mitk::Image::GetVtkImageData(int t, int n)
{
if(m_Initialized==false)
{
if(GetSource().IsNull())
return NULL;
if(GetSource()->Updating()==false)
GetSource()->UpdateOutputInformation();
}
ImageDataItemPointer volume=GetVolumeData(t, n);
if(volume.GetPointer()==NULL || volume->GetVtkImageData(this) == NULL)
return NULL;
SlicedGeometry3D* geom3d = GetSlicedGeometry(t);
float *fspacing = const_cast<float *>(geom3d->GetFloatSpacing());
double dspacing[3] = {fspacing[0],fspacing[1],fspacing[2]};
volume->GetVtkImageData(this)->SetSpacing( dspacing );
return volume->GetVtkImageData(this);
}
mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidSlice(s,t,n)==false) return NULL;
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
// slice directly available?
int pos=GetSliceIndex(s,t,n);
if(m_Slices[pos].GetPointer()!=NULL)
return m_Slices[pos];
// is slice available as part of a volume that is available?
ImageDataItemPointer sl, ch, vol;
vol=m_Volumes[GetVolumeIndex(t,n)];
if((vol.GetPointer()!=NULL) && (vol->IsComplete()))
{
sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize));
sl->SetComplete(true);
return m_Slices[pos]=sl;
}
// is slice available as part of a channel that is available?
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
{
sl=new ImageDataItem(*ch, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize));
sl->SetComplete(true);
return m_Slices[pos]=sl;
}
// slice is unavailable. Can we calculate it?
if((GetSource().IsNotNull()) && (GetSource()->Updating()==false))
{
// ... wir mussen rechnen!!! ....
m_RequestedRegion.SetIndex(0, 0);
m_RequestedRegion.SetIndex(1, 0);
m_RequestedRegion.SetIndex(2, s);
m_RequestedRegion.SetIndex(3, t);
m_RequestedRegion.SetIndex(4, n);
m_RequestedRegion.SetSize(0, m_Dimensions[0]);
m_RequestedRegion.SetSize(1, m_Dimensions[1]);
m_RequestedRegion.SetSize(2, 1);
m_RequestedRegion.SetSize(3, 1);
m_RequestedRegion.SetSize(4, 1);
m_RequestedRegionInitialized=true;
GetSource()->Update();
if(IsSliceSet(s,t,n))
//yes: now we can call ourselves without the risk of a endless loop (see "if" above)
return GetSliceData(s,t,n,data,importMemoryManagement);
else
return NULL;
}
else
{
ImageDataItemPointer item = AllocateSliceData(s,t,n,data,importMemoryManagement);
item->SetComplete(true);
return item;
}
}
mitk::Image::ImageDataItemPointer mitk::Image::GetVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidVolume(t,n)==false) return NULL;
ImageDataItemPointer ch, vol;
// volume directly available?
int pos=GetVolumeIndex(t,n);
vol=m_Volumes[pos];
if((vol.GetPointer()!=NULL) && (vol->IsComplete()))
return vol;
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
// is volume available as part of a channel that is available?
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
{
vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize));
vol->SetComplete(true);
return m_Volumes[pos]=vol;
}
// let's see if all slices of the volume are set, so that we can (could) combine them to a volume
bool complete=true;
unsigned int s;
for(s=0;s<m_Dimensions[2];++s)
{
if(m_Slices[GetSliceIndex(s,t,n)].GetPointer()==NULL)
{
complete=false;
break;
}
}
if(complete)
{
// if there is only single slice we do not need to combine anything
if(m_Dimensions[2]<=1)
{
ImageDataItemPointer sl;
sl=GetSliceData(0,t,n,data,importMemoryManagement);
vol=new ImageDataItem(*sl, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory);
vol->SetComplete(true);
}
else
{
mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n);
vol=m_Volumes[pos];
// ok, let's combine the slices!
if(vol.GetPointer()==NULL)
vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true);
vol->SetComplete(true);
size_t size=m_OffsetTable[2]*(ptypeSize);
for(s=0;s<m_Dimensions[2];++s)
{
int posSl;
ImageDataItemPointer sl;
posSl=GetSliceIndex(s,t,n);
sl=m_Slices[posSl];
if(sl->GetParent()!=vol)
{
// copy data of slices in volume
size_t offset = ((size_t) s)*size;
std::memcpy(static_cast<char*>(vol->GetData())+offset, sl->GetData(), size);
// FIXME mitkIpPicDescriptor * pic = sl->GetPicDescriptor();
// replace old slice with reference to volume
sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*size);
sl->SetComplete(true);
//mitkIpFuncCopyTags(sl->GetPicDescriptor(), pic);
m_Slices[posSl]=sl;
}
}
//if(vol->GetPicDescriptor()->info->tags_head==NULL)
// mitkIpFuncCopyTags(vol->GetPicDescriptor(), m_Slices[GetSliceIndex(0,t,n)]->GetPicDescriptor());
}
return m_Volumes[pos]=vol;
}
// volume is unavailable. Can we calculate it?
if((GetSource().IsNotNull()) && (GetSource()->Updating()==false))
{
// ... wir muessen rechnen!!! ....
m_RequestedRegion.SetIndex(0, 0);
m_RequestedRegion.SetIndex(1, 0);
m_RequestedRegion.SetIndex(2, 0);
m_RequestedRegion.SetIndex(3, t);
m_RequestedRegion.SetIndex(4, n);
m_RequestedRegion.SetSize(0, m_Dimensions[0]);
m_RequestedRegion.SetSize(1, m_Dimensions[1]);
m_RequestedRegion.SetSize(2, m_Dimensions[2]);
m_RequestedRegion.SetSize(3, 1);
m_RequestedRegion.SetSize(4, 1);
m_RequestedRegionInitialized=true;
GetSource()->Update();
if(IsVolumeSet(t,n))
//yes: now we can call ourselves without the risk of a endless loop (see "if" above)
return GetVolumeData(t,n,data,importMemoryManagement);
else
return NULL;
}
else
{
ImageDataItemPointer item = AllocateVolumeData(t,n,data,importMemoryManagement);
item->SetComplete(true);
return item;
}
}
mitk::Image::ImageDataItemPointer mitk::Image::GetChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidChannel(n)==false) return NULL;
ImageDataItemPointer ch, vol;
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
return ch;
// let's see if all volumes are set, so that we can (could) combine them to a channel
if(IsChannelSet(n))
{
// if there is only one time frame we do not need to combine anything
if(m_Dimensions[3]<=1)
{
vol=GetVolumeData(0,n,data,importMemoryManagement);
ch=new ImageDataItem(*vol, m_ImageDescriptor, m_ImageDescriptor->GetNumberOfDimensions(), data, importMemoryManagement == ManageMemory);
ch->SetComplete(true);
}
else
{
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
ch=m_Channels[n];
// ok, let's combine the volumes!
if(ch.GetPointer()==NULL)
ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true);
ch->SetComplete(true);
size_t size=m_OffsetTable[m_Dimension-1]*(ptypeSize);
unsigned int t;
ImageDataItemPointerArray::iterator slicesIt = m_Slices.begin()+n*m_Dimensions[2]*m_Dimensions[3];
for(t=0;t<m_Dimensions[3];++t)
{
int posVol;
ImageDataItemPointer vol;
posVol=GetVolumeIndex(t,n);
vol=GetVolumeData(t,n,data,importMemoryManagement);
if(vol->GetParent()!=ch)
{
// copy data of volume in channel
size_t offset = ((size_t) t)*m_OffsetTable[3]*(ptypeSize);
std::memcpy(static_cast<char*>(ch->GetData())+offset, vol->GetData(), size);
// REVEIW FIX mitkIpPicDescriptor * pic = vol->GetPicDescriptor();
// replace old volume with reference to channel
vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory, offset);
vol->SetComplete(true);
//mitkIpFuncCopyTags(vol->GetPicDescriptor(), pic);
m_Volumes[posVol]=vol;
// get rid of slices - they may point to old volume
ImageDataItemPointer dnull=NULL;
for(unsigned int i = 0; i < m_Dimensions[2]; ++i, ++slicesIt)
{
assert(slicesIt != m_Slices.end());
*slicesIt = dnull;
}
}
}
// REVIEW FIX
// if(ch->GetPicDescriptor()->info->tags_head==NULL)
// mitkIpFuncCopyTags(ch->GetPicDescriptor(), m_Volumes[GetVolumeIndex(0,n)]->GetPicDescriptor());
}
return m_Channels[n]=ch;
}
// channel is unavailable. Can we calculate it?
if((GetSource().IsNotNull()) && (GetSource()->Updating()==false))
{
// ... wir muessen rechnen!!! ....
m_RequestedRegion.SetIndex(0, 0);
m_RequestedRegion.SetIndex(1, 0);
m_RequestedRegion.SetIndex(2, 0);
m_RequestedRegion.SetIndex(3, 0);
m_RequestedRegion.SetIndex(4, n);
m_RequestedRegion.SetSize(0, m_Dimensions[0]);
m_RequestedRegion.SetSize(1, m_Dimensions[1]);
m_RequestedRegion.SetSize(2, m_Dimensions[2]);
m_RequestedRegion.SetSize(3, m_Dimensions[3]);
m_RequestedRegion.SetSize(4, 1);
m_RequestedRegionInitialized=true;
GetSource()->Update();
// did it work?
if(IsChannelSet(n))
//yes: now we can call ourselves without the risk of a endless loop (see "if" above)
return GetChannelData(n,data,importMemoryManagement);
else
return NULL;
}
else
{
ImageDataItemPointer item = AllocateChannelData(n,data,importMemoryManagement);
item->SetComplete(true);
return item;
}
}
bool mitk::Image::IsSliceSet(int s, int t, int n) const
{
if(IsValidSlice(s,t,n)==false) return false;
if(m_Slices[GetSliceIndex(s,t,n)].GetPointer()!=NULL)
return true;
ImageDataItemPointer ch, vol;
vol=m_Volumes[GetVolumeIndex(t,n)];
if((vol.GetPointer()!=NULL) && (vol->IsComplete()))
return true;
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
return true;
return false;
}
bool mitk::Image::IsVolumeSet(int t, int n) const
{
if(IsValidVolume(t,n)==false) return false;
ImageDataItemPointer ch, vol;
// volume directly available?
vol=m_Volumes[GetVolumeIndex(t,n)];
if((vol.GetPointer()!=NULL) && (vol->IsComplete()))
return true;
// is volume available as part of a channel that is available?
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
return true;
// let's see if all slices of the volume are set, so that we can (could) combine them to a volume
unsigned int s;
for(s=0;s<m_Dimensions[2];++s)
if(m_Slices[GetSliceIndex(s,t,n)].GetPointer()==NULL)
return false;
return true;
}
bool mitk::Image::IsChannelSet(int n) const
{
if(IsValidChannel(n)==false) return false;
ImageDataItemPointer ch, vol;
ch=m_Channels[n];
if((ch.GetPointer()!=NULL) && (ch->IsComplete()))
return true;
// let's see if all volumes are set, so that we can (could) combine them to a channel
unsigned int t;
for(t=0;t<m_Dimensions[3];++t)
if(IsVolumeSet(t,n)==false)
return false;
return true;
}
bool mitk::Image::SetSlice(const void *data, int s, int t, int n)
{
// const_cast is no risk for ImportMemoryManagementType == CopyMemory
return SetImportSlice(const_cast<void*>(data), s, t, n, CopyMemory);
}
bool mitk::Image::SetVolume(const void *data, int t, int n)
{
// const_cast is no risk for ImportMemoryManagementType == CopyMemory
return SetImportVolume(const_cast<void*>(data), t, n, CopyMemory);
}
bool mitk::Image::SetChannel(const void *data, int n)
{
// const_cast is no risk for ImportMemoryManagementType == CopyMemory
return SetImportChannel(const_cast<void*>(data), n, CopyMemory);
}
bool mitk::Image::SetImportSlice(void *data, int s, int t, int n, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidSlice(s,t,n)==false) return false;
ImageDataItemPointer sl;
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
if(IsSliceSet(s,t,n))
{
sl=GetSliceData(s,t,n,data,importMemoryManagement);
if(sl->GetManageMemory()==false)
{
sl=AllocateSliceData(s,t,n,data,importMemoryManagement);
if(sl.GetPointer()==NULL) return false;
}
if ( sl->GetData() != data )
std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(ptypeSize));
sl->Modified();
//we have changed the data: call Modified()!
Modified();
}
else
{
sl=AllocateSliceData(s,t,n,data,importMemoryManagement);
if(sl.GetPointer()==NULL) return false;
if ( sl->GetData() != data )
std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(ptypeSize));
//we just added a missing slice, which is not regarded as modification.
//Therefore, we do not call Modified()!
}
return true;
}
bool mitk::Image::SetImportVolume(void *data, int t, int n, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidVolume(t,n)==false) return false;
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
ImageDataItemPointer vol;
if(IsVolumeSet(t,n))
{
vol=GetVolumeData(t,n,data,importMemoryManagement);
if(vol->GetManageMemory()==false)
{
vol=AllocateVolumeData(t,n,data,importMemoryManagement);
if(vol.GetPointer()==NULL) return false;
}
if ( vol->GetData() != data )
std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize));
vol->Modified();
vol->SetComplete(true);
//we have changed the data: call Modified()!
Modified();
}
else
{
vol=AllocateVolumeData(t,n,data,importMemoryManagement);
if(vol.GetPointer()==NULL) return false;
if ( vol->GetData() != data )
{
std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize));
}
vol->SetComplete(true);
this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( vol->GetData() );
//we just added a missing Volume, which is not regarded as modification.
//Therefore, we do not call Modified()!
}
return true;
}
bool mitk::Image::SetImportChannel(void *data, int n, ImportMemoryManagementType importMemoryManagement)
{
if(IsValidChannel(n)==false) return false;
// channel descriptor
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
ImageDataItemPointer ch;
if(IsChannelSet(n))
{
ch=GetChannelData(n,data,importMemoryManagement);
if(ch->GetManageMemory()==false)
{
ch=AllocateChannelData(n,data,importMemoryManagement);
if(ch.GetPointer()==NULL) return false;
}
if ( ch->GetData() != data )
std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize));
ch->Modified();
ch->SetComplete(true);
//we have changed the data: call Modified()!
Modified();
}
else
{
ch=AllocateChannelData(n,data,importMemoryManagement);
if(ch.GetPointer()==NULL) return false;
if ( ch->GetData() != data )
std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize));
ch->SetComplete(true);
this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( ch->GetData() );
//we just added a missing Channel, which is not regarded as modification.
//Therefore, we do not call Modified()!
}
return true;
}
void mitk::Image::Initialize()
{
ImageDataItemPointerArray::iterator it, end;
for( it=m_Slices.begin(), end=m_Slices.end(); it!=end; ++it )
{
(*it)=NULL;
}
for( it=m_Volumes.begin(), end=m_Volumes.end(); it!=end; ++it )
{
(*it)=NULL;
}
for( it=m_Channels.begin(), end=m_Channels.end(); it!=end; ++it )
{
(*it)=NULL;
}
m_CompleteData = NULL;
if( m_ImageStatistics == NULL)
{
m_ImageStatistics = new mitk::ImageStatisticsHolder( this );
}
SetRequestedRegionToLargestPossibleRegion();
}
void mitk::Image::Initialize(const mitk::ImageDescriptor::Pointer inDesc)
{
// store the descriptor
this->m_ImageDescriptor = inDesc;
// initialize image
this->Initialize( inDesc->GetChannelDescriptor(0).GetPixelType(), inDesc->GetNumberOfDimensions(), inDesc->GetDimensions(), 1 );
}
void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels)
{
Clear();
m_Dimension=dimension;
if(!dimensions)
itkExceptionMacro(<< "invalid zero dimension image");
unsigned int i;
for(i=0;i<dimension;++i)
{
if(dimensions[i]<1)
itkExceptionMacro(<< "invalid dimension[" << i << "]: " << dimensions[i]);
}
// create new array since the old was deleted
m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];
// initialize the first four dimensions to 1, the remaining 4 to 0
FILL_C_ARRAY(m_Dimensions, 4, 1u);
FILL_C_ARRAY((m_Dimensions+4), 4, 0u);
// copy in the passed dimension information
std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int)*m_Dimension);
this->m_ImageDescriptor = mitk::ImageDescriptor::New();
this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension );
for(i=0;i<4;++i)
{
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]);
}
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize(i, channels);
if(m_LargestPossibleRegion.GetNumberOfPixels()==0)
{
delete [] m_Dimensions;
m_Dimensions = NULL;
return;
}
for( unsigned int i=0u; i<channels; i++)
{
this->m_ImageDescriptor->AddNewChannel( type );
}
PlaneGeometry::Pointer planegeometry = PlaneGeometry::New();
planegeometry->InitializeStandardPlane(m_Dimensions[0], m_Dimensions[1]);
SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
slicedGeometry->InitializeEvenlySpaced(planegeometry, m_Dimensions[2]);
if(dimension>=4)
{
TimeBounds timebounds;
timebounds[0] = 0.0;
timebounds[1] = 1.0;
slicedGeometry->SetTimeBounds(timebounds);
}
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
for (TimeStepType step = 0; step < timeGeometry->CountTimeSteps(); ++step)
{
timeGeometry->GetGeometryForTimeStep(step)->ImageGeometryOn();
}
SetTimeGeometry(timeGeometry);
ImageDataItemPointer dnull=NULL;
m_Channels.assign(GetNumberOfChannels(), dnull);
m_Volumes.assign(GetNumberOfChannels()*m_Dimensions[3], dnull);
m_Slices.assign(GetNumberOfChannels()*m_Dimensions[3]*m_Dimensions[2], dnull);
ComputeOffsetTable();
Initialize();
m_Initialized = true;
}
void mitk::Image::Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int channels, int tDim )
{
mitk::ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
Geometry3D::Pointer geometry3D = geometry.Clone();
timeGeometry->Initialize(geometry3D.GetPointer(), tDim);
this->Initialize(type, *timeGeometry, channels, tDim);
}
void mitk::Image::Initialize(const mitk::PixelType& type, const mitk::TimeGeometry& geometry, unsigned int channels, int tDim )
{
unsigned int dimensions[5];
dimensions[0] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(0)+0.5);
dimensions[1] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(1)+0.5);
dimensions[2] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(2)+0.5);
dimensions[3] = (tDim > 0) ? tDim : geometry.CountTimeSteps();
dimensions[4] = 0;
unsigned int dimension = 2;
if ( dimensions[2] > 1 )
dimension = 3;
if ( dimensions[3] > 1 )
dimension = 4;
Initialize( type, dimension, dimensions, channels );
if (geometry.CountTimeSteps() > 1)
{
TimeGeometry::Pointer cloned = geometry.Clone();
SetTimeGeometry(cloned.GetPointer());
}
else
Superclass::SetGeometry(geometry.GetGeometryForTimeStep(0));
/* //Old //TODO_GOETZ Really necessary?
mitk::BoundingBox::BoundsArrayType bounds = geometry.GetBoundingBoxInWorld()->GetBounds();
if( (bounds[0] != 0.0) || (bounds[2] != 0.0) || (bounds[4] != 0.0) )
{
SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0);
mitk::Point3D origin; origin.Fill(0.0);
slicedGeometry->IndexToWorld(origin, origin);
bounds[1]-=bounds[0]; bounds[3]-=bounds[2]; bounds[5]-=bounds[4];
bounds[0] = 0.0; bounds[2] = 0.0; bounds[4] = 0.0;
this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension );
slicedGeometry->SetBounds(bounds);
slicedGeometry->GetIndexToWorldTransform()->SetOffset(origin.GetVnlVector().data_block());
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
SetTimeGeometry(timeGeometry);
}*/
}
void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim )
{
SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
slicedGeometry->InitializeEvenlySpaced(static_cast<Geometry2D*>(geometry2d.Clone().GetPointer()), sDim, flipped);
Initialize(type, *slicedGeometry, channels, tDim);
}
void mitk::Image::Initialize(const mitk::Image* image)
{
Initialize(image->GetPixelType(), *image->GetTimeGeometry());
}
void mitk::Image::Initialize(vtkImageData* vtkimagedata, int channels, int tDim, int sDim, int pDim)
{
if(vtkimagedata==NULL) return;
m_Dimension=vtkimagedata->GetDataDimension();
unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4];
for(i=0;i<m_Dimension;++i) tmpDimensions[i]=vtkimagedata->GetDimensions()[i];
if(m_Dimension<4)
{
unsigned int *p;
for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p)
*p=1;
}
if(pDim>=0)
{
tmpDimensions[1]=pDim;
if(m_Dimension < 2)
m_Dimension = 2;
}
if(sDim>=0)
{
tmpDimensions[2]=sDim;
if(m_Dimension < 3)
m_Dimension = 3;
}
if(tDim>=0)
{
tmpDimensions[3]=tDim;
if(m_Dimension < 4)
m_Dimension = 4;
}
switch ( vtkimagedata->GetScalarType() )
{
case VTK_BIT:
case VTK_CHAR:
//pixelType.Initialize(typeid(char), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<char>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_UNSIGNED_CHAR:
//pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<unsigned char>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_SHORT:
//pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<short>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_UNSIGNED_SHORT:
//pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<unsigned short>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_INT:
//pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<int>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_UNSIGNED_INT:
//pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<unsigned int>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_LONG:
//pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<long>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_UNSIGNED_LONG:
//pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<unsigned long>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_FLOAT:
//pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<float>(), m_Dimension, tmpDimensions, channels);
break;
case VTK_DOUBLE:
//pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents());
Initialize(mitk::MakeScalarPixelType<double>(), m_Dimension, tmpDimensions, channels);
break;
default:
break;
}
/*
Initialize(pixelType,
m_Dimension,
tmpDimensions,
channels);
*/
const double *spacinglist = vtkimagedata->GetSpacing();
Vector3D spacing;
FillVector3D(spacing, spacinglist[0], 1.0, 1.0);
if(m_Dimension>=2)
spacing[1]=spacinglist[1];
if(m_Dimension>=3)
spacing[2]=spacinglist[2];
// access origin of vtkImage
Point3D origin;
double vtkorigin[3];
vtkimagedata->GetOrigin(vtkorigin);
FillVector3D(origin, vtkorigin[0], 0.0, 0.0);
if(m_Dimension>=2)
origin[1]=vtkorigin[1];
if(m_Dimension>=3)
origin[2]=vtkorigin[2];
SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0);
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry* planeGeometry = static_cast<PlaneGeometry*>(slicedGeometry->GetGeometry2D(0));
planeGeometry->SetOrigin(origin);
// re-initialize SlicedGeometry3D
slicedGeometry->SetOrigin(origin);
slicedGeometry->SetSpacing(spacing);
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
SetTimeGeometry(timeGeometry);
delete [] tmpDimensions;
}
bool mitk::Image::IsValidSlice(int s, int t, int n) const
{
if(m_Initialized)
return ((s>=0) && (s<(int)m_Dimensions[2]) && (t>=0) && (t< (int) m_Dimensions[3]) && (n>=0) && (n< (int)GetNumberOfChannels()));
else
return false;
}
bool mitk::Image::IsValidVolume(int t, int n) const
{
if(m_Initialized)
return IsValidSlice(0, t, n);
else
return false;
}
bool mitk::Image::IsValidChannel(int n) const
{
if(m_Initialized)
return IsValidSlice(0, 0, n);
else
return false;
}
void mitk::Image::ComputeOffsetTable()
{
if(m_OffsetTable!=NULL)
delete [] m_OffsetTable;
m_OffsetTable=new size_t[m_Dimension>4 ? m_Dimension+1 : 4+1];
unsigned int i;
size_t num=1;
m_OffsetTable[0] = 1;
for (i=0; i < m_Dimension; ++i)
{
num *= m_Dimensions[i];
m_OffsetTable[i+1] = num;
}
for (;i < 4; ++i)
m_OffsetTable[i+1] = num;
}
bool mitk::Image::IsValidTimeStep(int t) const
{
return ( ( m_Dimension >= 4 && t <= (int)m_Dimensions[3] && t > 0 ) || (t == 0) );
}
void mitk::Image::Expand(unsigned int timeSteps)
{
if(timeSteps < 1) itkExceptionMacro(<< "Invalid timestep in Image!");
Superclass::Expand(timeSteps);
}
int mitk::Image::GetSliceIndex(int s, int t, int n) const
{
if(IsValidSlice(s,t,n)==false) return false;
return ((size_t)s)+((size_t) t)*m_Dimensions[2]+((size_t) n)*m_Dimensions[3]*m_Dimensions[2]; //??
}
int mitk::Image::GetVolumeIndex(int t, int n) const
{
if(IsValidVolume(t,n)==false) return false;
return ((size_t)t)+((size_t) n)*m_Dimensions[3]; //??
}
mitk::Image::ImageDataItemPointer mitk::Image::AllocateSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
int pos;
pos=GetSliceIndex(s,t,n);
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
// is slice available as part of a volume that is available?
ImageDataItemPointer sl, ch, vol;
vol=m_Volumes[GetVolumeIndex(t,n)];
if(vol.GetPointer()!=NULL)
{
sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize));
sl->SetComplete(true);
return m_Slices[pos]=sl;
}
// is slice available as part of a channel that is available?
ch=m_Channels[n];
if(ch.GetPointer()!=NULL)
{
sl=new ImageDataItem(*ch, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize));
sl->SetComplete(true);
return m_Slices[pos]=sl;
}
// allocate new volume (instead of a single slice to keep data together!)
m_Volumes[GetVolumeIndex(t,n)]=vol=AllocateVolumeData(t,n,NULL,importMemoryManagement);
sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize));
sl->SetComplete(true);
return m_Slices[pos]=sl;
////ALTERNATIVE:
//// allocate new slice
//sl=new ImageDataItem(*m_PixelType, 2, m_Dimensions);
//m_Slices[pos]=sl;
//return vol;
}
mitk::Image::ImageDataItemPointer mitk::Image::AllocateVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
int pos;
pos=GetVolumeIndex(t,n);
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
// is volume available as part of a channel that is available?
ImageDataItemPointer ch, vol;
ch=m_Channels[n];
if(ch.GetPointer()!=NULL)
{
vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data,importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize));
return m_Volumes[pos]=vol;
}
mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n);
// allocate new volume
if(importMemoryManagement == CopyMemory)
{
vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true);
if(data != NULL)
std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize));
}
else
{
vol=new ImageDataItem( chPixelType, 3, m_Dimensions, data, importMemoryManagement == ManageMemory);
}
m_Volumes[pos]=vol;
return vol;
}
mitk::Image::ImageDataItemPointer mitk::Image::AllocateChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement)
{
ImageDataItemPointer ch;
// allocate new channel
if(importMemoryManagement == CopyMemory)
{
const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize();
ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true);
if(data != NULL)
std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize));
}
else
{
ch=new ImageDataItem(this->m_ImageDescriptor, data, importMemoryManagement == ManageMemory);
}
m_Channels[n]=ch;
return ch;
}
unsigned int* mitk::Image::GetDimensions() const
{
return m_Dimensions;
}
void mitk::Image::Clear()
{
Superclass::Clear();
delete [] m_Dimensions;
m_Dimensions = NULL;
}
void mitk::Image::SetGeometry(Geometry3D* aGeometry3D)
{
// Please be aware of the 0.5 offset/pixel-center issue! See Geometry documentation for further information
if(aGeometry3D->GetImageGeometry()==false)
{
MITK_INFO << "WARNING: Applied a non-image geometry onto an image. Please be SURE that this geometry is pixel-center-based! If it is not, you need to call Geometry3D->ChangeImageGeometryConsideringOriginOffset(true) before calling image->setGeometry(..)\n";
}
Superclass::SetGeometry(aGeometry3D);
for (TimeStepType step = 0; step < GetTimeGeometry()->CountTimeSteps(); ++step)
GetTimeGeometry()->GetGeometryForTimeStep(step)->ImageGeometryOn();
}
void mitk::Image::PrintSelf(std::ostream& os, itk::Indent indent) const
{
unsigned char i;
if(m_Initialized)
{
os << indent << " Dimension: " << m_Dimension << std::endl;
os << indent << " Dimensions: ";
for(i=0; i < m_Dimension; ++i)
os << GetDimension(i) << " ";
os << std::endl;
for(unsigned int ch=0; ch < this->m_ImageDescriptor->GetNumberOfChannels(); ch++)
{
mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(ch);
os << indent << " Channel: " << this->m_ImageDescriptor->GetChannelName(ch) << std::endl;
os << indent << " PixelType: " << chPixelType.GetPixelTypeAsString() << std::endl;
os << indent << " BytesPerElement: " << chPixelType.GetSize() << std::endl;
os << indent << " ComponentType: " << chPixelType.GetComponentTypeAsString() << std::endl;
os << indent << " NumberOfComponents: " << chPixelType.GetNumberOfComponents() << std::endl;
os << indent << " BitsPerComponent: " << chPixelType.GetBitsPerComponent() << std::endl;
}
}
else
{
os << indent << " Image not initialized: m_Initialized: false" << std::endl;
}
Superclass::PrintSelf(os,indent);
}
bool mitk::Image::IsRotated() const
{
const mitk::Geometry3D* geo = this->GetGeometry();
bool ret = false;
if(geo)
{
const vnl_matrix_fixed<ScalarType, 3, 3> & mx = geo->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix();
mitk::ScalarType ref = 0;
for(short k = 0; k < 3; ++k)
ref += mx[k][k];
ref/=1000; // Arbitrary value; if a non-diagonal (nd) element is bigger then this, matrix is considered nd.
for(short i = 0; i < 3; ++i)
{
for(short j = 0; j < 3; ++j)
{
if(i != j)
{
if(std::abs(mx[i][j]) > ref) // matrix is nd
ret = true;
}
}
}
}
return ret;
}
mitk::ScalarType mitk::Image::GetScalarValueMin(int t) const
{
return m_ImageStatistics->GetScalarValueMin(t);
}
//## \brief Get the maximum for scalar images
mitk::ScalarType mitk::Image::GetScalarValueMax(int t) const
{
return m_ImageStatistics->GetScalarValueMax(t);
}
//## \brief Get the second smallest value for scalar images
mitk::ScalarType mitk::Image::GetScalarValue2ndMin(int t) const
{
return m_ImageStatistics->GetScalarValue2ndMin(t);
}
mitk::ScalarType mitk::Image::GetScalarValueMinNoRecompute( unsigned int t ) const
{
return m_ImageStatistics->GetScalarValueMinNoRecompute(t);
}
mitk::ScalarType mitk::Image::GetScalarValue2ndMinNoRecompute( unsigned int t ) const
{
return m_ImageStatistics->GetScalarValue2ndMinNoRecompute(t);
}
mitk::ScalarType mitk::Image::GetScalarValue2ndMax(int t) const
{
return m_ImageStatistics->GetScalarValue2ndMax(t);
}
mitk::ScalarType mitk::Image::GetScalarValueMaxNoRecompute( unsigned int t) const
{
return m_ImageStatistics->GetScalarValueMaxNoRecompute(t);
}
mitk::ScalarType mitk::Image::GetScalarValue2ndMaxNoRecompute( unsigned int t ) const
{
return m_ImageStatistics->GetScalarValue2ndMaxNoRecompute(t);
}
mitk::ScalarType mitk::Image::GetCountOfMinValuedVoxels(int t ) const
{
return m_ImageStatistics->GetCountOfMinValuedVoxels(t);
}
mitk::ScalarType mitk::Image::GetCountOfMaxValuedVoxels(int t) const
{
return m_ImageStatistics->GetCountOfMaxValuedVoxels(t);
}
unsigned int mitk::Image::GetCountOfMaxValuedVoxelsNoRecompute( unsigned int t ) const
{
return m_ImageStatistics->GetCountOfMaxValuedVoxelsNoRecompute(t);
}
unsigned int mitk::Image::GetCountOfMinValuedVoxelsNoRecompute( unsigned int t ) const
{
return m_ImageStatistics->GetCountOfMinValuedVoxelsNoRecompute(t);
}
bool mitk::Equal(const mitk::Image* rightHandSide, const mitk::Image* leftHandSide, ScalarType eps, bool verbose)
{
bool returnValue = true;
if( rightHandSide == NULL )
{
if(verbose)
MITK_INFO << "[( Image )] rightHandSide is NULL.";
return false;
}
if( leftHandSide == NULL )
{
if(verbose)
MITK_INFO << "[( Image )] leftHandSide is NULL.";
return false;
}
// Dimensionality
if( rightHandSide->GetDimension() != leftHandSide->GetDimension() )
{
if(verbose)
{
MITK_INFO << "[( Image )] Dimensionality differs.";
MITK_INFO << "rightHandSide is " << rightHandSide->GetDimension()
<< "leftHandSide is " << leftHandSide->GetDimension();
}
returnValue = false;
}
// Pair-wise dimension (size) comparison
unsigned int minDimensionality = std::min(rightHandSide->GetDimension(),leftHandSide->GetDimension());
for( unsigned int i=0; i< minDimensionality; ++i)
{
if( rightHandSide->GetDimension(i) != leftHandSide->GetDimension(i) )
{
returnValue = false;
if(verbose)
{
MITK_INFO << "[( Image )] dimension differs.";
MITK_INFO << "rightHandSide->GetDimension("<<i<<") is " << rightHandSide->GetDimension(i)
<< "leftHandSide->GetDimension("<<i<<") is " << leftHandSide->GetDimension(i);
}
}
}
// Pixeltype
mitk::PixelType pixelTypeRightHandSide = rightHandSide->GetPixelType();
mitk::PixelType pixelTypeLeftHandSide = leftHandSide->GetPixelType();
if( !( pixelTypeRightHandSide == pixelTypeLeftHandSide ) )
{
if(verbose)
{
MITK_INFO << "[( Image )] PixelType differs.";
MITK_INFO << "rightHandSide is " << pixelTypeRightHandSide.GetTypeAsString()
<< "leftHandSide is " << pixelTypeLeftHandSide.GetTypeAsString();
}
returnValue = false;
}
// Geometries
if( !mitk::Equal( leftHandSide->GetGeometry(),
rightHandSide->GetGeometry(), eps, verbose) )
{
if(verbose)
{
MITK_INFO << "[( Image )] Geometries differ.";
}
returnValue = false;
}
// Pixel values - default mode [ 0 threshold in difference ]
// compare only if all previous checks were successfull, otherwise the ITK filter will throw an exception
if( returnValue )
{
mitk::CompareImageDataFilter::Pointer compareFilter = mitk::CompareImageDataFilter::New();
compareFilter->SetInput(0, rightHandSide);
compareFilter->SetInput(1, leftHandSide);
+ compareFilter->SetTolerance(eps);
compareFilter->Update();
if(( !compareFilter->GetResult() ) )
{
returnValue = false;
if(verbose)
{
MITK_INFO << "[(Image)] Pixel values differ: ";
+ compareFilter->GetCompareResults().PrintSelf();
}
- compareFilter->GetCompareResults().PrintSelf();
}
}
return returnValue;
}
diff --git a/Core/Code/Testing/CMakeLists.txt b/Core/Code/Testing/CMakeLists.txt
index 2bde005f97..a880e9e3d4 100644
--- a/Core/Code/Testing/CMakeLists.txt
+++ b/Core/Code/Testing/CMakeLists.txt
@@ -1,261 +1,263 @@
# The core tests need relaxed compiler flags...
# TODO fix core tests to compile without these additional no-error flags
if(MSVC_VERSION)
# disable deprecated warnings (they would lead to errors)
mitkFunctionCheckCAndCXXCompilerFlags("/wd4996" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
else()
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
endif()
MITK_CREATE_MODULE_TESTS(LABELS MITK-Core)
# MITK_INSTALL_TARGETS(EXECUTABLES MitkTestDriver)
mitkAddCustomModuleTest(mitkVolumeCalculatorTest_Png2D-bw mitkVolumeCalculatorTest
${MITK_DATA_DIR}/Png2D-bw.png
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
mitkAddCustomModuleTest(mitkEventMapperTest_Test1And2 mitkEventMapperTest
${MITK_DATA_DIR}/TestStateMachine1.xml
${MITK_DATA_DIR}/TestStateMachine2.xml
)
mitkAddCustomModuleTest(mitkEventConfigTest_CreateObjectInDifferentWays mitkEventConfigTest
${MITK_SOURCE_DIR}/Core/Code/Testing/Resources/Interactions/StatemachineConfigTest.xml
)
mitkAddCustomModuleTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest
${MITK_DATA_DIR}/Pic3D.nrrd
${MITK_DATA_DIR}/BallBinary30x30x30.nrrd
)
mitkAddCustomModuleTest(mitkDataStorageTest_US4DCyl mitkDataStorageTest
${MITK_DATA_DIR}/US4DCyl.nrrd
)
mitkAddCustomModuleTest(mitkStateMachineFactoryTest_TestStateMachine1_2 mitkStateMachineFactoryTest
${MITK_DATA_DIR}/TestStateMachine1.xml
${MITK_DATA_DIR}/TestStateMachine2.xml
)
mitkAddCustomModuleTest(mitkDicomSeriesReaderTest_CTImage mitkDicomSeriesReaderTest
${MITK_DATA_DIR}/TinyCTAbdomen
${MITK_DATA_DIR}/DICOMReader/Broken-Series
)
mitkAddCustomModuleTest(mitkPointSetReaderTest mitkPointSetReaderTest
${MITK_DATA_DIR}/PointSetReaderTestData.mps
)
mitkAddCustomModuleTest(mitkImageTest_4DImageData mitkImageTest
${MITK_DATA_DIR}/US4DCyl.nrrd
)
mitkAddCustomModuleTest(mitkImageTest_2D+tImageData mitkImageTest
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
mitkAddCustomModuleTest(mitkImageTest_3DImageData mitkImageTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
+mitkAddCustomModuleTest(mitkImageEqualTest mitkImageEqualTest)
+
mitkAddCustomModuleTest(mitkImageTest_brainImage mitkImageTest
${MITK_DATA_DIR}/brain.mhd
)
mitkAddCustomModuleTest(mitkImageTest_3DImageData mitkImageGeneratorTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkLevelWindowManagerTest mitkLevelWindowManagerTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkMultiComponentImageDataComparisonFilterTest mitkMultiComponentImageDataComparisonFilterTest
${MITK_DATA_DIR}/NrrdWritingTestImage.jpg
)
mitkAddCustomModuleTest(mitkImageToItkTest mitkImageToItkTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkImageSliceSelectorTest mitkImageSliceSelectorTest
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
if(MITK_ENABLE_RENDERING_TESTING) ### since the rendering test's do not run in ubuntu, yet, we build them only for other systems or if the user explicitly sets the variable MITK_ENABLE_RENDERING_TESTING
mitkAddCustomModuleTest(mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2DTest
${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/rgbaImage640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3d640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2DColorTest #test for color property (=blue) Pic3D sagittal slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dColorBlue640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2DLevelWindowTest #test for levelwindow property (=blood) #Pic3D sagittal slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dLevelWindowBlood640x480REF.png #corresponding reference #screenshot
)
#mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dOpacity640x480 mitkImageVtkMapper2DOpacityTest #test for opacity (=0.5) Pic3D coronal slice
# ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dOpacity640x480REF.png corresponding reference screenshot
#)
mitkAddCustomModuleTest(mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DSwivelTest #test for a randomly chosen Pic3D swivelled slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dSwivel640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkPointSetVtkMapper2D_openMeAlone640x480 mitkPointSetVtkMapper2DTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAlone640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkPointSetVtkMapper2D_Pic3DPointSetForPic3D640x480 mitkPointSetVtkMapper2DImageTest
${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/PointSetForPic3D.mps #input point set and image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Pic3DPointSetForPic3D640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkPointSetVtkMapper2D_openMeAloneGlyphType640x480 mitkPointSetVtkMapper2DGlyphTypeTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneGlyphType640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkPointSetVtkMapper2D_openMeAloneTransformed640x480 mitkPointSetVtkMapper2DTransformedPointsTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneTransformedPoints640x480REF.png #corresponding reference screenshot
)
#Test reslice interpolation
#note: nearest mode is already tested by swivel test
mitkAddCustomModuleTest(ResliceInterpolationIsLinear mitkImageVtkMapper2DResliceInterpolationPropertyTest
1 #linear
${MITK_DATA_DIR}/Pic3D.nrrd
-V
${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefLinear.png #corresponding reference screenshot LINEAR
)
mitkAddCustomModuleTest(ResliceInterpolationIsCubic mitkImageVtkMapper2DResliceInterpolationPropertyTest
3 #cubic
${MITK_DATA_DIR}/Pic3D.nrrd
-V
${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefCubic.png #corresponding reference screenshot CUBIC
)
#End test reslice interpolation
#Overlays
mitkAddCustomModuleTest(mitkLabelOverlay3DRendering2DTest mitkLabelOverlay3DRendering2DTest #OverlayTest
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkLabelOverlay3DRendering2DTest.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkLabelOverlay3DRendering3DTest mitkLabelOverlay3DRendering3DTest #OverlayTest
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkLabelOverlay3DRendering3DTest.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkTextOverlay2DRenderingTest_ball mitkTextOverlay2DRenderingTest #OverlayTest
${MITK_DATA_DIR}/ball.stl #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkTextOverlay2DRenderingTest_ball.png #corresponding reference screenshot
)
#mitkAddCustomModuleTest(mitkTextOverlay2DLayouterRenderingTest_ball mitkTextOverlay2DLayouterRenderingTest #OverlayTest
# ${MITK_DATA_DIR}/ball.stl #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkTextOverlay2DLayouterRenderingTest_ball.png #corresponding reference screenshot
#)
mitkAddCustomModuleTest(mitkTextOverlay3DRendering2DTest_ball mitkTextOverlay3DRendering2DTest #OverlayTest
${MITK_DATA_DIR}/ball.stl #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkTextOverlay3DRendering2DTest_ball.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkTextOverlay3DRendering3DTest_ball mitkTextOverlay3DRendering3DTest #OverlayTest
${MITK_DATA_DIR}/ball.stl #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkTextOverlay3DRendering3DTest_ball.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkTextOverlay3DColorRenderingTest_ball mitkTextOverlay3DColorRenderingTest #OverlayTest
${MITK_DATA_DIR}/ball.stl #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/mitkTextOverlay3DColorRenderingTest_ball.png #corresponding reference screenshot
)
#End of overlayTests
# Testing of the rendering of binary images
#mitkAddCustomModuleTest(mitkImageVtkMapper2D_binaryTestImage640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
# ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImage640x480REF.png #corresponding reference screenshot
#)
#mitkAddCustomModuleTest(mitkImageVtkMapper2D_binaryTestImageWithRef640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
# ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImageWithRef640x480REF.png #corresponding reference screenshot
#)
# End of binary image tests
mitkAddCustomModuleTest(mitkSurfaceVtkMapper3DTest_TextureProperty mitkSurfaceVtkMapper3DTest
${MITK_DATA_DIR}/ToF-Data/Kinect_LiverPhantom.vtp
${MITK_DATA_DIR}/ToF-Data/Kinect_LiverPhantom_RGBImage.nrrd
-V
${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedLiver640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DTransferFunctionTest
${MITK_DATA_DIR}/Png2D-bw.png
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-TransferFunctionRGBImage640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkSurfaceGLMapper2DColorTest_RedBall mitkSurfaceGLMapper2DColorTest
${MITK_DATA_DIR}/ball.stl
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/ballColorRed640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkSurfaceGLMapper2DColorTest_DasArmeSchwein mitkSurfaceGLMapper2DColorTest
${MITK_DATA_DIR}/binary.stl
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryColorRed640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleTest(mitkSurfaceGLMapper2DOpacityTest_BallOpacity mitkSurfaceGLMapper2DOpacityTest #opacity = 50% (0.5)
${MITK_DATA_DIR}/ball.stl
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/ballOpacity640x480REF.png #corresponding reference screenshot
)
############################## DISABLED TESTS
#Removed due to high rendering error.
#mitkAddCustomModuleTest(mitkSurfaceVtkMapper3DTexturedSphereTest_Football mitkSurfaceVtkMapper3DTexturedSphereTest
# ${MITK_DATA_DIR}/RenderingTestData/texture.jpg #input texture
# -V
# ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedSphere640x480REF.png corresponding reference screenshot
#)
#mitkAddCustomModuleTest(mitkImageVtkMapper2DLookupTableTest_Png2D-bw mitkImageVtkMapper2DLookupTableTest
# ${MITK_DATA_DIR}/Png2D-bw.png
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-LookupTableRGBImage640x480REF.png #corresponding reference screenshot
#)
#mitkAddCustomModuleTest(mitkImageTest_color2DImage mitkImageTest
# ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg
#)
#mitkAddCustomModuleTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest
# ${MITK_DATA_DIR}/Pic3D.pic.gz ${MITK_DATA_DIR}/BallBinary30x30x30.pic.gz
#)
SET_PROPERTY(TEST mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw
# mitkImageVtkMapper2D_pic3dOpacity640x480
mitkSurfaceGLMapper2DOpacityTest_BallOpacity mitkSurfaceGLMapper2DColorTest_DasArmeSchwein mitkSurfaceGLMapper2DColorTest_RedBall mitkSurfaceVtkMapper3DTest_TextureProperty mitkPointSetVtkMapper2D_Pic3DPointSetForPic3D640x480 mitkPointSetVtkMapper2D_openMeAlone640x480 mitkPointSetVtkMapper2D_openMeAloneGlyphType640x480 mitkPointSetVtkMapper2D_openMeAloneTransformed640x480 #mitkSurfaceVtkMapper3DTexturedSphereTest_Football
PROPERTY RUN_SERIAL TRUE)
endif()
add_test(mitkPointSetLocaleTest ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkPointSetLocaleTest ${MITK_DATA_DIR}/pointSet.mps)
set_property(TEST mitkPointSetLocaleTest PROPERTY LABELS MITK-Core)
add_test(mitkImageWriterTest_nrrdImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg)
add_test(mitkImageWriterTest_2DPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/Png2D-bw.png)
add_test(mitkImageWriterTest_rgbPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/RenderingTestData/rgbImage.png)
add_test(mitkImageWriterTest_rgbaPNGImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} mitkImageWriterTest ${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png)
set_property(TEST mitkImageWriterTest_nrrdImage PROPERTY LABELS MITK-Core)
set_property(TEST mitkImageWriterTest_2DPNGImage PROPERTY LABELS MITK-Core)
set_property(TEST mitkImageWriterTest_rgbPNGImage PROPERTY LABELS MITK-Core)
set_property(TEST mitkImageWriterTest_rgbaPNGImage PROPERTY LABELS MITK-Core)
add_subdirectory(DICOMTesting)
diff --git a/Core/Code/Testing/mitkImageEqualTest.cpp b/Core/Code/Testing/mitkImageEqualTest.cpp
index 4d2d80125c..560b33ef4e 100644
--- a/Core/Code/Testing/mitkImageEqualTest.cpp
+++ b/Core/Code/Testing/mitkImageEqualTest.cpp
@@ -1,120 +1,129 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "mitkImage.h"
#include "mitkImageGenerator.h"
#include "mitkTestingMacros.h"
#include "mitkImageSliceSelector.h"
#include "mitkTestFixture.h"
class mitkImageEqualTestSuite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkImageEqualTestSuite);
MITK_TEST(Equal_CloneAndOriginal_ReturnsTrue);
MITK_TEST(Equal_InputIsNull_ReturnsFalse);
MITK_TEST(Equal_DifferentImageGeometry_ReturnsFalse);
MITK_TEST(Equal_DifferentPixelTypes_ReturnsFalse);
MITK_TEST(Equal_DifferentDimensions_ReturnsFalse);
MITK_TEST(Equal_DifferentDimensionalities_ReturnsFalse);
MITK_TEST(Equal_DifferentPixelValues_ReturnsFalse);
CPPUNIT_TEST_SUITE_END();
private:
/** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
mitk::Image::Pointer m_Image;
mitk::Image::Pointer m_AnotherImage;
public:
/**
* @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
*/
void setUp()
{
//generate a gradient test image
m_Image = mitk::ImageGenerator::GenerateGradientImage<unsigned char>(3u, 3u, 1u);
m_AnotherImage = m_Image->Clone();
}
void tearDown()
{
m_Image = NULL;
m_AnotherImage = NULL;
}
void Equal_CloneAndOriginal_ReturnsTrue()
{
MITK_ASSERT_EQUAL( m_Image, m_Image->Clone(), "A clone should be equal to its original.");
}
void Equal_InputIsNull_ReturnsFalse()
{
mitk::Image::Pointer image = NULL;
MITK_ASSERT_NOT_EQUAL( image, image, "Input is NULL. Result should be false.");
}
void Equal_DifferentImageGeometry_ReturnsFalse()
{
mitk::Point3D origin;
origin[0] = 0.0;
origin[1] = 0.0;
origin[2] = mitk::eps * 1.01;
m_AnotherImage->GetGeometry()->SetOrigin(origin);
MITK_ASSERT_NOT_EQUAL( m_Image, m_AnotherImage, "One origin was modified. Result should be false.");
}
void Equal_DifferentPixelTypes_ReturnsFalse()
{
m_AnotherImage = mitk::ImageGenerator::GenerateGradientImage<float>(3u, 3u, 1u);
MITK_ASSERT_NOT_EQUAL( m_Image, m_AnotherImage, "One pixel type is float, the other unsigned char. Result should be false.");
}
void Equal_DifferentDimensions_ReturnsFalse()
{
m_AnotherImage = mitk::ImageGenerator::GenerateGradientImage<unsigned char>(5u, 7u, 3u);
MITK_ASSERT_NOT_EQUAL( m_Image, m_AnotherImage, "Dimensions of first image are: (3, 3, 1). Dimensions of second image are: (5, 7, 3). Result should be false.");
}
void Equal_DifferentDimensionalities_ReturnsFalse()
{
//Select the first slice of a 2D image and compare it to the 3D original
mitk::ImageSliceSelector::Pointer sliceSelector = mitk::ImageSliceSelector::New();
sliceSelector->SetInput( m_Image );
sliceSelector->SetSliceNr( 0 );
sliceSelector->Update();
m_AnotherImage = sliceSelector->GetOutput();
MITK_ASSERT_NOT_EQUAL( m_Image, m_AnotherImage, "First image is 3D. Second image is 2D. Result should be false.");
}
void Equal_DifferentPixelValues_ReturnsFalse()
{
//todo: Replace the random images via simpler images with fixed values.
m_Image = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(3u, 3u);
m_AnotherImage = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(3u, 3u);
MITK_ASSERT_NOT_EQUAL( m_Image, m_AnotherImage, "We compare two random images. Result should be false.");
}
+
+ void Equal_EpsilonDifference_ReturnsTrue()
+ {
+ m_Image = mitk::ImageGenerator::GenerateRandomImage<double>(10, 10);
+ m_AnotherImage = m_Image->Clone();
+
+ MITK_TEST_CONDITION_REQUIRED(!mitk::Equal(m_Image, m_AnotherImage, 0, false), "Epsilon = 0.0 --> double images should not be regarded as equal");
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(m_Image, m_AnotherImage, 0.001, false), "Epsilon = 0.001 --> double images should be regarded as equal");
+ }
};
MITK_TEST_SUITE_REGISTRATION(mitkImageEqual)
diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp
index 51918d9bda..b362a806ac 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp
@@ -1,802 +1,817 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
#define __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionConstIteratorWithIndex.h>
#include <itkImageRegionIterator.h>
#include <itkArray.h>
#include <vnl/vnl_vector.h>
#include <boost/version.hpp>
#include <stdio.h>
#include <locale>
#define _USE_MATH_DEFINES
#include <math.h>
#include <boost/math/special_functions.hpp>
#include "itkPointShell.h"
using namespace boost::math;
namespace itk {
#define QBALL_ANAL_RECON_PI M_PI
template< class T, class TG, class TO, int L, int NODF>
AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::AnalyticalDiffusionQballReconstructionImageFilter() :
m_GradientDirectionContainer(NULL),
m_NumberOfGradientDirections(0),
m_NumberOfBaselineImages(1),
m_Threshold(NumericTraits< ReferencePixelType >::NonpositiveMin()),
m_BValue(1.0),
m_Lambda(0.0),
m_DirectionsDuplicated(false),
m_Delta1(0.001),
- m_Delta2(0.001)
+ m_Delta2(0.001),
+ m_UseMrtrixBasis(false)
{
// At least 1 inputs is necessary for a vector image.
// For images added one at a time we need at least six
this->SetNumberOfRequiredInputs( 1 );
}
template<
class TReferenceImagePixelType,
class TGradientImagePixelType,
class TOdfPixelType,
int NOrderL,
int NrOdfDirections>
typename itk::AnalyticalDiffusionQballReconstructionImageFilter<
TReferenceImagePixelType,TGradientImagePixelType,TOdfPixelType,
NOrderL,NrOdfDirections>::OdfPixelType
itk::AnalyticalDiffusionQballReconstructionImageFilter
<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,
NOrderL, NrOdfDirections>
::Normalize( OdfPixelType odf,
typename NumericTraits<ReferencePixelType>::AccumulateType b0 )
{
switch( m_NormalizationMethod )
{
case QBAR_STANDARD:
{
TOdfPixelType sum = 0;
for(int i=0; i<NrOdfDirections; i++)
{
sum += odf[i];
}
if(sum>0)
odf /= sum;
return odf;
break;
}
case QBAR_B_ZERO_B_VALUE:
{
for(int i=0; i<NrOdfDirections; i++)
{
odf[i] = ((TOdfPixelType)log((TOdfPixelType)b0)-odf[i])/m_BValue;
}
return odf;
break;
}
case QBAR_B_ZERO:
{
odf *= 1.0/b0;
return odf;
break;
}
case QBAR_NONE:
{
return odf;
break;
}
case QBAR_ADC_ONLY:
{
for(int i=0; i<NrOdfDirections; i++)
{
odf[i] = ((TOdfPixelType)log((TOdfPixelType)b0)-odf[i])/m_BValue;
}
return odf;
break;
}
case QBAR_RAW_SIGNAL:
{
return odf;
break;
}
case QBAR_SOLID_ANGLE:
{
for(int i=0; i<NrOdfDirections; i++)
odf[i] *= QBALL_ANAL_RECON_PI*4/NrOdfDirections;
break;
}
case QBAR_NONNEG_SOLID_ANGLE:
{
break;
}
}
return odf;
}
template<
class TReferenceImagePixelType,
class TGradientImagePixelType,
class TOdfPixelType,
int NOrderL,
int NrOdfDirections>
vnl_vector<TOdfPixelType>
itk::AnalyticalDiffusionQballReconstructionImageFilter
<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,
NOrderL, NrOdfDirections>
::PreNormalize( vnl_vector<TOdfPixelType> vec,
typename NumericTraits<ReferencePixelType>::AccumulateType b0 )
{
switch( m_NormalizationMethod )
{
case QBAR_STANDARD:
{
return vec;
break;
}
case QBAR_B_ZERO_B_VALUE:
{
int n = vec.size();
for(int i=0; i<n; i++)
{
if (vec[i]<=0)
vec[i] = 0.001;
vec[i] = log(vec[i]);
}
return vec;
break;
}
case QBAR_B_ZERO:
{
return vec;
break;
}
case QBAR_NONE:
{
return vec;
break;
}
case QBAR_ADC_ONLY:
{
int n = vec.size();
for(int i=0; i<n; i++)
{
if (vec[i]<=0)
vec[i] = 0.001;
vec[i] = log(vec[i]);
}
return vec;
break;
}
case QBAR_RAW_SIGNAL:
{
return vec;
break;
}
case QBAR_SOLID_ANGLE:
case QBAR_NONNEG_SOLID_ANGLE:
{
int n = vec.size();
double b0f = (double)b0;
for(int i=0; i<n; i++)
{
vec[i] = vec[i]/b0f;
if (vec[i]<0)
vec[i] = m_Delta1;
else if (vec[i]<m_Delta1)
vec[i] = m_Delta1/2 + vec[i]*vec[i]/(2*m_Delta1);
else if (vec[i]>=1)
vec[i] = 1-m_Delta2/2;
else if (vec[i]>=1-m_Delta2)
vec[i] = 1-m_Delta2/2-(1-vec[i])*(1-vec[i])/(2*m_Delta2);
vec[i] = log(-log(vec[i]));
}
return vec;
break;
}
}
return vec;
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::BeforeThreadedGenerateData()
{
// If we have more than 2 inputs, then each input, except the first is a
// gradient image. The number of gradient images must match the number of
// gradient directions.
//const unsigned int numberOfInputs = this->GetNumberOfInputs();
// There need to be at least 6 gradient directions to be able to compute the
// tensor basis
if( m_NumberOfGradientDirections < (L*L + L + 2)/2 + L )
{
itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (L*L + L + 2)/2 + L << " needed for SH-order " << L);
}
// Input must be an itk::VectorImage.
std::string gradientImageClassName(
this->ProcessObject::GetInput(0)->GetNameOfClass());
if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 )
{
itkExceptionMacro( <<
"There is only one Gradient image. I expect that to be a VectorImage. "
<< "But its of type: " << gradientImageClassName );
}
this->ComputeReconstructionMatrix();
typename GradientImagesType::Pointer img = static_cast< GradientImagesType * >(
this->ProcessObject::GetInput(0) );
m_BZeroImage = BZeroImageType::New();
m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin
m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction
m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
m_BZeroImage->Allocate();
m_ODFSumImage = BZeroImageType::New();
m_ODFSumImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
m_ODFSumImage->SetOrigin( img->GetOrigin() ); // Set the image origin
m_ODFSumImage->SetDirection( img->GetDirection() ); // Set the image direction
m_ODFSumImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
m_ODFSumImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
m_ODFSumImage->Allocate();
m_CoefficientImage = CoefficientImageType::New();
m_CoefficientImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
m_CoefficientImage->SetOrigin( img->GetOrigin() ); // Set the image origin
m_CoefficientImage->SetDirection( img->GetDirection() ); // Set the image direction
m_CoefficientImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
m_CoefficientImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
m_CoefficientImage->Allocate();
if(m_NormalizationMethod == QBAR_SOLID_ANGLE || m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE)
m_Lambda = 0.0;
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
ThreadIdType )
{
typename OutputImageType::Pointer outputImage =
static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
oit.GoToBegin();
ImageRegionIterator< BZeroImageType > oit2(m_BZeroImage, outputRegionForThread);
oit2.GoToBegin();
ImageRegionIterator< FloatImageType > oit3(m_ODFSumImage, outputRegionForThread);
oit3.GoToBegin();
ImageRegionIterator< CoefficientImageType > oit4(m_CoefficientImage, outputRegionForThread);
oit4.GoToBegin();
typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType;
typedef typename GradientImagesType::PixelType GradientVectorType;
typename GradientImagesType::Pointer gradientImagePointer = NULL;
// Would have liked a dynamic_cast here, but seems SGI doesn't like it
// The enum will ensure that an inappropriate cast is not done
gradientImagePointer = static_cast< GradientImagesType * >(
this->ProcessObject::GetInput(0) );
GradientIteratorType git(gradientImagePointer, outputRegionForThread );
git.GoToBegin();
// Compute the indicies of the baseline images and gradient images
std::vector<unsigned int> baselineind; // contains the indicies of
// the baseline images
std::vector<unsigned int> gradientind; // contains the indicies of
// the gradient images
for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
{
if(gdcit.Value().one_norm() <= 0.0)
baselineind.push_back(gdcit.Index());
else
gradientind.push_back(gdcit.Index());
}
if( m_DirectionsDuplicated )
{
int gradIndSize = gradientind.size();
for(int i=0; i<gradIndSize; i++)
gradientind.push_back(gradientind[i]);
}
while( !git.IsAtEnd() )
{
GradientVectorType b = git.Get();
typename NumericTraits<ReferencePixelType>::AccumulateType b0 = NumericTraits<ReferencePixelType>::Zero;
// Average the baseline image pixels
for(unsigned int i = 0; i < baselineind.size(); ++i)
{
b0 += b[baselineind[i]];
}
b0 /= this->m_NumberOfBaselineImages;
OdfPixelType odf(0.0);
typename CoefficientImageType::PixelType coeffPixel(0.0);
vnl_vector<TO> B(m_NumberOfGradientDirections);
if( (b0 != 0) && (b0 >= m_Threshold) )
{
for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ )
{
B[i] = static_cast<TO>(b[gradientind[i]]);
}
B = PreNormalize(B, b0);
if(m_NormalizationMethod == QBAR_SOLID_ANGLE)
{
vnl_vector<TO> coeffs(m_NumberCoefficients);
coeffs = ( (*m_CoeffReconstructionMatrix) * B );
coeffs[0] += 1.0/(2.0*sqrt(QBALL_ANAL_RECON_PI));
odf = ( (*m_SphericalHarmonicBasisMatrix) * coeffs ).data_block();
coeffPixel = coeffs.data_block();
}
else if(m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE)
{
/** this would be the place to implement a non-negative
* solver for quadratic programming problem:
* min .5*|| Bc-s ||^2 subject to -CLPc <= 4*pi*ones
* (refer to MICCAI 2009 Goh et al. "Estimating ODFs with PDF constraints")
* .5*|| Bc-s ||^2 == .5*c'B'Bc - x'B's + .5*s's
*/
itkExceptionMacro( << "Nonnegative Solid Angle not yet implemented");
}
else
{
vnl_vector<TO> coeffs(m_NumberCoefficients);
coeffs = ( (*m_CoeffReconstructionMatrix) * B );
coeffs[0] += 1.0/(2.0*sqrt(QBALL_ANAL_RECON_PI));
coeffPixel = coeffs.data_block();
odf = ( (*m_ReconstructionMatrix) * B ).data_block();
}
odf = Normalize(odf, b0);
}
oit.Set( odf );
oit2.Set( b0 );
float sum = 0;
for (int k=0; k<odf.Size(); k++)
sum += (float) odf[k];
oit3.Set( sum-1 );
oit4.Set(coeffPixel);
++oit; // odf image iterator
++oit3; // odf sum image iterator
++oit2; // b0 image iterator
++oit4; // coefficient image iterator
++git; // Gradient image iterator
}
std::cout << "One Thread finished reconstruction" << std::endl;
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::tofile2(vnl_matrix<double> *pA, std::string fname)
{
vnl_matrix<double> A = (*pA);
ofstream myfile;
std::locale C("C");
std::locale originalLocale = myfile.getloc();
myfile.imbue(C);
myfile.open (fname.c_str());
myfile << "A1=[";
for(int i=0; i<A.rows(); i++)
{
for(int j=0; j<A.columns(); j++)
{
myfile << A(i,j) << " ";
if(j==A.columns()-1 && i!=A.rows()-1)
myfile << ";";
}
}
myfile << "];";
myfile.close();
myfile.imbue( originalLocale );
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::Cart2Sph(double x, double y, double z, double *spherical)
{
double phi, theta, r;
r = sqrt(x*x+y*y+z*z);
if( r<mitk::eps )
{
theta = M_PI/2;
phi = M_PI/2;
}
else
{
theta = acos(z/r);
phi = atan2(y, x);
}
spherical[0] = phi;
spherical[1] = theta;
spherical[2] = r;
}
template< class T, class TG, class TO, int L, int NODF>
double AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
-::Yj(int m, int l, double theta, double phi)
+::Yj(int m, int l, double theta, double phi, bool useMRtrixBasis)
{
- if (m<0)
- return sqrt(2.0)*spherical_harmonic_r(l, -m, theta, phi);
- else if (m==0)
- return spherical_harmonic_r(l, m, theta, phi);
+ if (!useMRtrixBasis)
+ {
+ if (m<0)
+ return sqrt(2.0)*spherical_harmonic_r(l, -m, theta, phi);
+ else if (m==0)
+ return spherical_harmonic_r(l, m, theta, phi);
+ else
+ return pow(-1.0,m)*sqrt(2.0)*spherical_harmonic_i(l, m, theta, phi);
+ }
else
- return pow(-1.0,m)*sqrt(2.0)*spherical_harmonic_i(l, m, theta, phi);
+ {
+ double plm = legendre_p<double>(l,abs(m),-cos(theta));
+ double mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))*plm;
+ if (m>0)
+ return mag*cos(m*phi);
+ else if (m==0)
+ return mag;
+ else
+ return mag*sin(-m*phi);
+ }
return 0;
}
template< class T, class TG, class TO, int L, int NODF>
double AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::Legendre0(int l)
{
if( l%2 != 0 )
{
return 0;
}
else
{
double prod1 = 1.0;
for(int i=1;i<l;i+=2) prod1 *= i;
double prod2 = 1.0;
for(int i=2;i<=l;i+=2) prod2 *= i;
return pow(-1.0,l/2.0)*(prod1/prod2);
}
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::ComputeReconstructionMatrix()
{
//for(int i=-6;i<7;i++)
// std::cout << boost::math::legendre_p<double>(6, i, 0.65657) << std::endl;
if( m_NumberOfGradientDirections < (L*L + L + 2)/2 + L )
{
itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (L*L + L + 2)/2 + L << " needed for SH-order " << L);
}
{
// check for duplicate diffusion gradients
bool warning = false;
for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
{
for(GradientDirectionContainerType::ConstIterator gdcit2 = this->m_GradientDirectionContainer->Begin();
gdcit2 != this->m_GradientDirectionContainer->End(); ++gdcit2)
{
if(gdcit1.Value() == gdcit2.Value() && gdcit1.Index() != gdcit2.Index())
{
itkWarningMacro( << "Some of the Diffusion Gradients equal each other. Corresponding image data should be averaged before calling this filter." );
warning = true;
break;
}
}
if (warning) break;
}
// handle acquisition schemes where only half of the spherical
// shell is sampled by the gradient directions. In this case,
// each gradient direction is duplicated in negative direction.
vnl_vector<double> centerMass(3);
centerMass.fill(0.0);
int count = 0;
for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
{
if(gdcit1.Value().one_norm() > 0.0)
{
centerMass += gdcit1.Value();
count ++;
}
}
centerMass /= count;
if(centerMass.two_norm() > 0.1)
{
m_DirectionsDuplicated = true;
m_NumberOfGradientDirections *= 2;
}
}
vnl_matrix<double> *Q = new vnl_matrix<double>(3, m_NumberOfGradientDirections);
{
int i = 0;
for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
{
if(gdcit.Value().one_norm() > 0.0)
{
double x = gdcit.Value().get(0);
double y = gdcit.Value().get(1);
double z = gdcit.Value().get(2);
double cart[3];
Cart2Sph(x,y,z,cart);
(*Q)(0,i) = cart[0];
(*Q)(1,i) = cart[1];
(*Q)(2,i++) = cart[2];
}
}
if(m_DirectionsDuplicated)
{
for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
{
if(gdcit.Value().one_norm() > 0.0)
{
double x = gdcit.Value().get(0);
double y = gdcit.Value().get(1);
double z = gdcit.Value().get(2);
double cart[3];
Cart2Sph(x,y,z,cart);
(*Q)(0,i) = cart[0];
(*Q)(1,i) = cart[1];
(*Q)(2,i++) = cart[2];
}
}
}
}
int l = L;
m_NumberCoefficients = (int)(l*l + l + 2.0)/2.0 + l;
vnl_matrix<double>* B = new vnl_matrix<double>(m_NumberOfGradientDirections,m_NumberCoefficients);
vnl_matrix<double>* _L = new vnl_matrix<double>(m_NumberCoefficients,m_NumberCoefficients);
_L->fill(0.0);
vnl_matrix<double>* LL = new vnl_matrix<double>(m_NumberCoefficients,m_NumberCoefficients);
LL->fill(0.0);
vnl_matrix<double>* P = new vnl_matrix<double>(m_NumberCoefficients,m_NumberCoefficients);
P->fill(0.0);
vnl_matrix<double>* Inv = new vnl_matrix<double>(m_NumberCoefficients,m_NumberCoefficients);
P->fill(0.0);
vnl_vector<int>* lj = new vnl_vector<int>(m_NumberCoefficients);
m_LP = new vnl_vector<double>(m_NumberCoefficients);
for(unsigned int i=0; i<m_NumberOfGradientDirections; i++)
{
for(int k=0; k<=l; k+=2)
{
for(int m=-k; m<=k; m++)
{
int j = (k*k + k + 2)/2 + m - 1;
(*_L)(j,j) = -k*(k+1);
(*m_LP)(j) = -k*(k+1);
(*lj)[j] = k;
double phi = (*Q)(0,i);
double th = (*Q)(1,i);
- (*B)(i,j) = Yj(m,k,th,phi);
+ (*B)(i,j) = Yj(m,k,th,phi, m_UseMrtrixBasis);
}
}
}
//vnl_matrix<double> temp((*_L)*(*_L));
LL->update(*_L);
*LL *= *_L;
//tofile2(LL,"LL");
for(int i=0; i<m_NumberCoefficients; i++)
{
// here we leave out the 2*pi multiplication from Descoteaux
// this is because we do not want the real integral value
// but an average value over the equator.
if(m_NormalizationMethod == QBAR_SOLID_ANGLE || m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE)
{
(*P)(i,i) = 2.0*QBALL_ANAL_RECON_PI*Legendre0((*lj)[i]);
(*m_LP)(i) *= (*P)(i,i);
}
else
{
(*P)(i,i) = Legendre0((*lj)[i]);
}
}
m_B_t = new vnl_matrix<double>(B->transpose());
//tofile2(&m_B_t,"m_B_t");
vnl_matrix<double> B_t_B = (*m_B_t) * (*B);
//tofile2(&B_t_B,"B_t_B");
vnl_matrix<double> lambdaLL(m_NumberCoefficients,m_NumberCoefficients);
lambdaLL.update((*LL));
lambdaLL *= m_Lambda;
//tofile2(&lambdaLL,"lLL");
vnl_matrix<double> tmp( B_t_B + lambdaLL);
vnl_matrix_inverse<double> *pseudoInverse
= new vnl_matrix_inverse<double>( tmp );
(*Inv) = pseudoInverse->pinverse();
//tofile2(Inv,"Inv");
vnl_matrix<double> temp((*Inv) * (*m_B_t));
double fac1 = (1.0/(16.0*QBALL_ANAL_RECON_PI*QBALL_ANAL_RECON_PI));
switch(m_NormalizationMethod)
{
case QBAR_ADC_ONLY:
case QBAR_RAW_SIGNAL:
break;
case QBAR_STANDARD:
case QBAR_B_ZERO_B_VALUE:
case QBAR_B_ZERO:
case QBAR_NONE:
temp = (*P) * temp;
break;
case QBAR_SOLID_ANGLE:
temp = fac1 * (*P) * (*_L) * temp;
break;
case QBAR_NONNEG_SOLID_ANGLE:
break;
}
//tofile2(&temp,"A");
m_CoeffReconstructionMatrix = new vnl_matrix<TO>(m_NumberCoefficients,m_NumberOfGradientDirections);
for(int i=0; i<m_NumberCoefficients; i++)
{
for(unsigned int j=0; j<m_NumberOfGradientDirections; j++)
{
(*m_CoeffReconstructionMatrix)(i,j) = (float) temp(i,j);
}
}
// this code goes to the image adapter coeffs->odfs later
int NOdfDirections = NODF;
vnl_matrix_fixed<double, 3, NODF>* U =
itk::PointShell<NODF, vnl_matrix_fixed<double, 3, NODF> >::DistributePointShell();
m_SphericalHarmonicBasisMatrix = new vnl_matrix<TO>(NOdfDirections,m_NumberCoefficients);
vnl_matrix<double>* sphericalHarmonicBasisMatrix2
= new vnl_matrix<double>(NOdfDirections,m_NumberCoefficients);
for(int i=0; i<NOdfDirections; i++)
{
double x = (*U)(0,i);
double y = (*U)(1,i);
double z = (*U)(2,i);
double cart[3];
Cart2Sph(x,y,z,cart);
(*U)(0,i) = cart[0];
(*U)(1,i) = cart[1];
(*U)(2,i) = cart[2];
}
for(int i=0; i<NOdfDirections; i++)
{
for(int k=0; k<=l; k+=2)
{
for(int m=-k; m<=k; m++)
{
int j = (k*k + k + 2)/2 + m - 1;
double phi = (*U)(0,i);
double th = (*U)(1,i);
- (*m_SphericalHarmonicBasisMatrix)(i,j) = Yj(m,k,th,phi);
+ (*m_SphericalHarmonicBasisMatrix)(i,j) = Yj(m,k,th,phi,m_UseMrtrixBasis);
(*sphericalHarmonicBasisMatrix2)(i,j) = (*m_SphericalHarmonicBasisMatrix)(i,j);
}
}
}
m_ReconstructionMatrix = new vnl_matrix<TO>(NOdfDirections,m_NumberOfGradientDirections);
*m_ReconstructionMatrix = (*m_SphericalHarmonicBasisMatrix) * (*m_CoeffReconstructionMatrix);
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::SetGradientImage(const GradientDirectionContainerType *gradientDirection,
- const GradientImagesType *gradientImage )
+ const GradientImagesType *gradientImage )
{
- // Copy Gradient Direction Container
- this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
- for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin();
- it != gradientDirection->End(); it++)
- {
- this->m_GradientDirectionContainer->push_back(it.Value());
- }
+ // Copy Gradient Direction Container
+ this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
+ for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin();
+ it != gradientDirection->End(); it++)
+ {
+ this->m_GradientDirectionContainer->push_back(it.Value());
+ }
unsigned int numImages = gradientDirection->Size();
this->m_NumberOfBaselineImages = 0;
for(GradientDirectionContainerType::Iterator it = this->m_GradientDirectionContainer->Begin();
it != this->m_GradientDirectionContainer->End(); it++)
{
if(it.Value().one_norm() <= 0.0)
{
this->m_NumberOfBaselineImages++;
}
else // Normalize non-zero gradient directions
{
it.Value() = it.Value() / it.Value().two_norm();
}
}
this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages;
// ensure that the gradient image we received has as many components as
// the number of gradient directions
if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + m_NumberOfGradientDirections )
{
itkExceptionMacro( << m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages
<< "baselines = " << m_NumberOfGradientDirections + this->m_NumberOfBaselineImages
<< " directions specified but image has " << gradientImage->GetVectorLength()
<< " components.");
}
this->ProcessObject::SetNthInput( 0, const_cast< GradientImagesType* >(gradientImage) );
}
template< class T, class TG, class TO, int L, int NODF>
void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,L,NODF>
::PrintSelf(std::ostream& os, Indent indent) const
{
std::locale C("C");
std::locale originalLocale = os.getloc();
os.imbue(C);
Superclass::PrintSelf(os,indent);
os << indent << "OdfReconstructionMatrix: " << m_ReconstructionMatrix << std::endl;
if ( m_GradientDirectionContainer )
os << indent << "GradientDirectionContainer: " << m_GradientDirectionContainer << std::endl;
else
os << indent << "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
os << indent << "NumberOfGradientDirections: " << m_NumberOfGradientDirections << std::endl;
os << indent << "NumberOfBaselineImages: " << m_NumberOfBaselineImages << std::endl;
os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl;
os << indent << "BValue: " << m_BValue << std::endl;
os.imbue( originalLocale );
}
}
#endif // __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
index 2c1e91c897..44d65be144 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
@@ -1,282 +1,285 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkAnalyticalDiffusionQballReconstructionImageFilter_h_
#define __itkAnalyticalDiffusionQballReconstructionImageFilter_h_
#include "itkImageToImageFilter.h"
#include "vnl/vnl_vector_fixed.h"
#include "vnl/vnl_matrix.h"
#include "vnl/algo/vnl_svd.h"
#include "itkVectorContainer.h"
#include "itkVectorImage.h"
namespace itk{
/** \class AnalyticalDiffusionQballReconstructionImageFilter
* \brief This class takes as input one or more reference image (acquired in the
* absence of diffusion sensitizing gradients) and 'n' diffusion
* weighted images and their gradient directions and computes an image of
* orientation distribution function coefficients in a spherical harmonic basis.
*
* \par Inputs and Usage
* \par
* When you have the 'n' gradient and one or more reference images in a single
* multi-component image (VectorImage), you can specify the images as
* \code
* filter->SetGradientImage( directionsContainer, vectorImage );
* \endcode
* Note that this method is used to specify both the reference and gradient images.
* This is convenient when the DWI images are read in using the
* <a href="http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format">NRRD</a>
* format. Like the Nrrd format, the reference images are those components of the
* vectorImage whose gradient direction is (0,0,0). If more than one reference image
* is present, they are averaged prior to the reconstruction.
*
* \par Outputs
* The output image is an image of vectors that must be understood as ODFs:
* \code
* Image< Vector< TPixelType, OdfNrDirections >, 3 >
* \endcode
*
* \par Parameters
* \li Threshold - Threshold on the reference image data. The output ODF will
* be a null pdf for pixels in the reference image that have a value less
* than this.
* \li BValue - See the documentation of SetBValue().
* \li At least 6 gradient images must be specified for the filter to be able
* to run. If the input gradient directions g_i are majorly sampled on one half
* of the sqhere, then each input image I_i will be duplicated and assign -g_i
* in order to guarantee stability of the algorithm.
* \li OdfDirections - directions of resulting orientation distribution function
* \li EquatorNrSamplingPoints - number of sampling points on equator when
* performing Funk Radeon Transform (FRT)
* \li BasisFunctionCenters - the centers of the basis functions are used for
* the sRBF (spherical radial basis functions interpolation). If not set, they
* will be defaulted to equal m_EquatorNrSamplingPoints
*
* \par Template parameters
* The class is templated over
* \li the pixel type of the reference and gradient images
* (expected to be scalar data types)
* \li the internal representation of the ODF pixels (double, float etc).
* \li the number of OdfDirections
* \li the number of basis function centers for the sRBF
*
* \par References:
* \li<a href="http://www3.interscience.wiley.com/cgi-bin/fulltext/109800293/PDFSTART">[1]</a>
* <em>Tuch DS,
* "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72.</em>
*
*/
template< class TReferenceImagePixelType,
class TGradientImagePixelType,
class TOdfPixelType,
int NOrderL,
int NrOdfDirections>
class AnalyticalDiffusionQballReconstructionImageFilter :
public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >,
Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
{
public:
enum Normalization {
QBAR_STANDARD,
QBAR_B_ZERO_B_VALUE,
QBAR_B_ZERO,
QBAR_NONE,
QBAR_ADC_ONLY,
QBAR_RAW_SIGNAL,
QBAR_SOLID_ANGLE,
QBAR_NONNEG_SOLID_ANGLE
};
typedef AnalyticalDiffusionQballReconstructionImageFilter Self;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>,
Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > Superclass;
/** Method for creation through the object factory. */
itkNewMacro(Self)
/** Runtime information support. */
itkTypeMacro(AnalyticalDiffusionQballReconstructionImageFilter, ImageToImageFilter)
typedef TReferenceImagePixelType ReferencePixelType;
typedef TGradientImagePixelType GradientPixelType;
typedef Vector< TOdfPixelType, NrOdfDirections > OdfPixelType;
typedef TOdfPixelType BZeroPixelType;
/** Reference image data, This image is aquired in the absence
* of a diffusion sensitizing field gradient */
typedef typename Superclass::InputImageType ReferenceImageType;
typedef Image< OdfPixelType, 3 > OdfImageType;
typedef OdfImageType OutputImageType;
typedef Image< Vector< TOdfPixelType, (NOrderL*NOrderL + NOrderL + 2)/2 + NOrderL >, 3 > CoefficientImageType;
typedef Image< BZeroPixelType, 3 > BZeroImageType;
typedef typename Superclass::OutputImageRegionType
OutputImageRegionType;
/** Typedef defining one (of the many) gradient images. */
typedef Image< GradientPixelType, 3 > GradientImageType;
/** An alternative typedef defining one (of the many) gradient images.
* It will be assumed that the vectorImage has the same dimension as the
* Reference image and a vector length parameter of \c n (number of
* gradient directions)*/
typedef VectorImage< GradientPixelType, 3 > GradientImagesType;
/** Holds the ODF reconstruction matrix */
typedef vnl_matrix< TOdfPixelType >*
OdfReconstructionMatrixType;
typedef vnl_matrix< double > CoefficientMatrixType;
/** Holds each magnetic field gradient used to acquire one DWImage */
typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
/** Container to hold gradient directions of the 'n' DW measurements */
typedef VectorContainer< unsigned int,
GradientDirectionType > GradientDirectionContainerType;
/** set method to add gradient directions and its corresponding
* image. The image here is a VectorImage. The user is expected to pass the
* gradient directions in a container. The ith element of the container
* corresponds to the gradient direction of the ith component image the
* VectorImage. For the baseline image, a vector of all zeros
* should be set.*/
void SetGradientImage( const GradientDirectionContainerType *,
const GradientImagesType *image);
/** Get reference image */
virtual ReferenceImageType * GetReferenceImage()
{ return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); }
/** Return the gradient direction. idx is 0 based */
virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
{
if( idx >= m_NumberOfGradientDirections )
itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
return m_GradientDirectionContainer->ElementAt( idx+1 );
}
static void tofile2(vnl_matrix<double> *A, std::string fname);
static void Cart2Sph(double x, double y, double z, double* cart);
- static double Yj(int m, int k, double theta, double phi);
+ static double Yj(int m, int k, double theta, double phi, bool useMRtrixBasis = false);
double Legendre0(int l);
OdfPixelType Normalize(OdfPixelType odf, typename NumericTraits<ReferencePixelType>::AccumulateType b0 );
vnl_vector<TOdfPixelType> PreNormalize( vnl_vector<TOdfPixelType> vec, typename NumericTraits<ReferencePixelType>::AccumulateType b0 );
/** Threshold on the reference image data. The output ODF will be a null
* pdf for pixels in the reference image that have a value less than this
* threshold. */
itkSetMacro( Threshold, ReferencePixelType )
itkGetMacro( Threshold, ReferencePixelType )
itkSetMacro( NormalizationMethod, Normalization)
itkGetMacro( NormalizationMethod, Normalization )
typedef Image<float, 3> FloatImageType;
itkGetMacro( BZeroImage, typename BZeroImageType::Pointer)
itkGetMacro( ODFSumImage, typename FloatImageType::Pointer)
itkGetMacro( CoefficientImage, typename CoefficientImageType::Pointer)
itkSetMacro( BValue, TOdfPixelType)
#ifdef GetBValue
#undef GetBValue
#endif
itkGetConstReferenceMacro( BValue, TOdfPixelType)
itkSetMacro( Lambda, double )
itkGetMacro( Lambda, double )
+ itkSetMacro( UseMrtrixBasis, bool )
+
#ifdef ITK_USE_CONCEPT_CHECKING
/** Begin concept checking */
itkConceptMacro(ReferenceEqualityComparableCheck,
(Concept::EqualityComparable<ReferencePixelType>));
itkConceptMacro(TensorEqualityComparableCheck,
(Concept::EqualityComparable<OdfPixelType>));
itkConceptMacro(GradientConvertibleToDoubleCheck,
(Concept::Convertible<GradientPixelType, double>));
itkConceptMacro(DoubleConvertibleToTensorCheck,
(Concept::Convertible<double, OdfPixelType>));
itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
(Concept::AdditiveOperators<GradientPixelType, GradientPixelType,
ReferencePixelType>));
itkConceptMacro(ReferenceOStreamWritableCheck,
(Concept::OStreamWritable<ReferencePixelType>));
itkConceptMacro(TensorOStreamWritableCheck,
(Concept::OStreamWritable<OdfPixelType>));
/** End concept checking */
#endif
protected:
AnalyticalDiffusionQballReconstructionImageFilter();
~AnalyticalDiffusionQballReconstructionImageFilter() {};
void PrintSelf(std::ostream& os, Indent indent) const;
void ComputeReconstructionMatrix();
void BeforeThreadedGenerateData();
void ThreadedGenerateData( const
OutputImageRegionType &outputRegionForThread, ThreadIdType);
private:
OdfReconstructionMatrixType m_ReconstructionMatrix;
OdfReconstructionMatrixType m_CoeffReconstructionMatrix;
OdfReconstructionMatrixType m_SphericalHarmonicBasisMatrix;
/** container to hold gradient directions */
GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
/** Number of gradient measurements */
unsigned int m_NumberOfGradientDirections;
/** Number of baseline images */
unsigned int m_NumberOfBaselineImages;
/** Threshold on the reference image data */
ReferencePixelType m_Threshold;
/** LeBihan's b-value for normalizing tensors */
TOdfPixelType m_BValue;
typename BZeroImageType::Pointer m_BZeroImage;
double m_Lambda;
bool m_DirectionsDuplicated;
Normalization m_NormalizationMethod;
int m_NumberCoefficients;
vnl_matrix<double>* m_B_t;
vnl_vector<double>* m_LP;
FloatImageType::Pointer m_ODFSumImage;
typename CoefficientImageType::Pointer m_CoefficientImage;
TOdfPixelType m_Delta1;
TOdfPixelType m_Delta2;
+ bool m_UseMrtrixBasis;
};
}
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkAnalyticalDiffusionQballReconstructionImageFilter.cpp"
#endif
#endif //__itkAnalyticalDiffusionQballReconstructionImageFilter_h_
diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkMrtrixPeakImageConverter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkMrtrixPeakImageConverter.cpp
index 423e156d64..49a5fc6b7e 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkMrtrixPeakImageConverter.cpp
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkMrtrixPeakImageConverter.cpp
@@ -1,211 +1,211 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkMrtrixPeakImageConverter_cpp
#define __itkMrtrixPeakImageConverter_cpp
#include <time.h>
#include <stdio.h>
#include <stdlib.h>
#include "itkMrtrixPeakImageConverter.h"
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionConstIteratorWithIndex.h>
#include <itkImageRegionIterator.h>
#include <itkContinuousIndex.h>
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkPolyLine.h>
namespace itk {
template< class PixelType >
MrtrixPeakImageConverter< PixelType >::MrtrixPeakImageConverter():
m_NormalizationMethod(NO_NORM)
{
}
template< class PixelType >
void MrtrixPeakImageConverter< PixelType >
::GenerateData()
{
// output vector field
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
Vector<float, 4> spacing4 = m_InputImage->GetSpacing();
Point<float, 4> origin4 = m_InputImage->GetOrigin();
Matrix<double, 4, 4> direction4 = m_InputImage->GetDirection();
ImageRegion<4> imageRegion4 = m_InputImage->GetLargestPossibleRegion();
Vector<double, 3> spacing3;
Point<float, 3> origin3;
Matrix<double, 3, 3> direction3;
ImageRegion<3> imageRegion3;
spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2];
origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2];
for (int r=0; r<3; r++)
for (int c=0; c<3; c++)
direction3[r][c] = direction4[r][c];
imageRegion3.SetSize(0, imageRegion4.GetSize()[0]);
imageRegion3.SetSize(1, imageRegion4.GetSize()[1]);
imageRegion3.SetSize(2, imageRegion4.GetSize()[2]);
double minSpacing = spacing3[0];
if (spacing3[1]<minSpacing)
minSpacing = spacing3[1];
if (spacing3[2]<minSpacing)
minSpacing = spacing3[2];
m_DirectionImageContainer = DirectionImageContainerType::New();
typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
int x = m_InputImage->GetLargestPossibleRegion().GetSize(0);
int y = m_InputImage->GetLargestPossibleRegion().GetSize(1);
int z = m_InputImage->GetLargestPossibleRegion().GetSize(2);
int numDirs = m_InputImage->GetLargestPossibleRegion().GetSize(3)/3;
m_NumDirectionsImage = ItkUcharImgType::New();
m_NumDirectionsImage->SetSpacing( spacing3 );
m_NumDirectionsImage->SetOrigin( origin3 );
m_NumDirectionsImage->SetDirection( direction3 );
m_NumDirectionsImage->SetRegions( imageRegion3 );
m_NumDirectionsImage->Allocate();
m_NumDirectionsImage->FillBuffer(0);
for (int i=0; i<numDirs; i++)
{
ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New();
directionImage->SetSpacing( spacing3 );
directionImage->SetOrigin( origin3 );
directionImage->SetDirection( direction3 );
directionImage->SetRegions( imageRegion3 );
directionImage->Allocate();
Vector< PixelType, 3 > nullVec; nullVec.Fill(0.0);
directionImage->FillBuffer(nullVec);
m_DirectionImageContainer->InsertElement(m_DirectionImageContainer->Size(), directionImage);
}
double minangle = 0;
for (int i=0; i<numDirs; i++)
{
for (int a=0; a<x; a++)
for (int b=0; b<y; b++)
for (int c=0; c<z; c++)
{
// generate vector field
typename InputImageType::IndexType index;
index.SetElement(0,a);
index.SetElement(1,b);
index.SetElement(2,c);
vnl_vector<double> dirVec; dirVec.set_size(4);
for (int k=0; k<3; k++)
{
index.SetElement(3,k+i*3);
dirVec[k] = m_InputImage->GetPixel(index);
}
dirVec[3] = 0;
if (dirVec.magnitude()<0.0001)
continue;
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
itk::ContinuousIndex<double, 4> center;
center[0] = index[0];
center[1] = index[1];
center[2] = index[2];
center[3] = 0;
itk::Point<double, 4> worldCenter;
m_InputImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter );
switch (m_NormalizationMethod)
{
case NO_NORM:
break;
case SINGLE_VEC_NORM:
dirVec.normalize();
break;
}
dirVec.normalize();
dirVec = m_InputImage->GetDirection()*dirVec;
itk::Point<double> worldStart;
worldStart[0] = worldCenter[0]-dirVec[0]/2 * minSpacing;
worldStart[1] = worldCenter[1]-dirVec[1]/2 * minSpacing;
worldStart[2] = worldCenter[2]-dirVec[2]/2 * minSpacing;
vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
itk::Point<double> worldEnd;
worldEnd[0] = worldCenter[0]+dirVec[0]/2 * minSpacing;
worldEnd[1] = worldCenter[1]+dirVec[1]/2 * minSpacing;
worldEnd[2] = worldCenter[2]+dirVec[2]/2 * minSpacing;
id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
m_VtkCellArray->InsertNextCell(container);
// generate direction image
typename ItkDirectionImageType::IndexType index2;
index2[0] = a; index2[1] = b; index2[2] = c;
-// // workaround *********************************************
-// dirVec = m_InputImage->GetDirection()*dirVec;
-// dirVec.normalize();
-// // workaround *********************************************
+ // workaround *********************************************
+ dirVec = m_InputImage->GetDirection()*dirVec;
+ dirVec.normalize();
+ // workaround *********************************************
Vector< PixelType, 3 > pixel;
pixel.SetElement(0, dirVec[0]);
pixel.SetElement(1, dirVec[1]);
pixel.SetElement(2, dirVec[2]);
for (int j=0; j<numDirs; j++)
{
ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->ElementAt(j);
Vector< PixelType, 3 > tempPix = directionImage->GetPixel(index2);
if (tempPix.GetNorm()<0.01)
{
directionImage->SetPixel(index2, pixel);
break;
}
else
{
if ( fabs(dot_product(tempPix.GetVnlVector(), pixel.GetVnlVector()))>minangle )
{
minangle = fabs(dot_product(tempPix.GetVnlVector(), pixel.GetVnlVector()));
MITK_INFO << "Minimum angle: " << acos(minangle)*180.0/M_PI;
}
}
}
m_NumDirectionsImage->SetPixel(index2, m_NumDirectionsImage->GetPixel(index2)+1);
}
}
vtkSmartPointer<vtkPolyData> directionsPolyData = vtkSmartPointer<vtkPolyData>::New();
directionsPolyData->SetPoints(m_VtkPoints);
directionsPolyData->SetLines(m_VtkCellArray);
m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData);
}
}
#endif // __itkMrtrixPeakImageConverter_cpp
diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.cpp
new file mode 100644
index 0000000000..098bac7781
--- /dev/null
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.cpp
@@ -0,0 +1,96 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+#ifndef __itkShCoefficientImageExporter_cpp
+#define __itkShCoefficientImageExporter_cpp
+
+#include <time.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "itkShCoefficientImageExporter.h"
+#include <itkImageRegionIterator.h>
+#include <boost/math/special_functions.hpp>
+
+using namespace boost::math;
+
+namespace itk {
+
+template< class PixelType, int ShOrder >
+ShCoefficientImageExporter< PixelType, ShOrder >::ShCoefficientImageExporter()
+{
+
+}
+
+template< class PixelType, int ShOrder >
+void ShCoefficientImageExporter< PixelType, ShOrder >
+::GenerateData()
+{
+ if (m_InputImage.IsNull())
+ return;
+
+ Vector<float, 4> spacing4;
+ Point<float, 4> origin4;
+ Matrix<double, 4, 4> direction4; direction4.SetIdentity();
+ ImageRegion<4> imageRegion4;
+
+ Vector<double, 3> spacing3 = m_InputImage->GetSpacing();
+ Point<float, 3> origin3 = m_InputImage->GetOrigin();
+ Matrix<double, 3, 3> direction3 = m_InputImage->GetDirection();
+ ImageRegion<3> imageRegion3 = m_InputImage->GetLargestPossibleRegion();
+
+ spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
+ origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
+ for (int r=0; r<3; r++)
+ for (int c=0; c<3; c++)
+ direction4[r][c] = direction3[r][c];
+
+ imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
+ imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
+ imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
+ imageRegion4.SetSize(3, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder );
+
+ m_OutputImage = CoefficientImageType::New();
+ m_OutputImage->SetSpacing( spacing4 );
+ m_OutputImage->SetOrigin( origin4 );
+ m_OutputImage->SetDirection( direction4 );
+ m_OutputImage->SetRegions( imageRegion4 );
+ m_OutputImage->Allocate();
+ m_OutputImage->FillBuffer(0.0);
+
+ typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
+ InputIteratorType it(m_InputImage, m_InputImage->GetLargestPossibleRegion());
+ int numCoeffs = imageRegion4.GetSize(3);
+
+ while(!it.IsAtEnd())
+ {
+ CoefficientImageType::IndexType index;
+ index[0] = it.GetIndex()[0];
+ index[1] = it.GetIndex()[1];
+ index[2] = it.GetIndex()[2];
+
+ for (int i=0; i<numCoeffs; i++)
+ {
+ index[3] = i;
+ m_OutputImage->SetPixel(index, it.Get()[i]);
+ }
+
+ ++it;
+ }
+}
+
+}
+
+#endif // __itkShCoefficientImageExporter_cpp
diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.h
new file mode 100644
index 0000000000..ad629ede75
--- /dev/null
+++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkShCoefficientImageExporter.h
@@ -0,0 +1,79 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006-03-27 17:01:06 $
+ Version: $Revision: 1.12 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkShCoefficientImageExporter_h_
+#define __itkShCoefficientImageExporter_h_
+
+#include <itkOrientationDistributionFunction.h>
+
+namespace itk{
+/** \class ShCoefficientImageExporter
+ Converts FSL reconstructions of diffusionweighted images (4D images containing the sh coefficients) to qball images or 3D sh-coefficient images.
+*/
+
+template< class PixelType, int ShOrder >
+class ShCoefficientImageExporter : public ProcessObject
+{
+
+public:
+
+ enum NormalizationMethods {
+ NO_NORM,
+ SINGLE_VEC_NORM,
+ SPACING_COMPENSATION
+ };
+
+
+ typedef ShCoefficientImageExporter Self;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+ typedef ProcessObject Superclass;
+ typedef itk::Image< float, 4 > CoefficientImageType;
+ typedef Image< Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 > InputImageType;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self)
+
+ /** Runtime information support. */
+ itkTypeMacro(ShCoefficientImageExporter, ProcessObject)
+
+ // input
+ itkSetMacro( InputImage, typename InputImageType::Pointer) ///< sh coefficient image in FSL file format
+
+ // output
+ itkGetMacro( OutputImage, typename CoefficientImageType::Pointer) ///< mitk style image containing the SH coefficients
+
+ void GenerateData();
+
+protected:
+ ShCoefficientImageExporter();
+ ~ShCoefficientImageExporter(){}
+
+ typename InputImageType::Pointer m_InputImage;
+ CoefficientImageType::Pointer m_OutputImage;
+
+private:
+
+};
+
+}
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkShCoefficientImageExporter.cpp"
+#endif
+
+#endif //__itkShCoefficientImageExporter_h_
+
diff --git a/Modules/DiffusionImaging/DiffusionCore/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp
index 7ab9f2ec1b..6164793663 100644
--- a/Modules/DiffusionImaging/DiffusionCore/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp
+++ b/Modules/DiffusionImaging/DiffusionCore/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp
@@ -1,459 +1,483 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "mitkNrrdTensorImageReader.h"
#include "itkImageFileReader.h"
#include "itkImageRegionIterator.h"
#include "itkMetaDataObject.h"
#include "itkNrrdImageIO.h"
#include <itkNiftiImageIO.h>
#include "mitkITKImageImport.h"
#include "mitkImageDataItem.h"
namespace mitk
{
void NrrdTensorImageReader
::GenerateData()
{
if ( m_FileName == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
}
else
{
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
try
{
- MITK_INFO << "Trying to load dti as nifti ...";
std::string fname3 = "temp_dti.nii";
itksys::SystemTools::CopyAFile(m_FileName.c_str(), fname3.c_str());
- typedef itk::Image<float,4> ImageType;
+ typedef itk::VectorImage<float,3> ImageType;
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
- itksys::SystemTools::RemoveFile(fname3.c_str());
-
ImageType::Pointer img = reader->GetOutput();
- itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
-
- itk::ImageRegion< 3 > region;
- region.SetSize(0,size[0]);
- region.SetSize(1,size[1]);
- region.SetSize(2,size[2]);
- itk::Vector<double,3> spacing;
- spacing[0] = img->GetSpacing()[0];
- spacing[1] = img->GetSpacing()[1];
- spacing[2] = img->GetSpacing()[2];
- itk::Point<double,3> origin;
- origin[0] = img->GetOrigin()[0];
- origin[1] = img->GetOrigin()[1];
- origin[2] = img->GetOrigin()[2];
- itk::Matrix<double,3,3> direction;
- direction[0][0] = img->GetDirection()[0][0];
- direction[1][0] = img->GetDirection()[1][0];
- direction[2][0] = img->GetDirection()[2][0];
- direction[0][1] = img->GetDirection()[0][1];
- direction[1][1] = img->GetDirection()[1][1];
- direction[2][1] = img->GetDirection()[2][1];
- direction[0][2] = img->GetDirection()[0][2];
- direction[1][2] = img->GetDirection()[1][2];
- direction[2][2] = img->GetDirection()[2][2];
typedef itk::Image<itk::DiffusionTensor3D<float>,3> VecImgType;
- typedef VecImgType::PixelType FixPixType;
VecImgType::Pointer vecImg = VecImgType::New();
- vecImg->SetSpacing( spacing );
- vecImg->SetOrigin( origin );
- vecImg->SetDirection( direction );
- vecImg->SetRegions( region );
+ vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
+ vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
+ vecImg->SetDirection( img->GetDirection() ); // Set the image direction
+ vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
- while (!ot.IsAtEnd())
- {
- itk::DiffusionTensor3D<float> tensor;
- ImageType::IndexType idx;
- idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
+ itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
+ it = it.Begin();
- if (size[3]==6)
+ typedef ImageType::PixelType VarPixType;
+ typedef VecImgType::PixelType FixPixType;
+ int numComponents = img->GetNumberOfComponentsPerPixel();
+
+ if (numComponents==6)
+ {
+ MITK_INFO << "Trying to load dti as 6-comp nifti ...";
+ while (!it.IsAtEnd())
{
- for (int te=0; te<size[3]; te++)
- {
- idx[3] = te;
- tensor.SetElement(te, img->GetPixel(idx));
- }
+ VarPixType vec = it.Get();
+ FixPixType fixVec(vec.GetDataPointer());
+
+ itk::DiffusionTensor3D<float> tensor;
+ tensor.SetElement(0, vec.GetElement(0));
+ tensor.SetElement(1, vec.GetElement(1));
+ tensor.SetElement(2, vec.GetElement(2));
+ tensor.SetElement(3, vec.GetElement(3));
+ tensor.SetElement(4, vec.GetElement(4));
+ tensor.SetElement(5, vec.GetElement(5));
+
+ fixVec = tensor;
+
+ ot.Set(fixVec);
+ ++ot;
+ ++it;
}
- else if (size[3]==9)
+ }
+ else if(numComponents==9)
+ {
+ MITK_INFO << "Trying to load dti as 9-comp nifti ...";
+ while (!it.IsAtEnd())
{
- idx[3] = 0;
- tensor.SetElement(0, img->GetPixel(idx));
- idx[3] = 1;
- tensor.SetElement(1, img->GetPixel(idx));
- idx[3] = 2;
- tensor.SetElement(2, img->GetPixel(idx));
- idx[3] = 4;
- tensor.SetElement(3, img->GetPixel(idx));
- idx[3] = 5;
- tensor.SetElement(4, img->GetPixel(idx));
- idx[3] = 8;
- tensor.SetElement(5, img->GetPixel(idx));
+ VarPixType vec = it.Get();
+ itk::DiffusionTensor3D<float> tensor;
+ tensor.SetElement(0, vec.GetElement(0));
+ tensor.SetElement(1, vec.GetElement(1));
+ tensor.SetElement(2, vec.GetElement(2));
+ tensor.SetElement(3, vec.GetElement(4));
+ tensor.SetElement(4, vec.GetElement(5));
+ tensor.SetElement(5, vec.GetElement(8));
+
+ FixPixType fixVec(tensor);
+ ot.Set(fixVec);
+ ++ot;
+ ++it;
}
- else
- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
+ }
+ else if (numComponents==1)
+ {
+ MITK_INFO << "Trying to load dti as 4D nifti ...";
+ typedef itk::Image<float,4> ImageType;
+ itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
+ typedef itk::ImageFileReader<ImageType> FileReaderType;
+ FileReaderType::Pointer reader = FileReaderType::New();
+ reader->SetImageIO(io);
+ reader->SetFileName(this->m_FileName);
+ reader->Update();
+ ImageType::Pointer img = reader->GetOutput();
+
+ itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
+
+ while (!ot.IsAtEnd())
+ {
+ itk::DiffusionTensor3D<float> tensor;
+ ImageType::IndexType idx;
+ idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
+
+ if (size[3]==6)
+ {
+ for (int te=0; te<size[3]; te++)
+ {
+ idx[3] = te;
+ tensor.SetElement(te, img->GetPixel(idx));
+ }
+ }
+ else if (size[3]==9)
+ {
+ idx[3] = 0;
+ tensor.SetElement(0, img->GetPixel(idx));
+ idx[3] = 1;
+ tensor.SetElement(1, img->GetPixel(idx));
+ idx[3] = 2;
+ tensor.SetElement(2, img->GetPixel(idx));
+ idx[3] = 4;
+ tensor.SetElement(3, img->GetPixel(idx));
+ idx[3] = 5;
+ tensor.SetElement(4, img->GetPixel(idx));
+ idx[3] = 8;
+ tensor.SetElement(5, img->GetPixel(idx));
+ }
+ else
+ throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
- FixPixType fixVec(tensor);
- ot.Set(fixVec);
- ++ot;
+ FixPixType fixVec(tensor);
+ ot.Set(fixVec);
+ ++ot;
+ }
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
}
catch(...)
{
MITK_INFO << "Trying to load dti as nrrd ...";
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
typedef itk::Image<itk::DiffusionTensor3D<float>,3> VecImgType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot = ot.Begin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it = it.Begin();
typedef ImageType::PixelType VarPixType;
typedef VecImgType::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString;
bool readFrame = false;
double xx, xy, xz, yx, yy, yz, zx, zy, zz;
MeasurementFrameType measFrame;
measFrame.SetIdentity();
MeasurementFrameType measFrameTransp;
measFrameTransp.SetIdentity();
for (; itKey != imgMetaKeys.end(); itKey ++)
{
itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
if (itKey->find("measurement frame") != std::string::npos)
{
sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
yx>10e-10 || yy>10e-10 || yz>10e-10 ||
zx>10e-10 || zy>10e-10 || zz>10e-10 )
{
readFrame = true;
measFrame(0,0) = xx;
measFrame(0,1) = xy;
measFrame(0,2) = xz;
measFrame(1,0) = yx;
measFrame(1,1) = yy;
measFrame(1,2) = yz;
measFrame(2,0) = zx;
measFrame(2,1) = zy;
measFrame(2,2) = zz;
measFrameTransp = measFrame.GetTranspose();
}
}
}
if (numComponents==6)
{
while (!it.IsAtEnd())
{
// T'=RTR'
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
if(readFrame)
{
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
fixVec = tensor;
}
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
itk::DiffusionTensor3D<float> tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
typedef itk::Image<float,4> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(this->m_FileName);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
MITK_INFO << size;
while (!ot.IsAtEnd())
{
itk::DiffusionTensor3D<float> tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
-
- // idx[3] = 0;
- // tensor.SetElement(0, img->GetPixel(idx));
- // idx[3] = 1;
- // tensor.SetElement(1, img->GetPixel(idx));
- // idx[3] = 3;
- // tensor.SetElement(2, img->GetPixel(idx));
- // idx[3] = 2;
- // tensor.SetElement(3, img->GetPixel(idx));
- // idx[3] = 4;
- // tensor.SetElement(4, img->GetPixel(idx));
- // idx[3] = 5;
- // tensor.SetElement(5, img->GetPixel(idx));
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
else
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
}
this->GetOutput()->InitializeByItk(vecImg.GetPointer());
this->GetOutput()->SetVolume(vecImg->GetBufferPointer());
}
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
}
}
}
void NrrdTensorImageReader::GenerateOutputInformation()
{
}
const char* NrrdTensorImageReader
::GetFileName() const
{
return m_FileName.c_str();
}
void NrrdTensorImageReader
::SetFileName(const char* aFileName)
{
m_FileName = aFileName;
}
const char* NrrdTensorImageReader
::GetFilePrefix() const
{
return m_FilePrefix.c_str();
}
void NrrdTensorImageReader
::SetFilePrefix(const char* aFilePrefix)
{
m_FilePrefix = aFilePrefix;
}
const char* NrrdTensorImageReader
::GetFilePattern() const
{
return m_FilePattern.c_str();
}
void NrrdTensorImageReader
::SetFilePattern(const char* aFilePattern)
{
m_FilePattern = aFilePattern;
}
bool NrrdTensorImageReader
::CanReadFile(const std::string filename, const std::string /*filePrefix*/, const std::string /*filePattern*/)
{
// First check the extension
if( filename == "" )
{
return false;
}
std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
ext = itksys::SystemTools::LowerCase(ext);
if (ext == ".hdti" || ext == ".dti")
{
return true;
}
return false;
}
itk::DiffusionTensor3D<float> NrrdTensorImageReader
::ConvertMatrixTypeToFixedArrayType(const itk::DiffusionTensor3D<float>::Superclass::MatrixType & matrix)
{
/* | 0 1 2 |
* | X 3 4 |
* | X X 5 |
*/
itk::DiffusionTensor3D<float> arr;
arr.SetElement(0,matrix(0,0));
arr.SetElement(1,matrix(0,1));
arr.SetElement(2,matrix(0,2));
arr.SetElement(3,matrix(1,3));
arr.SetElement(4,matrix(1,4));
arr.SetElement(5,matrix(2,5));
return arr;
}
} //namespace MITK
diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt
index d45daf111d..3280d50d47 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt
+++ b/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt
@@ -1 +1,3 @@
-MITK_CREATE_MODULE_TESTS()
\ No newline at end of file
+MITK_CREATE_MODULE_TESTS()
+
+mitkAddCustomModuleTest(mitkImageReconstructionTest mitkImageReconstructionTest ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test.dwi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_dti.dti ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QN0.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA0.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA6.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA4.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA5.qbi)
diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake b/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake
index 2b1323b4e3..53141cf060 100644
--- a/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake
+++ b/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake
@@ -1,9 +1,10 @@
set(MODULE_TESTS
mitkFactoryRegistrationTest.cpp
)
set(MODULE_CUSTOM_TESTS
mitkPyramidImageRegistrationMethodTest.cpp
mitkDWHeadMotionCorrectionTest.cpp
+ mitkImageReconstructionTest.cpp
)
diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp
new file mode 100755
index 0000000000..8010609d10
--- /dev/null
+++ b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp
@@ -0,0 +1,156 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkImageCast.h>
+#include <mitkTensorImage.h>
+#include <mitkQBallImage.h>
+#include <mitkDiffusionImage.h>
+#include <mitkIOUtil.h>
+#include <mitkBaseDataIOFactory.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <itkDiffusionTensor3D.h>
+#include <mitkTestingMacros.h>
+#include <itkDiffusionTensor3DReconstructionImageFilter.h>
+#include <itkDiffusionTensor3D.h>
+#include <itkDiffusionQballReconstructionImageFilter.h>
+#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
+#include <mitkNrrdQBallImageWriter.h>
+
+using namespace std;
+
+int mitkImageReconstructionTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkImageReconstructionTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data")
+
+ try
+ {
+ RegisterDiffusionCoreObjectFactory();
+
+ mitk::DiffusionImage<short>::Pointer dwi = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData());
+
+ {
+ MITK_INFO << "Tensor reconstruction " << argv[2];
+ mitk::TensorImage::Pointer tensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData());
+ typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
+ TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->Update();
+ mitk::TensorImage::Pointer testImage = mitk::TensorImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, tensorImage, 0.0001, true), "tensor reconstruction test.");
+ }
+
+ {
+ MITK_INFO << "Numerical Q-ball reconstruction " << argv[3];
+ mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData());
+ typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, QBALL_ODFSIZE> QballReconstructionImageFilterType;
+ QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
+ filter->Update();
+ mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Numerical Q-ball reconstruction test.");
+ }
+
+ {
+ MITK_INFO << "Standard Q-ball reconstruction " << argv[4];
+ mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData());
+ typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->SetLambda(0.006);
+ filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
+ filter->Update();
+ mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Standard Q-ball reconstruction test.");
+ }
+
+ {
+ MITK_INFO << "CSA Q-ball reconstruction " << argv[5];
+ mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData());
+ typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->SetLambda(0.006);
+ filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
+ filter->Update();
+ mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "CSA Q-ball reconstruction test.");
+ }
+
+ {
+ MITK_INFO << "ADC profile reconstruction " << argv[6];
+ mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData());
+ typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->SetLambda(0.006);
+ filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY);
+ filter->Update();
+ mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "ADC profile reconstruction test.");
+ }
+
+ {
+ MITK_INFO << "Raw signal modeling " << argv[7];
+ mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData());
+ typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
+ filter->SetBValue(dwi->GetB_Value());
+ filter->SetLambda(0.006);
+ filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL);
+ filter->Update();
+ mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
+ testImage->InitializeByItk( filter->GetOutput() );
+ testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Raw signal modeling test.");
+ }
+ }
+ catch (itk::ExceptionObject e)
+ {
+ MITK_INFO << e;
+ return EXIT_FAILURE;
+ }
+ catch (std::exception e)
+ {
+ MITK_INFO << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_INFO << "ERROR!?!";
+ return EXIT_FAILURE;
+ }
+
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/DiffusionCore/files.cmake b/Modules/DiffusionImaging/DiffusionCore/files.cmake
index fae94626db..cb589f5d62 100644
--- a/Modules/DiffusionImaging/DiffusionCore/files.cmake
+++ b/Modules/DiffusionImaging/DiffusionCore/files.cmake
@@ -1,146 +1,147 @@
set(CPP_FILES
# DicomImport
DicomImport/mitkDicomDiffusionImageReader.cpp
# DicomImport/mitkGroupDiffusionHeadersFilter.cpp
DicomImport/mitkDicomDiffusionImageHeaderReader.cpp
DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp
DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp
DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp
DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp
# DataStructures
IODataStructures/mitkDiffusionCoreObjectFactory.cpp
# DataStructures -> DWI
IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp
IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp
IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp
IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp
IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp
IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp
IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp
IODataStructures/DiffusionWeightedImages/mitkImageToDiffusionImageSource.cpp
IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp
# DataStructures -> QBall
IODataStructures/QBallImages/mitkQBallImageSource.cpp
IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp
IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp
IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp
IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp
IODataStructures/QBallImages/mitkQBallImage.cpp
IODataStructures/QBallImages/mitkQBallImageSerializer.cpp
# DataStructures -> Tensor
IODataStructures/TensorImages/mitkTensorImageSource.cpp
IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp
IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp
IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp
IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp
IODataStructures/TensorImages/mitkTensorImage.cpp
IODataStructures/TensorImages/mitkTensorImageSerializer.cpp
#IODataStructures/mitkRegistrationObject.cpp
# Rendering
Rendering/vtkMaskedProgrammableGlyphFilter.cpp
Rendering/mitkCompositeMapper.cpp
Rendering/mitkVectorImageVtkGlyphMapper3D.cpp
Rendering/vtkOdfSource.cxx
Rendering/vtkThickPlane.cxx
Rendering/mitkOdfNormalizationMethodProperty.cpp
Rendering/mitkOdfScaleByProperty.cpp
Rendering/mitkPlanarFigureMapper3D.cpp
# Algorithms
Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp
Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp
Algorithms/itkDwiGradientLengthCorrectionFilter.cpp
# Registration Algorithms & Co.
Algorithms/Registration/mitkRegistrationWrapper.cpp
Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp
# MultishellProcessing
Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp
Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp
Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp
Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp
# Function Collection
mitkDiffusionFunctionCollection.cpp
)
set(H_FILES
# function Collection
mitkDiffusionFunctionCollection.h
# Rendering
Rendering/mitkDiffusionImageMapper.h
Rendering/mitkOdfVtkMapper2D.h
Rendering/mitkPlanarFigureMapper3D.h
# Reconstruction
Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h
Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h
Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h
Algorithms/Reconstruction/itkPointShell.h
Algorithms/Reconstruction/itkOrientationDistributionFunction.h
Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h
# MultishellProcessing
Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h
Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h
Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h
Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h
Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h
Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h
# IO Datastructures
IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h
# Algorithms
Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h
Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h
Algorithms/itkTensorDerivedMeasurementsFilter.h
Algorithms/itkBrainMaskExtractionImageFilter.h
Algorithms/itkB0ImageExtractionImageFilter.h
Algorithms/itkB0ImageExtractionToSeparateImageFilter.h
Algorithms/itkTensorImageToDiffusionImageFilter.h
Algorithms/itkTensorToL2NormImageFilter.h
Algorithms/itkGaussianInterpolateImageFunction.h
Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h
Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h
Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h
Algorithms/itkCartesianToPolarVectorImageFilter.h
Algorithms/itkPolarToCartesianVectorImageFilter.h
Algorithms/itkDistanceMapFilter.h
Algorithms/itkProjectionFilter.h
Algorithms/itkResidualImageFilter.h
Algorithms/itkExtractChannelFromRgbaImageFilter.h
Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h
Algorithms/itkMergeDiffusionImagesFilter.h
Algorithms/itkDwiPhantomGenerationFilter.h
Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.h
Algorithms/itkMrtrixPeakImageConverter.h
Algorithms/itkFslPeakImageConverter.h
Algorithms/itkShCoefficientImageImporter.h
+ Algorithms/itkShCoefficientImageExporter.h
Algorithms/itkOdfMaximaExtractionFilter.h
Algorithms/itkResampleDwiImageFilter.h
Algorithms/itkDwiGradientLengthCorrectionFilter.h
Algorithms/itkAdcImageFilter.h
Algorithms/itkSplitDWImageFilter.h
Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h
Algorithms/mitkDiffusionImageToDiffusionImageFilter.h
)
set( TOOL_FILES
)
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp
index c3fe379a38..ab53b96ec8 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp
@@ -1,317 +1,368 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkAddArtifactsToDwiImageFilter_txx
#define __itkAddArtifactsToDwiImageFilter_txx
#include <time.h>
#include <stdio.h>
#include <stdlib.h>
#include "itkAddArtifactsToDwiImageFilter.h"
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionConstIteratorWithIndex.h>
#include <itkImageRegionIterator.h>
#include <boost/progress.hpp>
#include <itkImageDuplicator.h>
#include <itkResampleDwiImageFilter.h>
#include <itkCropImageFilter.h>
#define _USE_MATH_DEFINES
#include <math.h>
namespace itk {
template< class TPixelType >
AddArtifactsToDwiImageFilter< TPixelType >
::AddArtifactsToDwiImageFilter()
: m_NoiseModel(NULL)
, m_FrequencyMap(NULL)
, m_kOffset(0)
, m_tLine(1)
, m_EddyGradientStrength(0.001)
, m_SimulateEddyCurrents(false)
, m_TE(100)
, m_AddGibbsRinging(false)
, m_Spikes(0)
, m_SpikeAmplitude(1)
, m_Wrap(1.0)
{
this->SetNumberOfRequiredInputs( 1 );
}
template< class TPixelType >
AddArtifactsToDwiImageFilter< TPixelType >::ComplexSliceType::Pointer AddArtifactsToDwiImageFilter< TPixelType >::RearrangeSlice(ComplexSliceType::Pointer slice)
{
ImageRegion<2> region = slice->GetLargestPossibleRegion();
typename ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New();
rearrangedSlice->SetLargestPossibleRegion( region );
rearrangedSlice->SetBufferedRegion( region );
rearrangedSlice->SetRequestedRegion( region );
rearrangedSlice->Allocate();
int xHalf = region.GetSize(0)/2;
int yHalf = region.GetSize(1)/2;
for (int y=0; y<region.GetSize(1); y++)
for (int x=0; x<region.GetSize(0); x++)
{
typename SliceType::IndexType idx;
idx[0]=x; idx[1]=y;
vcl_complex< SliceType::PixelType > pix = slice->GetPixel(idx);
if( idx[0] < xHalf )
idx[0] = idx[0] + xHalf;
else
idx[0] = idx[0] - xHalf;
if( idx[1] < yHalf )
idx[1] = idx[1] + yHalf;
else
idx[1] = idx[1] - yHalf;
rearrangedSlice->SetPixel(idx, pix);
}
return rearrangedSlice;
}
template< class TPixelType >
void AddArtifactsToDwiImageFilter< TPixelType >
::GenerateData()
{
+ m_StartTime = clock();
+ m_StatusText = "Starting simulation\n";
+
typename DiffusionImageType::Pointer inputImage = static_cast< DiffusionImageType * >( this->ProcessObject::GetInput(0) );
itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion();
typename itk::ImageDuplicator<DiffusionImageType>::Pointer duplicator = itk::ImageDuplicator<DiffusionImageType>::New();
duplicator->SetInputImage( inputImage );
duplicator->Update();
typename DiffusionImageType::Pointer outputImage = duplicator->GetOutput();
// is input slize size even?
int xMax=inputRegion.GetSize(0); int yMax=inputRegion.GetSize(1);
if ( xMax%2 == 1 )
xMax += 1;
if ( yMax%2 == 1 )
yMax += 1;
// create slice object
typename SliceType::Pointer slice = SliceType::New();
ImageRegion<2> sliceRegion;
sliceRegion.SetSize(0, xMax);
sliceRegion.SetSize(1, yMax);
slice->SetLargestPossibleRegion( sliceRegion );
slice->SetBufferedRegion( sliceRegion );
slice->SetRequestedRegion( sliceRegion );
slice->Allocate();
slice->FillBuffer(0.0);
ImageRegion<2> upsampledSliceRegion;
if (m_AddGibbsRinging)
{
upsampledSliceRegion.SetSize(0, xMax*2);
upsampledSliceRegion.SetSize(1, yMax*2);
}
// frequency map slice
typename SliceType::Pointer fMap = NULL;
if (m_FrequencyMap.IsNotNull())
{
fMap = SliceType::New();
fMap->SetLargestPossibleRegion( sliceRegion );
fMap->SetBufferedRegion( sliceRegion );
fMap->SetRequestedRegion( sliceRegion );
fMap->Allocate();
fMap->FillBuffer(0.0);
}
if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || m_kOffset>0.0 || m_AddGibbsRinging || m_SimulateEddyCurrents || m_Wrap<1.0)
{
ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Wrap);
itk::Point<double,3> shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2;
outputImage = DiffusionImageType::New();
outputImage->SetSpacing( inputImage->GetSpacing() );
outputImage->SetOrigin( shiftedOrigin );
outputImage->SetDirection( inputImage->GetDirection() );
outputImage->SetLargestPossibleRegion( croppedRegion );
outputImage->SetBufferedRegion( croppedRegion );
outputImage->SetRequestedRegion( croppedRegion );
outputImage->SetVectorLength( inputImage->GetVectorLength() );
outputImage->Allocate();
typename DiffusionImageType::PixelType temp;
temp.SetSize(inputImage->GetVectorLength());
temp.Fill(0.0);
outputImage->FillBuffer(temp);
int tempY=croppedRegion.GetSize(1);
if ( tempY%2 == 1 )
tempY += 1;
croppedRegion.SetSize(1, tempY);
MatrixType transform = inputImage->GetDirection();
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
transform[i][j] *= inputImage->GetSpacing()[j];
- MITK_INFO << "Adjusting complex signal";
+ MITK_INFO << this->GetTime()+" > Adjusting complex signal";
MITK_INFO << "line readout time: " << m_tLine;
MITK_INFO << "line offset: " << m_kOffset;
if (m_FrequencyMap.IsNotNull())
MITK_INFO << "frequency map is set";
else
MITK_INFO << "no frequency map set";
if (m_AddGibbsRinging)
MITK_INFO << "Gibbs ringing enabled";
else
MITK_INFO << "Gibbs ringing disabled";
if (m_SimulateEddyCurrents)
MITK_INFO << "Simulating eddy currents";
std::vector< int > spikeVolume;
for (int i=0; i<m_Spikes; i++)
spikeVolume.push_back(rand()%inputImage->GetVectorLength());
std::sort (spikeVolume.begin(), spikeVolume.end());
std::reverse (spikeVolume.begin(), spikeVolume.end());
+ m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n";
+ m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
+ unsigned long lastTick = 0;
boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2));
for (unsigned int g=0; g<inputImage->GetVectorLength(); g++)
{
std::vector< int > spikeSlice;
while (!spikeVolume.empty() && spikeVolume.back()==g)
{
spikeSlice.push_back(rand()%inputImage->GetLargestPossibleRegion().GetSize(2));
spikeVolume.pop_back();
}
std::sort (spikeSlice.begin(), spikeSlice.end());
std::reverse (spikeSlice.begin(), spikeSlice.end());
for (unsigned int z=0; z<inputRegion.GetSize(2); z++)
{
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
+ }
+
std::vector< SliceType::Pointer > compartmentSlices;
// extract slice from channel g
for (unsigned int y=0; y<sliceRegion.GetSize(1); y++)
for (unsigned int x=0; x<sliceRegion.GetSize(0); x++)
{
typename SliceType::IndexType index2D;
index2D[0]=x; index2D[1]=y;
typename DiffusionImageType::IndexType index3D;
index3D[0]=x; index3D[1]=y; index3D[2]=z;
SliceType::PixelType pix2D = (SliceType::PixelType)inputImage->GetPixel(index3D)[g];
slice->SetPixel(index2D, pix2D);
if (fMap.IsNotNull())
fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D));
}
if (m_AddGibbsRinging)
{
itk::ResampleImageFilter<SliceType, SliceType>::Pointer resampler = itk::ResampleImageFilter<SliceType, SliceType>::New();
resampler->SetInput(slice);
resampler->SetOutputParametersFromImage(slice);
resampler->SetSize(upsampledSliceRegion.GetSize());
resampler->SetOutputSpacing(slice->GetSpacing()/2);
resampler->Update();
typename SliceType::Pointer upslice = resampler->GetOutput();
compartmentSlices.push_back(upslice);
}
else
compartmentSlices.push_back(slice);
// fourier transform slice
typename ComplexSliceType::Pointer fSlice;
itk::Size<2> outSize; outSize.SetElement(0, xMax); outSize.SetElement(1, croppedRegion.GetSize()[1]);
typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New();
idft->SetCompartmentImages(compartmentSlices);
idft->SetkOffset(m_kOffset);
idft->SettLine(m_tLine);
idft->SetSimulateRelaxation(false);
idft->SetFrequencyMap(fMap);
idft->SetDiffusionGradientDirection(m_GradientList.at(g));
idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents);
idft->SetEddyGradientMagnitude(m_EddyGradientStrength);
idft->SetTE(m_TE);
idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0);
idft->SetDirectionMatrix(transform);
idft->SetOutSize(outSize);
int numSpikes = 0;
while (!spikeSlice.empty() && spikeSlice.back()==z)
{
numSpikes++;
spikeSlice.pop_back();
}
idft->SetSpikes(numSpikes);
idft->SetSpikeAmplitude(m_SpikeAmplitude);
idft->Update();
fSlice = idft->GetOutput();
// inverse fourier transform slice
typename SliceType::Pointer newSlice;
typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New();
dft->SetInput(fSlice);
dft->Update();
newSlice = dft->GetOutput();
// put slice back into channel g
for (unsigned int y=0; y<outputImage->GetLargestPossibleRegion().GetSize(1); y++)
for (unsigned int x=0; x<outputImage->GetLargestPossibleRegion().GetSize(0); x++)
{
typename DiffusionImageType::IndexType index3D;
index3D[0]=x; index3D[1]=y; index3D[2]=z;
typename DiffusionImageType::PixelType pix3D = outputImage->GetPixel(index3D);
typename SliceType::IndexType index2D;
index2D[0]=x; index2D[1]=y;
double signal = newSlice->GetPixel(index2D);
if (signal>0)
signal = floor(signal+0.5);
else
signal = ceil(signal-0.5);
pix3D[g] = signal;
outputImage->SetPixel(index3D, pix3D);
}
++disp;
+ unsigned long newTick = 50*disp.count()/disp.expected_count();
+ for (unsigned int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
}
}
+ m_StatusText += "\n\n";
}
if (m_NoiseModel!=NULL)
{
+ m_StatusText += this->GetTime()+" > Adding noise\n";
+ m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n";
+ m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
+ unsigned long lastTick = 0;
+
ImageRegionIterator<DiffusionImageType> it1 (outputImage, outputImage->GetLargestPossibleRegion());
- boost::progress_display disp2(outputImage->GetLargestPossibleRegion().GetNumberOfPixels());
+ boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetNumberOfPixels());
while(!it1.IsAtEnd())
{
- ++disp2;
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
+ }
+
+ ++disp;
+ unsigned long newTick = 50*disp.count()/disp.expected_count();
+ for (unsigned int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
typename DiffusionImageType::PixelType signal = it1.Get();
m_NoiseModel->AddNoise(signal);
it1.Set(signal);
++it1;
}
+ m_StatusText += "\n\n";
}
this->SetNthOutput(0, outputImage);
+ m_StatusText += "Finished simulation\n";
+ m_StatusText += "Simulation time: "+GetTime();
+}
+
+template< class TPixelType >
+std::string AddArtifactsToDwiImageFilter< TPixelType >::GetTime()
+{
+ unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC;
+ unsigned long hours = total/3600;
+ unsigned long minutes = (total%3600)/60;
+ unsigned long seconds = total%60;
+ std::string out = "";
+ out.append(boost::lexical_cast<std::string>(hours));
+ out.append(":");
+ out.append(boost::lexical_cast<std::string>(minutes));
+ out.append(":");
+ out.append(boost::lexical_cast<std::string>(seconds));
+ return out;
}
}
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h
index c4a9040d46..27f4b426ec 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h
@@ -1,103 +1,107 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkAddArtifactsToDwiImageFilter_h_
#define __itkAddArtifactsToDwiImageFilter_h_
#include "FiberTrackingExports.h"
#include <itkImageToImageFilter.h>
#include <itkVectorImage.h>
#include <itkKspaceImageFilter.h>
#include <itkDftImageFilter.h>
#include <mitkDiffusionNoiseModel.h>
#include <mitkDiffusionSignalModel.h>
namespace itk{
/**
* \brief Adds several artifacts to the input DWI. */
template< class TPixelType >
class AddArtifactsToDwiImageFilter :
public ImageToImageFilter< VectorImage< TPixelType, 3 >, VectorImage< TPixelType, 3 > >
{
public:
typedef AddArtifactsToDwiImageFilter Self;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
typedef ImageToImageFilter< VectorImage< TPixelType, 3 >, VectorImage< TPixelType, 3 > > Superclass;
/** Method for creation through the object factory. */
itkNewMacro(Self)
/** Runtime information support. */
itkTypeMacro(AddArtifactsToDwiImageFilter, ImageToImageFilter)
typedef typename Superclass::InputImageType DiffusionImageType;
typedef mitk::DiffusionNoiseModel<short> NoiseModelType;
typedef itk::Image< double, 2 > SliceType;
typedef typename itk::KspaceImageFilter< double >::OutputImageType ComplexSliceType;
typedef itk::Image<double, 3> ItkDoubleImgType;
typedef itk::Matrix<double, 3, 3> MatrixType;
void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; }
itkSetMacro( FrequencyMap, ItkDoubleImgType::Pointer )
itkSetMacro( kOffset, double )
itkSetMacro( tLine, double )
itkSetMacro( SimulateEddyCurrents, bool )
itkSetMacro( EddyGradientStrength, double )
void SetGradientList(mitk::DiffusionSignalModel<double>::GradientListType list) { m_GradientList=list; }
itkSetMacro( TE, double )
itkSetMacro( AddGibbsRinging, bool )
itkSetMacro( Spikes, int )
itkSetMacro( SpikeAmplitude, double )
itkSetMacro( Wrap, double )
+ itkGetMacro( StatusText, std::string )
protected:
AddArtifactsToDwiImageFilter();
~AddArtifactsToDwiImageFilter() {}
typename ComplexSliceType::Pointer RearrangeSlice(typename ComplexSliceType::Pointer slice);
+ std::string GetTime();
void GenerateData();
NoiseModelType* m_NoiseModel;
ItkDoubleImgType::Pointer m_FrequencyMap;
double m_kOffset;
double m_tLine;
bool m_SimulateEddyCurrents;
double m_EddyGradientStrength;
mitk::DiffusionSignalModel<double>::GradientListType m_GradientList;
double m_TE;
bool m_AddGibbsRinging; ///< causes ringing artifacts
int m_Spikes;
double m_SpikeAmplitude;
double m_Wrap;
+ std::string m_StatusText;
+ time_t m_StartTime;
private:
};
}
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkAddArtifactsToDwiImageFilter.cpp"
#endif
#endif //__itkAddArtifactsToDwiImageFilter_h_
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp
index bbf4f2acbd..28603a7c36 100755
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp
@@ -1,389 +1,363 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkEvaluateDirectionImagesFilter_cpp
#define __itkEvaluateDirectionImagesFilter_cpp
#include "itkEvaluateDirectionImagesFilter.h"
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionIterator.h>
#include <itkImageDuplicator.h>
#include <boost/progress.hpp>
#define _USE_MATH_DEFINES
#include <math.h>
namespace itk {
template< class PixelType >
EvaluateDirectionImagesFilter< PixelType >
::EvaluateDirectionImagesFilter():
m_ImageSet(NULL),
m_ReferenceImageSet(NULL),
m_IgnoreMissingDirections(false),
m_Eps(0.0001)
{
- this->SetNumberOfOutputs(2);
+ this->SetNumberOfIndexedOutputs(2);
}
template< class PixelType >
void EvaluateDirectionImagesFilter< PixelType >::GenerateData()
{
if (m_ImageSet.IsNull() || m_ReferenceImageSet.IsNull())
return;
DirectionImageContainerType::Pointer set1 = DirectionImageContainerType::New();
DirectionImageContainerType::Pointer set2 = DirectionImageContainerType::New();
for (int i=0; i<m_ImageSet->Size(); i++)
{
typename itk::ImageDuplicator< DirectionImageType >::Pointer duplicator = itk::ImageDuplicator< DirectionImageType >::New();
duplicator->SetInputImage( m_ImageSet->GetElement(i) );
duplicator->Update();
set1->InsertElement(i, dynamic_cast<DirectionImageType*>(duplicator->GetOutput()));
}
for (int i=0; i<m_ReferenceImageSet->Size(); i++)
{
typename itk::ImageDuplicator< DirectionImageType >::Pointer duplicator = itk::ImageDuplicator< DirectionImageType >::New();
duplicator->SetInputImage( m_ReferenceImageSet->GetElement(i) );
duplicator->Update();
set2->InsertElement(i, dynamic_cast<DirectionImageType*>(duplicator->GetOutput()));
}
m_ImageSet = set1;
m_ReferenceImageSet = set2;
// angular error image
typename OutputImageType::Pointer outputImage = OutputImageType::New();
outputImage->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
outputImage->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
outputImage->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
outputImage->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
outputImage->Allocate();
outputImage->FillBuffer(0.0);
this->SetNthOutput(0, outputImage);
// length error image
outputImage = OutputImageType::New();
outputImage->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
outputImage->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
outputImage->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
outputImage->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
outputImage->Allocate();
outputImage->FillBuffer(0.0);
this->SetNthOutput(1, outputImage);
if (m_MaskImage.IsNull())
{
m_MaskImage = UCharImageType::New();
m_MaskImage->SetOrigin( outputImage->GetOrigin() );
m_MaskImage->SetRegions( outputImage->GetLargestPossibleRegion() );
m_MaskImage->SetSpacing( outputImage->GetSpacing() );
m_MaskImage->SetDirection( outputImage->GetDirection() );
m_MaskImage->Allocate();
m_MaskImage->FillBuffer(1);
}
m_MeanAngularError = 0.0;
m_MedianAngularError = 0;
m_MaxAngularError = 0.0;
m_MinAngularError = itk::NumericTraits<float>::max();
m_VarAngularError = 0.0;
m_AngularErrorVector.clear();
m_MeanLengthError = 0.0;
m_MedianLengthError = 0;
m_MaxLengthError = 0.0;
m_MinLengthError = itk::NumericTraits<float>::max();
m_VarLengthError = 0.0;
m_LengthErrorVector.clear();
if (m_ImageSet.IsNull() || m_ReferenceImageSet.IsNull())
return;
outputImage = static_cast< OutputImageType* >(this->ProcessObject::GetOutput(0));
typename OutputImageType::Pointer outputImage2 = static_cast< OutputImageType* >(this->ProcessObject::GetOutput(1));
ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
ImageRegionIterator< OutputImageType > oit2(outputImage2, outputImage2->GetLargestPossibleRegion());
ImageRegionIterator< UCharImageType > mit(m_MaskImage, m_MaskImage->GetLargestPossibleRegion());
- int numImages = m_ImageSet->Size();
+ int numTestImages = m_ImageSet->Size();
int numReferenceImages = m_ReferenceImageSet->Size();
-
- // fill missing directions with zeros
- if (numImages>numReferenceImages)
- {
- DirectionType zeroDir; zeroDir.Fill(0.0);
- for (int i=0; i<numImages-numReferenceImages; i++)
- {
- DirectionImageType::Pointer img = DirectionImageType::New();
- img->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
- img->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
- img->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
- img->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
- img->Allocate();
- img->FillBuffer(zeroDir);
- m_ReferenceImageSet->InsertElement(m_ReferenceImageSet->Size(), img);
- }
- numReferenceImages = numImages;
- }
- else if (numReferenceImages>numImages)
- {
- DirectionType zeroDir; zeroDir.Fill(0.0);
- for (int i=0; i<numReferenceImages-numImages; i++)
- {
- DirectionImageType::Pointer img = DirectionImageType::New();
- img->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
- img->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
- img->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
- img->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
- img->Allocate();
- img->FillBuffer(zeroDir);
- m_ImageSet->InsertElement(m_ImageSet->Size(), img);
- }
- numImages = numReferenceImages;
- }
- int numDirections = numReferenceImages;
+ int maxNumDirections = std::max(numReferenceImages, numTestImages);
// matrix containing the angular error between the directions
- vnl_matrix< float > diffM; diffM.set_size(numDirections, numDirections);
+ vnl_matrix< float > diffM; diffM.set_size(maxNumDirections, maxNumDirections);
boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetSize()[0]*outputImage->GetLargestPossibleRegion().GetSize()[1]*outputImage->GetLargestPossibleRegion().GetSize()[2]);
while( !oit.IsAtEnd() )
{
++disp;
if( mit.Get()!=1 )
{
++oit;
++oit2;
++mit;
continue;
}
typename OutputImageType::IndexType index = oit.GetIndex();
float maxAngularError = 1.0;
diffM.fill(10); // initialize with invalid error value
// get number of valid directions (length > 0)
int numRefDirs = 0;
int numTestDirs = 0;
std::vector< vnl_vector_fixed< PixelType, 3 > > testDirs;
std::vector< vnl_vector_fixed< PixelType, 3 > > refDirs;
- for (int i=0; i<numDirections; i++)
+ for (int i=0; i<numReferenceImages; i++)
{
vnl_vector_fixed< PixelType, 3 > refDir = m_ReferenceImageSet->GetElement(i)->GetPixel(index).GetVnlVector();
if (refDir.magnitude() > m_Eps )
{
refDir.normalize();
refDirs.push_back(refDir);
numRefDirs++;
}
+ }
+ for (int i=0; i<numTestImages; i++)
+ {
vnl_vector_fixed< PixelType, 3 > testDir = m_ImageSet->GetElement(i)->GetPixel(index).GetVnlVector();
if (testDir.magnitude() > m_Eps )
{
testDir.normalize();
testDirs.push_back(testDir);
numTestDirs++;
}
}
// i: index of reference direction
// j: index of test direction
- for (int i=0; i<numDirections; i++) // for each reference direction
+ for (int i=0; i<maxNumDirections; i++) // for each reference direction
{
bool missingDir = false;
vnl_vector_fixed< PixelType, 3 > refDir;
if (i<numRefDirs) // normalize if not null
refDir = refDirs.at(i);
else if (m_IgnoreMissingDirections)
continue;
else
missingDir = true;
- for (int j=0; j<numDirections; j++) // and each test direction
+ for (int j=0; j<maxNumDirections; j++) // and each test direction
{
vnl_vector_fixed< PixelType, 3 > testDir;
if (j<numTestDirs) // normalize if not null
testDir = testDirs.at(j);
else if (m_IgnoreMissingDirections || missingDir)
continue;
else
missingDir = true;
// found missing direction
if (missingDir)
{
diffM[i][j] = -1;
continue;
}
// calculate angle between directions
diffM[i][j] = fabs(dot_product(refDir, testDir));
if (diffM[i][j] < maxAngularError)
maxAngularError = diffM[i][j];
if (diffM[i][j]>1.0)
diffM[i][j] = 1.0;
}
}
float angularError = 0.0;
float lengthError = 0.0;
int counter = 0;
vnl_matrix< float > diffM_copy = diffM;
- for (int k=0; k<numDirections; k++)
+ for (int k=0; k<maxNumDirections; k++)
{
float error = -1;
int a,b; a=-1; b=-1;
bool missingDir = false;
// i: index of reference direction
// j: index of test direction
// find smalles error between two directions (large value -> small error)
- for (int i=0; i<numDirections; i++)
- for (int j=0; j<numDirections; j++)
+ for (int i=0; i<maxNumDirections; i++)
+ for (int j=0; j<maxNumDirections; j++)
{
- if (diffM[i][j]>error && diffM[i][j]<2) // found valid error entry
+ if (diffM[i][j]>error && diffM[i][j]<2) // found valid error entry
{
error = diffM[i][j];
a = i;
b = j;
missingDir = false;
}
else if (diffM[i][j]<0 && error<0) // found missing direction
{
a = i;
b = j;
missingDir = true;
}
}
- if (a<0 || b<0 || m_IgnoreMissingDirections && missingDir)
+ if (a<0 || b<0 || (m_IgnoreMissingDirections && missingDir))
continue; // no more directions found
if (a>=numRefDirs && b>=numTestDirs)
{
MITK_INFO << "ERROR: missing test and reference direction. should not be possible. check code.";
continue;
}
// remove processed directions from error matrix
diffM.set_row(a, 10.0);
diffM.set_column(b, 10.0);
if (a>=numRefDirs) // missing reference direction (find next closest)
{
for (int i=0; i<numRefDirs; i++)
if (diffM_copy[i][b]>error)
{
error = diffM_copy[i][b];
a = i;
}
}
else if (b>=numTestDirs) // missing test direction (find next closest)
{
for (int i=0; i<numTestDirs; i++)
if (diffM_copy[a][i]>error)
{
error = diffM_copy[a][i];
b = i;
}
}
- float refLength = m_ReferenceImageSet->GetElement(a)->GetPixel(index).GetVnlVector().magnitude();
- float testLength = m_ImageSet->GetElement(b)->GetPixel(index).GetVnlVector().magnitude();
+ float refLength = 0;
+ float testLength = 1;
if (a>=numRefDirs || b>=numTestDirs || error<0)
error = 0;
+ else
+ {
+ refLength = m_ReferenceImageSet->GetElement(a)->GetPixel(index).GetVnlVector().magnitude();
+ testLength = m_ImageSet->GetElement(b)->GetPixel(index).GetVnlVector().magnitude();
+ }
m_LengthErrorVector.push_back( fabs(refLength-testLength) );
m_AngularErrorVector.push_back( acos(error)*180.0/M_PI );
m_MeanAngularError += m_AngularErrorVector.back();
m_MeanLengthError += m_LengthErrorVector.back();
angularError += m_AngularErrorVector.back();
lengthError += m_LengthErrorVector.back();
counter++;
}
if (counter>0)
{
lengthError /= counter;
angularError /= counter;
}
oit2.Set(lengthError);
oit.Set(angularError);
++oit;
++oit2;
++mit;
}
std::sort( m_AngularErrorVector.begin(), m_AngularErrorVector.end() );
m_MeanAngularError /= m_AngularErrorVector.size(); // mean
- for (int i=0; i<m_AngularErrorVector.size(); i++)
+ for (unsigned int i=0; i<m_AngularErrorVector.size(); i++)
{
float temp = m_AngularErrorVector.at(i) - m_MeanAngularError;
m_VarAngularError += temp*temp;
if ( m_AngularErrorVector.at(i)>m_MaxAngularError )
m_MaxAngularError = m_AngularErrorVector.at(i);
if ( m_AngularErrorVector.at(i)<m_MinAngularError )
m_MinAngularError = m_AngularErrorVector.at(i);
}
if (m_AngularErrorVector.size()>1)
{
m_VarAngularError /= (m_AngularErrorVector.size()-1); // variance
// median
if (m_AngularErrorVector.size()%2 == 0)
m_MedianAngularError = 0.5*( m_AngularErrorVector.at( m_AngularErrorVector.size()/2 ) + m_AngularErrorVector.at( m_AngularErrorVector.size()/2+1 ) );
else
m_MedianAngularError = m_AngularErrorVector.at( (m_AngularErrorVector.size()+1)/2 ) ;
}
std::sort( m_LengthErrorVector.begin(), m_LengthErrorVector.end() );
m_MeanLengthError /= m_LengthErrorVector.size(); // mean
- for (int i=0; i<m_LengthErrorVector.size(); i++)
+ for (unsigned int i=0; i<m_LengthErrorVector.size(); i++)
{
float temp = m_LengthErrorVector.at(i) - m_MeanLengthError;
m_VarLengthError += temp*temp;
if ( m_LengthErrorVector.at(i)>m_MaxLengthError )
m_MaxLengthError = m_LengthErrorVector.at(i);
if ( m_LengthErrorVector.at(i)<m_MinLengthError )
m_MinLengthError = m_LengthErrorVector.at(i);
}
if (m_LengthErrorVector.size()>1)
{
m_VarLengthError /= (m_LengthErrorVector.size()-1); // variance
// median
if (m_LengthErrorVector.size()%2 == 0)
m_MedianLengthError = 0.5*( m_LengthErrorVector.at( m_LengthErrorVector.size()/2 ) + m_LengthErrorVector.at( m_LengthErrorVector.size()/2+1 ) );
else
m_MedianLengthError = m_LengthErrorVector.at( (m_LengthErrorVector.size()+1)/2 ) ;
}
}
}
#endif // __itkEvaluateDirectionImagesFilter_cpp
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp
index 374ea1315f..b84c54ffc0 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp
@@ -1,254 +1,251 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "itkFibersFromPlanarFiguresFilter.h"
#define _USE_MATH_DEFINES
#include <math.h>
// MITK
#include <itkOrientationDistributionFunction.h>
#include <itkDiffusionQballGeneralizedFaImageFilter.h>
#include <mitkStandardFileLocations.h>
#include <mitkFiberBuilder.h>
#include <mitkMetropolisHastingsSampler.h>
#include <itkTensorImageToQBallImageFilter.h>
#include <mitkGibbsEnergyComputer.h>
#include <mitkRotationOperation.h>
#include <mitkInteractionConst.h>
// ITK
#include <itkImageDuplicator.h>
#include <itkResampleImageFilter.h>
#include <itkTimeProbe.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>
// MISC
-#include <fstream>
-#include <QFile>
-#include <tinyxml.h>
#include <math.h>
namespace itk{
FibersFromPlanarFiguresFilter::FibersFromPlanarFiguresFilter()
: m_Density(1000)
, m_FiberSampling(1)
, m_Tension(0)
, m_Continuity(0)
, m_Bias(0)
, m_FiberDistribution(DISTRIBUTE_UNIFORM)
, m_Variance(0.1)
{
}
FibersFromPlanarFiguresFilter::~FibersFromPlanarFiguresFilter()
{
}
void FibersFromPlanarFiguresFilter::GeneratePoints()
{
Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
randGen->SetSeed((unsigned int)0);
m_2DPoints.clear();
int count = 0;
while (count < m_Density)
{
mitk::Vector2D p;
switch (m_FiberDistribution) {
case DISTRIBUTE_GAUSSIAN:
p[0] = randGen->GetNormalVariate(0, m_Variance);
p[1] = randGen->GetNormalVariate(0, m_Variance);
break;
default:
p[0] = randGen->GetUniformVariate(-1, 1);
p[1] = randGen->GetUniformVariate(-1, 1);
}
if (sqrt(p[0]*p[0]+p[1]*p[1]) <= 1)
{
m_2DPoints.push_back(p);
count++;
}
}
}
// perform global tracking
void FibersFromPlanarFiguresFilter::GenerateData()
{
// check if enough fiducials are available
for (int i=0; i<m_Fiducials.size(); i++)
if (m_Fiducials.at(i).size()<2)
itkExceptionMacro("At least 2 fiducials needed per fiber bundle!");
for (int i=0; i<m_Fiducials.size(); i++)
{
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
vector< mitk::PlanarEllipse::Pointer > bundle = m_Fiducials.at(i);
vector< unsigned int > fliplist;
if (i<m_FlipList.size())
fliplist = m_FlipList.at(i);
else
fliplist.resize(bundle.size(), 0);
if (fliplist.size()<bundle.size())
fliplist.resize(bundle.size(), 0);
GeneratePoints();
for (int j=0; j<m_Density; j++)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
mitk::PlanarEllipse::Pointer figure = bundle.at(0);
mitk::Point2D p0 = figure->GetControlPoint(0);
mitk::Point2D p1 = figure->GetControlPoint(1);
mitk::Point2D p2 = figure->GetControlPoint(2);
mitk::Point2D p3 = figure->GetControlPoint(3);
double r1 = p0.EuclideanDistanceTo(p1);
double r2 = p0.EuclideanDistanceTo(p2);
mitk::Vector2D eDir = p1-p0; eDir.Normalize();
mitk::Vector2D tDir = p3-p0; tDir.Normalize();
// apply twist
vnl_matrix_fixed<double, 2, 2> tRot;
tRot[0][0] = tDir[0];
tRot[1][1] = tRot[0][0];
tRot[1][0] = sin(acos(tRot[0][0]));
tRot[0][1] = -tRot[1][0];
if (tDir[1]<0)
tRot.inplace_transpose();
m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector());
// apply new ellipse shape
vnl_vector_fixed< double, 2 > newP;
newP[0] = m_2DPoints.at(j)[0];
newP[1] = m_2DPoints.at(j)[1];
double alpha = acos(eDir[0]);
if (eDir[1]>0)
alpha = 2*M_PI-alpha;
vnl_matrix_fixed<double, 2, 2> eRot;
eRot[0][0] = cos(alpha);
eRot[1][1] = eRot[0][0];
eRot[1][0] = sin(alpha);
eRot[0][1] = -eRot[1][0];
newP = eRot*newP;
newP[0] *= r1;
newP[1] *= r2;
newP = eRot.transpose()*newP;
p0[0] += newP[0];
p0[1] += newP[1];
const mitk::Geometry2D* pfgeometry = figure->GetGeometry2D();
const mitk::PlaneGeometry* planeGeo = dynamic_cast<const mitk::PlaneGeometry*>(pfgeometry);
mitk::Point3D w, wc;
planeGeo->Map(p0, w);
wc = figure->GetWorldControlPoint(0);
vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
vnl_vector_fixed< double, 3 > n = planeGeo->GetNormalVnl();
for (int k=1; k<bundle.size(); k++)
{
figure = bundle.at(k);
p0 = figure->GetControlPoint(0);
p1 = figure->GetControlPoint(1);
p2 = figure->GetControlPoint(2);
p3 = figure->GetControlPoint(3);
r1 = p0.EuclideanDistanceTo(p1);
r2 = p0.EuclideanDistanceTo(p2);
eDir = p1-p0; eDir.Normalize();
mitk::Vector2D tDir2 = p3-p0; tDir2.Normalize();
mitk::Vector2D temp; temp.SetVnlVector(tRot.transpose() * tDir2.GetVnlVector());
// apply twist
tRot[0][0] = tDir[0]*tDir2[0] + tDir[1]*tDir2[1];
tRot[1][1] = tRot[0][0];
tRot[1][0] = sin(acos(tRot[0][0]));
tRot[0][1] = -tRot[1][0];
if (temp[1]<0)
tRot.inplace_transpose();
m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector());
tDir = tDir2;
// apply new ellipse shape
newP[0] = m_2DPoints.at(j)[0];
newP[1] = m_2DPoints.at(j)[1];
// calculate normal
mitk::Geometry2D* pfgeometry = const_cast<mitk::Geometry2D*>(figure->GetGeometry2D());
mitk::PlaneGeometry* planeGeo = dynamic_cast<mitk::PlaneGeometry*>(pfgeometry);
mitk::Vector3D perp = wc-planeGeo->ProjectPointOntoPlane(wc); perp.Normalize();
vnl_vector_fixed< double, 3 > n2 = planeGeo->GetNormalVnl();
wc = figure->GetWorldControlPoint(0);
// is flip needed?
if (dot_product(perp.GetVnlVector(),n2)>0 && dot_product(n,n2)<=0.00001)
newP[0] *= -1;
if (fliplist.at(k)>0)
newP[0] *= -1;
n = n2;
alpha = acos(eDir[0]);
if (eDir[1]>0)
alpha = 2*M_PI-alpha;
eRot[0][0] = cos(alpha);
eRot[1][1] = eRot[0][0];
eRot[1][0] = sin(alpha);
eRot[0][1] = -eRot[1][0];
newP = eRot*newP;
newP[0] *= r1;
newP[1] *= r2;
newP = eRot.transpose()*newP;
p0[0] += newP[0];
p0[1] += newP[1];
mitk::Point3D w;
planeGeo->Map(p0, w);
vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
}
m_VtkCellArray->InsertNextCell(container);
}
vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
fiberPolyData->SetPoints(m_VtkPoints);
fiberPolyData->SetLines(m_VtkCellArray);
mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(fiberPolyData);
mitkFiberBundle->DoFiberSmoothing(m_FiberSampling, m_Tension, m_Continuity, m_Bias);
m_FiberBundles.push_back(mitkFiberBundle);
}
}
}
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
index 1054a54cee..30fe205179 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
@@ -1,721 +1,882 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkStreamlineTrackingFilter_txx
#define __itkStreamlineTrackingFilter_txx
#include <time.h>
#include <stdio.h>
#include <stdlib.h>
#include "itkStreamlineTrackingFilter.h"
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionConstIteratorWithIndex.h>
#include <itkImageRegionIterator.h>
#define _USE_MATH_DEFINES
#include <math.h>
namespace itk {
//#define QBALL_RECON_PI M_PI
template< class TTensorPixelType, class TPDPixelType>
StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::StreamlineTrackingFilter():
m_FaThreshold(0.2),
m_StepSize(1),
m_MaxLength(10000),
m_SeedsPerVoxel(1),
m_F(1.0),
m_G(0.0),
m_Interpolate(true),
m_MinTractLength(0.0),
m_ResampleFibers(false)
{
// At least 1 inputs is necessary for a vector image.
// For images added one at a time we need at least six
this->SetNumberOfRequiredInputs( 1 );
+ this->SetNumberOfIndexedInputs(3);
}
template< class TTensorPixelType,
class TPDPixelType>
double StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::RoundToNearest(double num) {
return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5);
}
template< class TTensorPixelType,
class TPDPixelType>
void StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::BeforeThreadedGenerateData()
{
m_FiberPolyData = FiberPolyDataType::New();
m_Points = vtkPoints::New();
m_Cells = vtkCellArray::New();
- m_InputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
+ InputImageType* inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
m_ImageSize.resize(3);
- m_ImageSize[0] = m_InputImage->GetLargestPossibleRegion().GetSize()[0];
- m_ImageSize[1] = m_InputImage->GetLargestPossibleRegion().GetSize()[1];
- m_ImageSize[2] = m_InputImage->GetLargestPossibleRegion().GetSize()[2];
+ m_ImageSize[0] = inputImage->GetLargestPossibleRegion().GetSize()[0];
+ m_ImageSize[1] = inputImage->GetLargestPossibleRegion().GetSize()[1];
+ m_ImageSize[2] = inputImage->GetLargestPossibleRegion().GetSize()[2];
if (m_ImageSize[0]<3 || m_ImageSize[1]<3 || m_ImageSize[2]<3)
m_Interpolate = false;
m_ImageSpacing.resize(3);
- m_ImageSpacing[0] = m_InputImage->GetSpacing()[0];
- m_ImageSpacing[1] = m_InputImage->GetSpacing()[1];
- m_ImageSpacing[2] = m_InputImage->GetSpacing()[2];
+ m_ImageSpacing[0] = inputImage->GetSpacing()[0];
+ m_ImageSpacing[1] = inputImage->GetSpacing()[1];
+ m_ImageSpacing[2] = inputImage->GetSpacing()[2];
float minSpacing;
if(m_ImageSpacing[0]<m_ImageSpacing[1] && m_ImageSpacing[0]<m_ImageSpacing[2])
minSpacing = m_ImageSpacing[0];
else if (m_ImageSpacing[1] < m_ImageSpacing[2])
minSpacing = m_ImageSpacing[1];
else
minSpacing = m_ImageSpacing[2];
if (m_StepSize<0.1*minSpacing)
m_StepSize = 0.1*minSpacing;
if (m_ResampleFibers)
m_PointPistance = 0.5*minSpacing;
m_PolyDataContainer = itk::VectorContainer< int, FiberPolyDataType >::New();
- for (int i=0; i<this->GetNumberOfThreads(); i++)
+ for (unsigned int i=0; i<this->GetNumberOfThreads(); i++)
{
FiberPolyDataType poly = FiberPolyDataType::New();
m_PolyDataContainer->InsertElement(i, poly);
}
if (m_SeedImage.IsNull())
{
// initialize mask image
m_SeedImage = ItkUcharImgType::New();
- m_SeedImage->SetSpacing( m_InputImage->GetSpacing() );
- m_SeedImage->SetOrigin( m_InputImage->GetOrigin() );
- m_SeedImage->SetDirection( m_InputImage->GetDirection() );
- m_SeedImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
+ m_SeedImage->SetSpacing( inputImage->GetSpacing() );
+ m_SeedImage->SetOrigin( inputImage->GetOrigin() );
+ m_SeedImage->SetDirection( inputImage->GetDirection() );
+ m_SeedImage->SetRegions( inputImage->GetLargestPossibleRegion() );
m_SeedImage->Allocate();
m_SeedImage->FillBuffer(1);
}
if (m_MaskImage.IsNull())
{
// initialize mask image
m_MaskImage = ItkUcharImgType::New();
- m_MaskImage->SetSpacing( m_InputImage->GetSpacing() );
- m_MaskImage->SetOrigin( m_InputImage->GetOrigin() );
- m_MaskImage->SetDirection( m_InputImage->GetDirection() );
- m_MaskImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
+ m_MaskImage->SetSpacing( inputImage->GetSpacing() );
+ m_MaskImage->SetOrigin( inputImage->GetOrigin() );
+ m_MaskImage->SetDirection( inputImage->GetDirection() );
+ m_MaskImage->SetRegions( inputImage->GetLargestPossibleRegion() );
m_MaskImage->Allocate();
m_MaskImage->FillBuffer(1);
}
- m_FaImage = ItkFloatImgType::New();
- m_FaImage->SetSpacing( m_InputImage->GetSpacing() );
- m_FaImage->SetOrigin( m_InputImage->GetOrigin() );
- m_FaImage->SetDirection( m_InputImage->GetDirection() );
- m_FaImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
- m_FaImage->Allocate();
- m_FaImage->FillBuffer(0.0);
-
- m_PdImage = ItkPDImgType::New();
- m_PdImage->SetSpacing( m_InputImage->GetSpacing() );
- m_PdImage->SetOrigin( m_InputImage->GetOrigin() );
- m_PdImage->SetDirection( m_InputImage->GetDirection() );
- m_PdImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
- m_PdImage->Allocate();
-
- m_EmaxImage = ItkFloatImgType::New();
- m_EmaxImage->SetSpacing( m_InputImage->GetSpacing() );
- m_EmaxImage->SetOrigin( m_InputImage->GetOrigin() );
- m_EmaxImage->SetDirection( m_InputImage->GetDirection() );
- m_EmaxImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
- m_EmaxImage->Allocate();
- m_EmaxImage->FillBuffer(1.0);
+ bool useUserFaImage = true;
+ if (m_FaImage.IsNull())
+ {
+ m_FaImage = ItkFloatImgType::New();
+ m_FaImage->SetSpacing( inputImage->GetSpacing() );
+ m_FaImage->SetOrigin( inputImage->GetOrigin() );
+ m_FaImage->SetDirection( inputImage->GetDirection() );
+ m_FaImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+ m_FaImage->Allocate();
+ m_FaImage->FillBuffer(0.0);
+ useUserFaImage = false;
+ }
+
+ m_NumberOfInputs = 0;
+ for (unsigned int i=0; i<this->GetNumberOfIndexedInputs(); i++)
+ {
+ if (this->ProcessObject::GetInput(i)==NULL)
+ break;
+
+ ItkPDImgType::Pointer pdImage = ItkPDImgType::New();
+ pdImage->SetSpacing( inputImage->GetSpacing() );
+ pdImage->SetOrigin( inputImage->GetOrigin() );
+ pdImage->SetDirection( inputImage->GetDirection() );
+ pdImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+ pdImage->Allocate();
+ m_PdImage.push_back(pdImage);
+
+ ItkFloatImgType::Pointer emaxImage = ItkFloatImgType::New();
+ emaxImage->SetSpacing( inputImage->GetSpacing() );
+ emaxImage->SetOrigin( inputImage->GetOrigin() );
+ emaxImage->SetDirection( inputImage->GetDirection() );
+ emaxImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+ emaxImage->Allocate();
+ emaxImage->FillBuffer(1.0);
+ m_EmaxImage.push_back(emaxImage);
+
+ typename InputImageType::Pointer inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(i) );
+ m_InputImage.push_back(inputImage);
+
+ m_NumberOfInputs++;
+ }
+ MITK_INFO << "Processing " << m_NumberOfInputs << " tensor files";
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
typename TensorType::EigenValuesArrayType eigenvalues;
typename TensorType::EigenVectorsMatrixType eigenvectors;
+
+
for (int x=0; x<m_ImageSize[0]; x++)
for (int y=0; y<m_ImageSize[1]; y++)
for (int z=0; z<m_ImageSize[2]; z++)
{
typename InputImageType::IndexType index;
index[0] = x; index[1] = y; index[2] = z;
- typename InputImageType::PixelType tensor = m_InputImage->GetPixel(index);
-
- vnl_vector_fixed<double,3> dir;
- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
- dir[0] = eigenvectors(2, 0);
- dir[1] = eigenvectors(2, 1);
- dir[2] = eigenvectors(2, 2);
- dir.normalize();
- m_PdImage->SetPixel(index, dir);
- m_FaImage->SetPixel(index, tensor.GetFractionalAnisotropy());
- m_EmaxImage->SetPixel(index, 2/eigenvalues[2]);
+ for (int i=0; i<m_NumberOfInputs; i++)
+ {
+ typename InputImageType::PixelType tensor = m_InputImage.at(i)->GetPixel(index);
+ vnl_vector_fixed<double,3> dir;
+ tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
+ dir[0] = eigenvectors(2, 0);
+ dir[1] = eigenvectors(2, 1);
+ dir[2] = eigenvectors(2, 2);
+ dir.normalize();
+ m_PdImage.at(i)->SetPixel(index, dir);
+ if (!useUserFaImage)
+ m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)+tensor.GetFractionalAnisotropy());
+ m_EmaxImage.at(i)->SetPixel(index, 2/eigenvalues[2]);
+ }
+ if (!useUserFaImage)
+ m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)/m_NumberOfInputs);
}
if (m_Interpolate)
std::cout << "StreamlineTrackingFilter: using trilinear interpolation" << std::endl;
else
{
if (m_MinCurvatureRadius<0.0)
m_MinCurvatureRadius = 0.1*minSpacing;
std::cout << "StreamlineTrackingFilter: using nearest neighbor interpolation" << std::endl;
}
if (m_MinCurvatureRadius<0.0)
m_MinCurvatureRadius = 0.5*minSpacing;
std::cout << "StreamlineTrackingFilter: Min. curvature radius: " << m_MinCurvatureRadius << std::endl;
std::cout << "StreamlineTrackingFilter: FA threshold: " << m_FaThreshold << std::endl;
std::cout << "StreamlineTrackingFilter: stepsize: " << m_StepSize << " mm" << std::endl;
std::cout << "StreamlineTrackingFilter: f: " << m_F << std::endl;
std::cout << "StreamlineTrackingFilter: g: " << m_G << std::endl;
std::cout << "StreamlineTrackingFilter: starting streamline tracking" << std::endl;
}
template< class TTensorPixelType, class TPDPixelType>
void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType>
::CalculateNewPosition(itk::ContinuousIndex<double, 3>& pos, vnl_vector_fixed<double,3>& dir, typename InputImageType::IndexType& index)
{
- vnl_matrix_fixed< double, 3, 3 > rot = m_InputImage->GetDirection().GetTranspose();
+ vnl_matrix_fixed< double, 3, 3 > rot = m_InputImage.at(0)->GetDirection().GetTranspose();
dir = rot*dir;
if (true)
{
dir *= m_StepSize;
pos[0] += dir[0]/m_ImageSpacing[0];
pos[1] += dir[1]/m_ImageSpacing[1];
pos[2] += dir[2]/m_ImageSpacing[2];
index[0] = RoundToNearest(pos[0]);
index[1] = RoundToNearest(pos[1]);
index[2] = RoundToNearest(pos[2]);
}
else
{
dir[0] /= m_ImageSpacing[0];
dir[1] /= m_ImageSpacing[1];
dir[2] /= m_ImageSpacing[2];
int smallest = 0;
float x = 100000;
if (dir[0]>0)
{
if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps)
x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0];
else
x = fabs(pos[0]-std::ceil(pos[0])-0.5)/dir[0];
}
else if (dir[0]<0)
{
if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps)
x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0];
else
x = -fabs(pos[0]-std::floor(pos[0])+0.5)/dir[0];
}
float s = x;
float y = 100000;
if (dir[1]>0)
{
if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps)
y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1];
else
y = fabs(pos[1]-std::ceil(pos[1])-0.5)/dir[1];
}
else if (dir[1]<0)
{
if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps)
y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1];
else
y = -fabs(pos[1]-std::floor(pos[1])+0.5)/dir[1];
}
if (s>y)
{
s=y;
smallest = 1;
}
float z = 100000;
if (dir[2]>0)
{
if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps)
z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2];
else
z = fabs(pos[2]-std::ceil(pos[2])-0.5)/dir[2];
}
else if (dir[2]<0)
{
if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps)
z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2];
else
z = -fabs(pos[2]-std::floor(pos[2])+0.5)/dir[2];
}
if (s>z)
{
s=z;
smallest = 2;
}
-// MITK_INFO << "---------------------------------------------";
-// MITK_INFO << "s: " << s;
-// MITK_INFO << "dir: " << dir;
-// MITK_INFO << "old: " << pos[0] << ", " << pos[1] << ", " << pos[2];
+ // MITK_INFO << "---------------------------------------------";
+ // MITK_INFO << "s: " << s;
+ // MITK_INFO << "dir: " << dir;
+ // MITK_INFO << "old: " << pos[0] << ", " << pos[1] << ", " << pos[2];
pos[0] += dir[0]*s;
pos[1] += dir[1]*s;
pos[2] += dir[2]*s;
switch (smallest)
{
case 0:
if (dir[0]<0)
index[0] = std::floor(pos[0]);
else
index[0] = std::ceil(pos[0]);
index[1] = RoundToNearest(pos[1]);
index[2] = RoundToNearest(pos[2]);
break;
case 1:
if (dir[1]<0)
index[1] = std::floor(pos[1]);
else
index[1] = std::ceil(pos[1]);
index[0] = RoundToNearest(pos[0]);
index[2] = RoundToNearest(pos[2]);
break;
case 2:
if (dir[2]<0)
index[2] = std::floor(pos[2]);
else
index[2] = std::ceil(pos[2]);
index[1] = RoundToNearest(pos[1]);
index[0] = RoundToNearest(pos[0]);
}
-// float x = 100000;
-// if (dir[0]>0)
-// x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0];
-// else if (dir[0]<0)
-// x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0];
-// float s = x;
-
-// float y = 100000;
-// if (dir[1]>0)
-// y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1];
-// else if (dir[1]<0)
-// y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1];
-// if (s>y)
-// s=y;
-
-// float z = 100000;
-// if (dir[2]>0)
-// z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2];
-// else if (dir[2]<0)
-// z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2];
-
-// if (s>z)
-// s=z;
-// s *= 1.001;
-
-// pos[0] += dir[0]*s;
-// pos[1] += dir[1]*s;
-// pos[2] += dir[2]*s;
-
-// index[0] = RoundToNearest(pos[0]);
-// index[1] = RoundToNearest(pos[1]);
-// index[2] = RoundToNearest(pos[2]);
-
-// MITK_INFO << "new: " << pos[0] << ", " << pos[1] << ", " << pos[2];
+ // float x = 100000;
+ // if (dir[0]>0)
+ // x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0];
+ // else if (dir[0]<0)
+ // x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0];
+ // float s = x;
+
+ // float y = 100000;
+ // if (dir[1]>0)
+ // y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1];
+ // else if (dir[1]<0)
+ // y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1];
+ // if (s>y)
+ // s=y;
+
+ // float z = 100000;
+ // if (dir[2]>0)
+ // z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2];
+ // else if (dir[2]<0)
+ // z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2];
+
+ // if (s>z)
+ // s=z;
+ // s *= 1.001;
+
+ // pos[0] += dir[0]*s;
+ // pos[1] += dir[1]*s;
+ // pos[2] += dir[2]*s;
+
+ // index[0] = RoundToNearest(pos[0]);
+ // index[1] = RoundToNearest(pos[1]);
+ // index[2] = RoundToNearest(pos[2]);
+
+ // MITK_INFO << "new: " << pos[0] << ", " << pos[1] << ", " << pos[2];
}
}
template< class TTensorPixelType, class TPDPixelType>
bool StreamlineTrackingFilter< TTensorPixelType, TPDPixelType>
-::IsValidPosition(itk::ContinuousIndex<double, 3>& pos, typename InputImageType::IndexType &index, vnl_vector_fixed< float, 8 >& interpWeights)
+::IsValidPosition(itk::ContinuousIndex<double, 3>& pos, typename InputImageType::IndexType &index, vnl_vector_fixed< float, 8 >& interpWeights, int imageIdx)
{
- if (!m_InputImage->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0)
+ if (!m_InputImage.at(imageIdx)->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0)
return false;
if (m_Interpolate)
{
float frac_x = pos[0] - index[0];
float frac_y = pos[1] - index[1];
float frac_z = pos[2] - index[2];
if (frac_x<0)
{
index[0] -= 1;
frac_x += 1;
}
if (frac_y<0)
{
index[1] -= 1;
frac_y += 1;
}
if (frac_z<0)
{
index[2] -= 1;
frac_z += 1;
}
frac_x = 1-frac_x;
frac_y = 1-frac_y;
frac_z = 1-frac_z;
// int coordinates inside image?
if (index[0] < 0 || index[0] >= m_ImageSize[0]-1)
return false;
if (index[1] < 0 || index[1] >= m_ImageSize[1]-1)
return false;
if (index[2] < 0 || index[2] >= m_ImageSize[2]-1)
return false;
interpWeights[0] = ( frac_x)*( frac_y)*( frac_z);
interpWeights[1] = (1-frac_x)*( frac_y)*( frac_z);
interpWeights[2] = ( frac_x)*(1-frac_y)*( frac_z);
interpWeights[3] = ( frac_x)*( frac_y)*(1-frac_z);
interpWeights[4] = (1-frac_x)*(1-frac_y)*( frac_z);
interpWeights[5] = ( frac_x)*(1-frac_y)*(1-frac_z);
interpWeights[6] = (1-frac_x)*( frac_y)*(1-frac_z);
interpWeights[7] = (1-frac_x)*(1-frac_y)*(1-frac_z);
typename InputImageType::IndexType tmpIdx;
float FA = m_FaImage->GetPixel(index) * interpWeights[0];
tmpIdx = index; tmpIdx[0]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[1];
tmpIdx = index; tmpIdx[1]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[2];
tmpIdx = index; tmpIdx[2]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[3];
tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[4];
tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[5];
tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[6];
tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[7];
if (FA<m_FaThreshold)
return false;
}
else if (m_FaImage->GetPixel(index)<m_FaThreshold)
return false;
return true;
}
template< class TTensorPixelType, class TPDPixelType>
float StreamlineTrackingFilter< TTensorPixelType, TPDPixelType>
-::FollowStreamline(itk::ContinuousIndex<double, 3> pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids)
+::FollowStreamline(itk::ContinuousIndex<double, 3> pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids, int imageIdx)
{
float tractLength = 0;
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
typename TensorType::EigenValuesArrayType eigenvalues;
typename TensorType::EigenVectorsMatrixType eigenvectors;
vnl_vector_fixed< float, 8 > interpWeights;
typename InputImageType::IndexType index, indexOld;
indexOld[0] = -1; indexOld[1] = -1; indexOld[2] = -1;
itk::Point<double> worldPos;
float distance = 0;
float distanceInVoxel = 0;
// starting index and direction
index[0] = RoundToNearest(pos[0]);
index[1] = RoundToNearest(pos[1]);
index[2] = RoundToNearest(pos[2]);
- vnl_vector_fixed<double,3> dir = m_PdImage->GetPixel(index);
+
+ vnl_vector_fixed<double,3> dir = m_PdImage.at(imageIdx)->GetPixel(index);
dir *= dirSign; // reverse direction
vnl_vector_fixed<double,3> dirOld = dir;
if (dir.magnitude()<mitk::eps)
return tractLength;
for (int step=0; step< m_MaxLength/2; step++)
{
// get new position
CalculateNewPosition(pos, dir, index);
distance += m_StepSize;
tractLength += m_StepSize;
distanceInVoxel += m_StepSize;
// is new position valid (inside image, above FA threshold etc.)
- if (!IsValidPosition(pos, index, interpWeights)) // if not add last point and end streamline
+ if (!IsValidPosition(pos, index, interpWeights, imageIdx)) // if not add last point and end streamline
{
- m_InputImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos );
+ m_SeedImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos );
ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer()));
return tractLength;
}
else if (distance>=m_PointPistance)
{
- m_InputImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos );
+ m_SeedImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos );
ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer()));
distance = 0;
}
if (!m_Interpolate) // use nearest neighbour interpolation
{
if (indexOld!=index) // did we enter a new voxel? if yes, calculate new direction
{
- dir = m_PdImage->GetPixel(index); // get principal direction
-
- typename InputImageType::PixelType tensor = m_InputImage->GetPixel(index);
- float scale = m_EmaxImage->GetPixel(index);
- dir[0] = m_F*dir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2]));
- dir[1] = m_F*dir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2]));
- dir[2] = m_F*dir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2]));
- dir.normalize();
-
- float angle = dot_product(dirOld, dir);
- if (angle<0)
+ double minAngle = 0;
+ for (int img=0; img<m_NumberOfInputs; img++)
{
- dir *= -1;
- angle *= -1;
+ vnl_vector_fixed<double,3> newDir = m_PdImage.at(img)->GetPixel(index); // get principal direction
+ if (newDir.magnitude()<mitk::eps)
+ continue;
+
+ typename InputImageType::PixelType tensor = m_InputImage.at(img)->GetPixel(index);
+ float scale = m_EmaxImage.at(img)->GetPixel(index);
+ newDir[0] = m_F*newDir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2]));
+ newDir[1] = m_F*newDir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2]));
+ newDir[2] = m_F*newDir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2]));
+ newDir.normalize();
+
+ float angle = dot_product(dirOld, newDir);
+ if (angle<0)
+ {
+ newDir *= -1;
+ angle *= -1;
+ }
+
+ if (angle>minAngle)
+ {
+ minAngle = angle;
+ dir = newDir;
+ }
}
- float r = m_StepSize/(2*std::asin(std::acos(angle)/2));
+ //float r = m_StepSize/(2*std::asin(std::acos(minAngle)/2));
+ vnl_vector_fixed<double,3> v3 = dir+dirOld; v3 *= m_StepSize;
+ float a = m_StepSize;
+ float b = m_StepSize;
+ float c = v3.magnitude();
+ float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
+
if (r<m_MinCurvatureRadius)
+ {
return tractLength;
-
- if (dir.magnitude()<mitk::eps)
- dir = dirOld;
- else
- dirOld = dir;
+ }
+ dirOld = dir;
indexOld = index;
distanceInVoxel = 0;
}
else
dir = dirOld;
}
else // use trilinear interpolation (weights calculated in IsValidPosition())
{
- typename InputImageType::PixelType tensor = m_InputImage->GetPixel(index) * interpWeights[0];
- typename InputImageType::IndexType tmpIdx = index; tmpIdx[0]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[1];
- tmpIdx = index; tmpIdx[1]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[2];
- tmpIdx = index; tmpIdx[2]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[3];
- tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[4];
- tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[5];
- tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[6];
- tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
- tensor += m_InputImage->GetPixel(tmpIdx) * interpWeights[7];
+ typename InputImageType::PixelType tensor;
+
+ typename InputImageType::IndexType tmpIdx = index;
+ typename InputImageType::PixelType tmpTensor;
+
+ if (m_NumberOfInputs>1)
+ {
+ double minAngle = 0;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor = tmpTensor * interpWeights[0];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[0]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[1];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[1]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[2];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[2]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[3];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[4];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[5];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[6];
+
+ minAngle = 0;
+ tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
+ for (int img=0; img<m_NumberOfInputs; img++)
+ {
+ float angle = dot_product(dirOld, m_PdImage.at(img)->GetPixel(tmpIdx));
+ if (fabs(angle)>minAngle)
+ {
+ minAngle = angle;
+ tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx);
+ }
+ }
+ tensor += tmpTensor * interpWeights[7];
+ }
+ else
+ {
+ tensor = m_InputImage.at(0)->GetPixel(index) * interpWeights[0];
+ typename InputImageType::IndexType tmpIdx = index; tmpIdx[0]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[1];
+ tmpIdx = index; tmpIdx[1]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[2];
+ tmpIdx = index; tmpIdx[2]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[3];
+ tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[4];
+ tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[5];
+ tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[6];
+ tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
+ tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[7];
+ }
tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
dir[0] = eigenvectors(2, 0);
dir[1] = eigenvectors(2, 1);
dir[2] = eigenvectors(2, 2);
+ if (dir.magnitude()<mitk::eps)
+ continue;
dir.normalize();
float scale = 2/eigenvalues[2];
dir[0] = m_F*dir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2]));
dir[1] = m_F*dir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2]));
dir[2] = m_F*dir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2]));
dir.normalize();
float angle = dot_product(dirOld, dir);
if (angle<0)
{
dir *= -1;
angle *= -1;
}
- float r = m_StepSize/(2*std::asin(std::acos(angle)/2));
+ vnl_vector_fixed<double,3> v3 = dir+dirOld; v3 *= m_StepSize;
+ float a = m_StepSize;
+ float b = m_StepSize;
+ float c = v3.magnitude();
+ float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
+
if (r<m_MinCurvatureRadius)
return tractLength;
- if (dir.magnitude()<mitk::eps)
- dir = dirOld;
- else
- dirOld = dir;
-
+ dirOld = dir;
indexOld = index;
}
}
return tractLength;
}
template< class TTensorPixelType,
class TPDPixelType>
void StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
ThreadIdType threadId)
{
FiberPolyDataType poly = m_PolyDataContainer->GetElement(threadId);
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> Cells = vtkSmartPointer<vtkCellArray>::New();
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
typedef ImageRegionConstIterator< ItkUcharImgType > MaskIteratorType;
typedef ImageRegionConstIterator< ItkFloatImgType > FloatIteratorType;
typedef typename InputImageType::PixelType InputTensorType;
- InputIteratorType it(m_InputImage, outputRegionForThread );
- MaskIteratorType mit(m_SeedImage, outputRegionForThread );
+ MaskIteratorType sit(m_SeedImage, outputRegionForThread );
FloatIteratorType fit(m_FaImage, outputRegionForThread );
- MaskIteratorType mit2(m_MaskImage, outputRegionForThread );
-
+ MaskIteratorType mit(m_MaskImage, outputRegionForThread );
- it.GoToBegin();
- mit.GoToBegin();
- mit2.GoToBegin();
- fit.GoToBegin();
- itk::Point<double> worldPos;
- while( !it.IsAtEnd() )
+ for (int img=0; img<m_NumberOfInputs; img++)
{
- if (mit.Value()==0 || fit.Value()<m_FaThreshold || mit2.Value()==0)
- {
- ++mit;
- ++mit2;
- ++it;
- ++fit;
- continue;
- }
-
- for (int s=0; s<m_SeedsPerVoxel; s++)
+ sit.GoToBegin();
+ mit.GoToBegin();
+ fit.GoToBegin();
+ itk::Point<double> worldPos;
+ while( !sit.IsAtEnd() )
{
- vtkSmartPointer<vtkPolyLine> line = vtkSmartPointer<vtkPolyLine>::New();
- std::vector< vtkIdType > pointIDs;
- typename InputImageType::IndexType index = it.GetIndex();
- itk::ContinuousIndex<double, 3> start;
- unsigned int counter = 0;
-
- if (m_SeedsPerVoxel>1)
+ if (sit.Value()==0 || fit.Value()<m_FaThreshold || mit.Value()==0)
{
- start[0] = index[0]+(double)(rand()%99-49)/100;
- start[1] = index[1]+(double)(rand()%99-49)/100;
- start[2] = index[2]+(double)(rand()%99-49)/100;
+ ++sit;
+ ++mit;
+ ++fit;
+ continue;
}
- else
+
+ for (int s=0; s<m_SeedsPerVoxel; s++)
{
- start[0] = index[0];
- start[1] = index[1];
- start[2] = index[2];
- }
+ vtkSmartPointer<vtkPolyLine> line = vtkSmartPointer<vtkPolyLine>::New();
+ std::vector< vtkIdType > pointIDs;
+ typename InputImageType::IndexType index = sit.GetIndex();
+ itk::ContinuousIndex<double, 3> start;
+ unsigned int counter = 0;
- // forward tracking
- float tractLength = FollowStreamline(start, 1, points, pointIDs);
+ if (m_SeedsPerVoxel>1)
+ {
+ start[0] = index[0]+(double)(rand()%99-49)/100;
+ start[1] = index[1]+(double)(rand()%99-49)/100;
+ start[2] = index[2]+(double)(rand()%99-49)/100;
+ }
+ else
+ {
+ start[0] = index[0];
+ start[1] = index[1];
+ start[2] = index[2];
+ }
- // add ids to line
- counter += pointIDs.size();
- while (!pointIDs.empty())
- {
- line->GetPointIds()->InsertNextId(pointIDs.back());
- pointIDs.pop_back();
- }
+ // forward tracking
+ float tractLength = FollowStreamline(start, 1, points, pointIDs, img);
- // insert start point
- m_InputImage->TransformContinuousIndexToPhysicalPoint( start, worldPos );
- line->GetPointIds()->InsertNextId(points->InsertNextPoint(worldPos.GetDataPointer()));
+ // add ids to line
+ counter += pointIDs.size();
+ while (!pointIDs.empty())
+ {
+ line->GetPointIds()->InsertNextId(pointIDs.back());
+ pointIDs.pop_back();
+ }
- // backward tracking
- tractLength += FollowStreamline(start, -1, points, pointIDs);
+ // insert start point
+ m_SeedImage->TransformContinuousIndexToPhysicalPoint( start, worldPos );
+ line->GetPointIds()->InsertNextId(points->InsertNextPoint(worldPos.GetDataPointer()));
- counter += pointIDs.size();
+ // backward tracking
+ tractLength += FollowStreamline(start, -1, points, pointIDs, img);
- if (tractLength<m_MinTractLength || counter<2)
- continue;
+ counter += pointIDs.size();
- // add ids to line
- for (int i=0; i<pointIDs.size(); i++)
- line->GetPointIds()->InsertNextId(pointIDs.at(i));
+ //MITK_INFO << "Tract length " << tractLength;
- Cells->InsertNextCell(line);
+ if (tractLength<m_MinTractLength || counter<2)
+ continue;
+
+ // add ids to line
+ for (unsigned int i=0; i<pointIDs.size(); i++)
+ line->GetPointIds()->InsertNextId(pointIDs.at(i));
+
+ Cells->InsertNextCell(line);
+ }
+ ++sit;
+ ++mit;
+ ++fit;
}
- ++mit;
- ++mit2;
- ++it;
- ++fit;
}
poly->SetPoints(points);
poly->SetLines(Cells);
std::cout << "Thread " << threadId << " finished tracking" << std::endl;
}
template< class TTensorPixelType,
class TPDPixelType>
vtkSmartPointer< vtkPolyData > StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::AddPolyData(FiberPolyDataType poly1, FiberPolyDataType poly2)
{
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = poly1->GetLines();
vtkSmartPointer<vtkPoints> vNewPoints = poly1->GetPoints();
vtkSmartPointer<vtkCellArray> vLines = poly2->GetLines();
vLines->InitTraversal();
for( int i=0; i<vLines->GetNumberOfCells(); i++ )
{
vtkIdType numPoints(0);
vtkIdType* points(NULL);
vLines->GetNextCell ( numPoints, points );
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for( int j=0; j<numPoints; j++)
{
vtkIdType id = vNewPoints->InsertNextPoint(poly2->GetPoint(points[j]));
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
}
// initialize polydata
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
return vNewPolyData;
}
template< class TTensorPixelType,
class TPDPixelType>
void StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::AfterThreadedGenerateData()
{
MITK_INFO << "Generating polydata ";
m_FiberPolyData = m_PolyDataContainer->GetElement(0);
- for (int i=1; i<this->GetNumberOfThreads(); i++)
+ for (unsigned int i=1; i<this->GetNumberOfThreads(); i++)
{
m_FiberPolyData = AddPolyData(m_FiberPolyData, m_PolyDataContainer->GetElement(i));
}
MITK_INFO << "done";
}
template< class TTensorPixelType,
class TPDPixelType>
void StreamlineTrackingFilter< TTensorPixelType,
TPDPixelType>
::PrintSelf(std::ostream& os, Indent indent) const
{
}
}
#endif // __itkDiffusionQballPrincipleDirectionsImageFilter_txx
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h
index b24f0c1175..7d588adad0 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h
@@ -1,139 +1,141 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
/*===================================================================
This file is based heavily on a corresponding ITK filter.
===================================================================*/
#ifndef __itkStreamlineTrackingFilter_h_
#define __itkStreamlineTrackingFilter_h_
#include "FiberTrackingExports.h"
#include <itkImageToImageFilter.h>
#include <itkVectorContainer.h>
#include <itkVectorImage.h>
#include <itkDiffusionTensor3D.h>
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkPolyLine.h>
namespace itk{
/**
* \brief Performes deterministic streamline tracking on the input tensor image. */
template< class TTensorPixelType, class TPDPixelType=double>
class StreamlineTrackingFilter :
public ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >,
Image< Vector< TPDPixelType, 3 >, 3 > >
{
public:
typedef StreamlineTrackingFilter Self;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
typedef ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > Superclass;
/** Method for creation through the object factory. */
itkNewMacro(Self)
/** Runtime information support. */
itkTypeMacro(StreamlineTrackingFilter, ImageToImageFilter)
typedef TTensorPixelType TensorComponentType;
typedef TPDPixelType DirectionPixelType;
typedef typename Superclass::InputImageType InputImageType;
typedef typename Superclass::OutputImageType OutputImageType;
typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Image<float, 3> ItkFloatImgType;
typedef itk::Image< vnl_vector_fixed<double,3>, 3> ItkPDImgType;
typedef vtkSmartPointer< vtkPolyData > FiberPolyDataType;
itkGetMacro( FiberPolyData, FiberPolyDataType )
itkSetMacro( SeedImage, ItkUcharImgType::Pointer)
itkSetMacro( MaskImage, ItkUcharImgType::Pointer)
+ itkSetMacro( FaImage, ItkFloatImgType::Pointer)
itkSetMacro( SeedsPerVoxel, int)
itkSetMacro( FaThreshold, float)
itkSetMacro( StepSize, float)
itkSetMacro( F, float )
itkSetMacro( G, float )
itkSetMacro( Interpolate, bool )
itkSetMacro( MinTractLength, float )
itkGetMacro( MinTractLength, float )
itkSetMacro( MinCurvatureRadius, float )
itkGetMacro( MinCurvatureRadius, float )
itkSetMacro( ResampleFibers, bool )
protected:
StreamlineTrackingFilter();
~StreamlineTrackingFilter() {}
void PrintSelf(std::ostream& os, Indent indent) const;
void CalculateNewPosition(itk::ContinuousIndex<double, 3>& pos, vnl_vector_fixed<double,3>& dir, typename InputImageType::IndexType& index);
- float FollowStreamline(itk::ContinuousIndex<double, 3> pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids);
- bool IsValidPosition(itk::ContinuousIndex<double, 3>& pos, typename InputImageType::IndexType& index, vnl_vector_fixed< float, 8 >& interpWeights);
+ float FollowStreamline(itk::ContinuousIndex<double, 3> pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids, int imageIdx);
+ bool IsValidPosition(itk::ContinuousIndex<double, 3>& pos, typename InputImageType::IndexType& index, vnl_vector_fixed< float, 8 >& interpWeights, int imageIdx);
double RoundToNearest(double num);
void BeforeThreadedGenerateData();
void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId);
void AfterThreadedGenerateData();
FiberPolyDataType AddPolyData(FiberPolyDataType poly1, FiberPolyDataType poly2);
FiberPolyDataType m_FiberPolyData;
vtkSmartPointer<vtkPoints> m_Points;
vtkSmartPointer<vtkCellArray> m_Cells;
- ItkFloatImgType::Pointer m_EmaxImage;
+ std::vector< ItkFloatImgType::Pointer > m_EmaxImage;
ItkFloatImgType::Pointer m_FaImage;
- ItkPDImgType::Pointer m_PdImage;
- typename InputImageType::Pointer m_InputImage;
+ std::vector< ItkPDImgType::Pointer > m_PdImage;
+ std::vector< typename InputImageType::Pointer > m_InputImage;
+ int m_NumberOfInputs;
float m_FaThreshold;
float m_MinCurvatureRadius;
float m_StepSize;
int m_MaxLength;
float m_MinTractLength;
int m_SeedsPerVoxel;
float m_F;
float m_G;
std::vector< int > m_ImageSize;
std::vector< float > m_ImageSpacing;
ItkUcharImgType::Pointer m_SeedImage;
ItkUcharImgType::Pointer m_MaskImage;
bool m_Interpolate;
float m_PointPistance;
bool m_ResampleFibers;
itk::VectorContainer< int, FiberPolyDataType >::Pointer m_PolyDataContainer;
private:
};
}
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkStreamlineTrackingFilter.cpp"
#endif
#endif //__itkStreamlineTrackingFilter_h_
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
index 7426885b1d..732b38f10e 100755
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp
@@ -1,707 +1,959 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "itkTractsToDWIImageFilter.h"
#include <boost/progress.hpp>
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkPolyLine.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <itkResampleImageFilter.h>
#include <itkNearestNeighborInterpolateImageFunction.h>
#include <itkBSplineInterpolateImageFunction.h>
#include <itkCastImageFilter.h>
#include <itkImageFileWriter.h>
#include <itkRescaleIntensityImageFilter.h>
#include <itkWindowedSincInterpolateImageFunction.h>
#include <itkResampleDwiImageFilter.h>
#include <itkKspaceImageFilter.h>
#include <itkDftImageFilter.h>
#include <itkAddImageFilter.h>
#include <itkConstantPadImageFilter.h>
#include <itkCropImageFilter.h>
+#include <mitkAstroStickModel.h>
+#include <vtkTransform.h>
+#include <iostream>
+#include <fstream>
+#include <itkImageDuplicator.h>
+#include <boost/lexical_cast.hpp>
namespace itk
{
template< class PixelType >
TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter()
: m_CircleDummy(false)
, m_VolumeAccuracy(10)
, m_AddGibbsRinging(false)
, m_NumberOfRepetitions(1)
, m_EnforcePureFiberVoxels(false)
, m_InterpolationShrink(1000)
, m_FiberRadius(0)
, m_SignalScale(25)
, m_kOffset(0)
, m_tLine(1)
, m_UseInterpolation(false)
, m_SimulateRelaxation(true)
, m_tInhom(50)
, m_TE(100)
, m_FrequencyMap(NULL)
, m_EddyGradientStrength(0.001)
, m_SimulateEddyCurrents(false)
, m_Spikes(0)
, m_Wrap(1.0)
+ , m_NoiseModel(NULL)
, m_SpikeAmplitude(1)
+ , m_AddMotionArtifact(false)
{
m_Spacing.Fill(2.5); m_Origin.Fill(0.0);
m_DirectionMatrix.SetIdentity();
m_ImageRegion.SetSize(0, 10);
m_ImageRegion.SetSize(1, 10);
m_ImageRegion.SetSize(2, 10);
+
+ m_MaxTranslation.Fill(0.0);
+ m_MaxRotation.Fill(0.0);
+
+ m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
+ m_RandGen->SetSeed();
}
template< class PixelType >
TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter()
{
}
template< class PixelType >
TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images )
{
// create slice object
ImageRegion<2> sliceRegion;
sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
Vector< double, 2 > sliceSpacing;
sliceSpacing[0] = m_UpsampledSpacing[0];
sliceSpacing[1] = m_UpsampledSpacing[1];
// frequency map slice
SliceType::Pointer fMapSlice = NULL;
if (m_FrequencyMap.IsNotNull())
{
fMapSlice = SliceType::New();
ImageRegion<2> region;
region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]);
region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]);
fMapSlice->SetLargestPossibleRegion( region );
fMapSlice->SetBufferedRegion( region );
fMapSlice->SetRequestedRegion( region );
fMapSlice->Allocate();
}
DoubleDwiType::Pointer newImage = DoubleDwiType::New();
newImage->SetSpacing( m_Spacing );
newImage->SetOrigin( m_Origin );
newImage->SetDirection( m_DirectionMatrix );
newImage->SetLargestPossibleRegion( m_ImageRegion );
newImage->SetBufferedRegion( m_ImageRegion );
newImage->SetRequestedRegion( m_ImageRegion );
newImage->SetVectorLength( images.at(0)->GetVectorLength() );
newImage->Allocate();
MatrixType transform = m_DirectionMatrix;
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
{
if (j<2)
transform[i][j] *= m_UpsampledSpacing[j];
else
transform[i][j] *= m_Spacing[j];
}
- std::vector< int > spikeVolume;
+ std::vector< unsigned int > spikeVolume;
for (int i=0; i<m_Spikes; i++)
spikeVolume.push_back(rand()%images.at(0)->GetVectorLength());
std::sort (spikeVolume.begin(), spikeVolume.end());
std::reverse (spikeVolume.begin(), spikeVolume.end());
- boost::progress_display disp(images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2));
+ m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n";
+ m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
+ unsigned long lastTick = 0;
+
+ boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2));
for (unsigned int g=0; g<images.at(0)->GetVectorLength(); g++)
{
std::vector< int > spikeSlice;
while (!spikeVolume.empty() && spikeVolume.back()==g)
{
spikeSlice.push_back(rand()%images.at(0)->GetLargestPossibleRegion().GetSize(2));
spikeVolume.pop_back();
}
std::sort (spikeSlice.begin(), spikeSlice.end());
std::reverse (spikeSlice.begin(), spikeSlice.end());
for (unsigned int z=0; z<images.at(0)->GetLargestPossibleRegion().GetSize(2); z++)
{
std::vector< SliceType::Pointer > compartmentSlices;
std::vector< double > t2Vector;
for (unsigned int i=0; i<images.size(); i++)
{
DiffusionSignalModel<double>* signalModel;
if (i<m_FiberModels.size())
signalModel = m_FiberModels.at(i);
else
signalModel = m_NonFiberModels.at(i-m_FiberModels.size());
SliceType::Pointer slice = SliceType::New();
slice->SetLargestPossibleRegion( sliceRegion );
slice->SetBufferedRegion( sliceRegion );
slice->SetRequestedRegion( sliceRegion );
slice->SetSpacing(sliceSpacing);
slice->Allocate();
slice->FillBuffer(0.0);
// extract slice from channel g
for (unsigned int y=0; y<images.at(0)->GetLargestPossibleRegion().GetSize(1); y++)
for (unsigned int x=0; x<images.at(0)->GetLargestPossibleRegion().GetSize(0); x++)
{
SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y;
DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]);
if (fMapSlice.IsNotNull() && i==0)
fMapSlice->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D));
}
compartmentSlices.push_back(slice);
t2Vector.push_back(signalModel->GetT2());
}
+ if (this->GetAbortGenerateData())
+ return NULL;
+
// create k-sapce (inverse fourier transform slices)
itk::Size<2> outSize; outSize.SetElement(0, m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_ImageRegion.GetSize(1));
itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New();
idft->SetCompartmentImages(compartmentSlices);
idft->SetT2(t2Vector);
idft->SetkOffset(m_kOffset);
idft->SettLine(m_tLine);
idft->SetTE(m_TE);
idft->SetTinhom(m_tInhom);
idft->SetSimulateRelaxation(m_SimulateRelaxation);
idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents);
idft->SetEddyGradientMagnitude(m_EddyGradientStrength);
idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0);
idft->SetDirectionMatrix(transform);
idft->SetDiffusionGradientDirection(m_FiberModels.at(0)->GetGradientDirection(g));
idft->SetFrequencyMap(fMapSlice);
idft->SetSignalScale(m_SignalScale);
idft->SetOutSize(outSize);
int numSpikes = 0;
while (!spikeSlice.empty() && spikeSlice.back()==z)
{
numSpikes++;
spikeSlice.pop_back();
}
idft->SetSpikes(numSpikes);
idft->SetSpikeAmplitude(m_SpikeAmplitude);
idft->Update();
ComplexSliceType::Pointer fSlice;
fSlice = idft->GetOutput();
- for (unsigned int i=0; i<m_KspaceArtifacts.size(); i++)
- fSlice = m_KspaceArtifacts.at(i)->AddArtifact(fSlice);
+ ++disp;
+ unsigned long newTick = 50*disp.count()/disp.expected_count();
+ for (int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
// fourier transform slice
SliceType::Pointer newSlice;
itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New();
dft->SetInput(fSlice);
dft->Update();
newSlice = dft->GetOutput();
// put slice back into channel g
for (unsigned int y=0; y<fSlice->GetLargestPossibleRegion().GetSize(1); y++)
for (unsigned int x=0; x<fSlice->GetLargestPossibleRegion().GetSize(0); x++)
{
DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y;
DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D);
pix3D[g] = newSlice->GetPixel(index2D);
newImage->SetPixel(index3D, pix3D);
}
-
++disp;
+ newTick = 50*disp.count()/disp.expected_count();
+ for (int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
}
}
+ m_StatusText += "\n\n";
return newImage;
}
template< class PixelType >
void TractsToDWIImageFilter< PixelType >::GenerateData()
{
+ m_StartTime = clock();
+ m_StatusText = "Starting simulation\n";
+
// check input data
if (m_FiberBundle.IsNull())
itkExceptionMacro("Input fiber bundle is NULL!");
int numFibers = m_FiberBundle->GetNumFibers();
if (numFibers<=0)
itkExceptionMacro("Input fiber bundle contains no fibers!");
if (m_FiberModels.empty())
itkExceptionMacro("No diffusion model for fiber compartments defined!");
if (m_EnforcePureFiberVoxels)
while (m_FiberModels.size()>1)
m_FiberModels.pop_back();
if (m_NonFiberModels.empty())
itkExceptionMacro("No diffusion model for non-fiber compartments defined!");
int baselineIndex = m_FiberModels[0]->GetFirstBaselineIndex();
if (baselineIndex<0)
itkExceptionMacro("No baseline index found!");
- // define output image geometry
- if (m_TissueMask.IsNotNull()) // if available use mask image geometry
- {
- // use input tissue mask
- m_Spacing = m_TissueMask->GetSpacing();
- m_Origin = m_TissueMask->GetOrigin();
- m_DirectionMatrix = m_TissueMask->GetDirection();
- m_ImageRegion = m_TissueMask->GetLargestPossibleRegion();
- MITK_INFO << "Using tissue mask";
- }
-
// initialize output dwi image
ImageRegion<3> croppedRegion = m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Wrap);
itk::Point<double,3> shiftedOrigin = m_Origin; shiftedOrigin[1] += (m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Spacing[1]/2;
typename OutputImageType::Pointer outImage = OutputImageType::New();
outImage->SetSpacing( m_Spacing );
outImage->SetOrigin( shiftedOrigin );
outImage->SetDirection( m_DirectionMatrix );
outImage->SetLargestPossibleRegion( croppedRegion );
outImage->SetBufferedRegion( croppedRegion );
outImage->SetRequestedRegion( croppedRegion );
outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
outImage->Allocate();
typename OutputImageType::PixelType temp;
temp.SetSize(m_FiberModels[0]->GetNumGradients());
temp.Fill(0.0);
outImage->FillBuffer(temp);
// ADJUST GEOMETRY FOR FURTHER PROCESSING
// is input slize size a power of two?
unsigned int x=m_ImageRegion.GetSize(0); unsigned int y=m_ImageRegion.GetSize(1);
if ( x%2 == 1 )
m_ImageRegion.SetSize(0, x+1);
if ( y%2 == 1 )
m_ImageRegion.SetSize(1, y+1);
// apply in-plane upsampling
double upsampling = 1;
if (m_AddGibbsRinging)
{
+ m_StatusText += "Gibbs ringing enabled\n";
MITK_INFO << "Adding ringing artifacts.";
upsampling = 2;
}
m_UpsampledSpacing = m_Spacing;
m_UpsampledSpacing[0] /= upsampling;
m_UpsampledSpacing[1] /= upsampling;
m_UpsampledImageRegion = m_ImageRegion;
m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*upsampling);
m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*upsampling);
+ m_UpsampledOrigin = m_Origin;
+ m_UpsampledOrigin[0] -= m_Spacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2;
+ m_UpsampledOrigin[1] -= m_Spacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2;
+ m_UpsampledOrigin[2] -= m_Spacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2;
// generate double images to store the individual compartment signals
std::vector< DoubleDwiType::Pointer > compartments;
for (unsigned int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
{
DoubleDwiType::Pointer doubleDwi = DoubleDwiType::New();
doubleDwi->SetSpacing( m_UpsampledSpacing );
- doubleDwi->SetOrigin( m_Origin );
+ doubleDwi->SetOrigin( m_UpsampledOrigin );
doubleDwi->SetDirection( m_DirectionMatrix );
doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion );
doubleDwi->SetBufferedRegion( m_UpsampledImageRegion );
doubleDwi->SetRequestedRegion( m_UpsampledImageRegion );
doubleDwi->SetVectorLength( m_FiberModels[0]->GetNumGradients() );
doubleDwi->Allocate();
DoubleDwiType::PixelType pix;
pix.SetSize(m_FiberModels[0]->GetNumGradients());
pix.Fill(0.0);
doubleDwi->FillBuffer(pix);
compartments.push_back(doubleDwi);
}
// initialize volume fraction images
m_VolumeFractions.clear();
for (unsigned int i=0; i<m_FiberModels.size()+m_NonFiberModels.size(); i++)
{
ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New();
doubleImg->SetSpacing( m_UpsampledSpacing );
- doubleImg->SetOrigin( m_Origin );
+ doubleImg->SetOrigin( m_UpsampledOrigin );
doubleImg->SetDirection( m_DirectionMatrix );
doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion );
doubleImg->SetBufferedRegion( m_UpsampledImageRegion );
doubleImg->SetRequestedRegion( m_UpsampledImageRegion );
doubleImg->Allocate();
doubleImg->FillBuffer(0);
m_VolumeFractions.push_back(doubleImg);
}
// resample mask image and frequency map to fit upsampled geometry
if (m_AddGibbsRinging)
{
if (m_TissueMask.IsNotNull())
{
// rescale mask image (otherwise there are problems with the resampling)
itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::Pointer rescaler = itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::New();
rescaler->SetInput(0,m_TissueMask);
rescaler->SetOutputMaximum(100);
rescaler->SetOutputMinimum(0);
rescaler->Update();
// resample mask image
itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer resampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
resampler->SetInput(rescaler->GetOutput());
resampler->SetOutputParametersFromImage(m_TissueMask);
resampler->SetSize(m_UpsampledImageRegion.GetSize());
resampler->SetOutputSpacing(m_UpsampledSpacing);
+ resampler->SetOutputOrigin(m_UpsampledOrigin);
resampler->Update();
m_TissueMask = resampler->GetOutput();
}
// resample frequency map
if (m_FrequencyMap.IsNotNull())
{
itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::Pointer resampler = itk::ResampleImageFilter<ItkDoubleImgType, ItkDoubleImgType>::New();
resampler->SetInput(m_FrequencyMap);
resampler->SetOutputParametersFromImage(m_FrequencyMap);
resampler->SetSize(m_UpsampledImageRegion.GetSize());
resampler->SetOutputSpacing(m_UpsampledSpacing);
+ resampler->SetOutputOrigin(m_UpsampledOrigin);
resampler->Update();
m_FrequencyMap = resampler->GetOutput();
}
}
+
// no input tissue mask is set -> create default
+ bool maskImageSet = true;
if (m_TissueMask.IsNull())
{
+ m_StatusText += "No tissue mask set\n";
+ MITK_INFO << "No tissue mask set";
m_TissueMask = ItkUcharImgType::New();
m_TissueMask->SetSpacing( m_UpsampledSpacing );
- m_TissueMask->SetOrigin( m_Origin );
+ m_TissueMask->SetOrigin( m_UpsampledOrigin );
m_TissueMask->SetDirection( m_DirectionMatrix );
m_TissueMask->SetLargestPossibleRegion( m_UpsampledImageRegion );
m_TissueMask->SetBufferedRegion( m_UpsampledImageRegion );
m_TissueMask->SetRequestedRegion( m_UpsampledImageRegion );
m_TissueMask->Allocate();
m_TissueMask->FillBuffer(1);
+ maskImageSet = false;
+ }
+ else
+ {
+ m_StatusText += "Using tissue mask\n";
+ MITK_INFO << "Using tissue mask";
}
m_ImageRegion = croppedRegion;
x=m_ImageRegion.GetSize(0); y=m_ImageRegion.GetSize(1);
if ( x%2 == 1 )
m_ImageRegion.SetSize(0, x+1);
if ( y%2 == 1 )
m_ImageRegion.SetSize(1, y+1);
// resample fiber bundle for sufficient voxel coverage
+ m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n";
double segmentVolume = 0.0001;
float minSpacing = 1;
if(m_UpsampledSpacing[0]<m_UpsampledSpacing[1] && m_UpsampledSpacing[0]<m_UpsampledSpacing[2])
minSpacing = m_UpsampledSpacing[0];
else if (m_UpsampledSpacing[1] < m_UpsampledSpacing[2])
minSpacing = m_UpsampledSpacing[1];
else
minSpacing = m_UpsampledSpacing[2];
FiberBundleType fiberBundle = m_FiberBundle->GetDeepCopy();
fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy);
double mmRadius = m_FiberRadius/1000;
if (mmRadius>0)
segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy;
double interpFact = 2*atan(-0.5*m_InterpolationShrink);
double maxVolume = 0;
+ double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2];
+
+ if (m_AddMotionArtifact)
+ {
+ if (m_RandomMotion)
+ {
+ m_StatusText += "Adding random motion artifacts:\n";
+ m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast<std::string>(m_MaxRotation) + "°\n";
+ m_StatusText += "Maximum translation: +/-" + boost::lexical_cast<std::string>(m_MaxTranslation) + "mm\n";
+ }
+ else
+ {
+ m_StatusText += "Adding linear motion artifacts:\n";
+ m_StatusText += "Maximum rotation: " + boost::lexical_cast<std::string>(m_MaxRotation) + "°\n";
+ m_StatusText += "Maximum translation: " + boost::lexical_cast<std::string>(m_MaxTranslation) + "mm\n";
+ }
+ MITK_INFO << "Adding motion artifacts";
+ MITK_INFO << "Maximum rotation: " << m_MaxRotation;
+ MITK_INFO << "Maxmimum translation: " << m_MaxTranslation;
+ }
+ maxVolume = 0;
+ m_StatusText += "\n"+this->GetTime()+" > Generating signal of " + boost::lexical_cast<std::string>(m_FiberModels.size()) + " fiber compartments\n";
MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments";
- vtkSmartPointer<vtkPolyData> fiberPolyData = fiberBundle->GetFiberPolyData();
- boost::progress_display disp(numFibers);
- for( int i=0; i<numFibers; i++ )
+ boost::progress_display disp(numFibers*m_FiberModels.at(0)->GetNumGradients());
+
+ ofstream logFile;
+ logFile.open("fiberfox_motion.log");
+ logFile << "0 rotation: 0,0,0; translation: 0,0,0\n";
+
+ // get transform for motion artifacts
+ FiberBundleType fiberBundleTransformed = fiberBundle;
+ VectorType rotation = m_MaxRotation/m_FiberModels.at(0)->GetNumGradients();
+ VectorType translation = m_MaxTranslation/m_FiberModels.at(0)->GetNumGradients();
+
+ // creat image to hold transformed mask (motion artifact)
+ ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New();
+ itk::ImageDuplicator<ItkUcharImgType>::Pointer duplicator = itk::ImageDuplicator<ItkUcharImgType>::New();
+ duplicator->SetInputImage(m_TissueMask);
+ duplicator->Update();
+ tempTissueMask = duplicator->GetOutput();
+
+ // second upsampling needed for motion artifacts
+ ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion;
+ itk::Vector<double,3> upsampledSpacing = m_UpsampledSpacing;
+ upsampledSpacing[0] /= 4;
+ upsampledSpacing[1] /= 4;
+ upsampledSpacing[2] /= 4;
+ upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4);
+ upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4);
+ upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4);
+ itk::Point<double,3> upsampledOrigin = m_UpsampledOrigin;
+ upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2;
+ upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2;
+ upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2;
+ ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New();
+ itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::Pointer upsampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
+ upsampler->SetInput(m_TissueMask);
+ upsampler->SetOutputParametersFromImage(m_TissueMask);
+ upsampler->SetSize(upsampledImageRegion.GetSize());
+ upsampler->SetOutputSpacing(upsampledSpacing);
+ upsampler->SetOutputOrigin(upsampledOrigin);
+ itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType>::Pointer nn_interpolator
+ = itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType>::New();
+ upsampler->SetInterpolator(nn_interpolator);
+ upsampler->Update();
+ upsampledTissueMask = upsampler->GetOutput();
+
+ m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n";
+ m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
+ unsigned int lastTick = 0;
+
+ for (int g=0; g<m_FiberModels.at(0)->GetNumGradients(); g++)
{
- vtkCell* cell = fiberPolyData->GetCell(i);
- int numPoints = cell->GetNumberOfPoints();
- vtkPoints* points = cell->GetPoints();
+ vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData();
+
+ ItkDoubleImgType::Pointer intraAxonalVolume = ItkDoubleImgType::New();
+ intraAxonalVolume->SetSpacing( m_UpsampledSpacing );
+ intraAxonalVolume->SetOrigin( m_UpsampledOrigin );
+ intraAxonalVolume->SetDirection( m_DirectionMatrix );
+ intraAxonalVolume->SetLargestPossibleRegion( m_UpsampledImageRegion );
+ intraAxonalVolume->SetBufferedRegion( m_UpsampledImageRegion );
+ intraAxonalVolume->SetRequestedRegion( m_UpsampledImageRegion );
+ intraAxonalVolume->Allocate();
+ intraAxonalVolume->FillBuffer(0);
+
+ // generate fiber signal
+ for( int i=0; i<numFibers; i++ )
+ {
+ vtkCell* cell = fiberPolyData->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
- if (numPoints<2)
- continue;
+ if (numPoints<2)
+ continue;
- for( int j=0; j<numPoints; j++)
- {
- double* temp = points->GetPoint(j);
- itk::Point<float, 3> vertex = GetItkPoint(temp);
- itk::Vector<double> v = GetItkVector(temp);
+ for( int j=0; j<numPoints; j++)
+ {
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
+ }
- itk::Vector<double, 3> dir(3);
- if (j<numPoints-1)
- dir = GetItkVector(points->GetPoint(j+1))-v;
- else
- dir = v-GetItkVector(points->GetPoint(j-1));
+ double* temp = points->GetPoint(j);
+ itk::Point<float, 3> vertex = GetItkPoint(temp);
+ itk::Vector<double> v = GetItkVector(temp);
- itk::Index<3> idx;
- itk::ContinuousIndex<float, 3> contIndex;
- m_TissueMask->TransformPhysicalPointToIndex(vertex, idx);
- m_TissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
+ itk::Vector<double, 3> dir(3);
+ if (j<numPoints-1)
+ dir = GetItkVector(points->GetPoint(j+1))-v;
+ else
+ dir = v-GetItkVector(points->GetPoint(j-1));
- if (!m_UseInterpolation) // use nearest neighbour interpolation
- {
- if (!m_TissueMask->GetLargestPossibleRegion().IsInside(idx) || m_TissueMask->GetPixel(idx)<=0)
+ if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2])
continue;
- // generate signal for each fiber compartment
- for (unsigned int k=0; k<m_FiberModels.size(); k++)
+ itk::Index<3> idx;
+ itk::ContinuousIndex<float, 3> contIndex;
+ tempTissueMask->TransformPhysicalPointToIndex(vertex, idx);
+ tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
+
+ if (!m_UseInterpolation) // use nearest neighbour interpolation
{
- DoubleDwiType::Pointer doubleDwi = compartments.at(k);
- m_FiberModels[k]->SetFiberDirection(dir);
- DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx);
- pix += segmentVolume*m_FiberModels[k]->SimulateMeasurement();
- doubleDwi->SetPixel(idx, pix );
- if (pix[baselineIndex]>maxVolume)
- maxVolume = pix[baselineIndex];
+ if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0)
+ continue;
+
+ // generate signal for each fiber compartment
+ for (unsigned int k=0; k<m_FiberModels.size(); k++)
+ {
+ DoubleDwiType::Pointer doubleDwi = compartments.at(k);
+ m_FiberModels[k]->SetFiberDirection(dir);
+ DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx);
+ pix[g] += segmentVolume*m_FiberModels[k]->SimulateMeasurement(g);
+
+ if (pix[g]!=pix[g])
+ {
+ std::cout << "pix[g] " << pix[g] << std::endl;
+ std::cout << "dir " << dir << std::endl;
+ std::cout << "segmentVolume " << segmentVolume << std::endl;
+ std::cout << "m_FiberModels[k]->SimulateMeasurement(g) " << m_FiberModels[k]->SimulateMeasurement(g) << std::endl;
+ }
+
+ doubleDwi->SetPixel(idx, pix );
+
+ double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume;
+ intraAxonalVolume->SetPixel(idx, vol );
+
+ if (g==0 && vol>maxVolume)
+ maxVolume = vol;
+ }
+ continue;
}
- continue;
- }
- double frac_x = contIndex[0] - idx[0];
- double frac_y = contIndex[1] - idx[1];
- double frac_z = contIndex[2] - idx[2];
- if (frac_x<0)
- {
- idx[0] -= 1;
- frac_x += 1;
- }
- if (frac_y<0)
- {
- idx[1] -= 1;
- frac_y += 1;
- }
- if (frac_z<0)
- {
- idx[2] -= 1;
- frac_z += 1;
- }
+ double frac_x = contIndex[0] - idx[0]; double frac_y = contIndex[1] - idx[1]; double frac_z = contIndex[2] - idx[2];
+ if (frac_x<0)
+ {
+ idx[0] -= 1;
+ frac_x += 1;
+ }
+ if (frac_y<0)
+ {
+ idx[1] -= 1;
+ frac_y += 1;
+ }
+ if (frac_z<0)
+ {
+ idx[2] -= 1;
+ frac_z += 1;
+ }
- frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5;
- frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5;
- frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5;
+ frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5;
+ frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5;
+ frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5;
- // use trilinear interpolation
- itk::Index<3> newIdx;
- for (int x=0; x<2; x++)
- {
- frac_x = 1-frac_x;
- for (int y=0; y<2; y++)
+ // use trilinear interpolation
+ itk::Index<3> newIdx;
+ for (int x=0; x<2; x++)
{
- frac_y = 1-frac_y;
- for (int z=0; z<2; z++)
+ frac_x = 1-frac_x;
+ for (int y=0; y<2; y++)
{
- frac_z = 1-frac_z;
+ frac_y = 1-frac_y;
+ for (int z=0; z<2; z++)
+ {
+ frac_z = 1-frac_z;
- newIdx[0] = idx[0]+x;
- newIdx[1] = idx[1]+y;
- newIdx[2] = idx[2]+z;
+ newIdx[0] = idx[0]+x;
+ newIdx[1] = idx[1]+y;
+ newIdx[2] = idx[2]+z;
- double frac = frac_x*frac_y*frac_z;
+ double frac = frac_x*frac_y*frac_z;
- // is position valid?
- if (!m_TissueMask->GetLargestPossibleRegion().IsInside(newIdx) || m_TissueMask->GetPixel(newIdx)<=0)
- continue;
+ // is position valid?
+ if (!tempTissueMask->GetLargestPossibleRegion().IsInside(newIdx) || tempTissueMask->GetPixel(newIdx)<=0)
+ continue;
- // generate signal for each fiber compartment
- for (unsigned int k=0; k<m_FiberModels.size(); k++)
- {
- DoubleDwiType::Pointer doubleDwi = compartments.at(k);
- m_FiberModels[k]->SetFiberDirection(dir);
- DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx);
- pix += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement();
- doubleDwi->SetPixel(newIdx, pix );
- if (pix[baselineIndex]>maxVolume)
- maxVolume = pix[baselineIndex];
+ // generate signal for each fiber compartment
+ for (unsigned int k=0; k<m_FiberModels.size(); k++)
+ {
+ DoubleDwiType::Pointer doubleDwi = compartments.at(k);
+ m_FiberModels[k]->SetFiberDirection(dir);
+ DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx);
+ pix[g] += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement(g);
+ doubleDwi->SetPixel(newIdx, pix );
+
+ double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume;
+ intraAxonalVolume->SetPixel(idx, vol );
+
+ if (g==0 && vol>maxVolume)
+ maxVolume = vol;
+ }
}
}
}
}
+ ++disp;
+ unsigned long newTick = 50*disp.count()/disp.expected_count();
+ for (int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
}
- ++disp;
- }
- MITK_INFO << "Generating signal of " << m_NonFiberModels.size() << " non-fiber compartments";
- ImageRegionIterator<ItkUcharImgType> it3(m_TissueMask, m_TissueMask->GetLargestPossibleRegion());
- boost::progress_display disp3(m_TissueMask->GetLargestPossibleRegion().GetNumberOfPixels());
- double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2];
+ // generate non-fiber signal
+ ImageRegionIterator<ItkUcharImgType> it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion());
+ double fact = 1;
+ if (m_FiberRadius<0.0001)
+ fact = voxelVolume/maxVolume;
+ while(!it3.IsAtEnd())
+ {
+ if (it3.Get()>0)
+ {
+ DoubleDwiType::IndexType index = it3.GetIndex();
- double fact = 1;
- if (m_FiberRadius<0.0001)
- fact = voxelVolume/maxVolume;
+ // get fiber volume fraction
+ DoubleDwiType::Pointer fiberDwi = compartments.at(0);
+ DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment
+ if (fact>1) // auto scale intra-axonal if no fiber radius is specified
+ {
+ fiberPix[g] *= fact;
+ fiberDwi->SetPixel(index, fiberPix);
+ }
+ double f = intraAxonalVolume->GetPixel(index)*fact;
- while(!it3.IsAtEnd())
- {
- DoubleDwiType::IndexType index = it3.GetIndex();
+ if (f>voxelVolume || (f>0.0 && m_EnforcePureFiberVoxels) ) // more fiber than space in voxel?
+ {
+ fiberPix[g] *= voxelVolume/f;
+ fiberDwi->SetPixel(index, fiberPix);
+ m_VolumeFractions.at(0)->SetPixel(index, 1);
+ }
+ else
+ {
+ m_VolumeFractions.at(0)->SetPixel(index, f/voxelVolume);
- if (it3.Get()>0)
- {
- // get fiber volume fraction
- DoubleDwiType::Pointer fiberDwi = compartments.at(0);
- DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment
- if (fact>1) // auto scale intra-axonal if no fiber radius is specified
- {
- fiberPix *= fact;
- fiberDwi->SetPixel(index, fiberPix);
+ double nonf = voxelVolume-f; // non-fiber volume
+ double inter = 0;
+ if (m_FiberModels.size()>1)
+ inter = nonf * f/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f
+ double other = nonf - inter; // rest of compartment
+ double singleinter = inter/(m_FiberModels.size()-1);
+
+ // adjust non-fiber and intra-axonal signal
+ for (unsigned int i=1; i<m_FiberModels.size(); i++)
+ {
+ DoubleDwiType::Pointer doubleDwi = compartments.at(i);
+ DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
+ if (f>0)
+ pix[g] /= f;
+ pix[g] *= singleinter;
+ doubleDwi->SetPixel(index, pix);
+ m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume);
+ }
+ for (unsigned int i=0; i<m_NonFiberModels.size(); i++)
+ {
+ DoubleDwiType::Pointer doubleDwi = compartments.at(i+m_FiberModels.size());
+ DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
+ // if (dynamic_cast< mitk::AstroStickModel<double>* >(m_NonFiberModels.at(i)))
+ // {
+ // mitk::AstroStickModel<double>* model = dynamic_cast< mitk::AstroStickModel<double>* >(m_NonFiberModels.at(i));
+ // model->SetSeed(8111984);
+ // }
+ pix[g] += m_NonFiberModels[i]->SimulateMeasurement(g)*other*m_NonFiberModels[i]->GetWeight();
+ doubleDwi->SetPixel(index, pix);
+ m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight());
+ }
+ }
}
- double f = fiberPix[baselineIndex];
+ ++it3;
+ }
- if (f>voxelVolume || (f>0.0 && m_EnforcePureFiberVoxels) ) // more fiber than space in voxel?
+ // move fibers
+ if (m_AddMotionArtifact)
+ {
+ if (m_RandomMotion)
{
- fiberDwi->SetPixel(index, fiberPix*voxelVolume/f);
- m_VolumeFractions.at(0)->SetPixel(index, 1);
+ fiberBundleTransformed = fiberBundle->GetDeepCopy();
+ rotation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[0]*2)-m_MaxRotation[0];
+ rotation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[1]*2)-m_MaxRotation[1];
+ rotation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[2]*2)-m_MaxRotation[2];
+ translation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[0]*2)-m_MaxTranslation[0];
+ translation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[1]*2)-m_MaxTranslation[1];
+ translation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[2]*2)-m_MaxTranslation[2];
}
- else
- {
- m_VolumeFractions.at(0)->SetPixel(index, f/voxelVolume);
- double nonf = voxelVolume-f; // non-fiber volume
- double inter = 0;
- if (m_FiberModels.size()>1)
- inter = nonf * f/voxelVolume; // intra-axonal fraction of non fiber compartment scales linearly with f
- double other = nonf - inter; // rest of compartment
- double singleinter = inter/(m_FiberModels.size()-1);
+ // rotate mask image
+ if (maskImageSet)
+ {
+ ImageRegionIterator<ItkUcharImgType> maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion());
+ tempTissueMask->FillBuffer(0);
- // adjust non-fiber and intra-axonal signal
- for (unsigned int i=1; i<m_FiberModels.size(); i++)
- {
- DoubleDwiType::Pointer doubleDwi = compartments.at(i);
- DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
- if (pix[baselineIndex]>0)
- pix /= pix[baselineIndex];
- pix *= singleinter;
- doubleDwi->SetPixel(index, pix);
- m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume);
- }
- for (unsigned int i=0; i<m_NonFiberModels.size(); i++)
+ while(!maskIt.IsAtEnd())
{
- DoubleDwiType::Pointer doubleDwi = compartments.at(i+m_FiberModels.size());
- DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index) + m_NonFiberModels[i]->SimulateMeasurement()*other*m_NonFiberModels[i]->GetWeight();
- doubleDwi->SetPixel(index, pix);
- m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight());
+ if (maskIt.Get()<=0)
+ {
+ ++maskIt;
+ continue;
+ }
+
+ DoubleDwiType::IndexType index = maskIt.GetIndex();
+ itk::Point<double, 3> point;
+ upsampledTissueMask->TransformIndexToPhysicalPoint(index, point);
+ if (m_RandomMotion)
+ point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]);
+ else
+ point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1));
+
+ tempTissueMask->TransformPhysicalPointToIndex(point, index);
+ if (tempTissueMask->GetLargestPossibleRegion().IsInside(index))
+ tempTissueMask->SetPixel(index,100);
+ ++maskIt;
}
}
+
+ // rotate fibers
+ logFile << g+1 << " rotation:" << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";";
+ logFile << " translation:" << translation[0] << "," << translation[1] << "," << translation[2] << "\n";
+ fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]);
}
- ++it3;
- ++disp3;
+ }
+ logFile.close();
+ m_StatusText += "\n\n";
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
}
// do k-space stuff
DoubleDwiType::Pointer doubleOutImage;
- if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || !m_KspaceArtifacts.empty() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents || m_AddGibbsRinging || m_Wrap<1.0)
+ if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents || m_AddGibbsRinging || m_Wrap<1.0)
{
+ m_StatusText += this->GetTime()+" > Adjusting complex signal\n";
MITK_INFO << "Adjusting complex signal";
doubleOutImage = DoKspaceStuff(compartments);
m_SignalScale = 1;
}
else
{
+ m_StatusText += this->GetTime()+" > Summing compartments\n";
MITK_INFO << "Summing compartments";
doubleOutImage = compartments.at(0);
for (unsigned int i=1; i<compartments.size(); i++)
{
itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New();
adder->SetInput1(doubleOutImage);
adder->SetInput2(compartments.at(i));
adder->Update();
doubleOutImage = adder->GetOutput();
}
}
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
+ }
+ m_StatusText += this->GetTime()+" > Finalizing image\n";
MITK_INFO << "Finalizing image";
unsigned int window = 0;
unsigned int min = itk::NumericTraits<unsigned int>::max();
ImageRegionIterator<OutputImageType> it4 (outImage, outImage->GetLargestPossibleRegion());
DoubleDwiType::PixelType signal; signal.SetSize(m_FiberModels[0]->GetNumGradients());
- boost::progress_display disp4(outImage->GetLargestPossibleRegion().GetNumberOfPixels());
+ boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels());
+
+ m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n";
+ m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*";
+ lastTick = 0;
+
while(!it4.IsAtEnd())
{
- ++disp4;
+ if (this->GetAbortGenerateData())
+ {
+ m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n";
+ return;
+ }
+
+ ++disp2;
+ unsigned long newTick = 50*disp2.count()/disp2.expected_count();
+ for (int tick = 0; tick<(newTick-lastTick); tick++)
+ m_StatusText += "*";
+ lastTick = newTick;
+
typename OutputImageType::IndexType index = it4.GetIndex();
signal = doubleOutImage->GetPixel(index)*m_SignalScale;
- if (m_NoiseModel->GetNoiseVariance() > 0)
+ if (m_NoiseModel!=NULL)
{
DoubleDwiType::PixelType accu = signal; accu.Fill(0.0);
for (unsigned int i=0; i<m_NumberOfRepetitions; i++)
{
DoubleDwiType::PixelType temp = signal;
m_NoiseModel->AddNoise(temp);
accu += temp;
}
signal = accu/m_NumberOfRepetitions;
}
for (unsigned int i=0; i<signal.Size(); i++)
{
if (signal[i]>0)
signal[i] = floor(signal[i]+0.5);
else
signal[i] = ceil(signal[i]-0.5);
if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]>window)
window = signal[i];
if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]<min)
min = signal[i];
}
it4.Set(signal);
++it4;
}
window -= min;
unsigned int level = window/2 + min;
m_LevelWindow.SetLevelWindow(level, window);
this->SetNthOutput(0, outImage);
+
+ m_StatusText += "\n\n";
+ m_StatusText += "Finished simulation\n";
+ m_StatusText += "Simulation time: "+GetTime();
}
template< class PixelType >
itk::Point<float, 3> TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3])
{
itk::Point<float, 3> itkPoint;
itkPoint[0] = point[0];
itkPoint[1] = point[1];
itkPoint[2] = point[2];
return itkPoint;
}
template< class PixelType >
itk::Vector<double, 3> TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3])
{
itk::Vector<double, 3> itkVector;
itkVector[0] = point[0];
itkVector[1] = point[1];
itkVector[2] = point[2];
return itkVector;
}
template< class PixelType >
vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3])
{
vnl_vector_fixed<double, 3> vnlVector;
vnlVector[0] = point[0];
vnlVector[1] = point[1];
vnlVector[2] = point[2];
return vnlVector;
}
template< class PixelType >
vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector<float,3>& vector)
{
vnl_vector_fixed<double, 3> vnlVector;
vnlVector[0] = vector[0];
vnlVector[1] = vector[1];
vnlVector[2] = vector[2];
return vnlVector;
}
+template< class PixelType >
+std::string TractsToDWIImageFilter< PixelType >::GetTime()
+{
+ unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC;
+ unsigned long hours = total/3600;
+ unsigned long minutes = (total%3600)/60;
+ unsigned long seconds = total%60;
+ std::string out = "";
+ out.append(boost::lexical_cast<std::string>(hours));
+ out.append(":");
+ out.append(boost::lexical_cast<std::string>(minutes));
+ out.append(":");
+ out.append(boost::lexical_cast<std::string>(seconds));
+ return out;
+}
+
}
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h
index 4d7f6437b7..93adf86e9e 100755
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h
@@ -1,161 +1,170 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef __itkTractsToDWIImageFilter_h__
#define __itkTractsToDWIImageFilter_h__
// MITK
#include <mitkFiberBundleX.h>
#include <mitkDiffusionSignalModel.h>
#include <mitkDiffusionNoiseModel.h>
-#include <mitkKspaceArtifact.h>
// ITK
#include <itkImage.h>
#include <itkVectorImage.h>
#include <itkImageSource.h>
#include <itkVnlForwardFFTImageFilter.h>
#include <itkVnlInverseFFTImageFilter.h>
+#include <itkTimeProbe.h>
#include <cmath>
+#include <ctime>
namespace itk
{
/**
* \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. */
template< class PixelType >
class TractsToDWIImageFilter : public ImageSource< itk::VectorImage< PixelType, 3 > >
{
public:
typedef TractsToDWIImageFilter Self;
typedef ImageSource< itk::VectorImage< PixelType, 3 > > Superclass;
typedef SmartPointer< Self > Pointer;
typedef SmartPointer< const Self > ConstPointer;
typedef typename Superclass::OutputImageType OutputImageType;
typedef itk::Image<double, 3> ItkDoubleImgType;
typedef itk::Image<float, 3> ItkFloatImgType;
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef mitk::FiberBundleX::Pointer FiberBundleType;
typedef itk::VectorImage< double, 3 > DoubleDwiType;
- typedef std::vector< mitk::KspaceArtifact<double>* > KspaceArtifactList;
typedef std::vector< mitk::DiffusionSignalModel<double>* > DiffusionModelList;
typedef itk::Matrix<double, 3, 3> MatrixType;
typedef mitk::DiffusionNoiseModel<double> NoiseModelType;
typedef itk::Image< double, 2 > SliceType;
typedef itk::VnlForwardFFTImageFilter<SliceType>::OutputImageType ComplexSliceType;
typedef itk::Vector< double,3> VectorType;
typedef itk::Point< double,3> PointType;
itkNewMacro(Self)
itkTypeMacro( TractsToDWIImageFilter, ImageToImageFilter )
// input
itkSetMacro( SignalScale, double )
itkSetMacro( FiberRadius, double )
itkSetMacro( InterpolationShrink, double ) ///< large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation)
itkSetMacro( VolumeAccuracy, unsigned int ) ///< determines fiber sampling density and thereby the accuracy of the fiber volume fraction
itkSetMacro( FiberBundle, FiberBundleType ) ///< input fiber bundle
itkSetMacro( Spacing, VectorType ) ///< output image spacing
itkSetMacro( Origin, PointType ) ///< output image origin
itkSetMacro( DirectionMatrix, MatrixType ) ///< output image rotation
itkSetMacro( EnforcePureFiberVoxels, bool ) ///< treat all voxels containing at least one fiber as fiber-only (actually disable non-fiber compartments for this voxel).
itkSetMacro( ImageRegion, ImageRegion<3> ) ///< output image size
itkSetMacro( NumberOfRepetitions, unsigned int ) ///< number of acquisition repetitions to reduce noise (default is no additional repetition)
itkSetMacro( TissueMask, ItkUcharImgType::Pointer ) ///< voxels outside of this binary mask contain only noise (are treated as air)
void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; } ///< generates the noise added to the image values
void SetFiberModels(DiffusionModelList modelList){ m_FiberModels = modelList; } ///< generate signal of fiber compartments
void SetNonFiberModels(DiffusionModelList modelList){ m_NonFiberModels = modelList; } ///< generate signal of non-fiber compartments
- void SetKspaceArtifacts(KspaceArtifactList artifactList){ m_KspaceArtifacts = artifactList; }
mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; }
itkSetMacro( FrequencyMap, ItkDoubleImgType::Pointer )
itkSetMacro( kOffset, double )
itkSetMacro( tLine, double )
itkSetMacro( tInhom, double )
itkSetMacro( TE, double )
itkSetMacro( UseInterpolation, bool )
itkSetMacro( SimulateEddyCurrents, bool )
itkSetMacro( SimulateRelaxation, bool )
itkSetMacro( EddyGradientStrength, double )
itkSetMacro( AddGibbsRinging, bool )
itkSetMacro( Spikes, int )
itkSetMacro( SpikeAmplitude, double )
itkSetMacro( Wrap, double )
+ itkSetMacro( MaxTranslation, VectorType )
+ itkSetMacro( MaxRotation, VectorType )
+ itkSetMacro( AddMotionArtifact, bool )
+ itkSetMacro( RandomMotion, bool )
+ itkGetMacro( StatusText, std::string )
// output
std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions(){ return m_VolumeFractions; }
void GenerateData();
protected:
TractsToDWIImageFilter();
virtual ~TractsToDWIImageFilter();
itk::Point<float, 3> GetItkPoint(double point[3]);
itk::Vector<double, 3> GetItkVector(double point[3]);
vnl_vector_fixed<double, 3> GetVnlVector(double point[3]);
vnl_vector_fixed<double, 3> GetVnlVector(Vector< float, 3 >& vector);
+ std::string GetTime();
/** Transform generated image compartment by compartment, channel by channel and slice by slice using FFT and add k-space artifacts. */
DoubleDwiType::Pointer DoKspaceStuff(std::vector< DoubleDwiType::Pointer >& images);
-// /** Rearrange FFT output to shift low frequencies to the iamge center (correct itk). */
-// TractsToDWIImageFilter::ComplexSliceType::Pointer RearrangeSlice(ComplexSliceType::Pointer slice);
-
itk::Vector<double,3> m_Spacing; ///< output image spacing
itk::Vector<double,3> m_UpsampledSpacing;
itk::Point<double,3> m_Origin; ///< output image origin
+ itk::Point<double,3> m_UpsampledOrigin;
MatrixType m_DirectionMatrix; ///< output image rotation
ImageRegion<3> m_ImageRegion; ///< output image size
ImageRegion<3> m_UpsampledImageRegion;
ItkUcharImgType::Pointer m_TissueMask; ///< voxels outside of this binary mask contain only noise (are treated as air)
ItkDoubleImgType::Pointer m_FrequencyMap; ///< map of the B0 inhomogeneities
double m_kOffset;
double m_tLine;
double m_TE;
double m_tInhom;
FiberBundleType m_FiberBundle; ///< input fiber bundle
DiffusionModelList m_FiberModels; ///< generate signal of fiber compartments
DiffusionModelList m_NonFiberModels; ///< generate signal of non-fiber compartments
- KspaceArtifactList m_KspaceArtifacts;
NoiseModelType* m_NoiseModel; ///< generates the noise added to the image values
bool m_CircleDummy;
unsigned int m_VolumeAccuracy;
bool m_AddGibbsRinging; ///< causes ringing artifacts
unsigned int m_NumberOfRepetitions;
bool m_EnforcePureFiberVoxels;
double m_InterpolationShrink;
double m_FiberRadius;
double m_SignalScale;
mitk::LevelWindow m_LevelWindow;
bool m_UseInterpolation;
std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions; ///< one double image for each compartment containing the corresponding volume fraction per voxel
bool m_SimulateRelaxation;
bool m_SimulateEddyCurrents;
double m_EddyGradientStrength;
int m_Spikes;
double m_SpikeAmplitude;
double m_Wrap;
+ VectorType m_MaxTranslation;
+ VectorType m_MaxRotation;
+ bool m_AddMotionArtifact;
+ bool m_RandomMotion;
+ itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
+ std::string m_StatusText;
+ time_t m_StartTime;
};
}
#include "itkTractsToDWIImageFilter.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp
index a24e174713..e2857935cd 100644
--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp
@@ -1,836 +1,832 @@
#include "itkTractsToVectorImageFilter.h"
// VTK
#include <vtkPolyLine.h>
#include <vtkCellArray.h>
#include <vtkCellData.h>
// ITK
#include <itkTimeProbe.h>
#include <itkImageRegionIterator.h>
// misc
#define _USE_MATH_DEFINES
#include <math.h>
#include <boost/progress.hpp>
namespace itk{
static bool CompareVectorLengths(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2)
{
return (v1.magnitude()>v2.magnitude());
}
template< class PixelType >
TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter():
m_AngularThreshold(0.7),
m_MaskImage(NULL),
m_NumDirectionsImage(NULL),
m_NormalizeVectors(false),
m_Epsilon(0.999),
m_UseWorkingCopy(true),
m_MaxNumDirections(3),
m_UseTrilinearInterpolation(false),
m_Thres(0.5)
{
this->SetNumberOfRequiredOutputs(1);
}
template< class PixelType >
TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter()
{
}
template< class PixelType >
vnl_vector_fixed<double, 3> TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[3])
{
vnl_vector_fixed<double, 3> vnlVector;
vnlVector[0] = point[0];
vnlVector[1] = point[1];
vnlVector[2] = point[2];
return vnlVector;
}
template< class PixelType >
itk::Point<float, 3> TractsToVectorImageFilter< PixelType >::GetItkPoint(double point[3])
{
itk::Point<float, 3> itkPoint;
itkPoint[0] = point[0];
itkPoint[1] = point[1];
itkPoint[2] = point[2];
return itkPoint;
}
template< class PixelType >
void TractsToVectorImageFilter< PixelType >::GenerateData()
{
mitk::Geometry3D::Pointer geometry = m_FiberBundle->GetGeometry();
// calculate new image parameters
itk::Vector<double> spacing;
itk::Point<double> origin;
itk::Matrix<double, 3, 3> direction;
ImageRegion<3> imageRegion;
if (!m_MaskImage.IsNull())
{
spacing = m_MaskImage->GetSpacing();
imageRegion = m_MaskImage->GetLargestPossibleRegion();
origin = m_MaskImage->GetOrigin();
direction = m_MaskImage->GetDirection();
}
else
{
spacing = geometry->GetSpacing();
origin = geometry->GetOrigin();
mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
origin[0] += bounds.GetElement(0);
origin[1] += bounds.GetElement(2);
origin[2] += bounds.GetElement(4);
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
direction[j][i] = geometry->GetMatrixColumn(i)[j];
imageRegion.SetSize(0, geometry->GetExtent(0));
imageRegion.SetSize(1, geometry->GetExtent(1));
imageRegion.SetSize(2, geometry->GetExtent(2));
m_MaskImage = ItkUcharImgType::New();
m_MaskImage->SetSpacing( spacing );
m_MaskImage->SetOrigin( origin );
m_MaskImage->SetDirection( direction );
m_MaskImage->SetRegions( imageRegion );
m_MaskImage->Allocate();
m_MaskImage->FillBuffer(1);
}
OutputImageType::RegionType::SizeType outImageSize = imageRegion.GetSize();
m_OutImageSpacing = m_MaskImage->GetSpacing();
m_ClusteredDirectionsContainer = ContainerType::New();
// initialize crossings image
m_CrossingsImage = ItkUcharImgType::New();
m_CrossingsImage->SetSpacing( spacing );
m_CrossingsImage->SetOrigin( origin );
m_CrossingsImage->SetDirection( direction );
m_CrossingsImage->SetRegions( imageRegion );
m_CrossingsImage->Allocate();
m_CrossingsImage->FillBuffer(0);
// initialize num directions image
m_NumDirectionsImage = ItkUcharImgType::New();
m_NumDirectionsImage->SetSpacing( spacing );
m_NumDirectionsImage->SetOrigin( origin );
m_NumDirectionsImage->SetDirection( direction );
m_NumDirectionsImage->SetRegions( imageRegion );
m_NumDirectionsImage->Allocate();
m_NumDirectionsImage->FillBuffer(0);
// resample fiber bundle
float minSpacing = 1;
if(m_OutImageSpacing[0]<m_OutImageSpacing[1] && m_OutImageSpacing[0]<m_OutImageSpacing[2])
minSpacing = m_OutImageSpacing[0];
else if (m_OutImageSpacing[1] < m_OutImageSpacing[2])
minSpacing = m_OutImageSpacing[1];
else
minSpacing = m_OutImageSpacing[2];
if (m_UseWorkingCopy)
m_FiberBundle = m_FiberBundle->GetDeepCopy();
// resample fiber bundle for sufficient voxel coverage
- m_FiberBundle->ResampleFibers(minSpacing/10);
+ m_FiberBundle->ResampleFibers(minSpacing/3);
// iterate over all fibers
vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
vtkSmartPointer<vtkCellArray> vLines = fiberPolyData->GetLines();
vLines->InitTraversal();
int numFibers = m_FiberBundle->GetNumFibers();
itk::TimeProbe clock;
m_DirectionsContainer = ContainerType::New();
if (m_UseTrilinearInterpolation)
MITK_INFO << "Generating directions from tractogram (trilinear interpolation)";
else
MITK_INFO << "Generating directions from tractogram";
boost::progress_display disp(numFibers);
for( int i=0; i<numFibers; i++ )
{
++disp;
clock.Start();
vtkIdType numPoints(0);
vtkIdType* points(NULL);
vLines->GetNextCell ( numPoints, points );
if (numPoints<2)
continue;
itk::Index<3> index; index.Fill(0);
itk::ContinuousIndex<float, 3> contIndex;
vnl_vector_fixed<double, 3> dir, wDir;
itk::Point<float, 3> worldPos;
vnl_vector<double> v;
for( int j=0; j<numPoints-1; j++)
{
double* temp = fiberPolyData->GetPoint(points[j]);
worldPos = GetItkPoint(temp);
v = GetVnlVector(temp);
dir = GetVnlVector(fiberPolyData->GetPoint(points[j+1]))-v;
dir.normalize();
m_MaskImage->TransformPhysicalPointToIndex(worldPos, index);
m_MaskImage->TransformPhysicalPointToContinuousIndex(worldPos, contIndex);
if (m_MaskImage->GetPixel(index)==0)
continue;
if (!m_UseTrilinearInterpolation)
{
if (index[0] < 0 || index[0] >= outImageSize[0])
continue;
if (index[1] < 0 || index[1] >= outImageSize[1])
continue;
if (index[2] < 0 || index[2] >= outImageSize[2])
continue;
int idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2]);
DirectionContainerType::Pointer dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), dir);
}
else
{
dirCont->InsertElement(0, dir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
continue;
}
float frac_x = contIndex[0] - index[0];
float frac_y = contIndex[1] - index[1];
float frac_z = contIndex[2] - index[2];
if (frac_x<0)
{
index[0] -= 1;
frac_x += 1;
}
if (frac_y<0)
{
index[1] -= 1;
frac_y += 1;
}
if (frac_z<0)
{
index[2] -= 1;
frac_z += 1;
}
frac_x = 1-frac_x;
frac_y = 1-frac_y;
frac_z = 1-frac_z;
// int coordinates inside image?
if (index[0] < 0 || index[0] >= outImageSize[0]-1)
continue;
if (index[1] < 0 || index[1] >= outImageSize[1]-1)
continue;
if (index[2] < 0 || index[2] >= outImageSize[2]-1)
continue;
DirectionContainerType::Pointer dirCont;
int idx;
wDir = dir;
float weight = ( frac_x)*( frac_y)*( frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2] );
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = ( frac_x)*(1-frac_y)*( frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0] + outImageSize[0]*(index[1]+1+ outImageSize[1]*index[2] );
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = ( frac_x)*( frac_y)*(1-frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2]+outImageSize[1]);
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = ( frac_x)*(1-frac_y)*(1-frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0] + outImageSize[0]*(index[1]+1+ outImageSize[1]*index[2]+outImageSize[1]);
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = (1-frac_x)*( frac_y)*( frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0]+1 + outImageSize[0]*(index[1] + outImageSize[1]*index[2] );
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = (1-frac_x)*( frac_y)*(1-frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0]+1 + outImageSize[0]*(index[1] + outImageSize[1]*index[2]+outImageSize[1]);
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = (1-frac_x)*(1-frac_y)*( frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0]+1 + outImageSize[0]*(index[1]+1+ outImageSize[1]*index[2] );
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
wDir = dir;
weight = (1-frac_x)*(1-frac_y)*(1-frac_z);
if (weight>m_Thres)
{
wDir *= weight;
idx = index[0]+1 + outImageSize[0]*(index[1]+1+ outImageSize[1]*index[2]+outImageSize[1]);
dirCont = DirectionContainerType::New();
if (m_DirectionsContainer->IndexExists(idx))
{
dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull())
{
dirCont = DirectionContainerType::New();
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
else
dirCont->InsertElement(dirCont->Size(), wDir);
}
else
{
dirCont->InsertElement(0, wDir);
m_DirectionsContainer->InsertElement(idx, dirCont);
}
}
}
clock.Stop();
}
vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
itk::ImageRegionIterator<ItkUcharImgType> dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<ItkUcharImgType> crossIt(m_CrossingsImage, m_CrossingsImage->GetLargestPossibleRegion());
m_DirectionImageContainer = DirectionImageContainerType::New();
int maxNumDirections = 0;
MITK_INFO << "Clustering directions";
boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]);
for(crossIt.GoToBegin(); !crossIt.IsAtEnd(); ++crossIt)
{
++disp2;
OutputImageType::IndexType index = crossIt.GetIndex();
int idx = index[0]+(index[1]+index[2]*outImageSize[1])*outImageSize[0];
if (!m_DirectionsContainer->IndexExists(idx))
{
++dirIt;
continue;
}
DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx);
if (dirCont.IsNull() || index[0] < 0 || index[0] >= outImageSize[0] || index[1] < 0 || index[1] >= outImageSize[1] || index[2] < 0 || index[2] >= outImageSize[2])
{
++dirIt;
continue;
}
std::vector< DirectionType > directions;
for (int i=0; i<dirCont->Size(); i++)
if (dirCont->ElementAt(i).magnitude()>0.0001)
directions.push_back(dirCont->ElementAt(i));
if (!directions.empty())
directions = FastClustering(directions);
std::sort( directions.begin(), directions.end(), CompareVectorLengths );
if ( directions.size() > maxNumDirections )
{
for (int i=maxNumDirections; i<std::min((int)directions.size(), m_MaxNumDirections); i++)
{
ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New();
directionImage->SetSpacing( spacing );
directionImage->SetOrigin( origin );
directionImage->SetDirection( direction );
directionImage->SetRegions( imageRegion );
directionImage->Allocate();
Vector< float, 3 > nullVec; nullVec.Fill(0.0);
directionImage->FillBuffer(nullVec);
m_DirectionImageContainer->InsertElement(i, directionImage);
}
maxNumDirections = std::min((int)directions.size(), m_MaxNumDirections);
}
int numDir = directions.size();
if (numDir>m_MaxNumDirections)
numDir = m_MaxNumDirections;
for (int i=0; i<numDir; i++)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
itk::ContinuousIndex<float, 3> center;
center[0] = index[0];
center[1] = index[1];
center[2] = index[2];
itk::Point<float> worldCenter;
m_MaskImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter );
-
- // workaround *********************************************
- //DirectionType dir = m_MaskImage->GetDirection()*directions.at(i);
DirectionType dir = directions.at(i);
- // workaround *********************************************
// set direction image pixel
ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->GetElement(i);
Vector< float, 3 > pixel;
pixel.SetElement(0, dir[0]);
pixel.SetElement(1, dir[1]);
pixel.SetElement(2, dir[2]);
directionImage->SetPixel(index, pixel);
// add direction to vector field (with spacing compensation)
itk::Point<float> worldStart;
worldStart[0] = worldCenter[0]-dir[0]/2*minSpacing;
worldStart[1] = worldCenter[1]-dir[1]/2*minSpacing;
worldStart[2] = worldCenter[2]-dir[2]/2*minSpacing;
vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
itk::Point<float> worldEnd;
worldEnd[0] = worldCenter[0]+dir[0]/2*minSpacing;
worldEnd[1] = worldCenter[1]+dir[1]/2*minSpacing;
worldEnd[2] = worldCenter[2]+dir[2]/2*minSpacing;
id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer());
container->GetPointIds()->InsertNextId(id);
m_VtkCellArray->InsertNextCell(container);
}
dirIt.Set(numDir);
++dirIt;
}
vtkSmartPointer<vtkPolyData> directionsPolyData = vtkSmartPointer<vtkPolyData>::New();
directionsPolyData->SetPoints(m_VtkPoints);
directionsPolyData->SetLines(m_VtkCellArray);
m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData);
}
template< class PixelType >
std::vector< vnl_vector_fixed< double, 3 > > TractsToVectorImageFilter< PixelType >::FastClustering(std::vector< vnl_vector_fixed< double, 3 > >& inDirs)
{
std::vector< vnl_vector_fixed< double, 3 > > outDirs;
if (inDirs.empty())
return outDirs;
vnl_vector_fixed< double, 3 > oldMean, currentMean, workingMean;
std::vector< vnl_vector_fixed< double, 3 > > normalizedDirs;
std::vector< int > touched;
for (int i=0; i<inDirs.size(); i++)
{
normalizedDirs.push_back(inDirs[i]);
normalizedDirs.back().normalize();
}
// initialize
float max = 0.0;
touched.resize(inDirs.size(), 0);
bool free = true;
currentMean = inDirs[0]; // initialize first seed
while (free)
{
oldMean.fill(0.0);
// start mean-shift clustering
float angle = 0.0;
int counter = 0;
while ((currentMean-oldMean).magnitude()>0.0001)
{
counter = 0;
oldMean = currentMean;
workingMean = oldMean;
workingMean.normalize();
currentMean.fill(0.0);
for (int i=0; i<normalizedDirs.size(); i++)
{
angle = dot_product(workingMean, normalizedDirs[i]);
if (angle>=m_AngularThreshold)
{
currentMean += inDirs[i];
touched[i] = 1;
counter++;
}
else if (-angle>=m_AngularThreshold)
{
currentMean -= inDirs[i];
touched[i] = 1;
counter++;
}
}
}
// found stable mean
if (counter>0)
{
currentMean /= counter;
float mag = currentMean.magnitude();
if (mag>0)
{
if (mag>max)
max = mag;
outDirs.push_back(currentMean);
}
}
// find next unused seed
free = false;
for (int i=0; i<touched.size(); i++)
if (touched[i]==0)
{
currentMean = inDirs[i];
free = true;
}
}
if (m_NormalizeVectors)
for (int i=0; i<outDirs.size(); i++)
outDirs[i].normalize();
else if (max>0)
for (int i=0; i<outDirs.size(); i++)
outDirs[i] /= max;
if (inDirs.size()==outDirs.size())
return outDirs;
else
return FastClustering(outDirs);
}
template< class PixelType >
std::vector< vnl_vector_fixed< double, 3 > > TractsToVectorImageFilter< PixelType >::Clustering(std::vector< vnl_vector_fixed< double, 3 > >& inDirs)
{
std::vector< vnl_vector_fixed< double, 3 > > outDirs;
if (inDirs.empty())
return outDirs;
vnl_vector_fixed< double, 3 > oldMean, currentMean, workingMean;
std::vector< vnl_vector_fixed< double, 3 > > normalizedDirs;
std::vector< int > touched;
for (int i=0; i<inDirs.size(); i++)
{
normalizedDirs.push_back(inDirs[i]);
normalizedDirs.back().normalize();
}
// initialize
float max = 0.0;
touched.resize(inDirs.size(), 0);
for (int j=0; j<inDirs.size(); j++)
{
currentMean = inDirs[j];
oldMean.fill(0.0);
// start mean-shift clustering
float angle = 0.0;
int counter = 0;
while ((currentMean-oldMean).magnitude()>0.0001)
{
counter = 0;
oldMean = currentMean;
workingMean = oldMean;
workingMean.normalize();
currentMean.fill(0.0);
for (int i=0; i<normalizedDirs.size(); i++)
{
angle = dot_product(workingMean, normalizedDirs[i]);
if (angle>=m_AngularThreshold)
{
currentMean += inDirs[i];
counter++;
}
else if (-angle>=m_AngularThreshold)
{
currentMean -= inDirs[i];
counter++;
}
}
}
// found stable mean
if (counter>0)
{
bool add = true;
vnl_vector_fixed< double, 3 > normMean = currentMean;
normMean.normalize();
for (int i=0; i<outDirs.size(); i++)
{
vnl_vector_fixed< double, 3 > dir = outDirs[i];
dir.normalize();
if ((normMean-dir).magnitude()<=0.0001)
{
add = false;
break;
}
}
currentMean /= counter;
if (add)
{
float mag = currentMean.magnitude();
if (mag>0)
{
if (mag>max)
max = mag;
outDirs.push_back(currentMean);
}
}
}
}
if (m_NormalizeVectors)
for (int i=0; i<outDirs.size(); i++)
outDirs[i].normalize();
else if (max>0)
for (int i=0; i<outDirs.size(); i++)
outDirs[i] /= max;
if (inDirs.size()==outDirs.size())
return outDirs;
else
return FastClustering(outDirs);
}
template< class PixelType >
TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::MeanShiftClustering(DirectionContainerType::Pointer dirCont)
{
DirectionContainerType::Pointer container = DirectionContainerType::New();
float max = 0;
for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it)
{
vnl_vector_fixed<double, 3> mean = ClusterStep(dirCont, it.Value());
if (mean.is_zero())
continue;
bool addMean = true;
for (DirectionContainerType::ConstIterator it2 = container->Begin(); it2!=container->End(); ++it2)
{
vnl_vector_fixed<double, 3> dir = it2.Value();
float angle = fabs(dot_product(mean, dir)/(mean.magnitude()*dir.magnitude()));
if (angle>=m_Epsilon)
{
addMean = false;
break;
}
}
if (addMean)
{
if (m_NormalizeVectors)
mean.normalize();
else if (mean.magnitude()>max)
max = mean.magnitude();
container->InsertElement(container->Size(), mean);
}
}
// max normalize voxel directions
if (max>0 && !m_NormalizeVectors)
for (int i=0; i<container->Size(); i++)
container->ElementAt(i) /= max;
if (container->Size()<dirCont->Size())
return MeanShiftClustering(container);
else
return container;
}
template< class PixelType >
vnl_vector_fixed<double, 3> TractsToVectorImageFilter< PixelType >::ClusterStep(DirectionContainerType::Pointer dirCont, vnl_vector_fixed<double, 3> currentMean)
{
vnl_vector_fixed<double, 3> newMean; newMean.fill(0);
for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it)
{
vnl_vector_fixed<double, 3> dir = it.Value();
float angle = dot_product(currentMean, dir)/(currentMean.magnitude()*dir.magnitude());
if (angle>=m_AngularThreshold)
newMean += dir;
else if (-angle>=m_AngularThreshold)
newMean -= dir;
}
if (fabs(dot_product(currentMean, newMean)/(currentMean.magnitude()*newMean.magnitude()))>=m_Epsilon || newMean.is_zero())
return newMean;
else
return ClusterStep(dirCont, newMean);
}
}
diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
index 8214f30e9a..342f500bce 100755
--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
@@ -1,1800 +1,1965 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#define _USE_MATH_DEFINES
#include "mitkFiberBundleX.h"
#include <mitkPlanarCircle.h>
#include <mitkPlanarPolygon.h>
#include <mitkPlanarFigureComposite.h>
#include "mitkImagePixelReadAccessor.h"
#include <mitkPixelTypeMultiplex.h>
#include <vtkPointData.h>
#include <vtkDataArray.h>
#include <vtkUnsignedCharArray.h>
#include <vtkPolyLine.h>
#include <vtkCellArray.h>
#include <vtkCellData.h>
#include <vtkIdFilter.h>
#include <vtkClipPolyData.h>
#include <vtkPlane.h>
#include <vtkDoubleArray.h>
#include <vtkKochanekSpline.h>
#include <vtkParametricFunctionSource.h>
#include <vtkParametricSpline.h>
#include <vtkPolygon.h>
#include <vtkCleanPolyData.h>
#include <cmath>
#include <boost/progress.hpp>
+#include <vtkTransformPolyDataFilter.h>
const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient";
//const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity";
const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values";
const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom";
const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs";
using namespace std;
mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData )
: m_CurrentColorCoding(NULL)
, m_NumFibers(0)
, m_FiberSampling(0)
{
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
if (fiberPolyData != NULL)
{
m_FiberPolyData = fiberPolyData;
//m_FiberPolyData->DeepCopy(fiberPolyData);
this->DoColorCodingOrientationBased();
}
this->UpdateFiberGeometry();
this->SetColorCoding(COLORCODING_ORIENTATION_BASED);
this->GenerateFiberIds();
}
mitk::FiberBundleX::~FiberBundleX()
{
}
mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy()
{
mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData);
newFib->SetColorCoding(m_CurrentColorCoding);
return newFib;
}
vtkSmartPointer<vtkPolyData> mitk::FiberBundleX::GeneratePolyDataByIds(std::vector<long> fiberIds)
{
MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n";
MITK_DEBUG << "Number of new Fibers: " << fiberIds.size();
// iterate through the vectorcontainer hosting all desired fiber Ids
vtkSmartPointer<vtkPolyData> newFiberPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> newLineSet = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> newPointSet = vtkSmartPointer<vtkPoints>::New();
// if FA array available, initialize fa double array
// if color orient array is available init color array
vtkSmartPointer<vtkDoubleArray> faValueArray;
vtkSmartPointer<vtkUnsignedCharArray> colorsT;
//colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
int componentSize = sizeof(rgba);
if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){
MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle";
faValueArray = vtkSmartPointer<vtkDoubleArray>::New();
}
if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){
MITK_DEBUG << "colorValues available, init array for new fiberbundle";
colorsT = vtkUnsignedCharArray::New();
colorsT->SetNumberOfComponents(componentSize);
colorsT->SetName(COLORCODING_ORIENTATION_BASED);
}
std::vector<long>::iterator finIt = fiberIds.begin();
while ( finIt != fiberIds.end() )
{
if (*finIt < 0 || *finIt>GetNumFibers()){
MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt;
break;
}
vtkSmartPointer<vtkCell> fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber);
vtkSmartPointer<vtkPoints> fibPoints = fiber->GetPoints();
vtkSmartPointer<vtkPolyLine> newFiber = vtkSmartPointer<vtkPolyLine>::New();
newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() );
for(int i=0; i<fibPoints->GetNumberOfPoints(); i++)
{
// MITK_DEBUG << "id: " << fiber->GetPointId(i);
// MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2];
newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints());
newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]);
if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){
// MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i));
}
if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){
// MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0];
}
}
newLineSet->InsertNextCell(newFiber);
++finIt;
}
newFiberPolyData->SetPoints(newPointSet);
newFiberPolyData->SetLines(newLineSet);
MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints();
MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines();
MITK_DEBUG << "=====================\n";
// mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData);
return newFiberPolyData;
}
// merge two fiber bundles
mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib)
{
if (fib==NULL)
{
MITK_WARN << "trying to call AddBundle with NULL argument";
return NULL;
}
MITK_INFO << "Adding fibers";
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
// add current fiber bundle
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
}
// add new fiber bundle
for (int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
{
vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double p[3];
points->GetPoint(j, p);
vtkIdType id = vNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
}
// initialize polydata
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData);
return newFib;
}
// subtract two fiber bundles
mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib)
{
MITK_INFO << "Subtracting fibers";
vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
// iterate over current fibers
- int numFibers = GetNumFibers();
- boost::progress_display disp(numFibers);
- for( int i=0; i<numFibers; i++ )
+ boost::progress_display disp(m_NumFibers);
+ for( int i=0; i<m_NumFibers; i++ )
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (points==NULL || numPoints<=0)
continue;
int numFibers2 = fib->GetNumFibers();
bool contained = false;
for( int i2=0; i2<numFibers2; i2++ )
{
vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i2);
int numPoints2 = cell2->GetNumberOfPoints();
vtkPoints* points2 = cell2->GetPoints();
- if (points2==NULL || numPoints2<=0)
+ if (points2==NULL)// || numPoints2<=0)
continue;
// check endpoints
- itk::Point<float, 3> point_start = GetItkPoint(points->GetPoint(0));
- itk::Point<float, 3> point_end = GetItkPoint(points->GetPoint(numPoints-1));
- itk::Point<float, 3> point2_start = GetItkPoint(points2->GetPoint(0));
- itk::Point<float, 3> point2_end = GetItkPoint(points2->GetPoint(numPoints2-1));
-
- if (point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps ||
- point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)
+ if (numPoints2==numPoints)
{
- // further checking ???
- if (numPoints2==numPoints)
+ itk::Point<float, 3> point_start = GetItkPoint(points->GetPoint(0));
+ itk::Point<float, 3> point_end = GetItkPoint(points->GetPoint(numPoints-1));
+ itk::Point<float, 3> point2_start = GetItkPoint(points2->GetPoint(0));
+ itk::Point<float, 3> point2_end = GetItkPoint(points2->GetPoint(numPoints2-1));
+
+ if (point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps ||
+ point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)
+ {
+ // further checking ???
contained = true;
+ break;
+ }
}
}
// add to result because fiber is not subtracted
if (!contained)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for( int j=0; j<numPoints; j++)
{
vtkIdType id = vNewPoints->InsertNextPoint(points->GetPoint(j));
container->GetPointIds()->InsertNextId(id);
}
vNewLines->InsertNextCell(container);
}
}
if(vNewLines->GetNumberOfCells()==0)
return NULL;
// initialize polydata
vNewPolyData->SetPoints(vNewPoints);
vNewPolyData->SetLines(vNewLines);
// initialize fiber bundle
- mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData);
- return newFib;
+ return mitk::FiberBundleX::New(vNewPolyData);
}
itk::Point<float, 3> mitk::FiberBundleX::GetItkPoint(double point[3])
{
itk::Point<float, 3> itkPoint;
itkPoint[0] = point[0];
itkPoint[1] = point[1];
itkPoint[2] = point[2];
return itkPoint;
}
/*
* set polydata (additional flag to recompute fiber geometry, default = true)
*/
void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer<vtkPolyData> fiberPD, bool updateGeometry)
{
if (fiberPD == NULL)
this->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
else
{
m_FiberPolyData->DeepCopy(fiberPD);
DoColorCodingOrientationBased();
}
m_NumFibers = m_FiberPolyData->GetNumberOfLines();
if (updateGeometry)
UpdateFiberGeometry();
SetColorCoding(COLORCODING_ORIENTATION_BASED);
GenerateFiberIds();
}
/*
* return vtkPolyData
*/
vtkSmartPointer<vtkPolyData> mitk::FiberBundleX::GetFiberPolyData()
{
return m_FiberPolyData;
}
void mitk::FiberBundleX::DoColorCodingOrientationBased()
{
//===== FOR WRITING A TEST ========================
// colorT size == tupelComponents * tupelElements
// compare color results
// to cover this code 100% also polydata needed, where colorarray already exists
// + one fiber with exactly 1 point
// + one fiber with 0 points
//=================================================
/* make sure that processing colorcoding is only called when necessary */
if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) &&
m_FiberPolyData->GetNumberOfPoints() ==
m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() )
{
// fiberstructure is already colorcoded
MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ;
this->ResetFiberOpacity();
this->SetColorCoding(COLORCODING_ORIENTATION_BASED);
return;
}
/* Finally, execute color calculation */
vtkPoints* extrPoints = NULL;
extrPoints = m_FiberPolyData->GetPoints();
int numOfPoints = 0;
if (extrPoints!=NULL)
numOfPoints = extrPoints->GetNumberOfPoints();
//colors and alpha value for each single point, RGBA = 4 components
unsigned char rgba[4] = {0,0,0,0};
// int componentSize = sizeof(rgba);
int componentSize = 4;
vtkSmartPointer<vtkUnsignedCharArray> colorsT = vtkSmartPointer<vtkUnsignedCharArray>::New();
colorsT->Allocate(numOfPoints * componentSize);
colorsT->SetNumberOfComponents(componentSize);
colorsT->SetName(COLORCODING_ORIENTATION_BASED);
/* checkpoint: does polydata contain any fibers */
int numOfFibers = m_FiberPolyData->GetNumberOfLines();
if (numOfFibers < 1) {
MITK_DEBUG << "\n ========= Number of Fibers is 0 and below ========= \n";
return;
}
/* extract single fibers of fiberBundle */
vtkCellArray* fiberList = m_FiberPolyData->GetLines();
fiberList->InitTraversal();
for (int fi=0; fi<numOfFibers; ++fi) {
vtkIdType* idList; // contains the point id's of the line
vtkIdType pointsPerFiber; // number of points for current line
fiberList->GetNextCell(pointsPerFiber, idList);
// MITK_DEBUG << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ;
/* single fiber checkpoints: is number of points valid */
if (pointsPerFiber > 1)
{
/* operate on points of single fiber */
for (int i=0; i <pointsPerFiber; ++i)
{
/* process all points except starting and endpoint
* for calculating color value take current point, previous point and next point */
if (i<pointsPerFiber-1 && i > 0)
{
/* The color value of the current point is influenced by the previous point and next point. */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
vnl_vector_fixed< double, 3 > diff1;
diff1 = currentPntvtk - nextPntvtk;
vnl_vector_fixed< double, 3 > diff2;
diff2 = currentPntvtk - prevPntvtk;
vnl_vector_fixed< double, 3 > diff;
diff = (diff1 - diff2) / 2.0;
diff.normalize();
rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0]));
rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1]));
rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2]));
rgba[3] = (unsigned char) (255.0);
} else if (i==0) {
/* First point has no previous point, therefore only diff1 is taken */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
vnl_vector_fixed< double, 3 > diff1;
diff1 = currentPntvtk - nextPntvtk;
diff1.normalize();
rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0]));
rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1]));
rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2]));
rgba[3] = (unsigned char) (255.0);
} else if (i==pointsPerFiber-1) {
/* Last point has no next point, therefore only diff2 is taken */
vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
vnl_vector_fixed< double, 3 > diff2;
diff2 = currentPntvtk - prevPntvtk;
diff2.normalize();
rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0]));
rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1]));
rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2]));
rgba[3] = (unsigned char) (255.0);
}
colorsT->InsertTupleValue(idList[i], rgba);
} //end for loop
} else if (pointsPerFiber == 1) {
/* a single point does not define a fiber (use vertex mechanisms instead */
continue;
// colorsT->InsertTupleValue(0, rgba);
} else {
MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ;
continue;
}
}//end for loop
m_FiberPolyData->GetPointData()->AddArray(colorsT);
/*=========================
- this is more relevant for renderer than for fiberbundleX datastructure
- think about sourcing this to a explicit method which coordinates colorcoding */
this->SetColorCoding(COLORCODING_ORIENTATION_BASED);
// ===========================
//mini test, shall be ported to MITK TESTINGS!
if (colorsT->GetSize() != numOfPoints*componentSize)
MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY";
}
void mitk::FiberBundleX::DoColorCodingFaBased()
{
if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 )
return;
this->SetColorCoding(COLORCODING_FA_BASED);
MITK_DEBUG << "FBX: done CC FA based";
this->GenerateFiberIds();
}
void mitk::FiberBundleX::DoUseFaFiberOpacity()
{
if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 )
return;
if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 )
return;
vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED);
vtkUnsignedCharArray* ColorArray = dynamic_cast<vtkUnsignedCharArray*> (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED));
for(long i=0; i<ColorArray->GetNumberOfTuples(); i++) {
double faValue = FAValArray->GetValue(i);
faValue = faValue * 255.0;
ColorArray->SetComponent(i,3, (unsigned char) faValue );
}
this->SetColorCoding(COLORCODING_ORIENTATION_BASED);
MITK_DEBUG << "FBX: done CC OPACITY";
this->GenerateFiberIds();
}
void mitk::FiberBundleX::ResetFiberOpacity() {
vtkUnsignedCharArray* ColorArray = dynamic_cast<vtkUnsignedCharArray*> (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED));
if (ColorArray==NULL)
return;
for(long i=0; i<ColorArray->GetNumberOfTuples(); i++)
ColorArray->SetComponent(i,3, 255.0 );
}
void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage)
{
- mitkPixelTypeMultiplex1( SetFAMap, FAimage->GetPixelType(), FAimage );
+ mitkPixelTypeMultiplex1( SetFAMap, FAimage->GetPixelType(), FAimage );
}
template <typename TPixel>
void mitk::FiberBundleX::SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer FAimage)
{
- MITK_DEBUG << "SetFAMap";
- vtkSmartPointer<vtkDoubleArray> faValues = vtkSmartPointer<vtkDoubleArray>::New();
- faValues->SetName(COLORCODING_FA_BASED);
- faValues->Allocate(m_FiberPolyData->GetNumberOfPoints());
- faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints());
-
- mitk::ImagePixelReadAccessor<TPixel,3> readFAimage (FAimage, FAimage->GetVolumeData(0));
-
- vtkPoints* pointSet = m_FiberPolyData->GetPoints();
- for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
- {
- Point3D px;
- px[0] = pointSet->GetPoint(i)[0];
- px[1] = pointSet->GetPoint(i)[1];
- px[2] = pointSet->GetPoint(i)[2];
- double faPixelValue = 1-readFAimage.GetPixelByWorldCoordinates(px);
- faValues->InsertValue(i, faPixelValue);
- }
-
- m_FiberPolyData->GetPointData()->AddArray(faValues);
- this->GenerateFiberIds();
-
- if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED))
- MITK_DEBUG << "FA VALUE ARRAY SET";
+ MITK_DEBUG << "SetFAMap";
+ vtkSmartPointer<vtkDoubleArray> faValues = vtkSmartPointer<vtkDoubleArray>::New();
+ faValues->SetName(COLORCODING_FA_BASED);
+ faValues->Allocate(m_FiberPolyData->GetNumberOfPoints());
+ faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints());
+
+ mitk::ImagePixelReadAccessor<TPixel,3> readFAimage (FAimage, FAimage->GetVolumeData(0));
+
+ vtkPoints* pointSet = m_FiberPolyData->GetPoints();
+ for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
+ {
+ Point3D px;
+ px[0] = pointSet->GetPoint(i)[0];
+ px[1] = pointSet->GetPoint(i)[1];
+ px[2] = pointSet->GetPoint(i)[2];
+ double faPixelValue = 1-readFAimage.GetPixelByWorldCoordinates(px);
+ faValues->InsertValue(i, faPixelValue);
+ }
+
+ m_FiberPolyData->GetPointData()->AddArray(faValues);
+ this->GenerateFiberIds();
+
+ if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED))
+ MITK_DEBUG << "FA VALUE ARRAY SET";
}
void mitk::FiberBundleX::GenerateFiberIds()
{
if (m_FiberPolyData == NULL)
return;
vtkSmartPointer<vtkIdFilter> idFiberFilter = vtkSmartPointer<vtkIdFilter>::New();
idFiberFilter->SetInputData(m_FiberPolyData);
idFiberFilter->CellIdsOn();
// idFiberFilter->PointIdsOn(); // point id's are not needed
idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY);
idFiberFilter->FieldDataOn();
idFiberFilter->Update();
m_FiberIdDataSet = idFiberFilter->GetOutput();
MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells();
}
mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint)
{
vtkSmartPointer<vtkPolyData> polyData = m_FiberPolyData;
if (anyPoint)
{
float minSpacing = 1;
if(mask->GetSpacing()[0]<mask->GetSpacing()[1] && mask->GetSpacing()[0]<mask->GetSpacing()[2])
minSpacing = mask->GetSpacing()[0];
else if (mask->GetSpacing()[1] < mask->GetSpacing()[2])
minSpacing = mask->GetSpacing()[1];
else
minSpacing = mask->GetSpacing()[2];
mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy();
fibCopy->ResampleFibers(minSpacing/10);
polyData = fibCopy->GetFiberPolyData();
}
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Extracting fibers";
boost::progress_display disp(m_NumFibers);
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = polyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkCell* cellOriginal = m_FiberPolyData->GetCell(i);
int numPointsOriginal = cellOriginal->GetNumberOfPoints();
vtkPoints* pointsOriginal = cellOriginal->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
if (numPoints>1 && numPointsOriginal)
{
if (anyPoint)
{
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
itk::Point<float, 3> itkP;
itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2];
itk::Index<3> idx;
mask->TransformPhysicalPointToIndex(itkP, idx);
if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) )
{
for (int k=0; k<numPointsOriginal; k++)
{
double* p = pointsOriginal->GetPoint(k);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
break;
}
}
}
else
{
double* start = pointsOriginal->GetPoint(0);
itk::Point<float, 3> itkStart;
itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2];
itk::Index<3> idxStart;
mask->TransformPhysicalPointToIndex(itkStart, idxStart);
double* end = pointsOriginal->GetPoint(numPointsOriginal-1);
itk::Point<float, 3> itkEnd;
itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2];
itk::Index<3> idxEnd;
mask->TransformPhysicalPointToIndex(itkEnd, idxEnd);
if ( mask->GetPixel(idxStart)>0 && mask->GetPixel(idxEnd)>0 && mask->GetLargestPossibleRegion().IsInside(idxStart) && mask->GetLargestPossibleRegion().IsInside(idxEnd) )
{
for (int j=0; j<numPointsOriginal; j++)
{
double* p = pointsOriginal->GetPoint(j);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
}
}
}
vtkNewCells->InsertNextCell(container);
}
if (vtkNewCells->GetNumberOfCells()<=0)
return NULL;
vtkSmartPointer<vtkPolyData> newPolyData = vtkSmartPointer<vtkPolyData>::New();
newPolyData->SetPoints(vtkNewPoints);
newPolyData->SetLines(vtkNewCells);
return mitk::FiberBundleX::New(newPolyData);
}
mitk::FiberBundleX::Pointer mitk::FiberBundleX::RemoveFibersOutside(ItkUcharImgType* mask, bool invert)
{
float minSpacing = 1;
if(mask->GetSpacing()[0]<mask->GetSpacing()[1] && mask->GetSpacing()[0]<mask->GetSpacing()[2])
minSpacing = mask->GetSpacing()[0];
else if (mask->GetSpacing()[1] < mask->GetSpacing()[2])
minSpacing = mask->GetSpacing()[1];
else
minSpacing = mask->GetSpacing()[2];
mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy();
fibCopy->ResampleFibers(minSpacing/10);
vtkSmartPointer<vtkPolyData> polyData =fibCopy->GetFiberPolyData();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Cutting fibers";
boost::progress_display disp(m_NumFibers);
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = polyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
if (numPoints>1)
{
int newNumPoints = 0;
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
itk::Point<float, 3> itkP;
itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2];
itk::Index<3> idx;
mask->TransformPhysicalPointToIndex(itkP, idx);
if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) && !invert )
{
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
newNumPoints++;
}
else if ( (mask->GetPixel(idx)<=0 || !mask->GetLargestPossibleRegion().IsInside(idx)) && invert )
{
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
newNumPoints++;
}
else if (newNumPoints>0)
{
vtkNewCells->InsertNextCell(container);
newNumPoints = 0;
container = vtkSmartPointer<vtkPolyLine>::New();
}
}
if (newNumPoints>0)
vtkNewCells->InsertNextCell(container);
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return NULL;
vtkSmartPointer<vtkPolyData> newPolyData = vtkSmartPointer<vtkPolyData>::New();
newPolyData->SetPoints(vtkNewPoints);
newPolyData->SetLines(vtkNewCells);
- return mitk::FiberBundleX::New(newPolyData);
+ mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newPolyData);
+ newFib->ResampleFibers(minSpacing/2);
+ return newFib;
}
mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(mitk::PlanarFigure* pf)
{
if (pf==NULL)
return NULL;
std::vector<long> tmp = ExtractFiberIdSubset(pf);
if (tmp.size()<=0)
return mitk::FiberBundleX::New();
vtkSmartPointer<vtkPolyData> pTmp = GeneratePolyDataByIds(tmp);
return mitk::FiberBundleX::New(pTmp);
}
std::vector<long> mitk::FiberBundleX::ExtractFiberIdSubset(mitk::PlanarFigure* pf)
{
MITK_DEBUG << "Extracting fibers!";
// vector which is returned, contains all extracted FiberIds
std::vector<long> FibersInROI;
if (pf==NULL)
return FibersInROI;
/* Handle type of planarfigure */
// if incoming pf is a pfc
mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast<mitk::PlanarFigureComposite*>(pf);
if (!pfcomp.IsNull()) {
// process requested boolean operation of PFC
switch (pfcomp->getOperationType()) {
case 0:
{
MITK_DEBUG << "AND PROCESSING";
//AND
//temporarly store results of the child in this vector, we need that to accumulate the
std::vector<long> childResults = this->ExtractFiberIdSubset(pfcomp->getChildAt(0));
MITK_DEBUG << "first roi got fibers in ROI: " << childResults.size();
MITK_DEBUG << "sorting...";
std::sort(childResults.begin(), childResults.end());
MITK_DEBUG << "sorting done";
std::vector<long> AND_Assamblage(childResults.size());
//std::vector<unsigned long> AND_Assamblage;
fill(AND_Assamblage.begin(), AND_Assamblage.end(), -1);
//AND_Assamblage.reserve(childResults.size()); //max size AND can reach anyway
std::vector<long>::iterator it;
for (int i=1; i<pfcomp->getNumberOfChildren(); ++i)
{
std::vector<long> tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i));
MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size();
sort(tmpChild.begin(), tmpChild.end());
it = std::set_intersection(childResults.begin(), childResults.end(),
tmpChild.begin(), tmpChild.end(),
AND_Assamblage.begin() );
}
MITK_DEBUG << "resize Vector";
long i=0;
while (i < AND_Assamblage.size() && AND_Assamblage[i] != -1){ //-1 represents a placeholder in the array
++i;
}
AND_Assamblage.resize(i);
MITK_DEBUG << "returning AND vector, size: " << AND_Assamblage.size();
return AND_Assamblage;
// break;
}
case 1:
{
//OR
std::vector<long> OR_Assamblage = this->ExtractFiberIdSubset(pfcomp->getChildAt(0));
std::vector<long>::iterator it;
MITK_DEBUG << OR_Assamblage.size();
for (int i=1; i<pfcomp->getNumberOfChildren(); ++i) {
it = OR_Assamblage.end();
std::vector<long> tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i));
OR_Assamblage.insert(it, tmpChild.begin(), tmpChild.end());
MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size() << " OR Assamblage: " << OR_Assamblage.size();
}
sort(OR_Assamblage.begin(), OR_Assamblage.end());
it = unique(OR_Assamblage.begin(), OR_Assamblage.end());
OR_Assamblage.resize( it - OR_Assamblage.begin() );
MITK_DEBUG << "returning OR vector, size: " << OR_Assamblage.size();
return OR_Assamblage;
}
case 2:
{
//NOT
//get IDs of all fibers
std::vector<long> childResults;
childResults.reserve(this->GetNumFibers());
vtkSmartPointer<vtkDataArray> idSet = m_FiberIdDataSet->GetCellData()->GetArray(FIBER_ID_ARRAY);
MITK_DEBUG << "m_NumOfFib: " << this->GetNumFibers() << " cellIdNum: " << idSet->GetNumberOfTuples();
for(long i=0; i<this->GetNumFibers(); i++)
{
MITK_DEBUG << "i: " << i << " idset: " << idSet->GetTuple(i)[0];
childResults.push_back(idSet->GetTuple(i)[0]);
}
std::sort(childResults.begin(), childResults.end());
std::vector<long> NOT_Assamblage(childResults.size());
//fill it with -1, otherwise 0 will be stored and 0 can also be an ID of fiber!
fill(NOT_Assamblage.begin(), NOT_Assamblage.end(), -1);
std::vector<long>::iterator it;
for (long i=0; i<pfcomp->getNumberOfChildren(); ++i)
{
std::vector<long> tmpChild = ExtractFiberIdSubset(pfcomp->getChildAt(i));
sort(tmpChild.begin(), tmpChild.end());
it = std::set_difference(childResults.begin(), childResults.end(),
tmpChild.begin(), tmpChild.end(),
NOT_Assamblage.begin() );
}
MITK_DEBUG << "resize Vector";
long i=0;
while (NOT_Assamblage[i] != -1){ //-1 represents a placeholder in the array
++i;
}
NOT_Assamblage.resize(i);
return NOT_Assamblage;
}
default:
MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ;
break;
}
}
else
{
mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D();
const mitk::PlaneGeometry* planeGeometry = dynamic_cast<const mitk::PlaneGeometry*> (pfgeometry.GetPointer());
Vector3D planeNormal = planeGeometry->GetNormal();
planeNormal.Normalize();
Point3D planeOrigin = planeGeometry->GetOrigin();
MITK_DEBUG << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl;
MITK_DEBUG << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl;
std::vector<int> PointsOnPlane; // contains all pointIds which are crossing the cutting plane
std::vector<int> PointsInROI; // based on PointsOnPlane, all ROI relevant point IDs are stored here
/* Define cutting plane by ROI (PlanarFigure) */
vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]);
plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]);
/* get all points/fibers cutting the plane */
MITK_DEBUG << "start clipping";
vtkSmartPointer<vtkClipPolyData> clipper = vtkSmartPointer<vtkClipPolyData>::New();
clipper->SetInputData(m_FiberIdDataSet);
clipper->SetClipFunction(plane);
clipper->GenerateClipScalarsOn();
clipper->GenerateClippedOutputOn();
clipper->Update();
vtkSmartPointer<vtkPolyData> clipperout = clipper->GetClippedOutput();
MITK_DEBUG << "end clipping";
MITK_DEBUG << "init and update clipperoutput";
// clipperout->GetPointData()->Initialize();
// clipperout->Update(); //VTK6_TODO
MITK_DEBUG << "init and update clipperoutput completed";
MITK_DEBUG << "STEP 1: find all points which have distance 0 to the given plane";
/*======STEP 1======
* extract all points, which are crossing the plane */
// Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index
vtkSmartPointer<vtkDataArray> distanceList = clipperout->GetPointData()->GetScalars();
vtkIdType sizeOfList = distanceList->GetNumberOfTuples();
PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then!
* size of list can be optimized by reducing allocation, but be aware of iterator and vector size*/
for (int i=0; i<sizeOfList; ++i) {
double *distance = distanceList->GetTuple(i);
// check if point is on plane.
// 0.01 due to some approximation errors when calculating distance
if (distance[0] >= -0.01 && distance[0] <= 0.01)
PointsOnPlane.push_back(i);
}
MITK_DEBUG << "Num Of points on plane: " << PointsOnPlane.size();
MITK_DEBUG << "Step 2: extract Interesting points with respect to given extraction planarFigure";
PointsInROI.reserve(PointsOnPlane.size());
/*=======STEP 2=====
* extract ROI relevant pointIds */
mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New();
mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New();
if ( pf->GetNameOfClass() == circleName->GetNameOfClass() )
{
//calculate circle radius
mitk::Point3D V1w = pf->GetWorldControlPoint(0); //centerPoint
mitk::Point3D V2w = pf->GetWorldControlPoint(1); //radiusPoint
double distPF = V1w.EuclideanDistanceTo(V2w);
for (int i=0; i<PointsOnPlane.size(); i++)
{
//distance between circle radius and given point
double XdistPnt = sqrt((double) (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) * (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) +
- (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) * (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) +
- (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2]) * (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2])) ;
+ (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) * (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) +
+ (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2]) * (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2])) ;
if( XdistPnt <= distPF)
PointsInROI.push_back(PointsOnPlane[i]);
}
}
else if ( pf->GetNameOfClass() == polyName->GetNameOfClass() )
{
//create vtkPolygon using controlpoints from planarFigure polygon
vtkSmartPointer<vtkPolygon> polygonVtk = vtkSmartPointer<vtkPolygon>::New();
//get the control points from pf and insert them to vtkPolygon
unsigned int nrCtrlPnts = pf->GetNumberOfControlPoints();
for (int i=0; i<nrCtrlPnts; ++i)
{
polygonVtk->GetPoints()->InsertNextPoint((double)pf->GetWorldControlPoint(i)[0], (double)pf->GetWorldControlPoint(i)[1], (double)pf->GetWorldControlPoint(i)[2] );
}
//prepare everything for using pointInPolygon function
double n[3];
polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(),
static_cast<double*>(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n);
double bounds[6];
polygonVtk->GetPoints()->GetBounds(bounds);
for (int i=0; i<PointsOnPlane.size(); i++)
{
double checkIn[3] = {clipperout->GetPoint(PointsOnPlane[i])[0], clipperout->GetPoint(PointsOnPlane[i])[1], clipperout->GetPoint(PointsOnPlane[i])[2]};
int isInPolygon = polygonVtk->PointInPolygon(checkIn, polygonVtk->GetPoints()->GetNumberOfPoints()
, static_cast<double*>(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n);
if( isInPolygon )
PointsInROI.push_back(PointsOnPlane[i]);
}
}
MITK_DEBUG << "Step3: Identify fibers";
// we need to access the fiberId Array, so make sure that this array is available
if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY))
{
MITK_DEBUG << "ERROR: FiberID array does not exist, no correlation between points and fiberIds possible! Make sure calling GenerateFiberIds()";
return FibersInROI; // FibersInRoi is empty then
}
if (PointsInROI.size()<=0)
return FibersInROI;
// prepare a structure where each point id is represented as an indexId.
// vector looks like: | pntId | fiberIdx |
std::vector< long > pointindexFiberMap;
// walk through the whole subline section and create an vector sorted by point index
vtkCellArray *clipperlines = clipperout->GetLines();
clipperlines->InitTraversal();
long numOfLineCells = clipperlines->GetNumberOfCells();
long numofClippedPoints = clipperout->GetNumberOfPoints();
pointindexFiberMap.resize(numofClippedPoints);
//prepare resulting vector
FibersInROI.reserve(PointsInROI.size());
MITK_DEBUG << "\n===== Pointindex based structure initialized ======\n";
// go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id.
for (int i=0, ic=0 ; i<numOfLineCells; i++, ic+=3)
{ //ic is the index counter for the cells hosting the desired information, eg. 2 | 45 | 46. each cell consits of 3 items.
vtkIdType npts;
vtkIdType *pts;
clipperlines->GetCell(ic, npts, pts);
// go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. eg. idx[0]=45; idx[1]=46
for (long j=0; j<npts; j++)
{
// MITK_DEBUG << "writing fiber id: " << clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0] << " to pointId: " << pts[j];
pointindexFiberMap[ pts[j] ] = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0];
// MITK_DEBUG << "in array: " << pointindexFiberMap[ pts[j] ];
}
}
MITK_DEBUG << "\n===== Pointindex based structure finalized ======\n";
// get all Points in ROI with according fiberID
for (long k = 0; k < PointsInROI.size(); k++)
{
//MITK_DEBUG << "point " << PointsInROI[k] << " belongs to fiber " << pointindexFiberMap[ PointsInROI[k] ];
if (pointindexFiberMap[ PointsInROI[k] ]<=GetNumFibers() && pointindexFiberMap[ PointsInROI[k] ]>=0)
FibersInROI.push_back(pointindexFiberMap[ PointsInROI[k] ]);
else
MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected";
}
m_PointsRoi = PointsInROI;
}
// detecting fiberId duplicates
MITK_DEBUG << "check for duplicates";
sort(FibersInROI.begin(), FibersInROI.end());
bool hasDuplicats = false;
for(long i=0; i<FibersInROI.size()-1; ++i)
{
if(FibersInROI[i] == FibersInROI[i+1])
hasDuplicats = true;
}
if(hasDuplicats)
{
std::vector<long>::iterator it;
it = unique (FibersInROI.begin(), FibersInROI.end());
FibersInROI.resize( it - FibersInROI.begin() );
}
return FibersInROI;
}
void mitk::FiberBundleX::UpdateFiberGeometry()
{
vtkSmartPointer<vtkCleanPolyData> cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
cleaner->SetInputData(m_FiberPolyData);
cleaner->PointMergingOff();
cleaner->Update();
m_FiberPolyData = cleaner->GetOutput();
m_FiberLengths.clear();
m_MeanFiberLength = 0;
m_MedianFiberLength = 0;
m_LengthStDev = 0;
m_NumFibers = m_FiberPolyData->GetNumberOfCells();
if (m_NumFibers<=0) // no fibers present; apply default geometry
{
m_MinFiberLength = 0;
m_MaxFiberLength = 0;
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
geometry->SetImageGeometry(true);
float b[] = {0, 1, 0, 1, 0, 1};
geometry->SetFloatBounds(b);
SetGeometry(geometry);
return;
}
float min = itk::NumericTraits<float>::NonpositiveMin();
float max = itk::NumericTraits<float>::max();
float b[] = {max, min, max, min, max, min};
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
vtkCell* cell = m_FiberPolyData->GetCell(i);
int p = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
float length = 0;
for (int j=0; j<p; j++)
{
// calculate bounding box
double p1[3];
points->GetPoint(j, p1);
if (p1[0]<b[0])
b[0]=p1[0];
if (p1[0]>b[1])
b[1]=p1[0];
if (p1[1]<b[2])
b[2]=p1[1];
if (p1[1]>b[3])
b[3]=p1[1];
if (p1[2]<b[4])
b[4]=p1[2];
if (p1[2]>b[5])
b[5]=p1[2];
// calculate statistics
if (j<p-1)
{
double p2[3];
points->GetPoint(j+1, p2);
float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
length += dist;
}
}
m_FiberLengths.push_back(length);
m_MeanFiberLength += length;
if (i==0)
{
m_MinFiberLength = length;
m_MaxFiberLength = length;
}
else
{
if (length<m_MinFiberLength)
m_MinFiberLength = length;
if (length>m_MaxFiberLength)
m_MaxFiberLength = length;
}
}
m_MeanFiberLength /= m_NumFibers;
std::vector< float > sortedLengths = m_FiberLengths;
std::sort(sortedLengths.begin(), sortedLengths.end());
for (int i=0; i<m_NumFibers; i++)
m_LengthStDev += (m_MeanFiberLength-sortedLengths.at(i))*(m_MeanFiberLength-sortedLengths.at(i));
if (m_NumFibers>1)
m_LengthStDev /= (m_NumFibers-1);
else
m_LengthStDev = 0;
m_LengthStDev = std::sqrt(m_LengthStDev);
m_MedianFiberLength = sortedLengths.at(m_NumFibers/2);
// provide some border margin
for(int i=0; i<=4; i+=2)
b[i] -=10;
for(int i=1; i<=5; i+=2)
b[i] +=10;
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
geometry->SetFloatBounds(b);
this->SetGeometry(geometry);
}
std::vector<std::string> mitk::FiberBundleX::GetAvailableColorCodings()
{
std::vector<std::string> availableColorCodings;
int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays();
for(int i=0; i<numColors; i++)
{
availableColorCodings.push_back(m_FiberPolyData->GetPointData()->GetArrayName(i));
}
//this controlstructure shall be implemented by the calling method
if (availableColorCodings.empty())
MITK_DEBUG << "no colorcodings available in fiberbundleX";
return availableColorCodings;
}
char* mitk::FiberBundleX::GetCurrentColorCoding()
{
return m_CurrentColorCoding;
}
void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding)
{
if (requestedColorCoding==NULL)
return;
MITK_DEBUG << "SetColorCoding:" << requestedColorCoding;
if( strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) {
this->m_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED;
} else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) {
this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED;
} else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) {
this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM;
} else {
MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure";
this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers
}
}
+itk::Matrix< double, 3, 3 > mitk::FiberBundleX::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz)
+{
+ rx = rx*M_PI/180;
+ ry = ry*M_PI/180;
+ rz = rz*M_PI/180;
+
+ itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
+ rotX[1][1] = cos(rx);
+ rotX[2][2] = rotX[1][1];
+ rotX[1][2] = -sin(rx);
+ rotX[2][1] = -rotX[1][2];
+
+ itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
+ rotY[0][0] = cos(ry);
+ rotY[2][2] = rotY[0][0];
+ rotY[0][2] = sin(ry);
+ rotY[2][0] = -rotY[0][2];
+
+ itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
+ rotZ[0][0] = cos(rz);
+ rotZ[1][1] = rotZ[0][0];
+ rotZ[0][1] = -sin(rz);
+ rotZ[1][0] = -rotZ[0][1];
+
+ itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX;
+
+ m = rot*m;
+
+ return m;
+}
+
+itk::Point<float, 3> mitk::FiberBundleX::TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz)
+{
+ rx = rx*M_PI/180;
+ ry = ry*M_PI/180;
+ rz = rz*M_PI/180;
+
+ vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
+ rotX[1][1] = cos(rx);
+ rotX[2][2] = rotX[1][1];
+ rotX[1][2] = -sin(rx);
+ rotX[2][1] = -rotX[1][2];
+
+ vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
+ rotY[0][0] = cos(ry);
+ rotY[2][2] = rotY[0][0];
+ rotY[0][2] = sin(ry);
+ rotY[2][0] = -rotY[0][2];
+
+ vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
+ rotZ[0][0] = cos(rz);
+ rotZ[1][1] = rotZ[0][0];
+ rotZ[0][1] = -sin(rz);
+ rotZ[1][0] = -rotZ[0][1];
+
+ vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX;
+
+ mitk::Geometry3D::Pointer geom = this->GetGeometry();
+ mitk::Point3D center = geom->GetCenter();
+
+ point[0] -= center[0];
+ point[1] -= center[1];
+ point[2] -= center[2];
+ point = rot*point;
+ point[0] += center[0]+tx;
+ point[1] += center[1]+ty;
+ point[2] += center[2]+tz;
+ itk::Point<float, 3> out; out[0] = point[0]; out[1] = point[1]; out[2] = point[2];
+ return out;
+}
+
+void mitk::FiberBundleX::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz)
+{
+ rx = rx*M_PI/180;
+ ry = ry*M_PI/180;
+ rz = rz*M_PI/180;
+
+ vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
+ rotX[1][1] = cos(rx);
+ rotX[2][2] = rotX[1][1];
+ rotX[1][2] = -sin(rx);
+ rotX[2][1] = -rotX[1][2];
+
+ vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
+ rotY[0][0] = cos(ry);
+ rotY[2][2] = rotY[0][0];
+ rotY[0][2] = sin(ry);
+ rotY[2][0] = -rotY[0][2];
+
+ vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
+ rotZ[0][0] = cos(rz);
+ rotZ[1][1] = rotZ[0][0];
+ rotZ[0][1] = -sin(rz);
+ rotZ[1][0] = -rotZ[0][1];
+
+ vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX;
+
+ mitk::Geometry3D::Pointer geom = this->GetGeometry();
+ mitk::Point3D center = geom->GetCenter();
+
+ vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
+ vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
+
+ for (int i=0; i<m_NumFibers; i++)
+ {
+ vtkCell* cell = m_FiberPolyData->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
+
+ vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
+ for (int j=0; j<numPoints; j++)
+ {
+ double* p = points->GetPoint(j);
+ vnl_vector_fixed< double, 3 > dir;
+ dir[0] = p[0]-center[0];
+ dir[1] = p[1]-center[1];
+ dir[2] = p[2]-center[2];
+ dir = rot*dir;
+ dir[0] += center[0]+tx;
+ dir[1] += center[1]+ty;
+ dir[2] += center[2]+tz;
+ vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
+ container->GetPointIds()->InsertNextId(id);
+ }
+ vtkNewCells->InsertNextCell(container);
+ }
+
+ m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
+ m_FiberPolyData->SetPoints(vtkNewPoints);
+ m_FiberPolyData->SetLines(vtkNewCells);
+ UpdateColorCoding();
+ UpdateFiberGeometry();
+}
+
void mitk::FiberBundleX::RotateAroundAxis(double x, double y, double z)
{
- MITK_INFO << "Rotating fibers";
x = x*M_PI/180;
y = y*M_PI/180;
z = z*M_PI/180;
vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
rotX[1][1] = cos(x);
rotX[2][2] = rotX[1][1];
rotX[1][2] = -sin(x);
rotX[2][1] = -rotX[1][2];
vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
rotY[0][0] = cos(y);
rotY[2][2] = rotY[0][0];
rotY[0][2] = sin(y);
rotY[2][0] = -rotY[0][2];
vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
rotZ[0][0] = cos(z);
rotZ[1][1] = rotZ[0][0];
rotZ[0][1] = -sin(z);
rotZ[1][0] = -rotZ[0][1];
mitk::Geometry3D::Pointer geom = this->GetGeometry();
mitk::Point3D center = geom->GetCenter();
- boost::progress_display disp(m_NumFibers);
-
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (int i=0; i<m_NumFibers; i++)
{
- ++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vnl_vector_fixed< double, 3 > dir;
dir[0] = p[0]-center[0];
dir[1] = p[1]-center[1];
dir[2] = p[2]-center[2];
dir = rotZ*rotY*rotX*dir;
dir[0] += center[0];
dir[1] += center[1];
dir[2] += center[2];
vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
}
void mitk::FiberBundleX::ScaleFibers(double x, double y, double z)
{
MITK_INFO << "Scaling fibers";
boost::progress_display disp(m_NumFibers);
mitk::Geometry3D* geom = this->GetGeometry();
mitk::Point3D c = geom->GetCenter();
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (int i=0; i<m_NumFibers; i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2];
p[0] *= x;
p[1] *= y;
p[2] *= z;
p[0] += c[0]; p[1] += c[1]; p[2] += c[2];
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
}
void mitk::FiberBundleX::TranslateFibers(double x, double y, double z)
{
- MITK_INFO << "Translating fibers";
- boost::progress_display disp(m_NumFibers);
-
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (int i=0; i<m_NumFibers; i++)
{
- ++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
p[0] += x;
p[1] += y;
p[2] += z;
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
}
void mitk::FiberBundleX::MirrorFibers(unsigned int axis)
{
if (axis>2)
return;
MITK_INFO << "Mirroring fibers";
boost::progress_display disp(m_NumFibers);
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
p[axis] = -p[axis];
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
}
bool mitk::FiberBundleX::ApplyCurvatureThreshold(float minRadius, bool deleteFibers)
{
if (minRadius<0)
return true;
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Applying curvature threshold";
boost::progress_display disp(m_FiberPolyData->GetNumberOfCells());
for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
{
++disp ;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
// calculate curvatures
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints-2; j++)
{
double p1[3];
points->GetPoint(j, p1);
double p2[3];
points->GetPoint(j+1, p2);
double p3[3];
points->GetPoint(j+2, p3);
vnl_vector_fixed< float, 3 > v1, v2, v3;
v1[0] = p2[0]-p1[0];
v1[1] = p2[1]-p1[1];
v1[2] = p2[2]-p1[2];
v2[0] = p3[0]-p2[0];
v2[1] = p3[1]-p2[1];
v2[2] = p3[2]-p2[2];
v3[0] = p1[0]-p3[0];
v3[1] = p1[1]-p3[1];
v3[2] = p1[2]-p3[2];
float a = v1.magnitude();
float b = v2.magnitude();
float c = v3.magnitude();
float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
container->GetPointIds()->InsertNextId(id);
if (deleteFibers && r<minRadius)
break;
if (r<minRadius)
{
j += 2;
vtkNewCells->InsertNextCell(container);
container = vtkSmartPointer<vtkPolyLine>::New();
}
else if (j==numPoints-3)
{
id = vtkNewPoints->InsertNextPoint(p2);
container->GetPointIds()->InsertNextId(id);
id = vtkNewPoints->InsertNextPoint(p3);
container->GetPointIds()->InsertNextId(id);
vtkNewCells->InsertNextCell(container);
}
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
return true;
}
bool mitk::FiberBundleX::RemoveShortFibers(float lengthInMM)
{
MITK_INFO << "Removing short fibers";
if (lengthInMM<=0 || lengthInMM<m_MinFiberLength)
{
MITK_INFO << "No fibers shorter than " << lengthInMM << " mm found!";
return true;
}
if (lengthInMM>m_MaxFiberLength) // can't remove all fibers
{
MITK_WARN << "Process aborted. No fibers would be left!";
return false;
}
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
float min = m_MaxFiberLength;
boost::progress_display disp(m_NumFibers);
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (m_FiberLengths.at(i)>=lengthInMM)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
if (m_FiberLengths.at(i)<min)
min = m_FiberLengths.at(i);
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
return true;
}
bool mitk::FiberBundleX::RemoveLongFibers(float lengthInMM)
{
if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength)
return true;
if (lengthInMM<m_MinFiberLength) // can't remove all fibers
return false;
vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
MITK_INFO << "Removing long fibers";
boost::progress_display disp(m_NumFibers);
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
if (m_FiberLengths.at(i)<=lengthInMM)
{
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
for (int j=0; j<numPoints; j++)
{
double* p = points->GetPoint(j);
vtkIdType id = vtkNewPoints->InsertNextPoint(p);
container->GetPointIds()->InsertNextId(id);
}
vtkNewCells->InsertNextCell(container);
}
}
if (vtkNewCells->GetNumberOfCells()<=0)
return false;
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkNewPoints);
m_FiberPolyData->SetLines(vtkNewCells);
UpdateColorCoding();
UpdateFiberGeometry();
return true;
}
void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias )
{
if (pointDistance<=0)
return;
vtkSmartPointer<vtkPoints> vtkSmoothPoints = vtkSmartPointer<vtkPoints>::New(); //in smoothpoints the interpolated points representing a fiber are stored.
//in vtkcells all polylines are stored, actually all id's of them are stored
vtkSmartPointer<vtkCellArray> vtkSmoothCells = vtkSmartPointer<vtkCellArray>::New(); //cellcontainer for smoothed lines
vtkIdType pointHelperCnt = 0;
MITK_INFO << "Smoothing fibers";
boost::progress_display disp(m_NumFibers);
for (int i=0; i<m_NumFibers; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
for (int j=0; j<numPoints; j++)
newPoints->InsertNextPoint(points->GetPoint(j));
float length = m_FiberLengths.at(i);
int sampling = std::ceil(length/pointDistance);
vtkSmartPointer<vtkKochanekSpline> xSpline = vtkSmartPointer<vtkKochanekSpline>::New();
vtkSmartPointer<vtkKochanekSpline> ySpline = vtkSmartPointer<vtkKochanekSpline>::New();
vtkSmartPointer<vtkKochanekSpline> zSpline = vtkSmartPointer<vtkKochanekSpline>::New();
xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity);
ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity);
zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity);
vtkSmartPointer<vtkParametricSpline> spline = vtkSmartPointer<vtkParametricSpline>::New();
spline->SetXSpline(xSpline);
spline->SetYSpline(ySpline);
spline->SetZSpline(zSpline);
spline->SetPoints(newPoints);
vtkSmartPointer<vtkParametricFunctionSource> functionSource = vtkSmartPointer<vtkParametricFunctionSource>::New();
functionSource->SetParametricFunction(spline);
functionSource->SetUResolution(sampling);
functionSource->SetVResolution(sampling);
functionSource->SetWResolution(sampling);
functionSource->Update();
vtkPolyData* outputFunction = functionSource->GetOutput();
vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber
vtkSmartPointer<vtkPolyLine> smoothLine = vtkSmartPointer<vtkPolyLine>::New();
smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints());
for (int j=0; j<smoothLine->GetNumberOfPoints(); j++)
{
smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt);
vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j));
}
vtkSmoothCells->InsertNextCell(smoothLine);
pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints();
}
m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
m_FiberPolyData->SetPoints(vtkSmoothPoints);
m_FiberPolyData->SetLines(vtkSmoothCells);
UpdateColorCoding();
UpdateFiberGeometry();
m_FiberSampling = 10/pointDistance;
}
void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance)
{
DoFiberSmoothing(pointDistance, 0, 0, 0 );
}
// Resample fiber to get equidistant points
void mitk::FiberBundleX::ResampleFibers(float pointDistance)
{
if (pointDistance<=0.00001)
return;
vtkSmartPointer<vtkPolyData> newPoly = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkCellArray> newCellArray = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
int numberOfLines = m_NumFibers;
MITK_INFO << "Resampling fibers";
boost::progress_display disp(m_NumFibers);
for (int i=0; i<numberOfLines; i++)
{
++disp;
vtkCell* cell = m_FiberPolyData->GetCell(i);
int numPoints = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
double* point = points->GetPoint(0);
vtkIdType pointId = newPoints->InsertNextPoint(point);
container->GetPointIds()->InsertNextId(pointId);
float dtau = 0;
int cur_p = 1;
itk::Vector<float,3> dR;
float normdR = 0;
for (;;)
{
while (dtau <= pointDistance && cur_p < numPoints)
{
itk::Vector<float,3> v1;
point = points->GetPoint(cur_p-1);
v1[0] = point[0];
v1[1] = point[1];
v1[2] = point[2];
itk::Vector<float,3> v2;
point = points->GetPoint(cur_p);
v2[0] = point[0];
v2[1] = point[1];
v2[2] = point[2];
dR = v2 - v1;
normdR = std::sqrt(dR.GetSquaredNorm());
dtau += normdR;
cur_p++;
}
if (dtau >= pointDistance)
{
itk::Vector<float,3> v1;
point = points->GetPoint(cur_p-1);
v1[0] = point[0];
v1[1] = point[1];
v1[2] = point[2];
itk::Vector<float,3> v2 = v1 - dR*( (dtau-pointDistance)/normdR );
pointId = newPoints->InsertNextPoint(v2.GetDataPointer());
container->GetPointIds()->InsertNextId(pointId);
}
else
{
point = points->GetPoint(numPoints-1);
pointId = newPoints->InsertNextPoint(point);
container->GetPointIds()->InsertNextId(pointId);
break;
}
dtau = dtau-pointDistance;
}
newCellArray->InsertNextCell(container);
}
newPoly->SetPoints(newPoints);
newPoly->SetLines(newCellArray);
m_FiberPolyData = newPoly;
UpdateFiberGeometry();
UpdateColorCoding();
m_FiberSampling = 10/pointDistance;
}
// reapply selected colorcoding in case polydata structure has changed
void mitk::FiberBundleX::UpdateColorCoding()
{
char* cc = GetCurrentColorCoding();
if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 )
DoColorCodingOrientationBased();
else if( strcmp (COLORCODING_FA_BASED,cc) == 0 )
DoColorCodingFaBased();
}
// reapply selected colorcoding in case polydata structure has changed
bool mitk::FiberBundleX::Equals(mitk::FiberBundleX* fib)
{
if (fib==NULL)
+ {
+ MITK_INFO << "Reference bundle is NULL!";
return false;
+ }
- mitk::FiberBundleX::Pointer tempFib = this->SubtractBundle(fib);
- mitk::FiberBundleX::Pointer tempFib2 = fib->SubtractBundle(this);
+ if (m_NumFibers!=fib->GetNumFibers())
+ {
+ MITK_INFO << "Unequal number of fibers!";
+ MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers();
+ return false;
+ }
- if (tempFib.IsNull() && tempFib2.IsNull())
- return true;
+ for (int i=0; i<m_NumFibers; i++)
+ {
+ vtkCell* cell = m_FiberPolyData->GetCell(i);
+ int numPoints = cell->GetNumberOfPoints();
+ vtkPoints* points = cell->GetPoints();
- return false;
+ vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i);
+ int numPoints2 = cell2->GetNumberOfPoints();
+ vtkPoints* points2 = cell2->GetPoints();
+
+ if (numPoints2!=numPoints)
+ {
+ MITK_INFO << "Unequal number of points in fiber " << i << "!";
+ MITK_INFO << numPoints2 << " vs. " << numPoints;
+ return false;
+ }
+
+ for (int j=0; j<numPoints; j++)
+ {
+ double* p1 = points->GetPoint(j);
+ double* p2 = points2->GetPoint(j);
+ if (fabs(p1[0]-p2[0])>0.0001 || fabs(p1[1]-p2[1])>0.0001 || fabs(p1[2]-p2[2])>0.0001)
+ {
+ MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!";
+ MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2];
+ MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2];
+ return false;
+ }
+ }
+ }
+
+ return true;
}
/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
void mitk::FiberBundleX::UpdateOutputInformation()
{
}
void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion()
{
}
bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion()
{
return false;
}
bool mitk::FiberBundleX::VerifyRequestedRegion()
{
return true;
}
void mitk::FiberBundleX::SetRequestedRegion(const itk::DataObject *data )
{
}
diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h
index 3b4e3479eb..31361727a3 100644
--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h
+++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h
@@ -1,160 +1,164 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_FiberBundleX_H
#define _MITK_FiberBundleX_H
//includes for MITK datastructure
#include <mitkBaseData.h>
#include "FiberTrackingExports.h"
#include <mitkImage.h>
//includes storing fiberdata
-#include <vtkSmartPointer.h> //may be replaced by class precompile argument
-#include <vtkPolyData.h> // may be replaced by class
-#include <vtkPoints.h> // my be replaced by class
+#include <vtkSmartPointer.h>
+#include <vtkPolyData.h>
+#include <vtkPoints.h>
#include <vtkDataSet.h>
+#include <vtkTransform.h>
//#include <QStringList>
#include <mitkPlanarFigure.h>
namespace mitk {
/**
* \brief Base Class for Fiber Bundles; */
class FiberTracking_EXPORT FiberBundleX : public BaseData
{
public:
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
// fiber colorcodings
static const char* COLORCODING_ORIENTATION_BASED;
static const char* COLORCODING_FA_BASED;
static const char* COLORCODING_CUSTOM;
static const char* FIBER_ID_ARRAY;
virtual void UpdateOutputInformation();
virtual void SetRequestedRegionToLargestPossibleRegion();
virtual bool RequestedRegionIsOutsideOfTheBufferedRegion();
virtual bool VerifyRequestedRegion();
virtual void SetRequestedRegion(const itk::DataObject *data );
mitkClassMacro( FiberBundleX, BaseData )
itkNewMacro( Self )
mitkNewMacro1Param(Self, vtkSmartPointer<vtkPolyData>) // custom constructor
// colorcoding related methods
void SetColorCoding(const char*);
void SetFAMap(mitk::Image::Pointer);
template <typename TPixel>
void SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer);
void DoColorCodingOrientationBased();
void DoColorCodingFaBased();
void DoUseFaFiberOpacity();
void ResetFiberOpacity();
// fiber smoothing/resampling
void ResampleFibers(float pointDistance = 1);
void DoFiberSmoothing(float pointDistance);
void DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias );
bool RemoveShortFibers(float lengthInMM);
bool RemoveLongFibers(float lengthInMM);
bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers);
void MirrorFibers(unsigned int axis);
void RotateAroundAxis(double x, double y, double z);
void TranslateFibers(double x, double y, double z);
void ScaleFibers(double x, double y, double z);
+ void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz);
+ itk::Point<float, 3> TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz);
+ itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz);
// add/subtract fibers
FiberBundleX::Pointer AddBundle(FiberBundleX* fib);
FiberBundleX::Pointer SubtractBundle(FiberBundleX* fib);
// fiber subset extraction
FiberBundleX::Pointer ExtractFiberSubset(PlanarFigure *pf);
std::vector<long> ExtractFiberIdSubset(PlanarFigure* pf);
FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint);
FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false);
vtkSmartPointer<vtkPolyData> GeneratePolyDataByIds( std::vector<long> ); // TODO: make protected
void GenerateFiberIds(); // TODO: make protected
// get/set data
void SetFiberPolyData(vtkSmartPointer<vtkPolyData>, bool updateGeometry = true);
vtkSmartPointer<vtkPolyData> GetFiberPolyData();
std::vector< std::string > GetAvailableColorCodings();
char* GetCurrentColorCoding();
itkGetMacro( NumFibers, int)
itkGetMacro( FiberSampling, int)
itkGetMacro( MinFiberLength, float )
itkGetMacro( MaxFiberLength, float )
itkGetMacro( MeanFiberLength, float )
itkGetMacro( MedianFiberLength, float )
itkGetMacro( LengthStDev, float )
std::vector<int> GetPointsRoi()
{
return m_PointsRoi;
}
// copy fiber bundle
mitk::FiberBundleX::Pointer GetDeepCopy();
// compare fiber bundles
bool Equals(FiberBundleX* fib);
protected:
FiberBundleX( vtkPolyData* fiberPolyData = NULL );
virtual ~FiberBundleX();
itk::Point<float, 3> GetItkPoint(double point[3]);
// calculate geometry from fiber extent
void UpdateFiberGeometry();
// calculate colorcoding values according to m_CurrentColorCoding
void UpdateColorCoding();
private:
// actual fiber container
vtkSmartPointer<vtkPolyData> m_FiberPolyData;
// contains fiber ids
vtkSmartPointer<vtkDataSet> m_FiberIdDataSet;
char* m_CurrentColorCoding;
int m_NumFibers;
std::vector< float > m_FiberLengths;
float m_MinFiberLength;
float m_MaxFiberLength;
float m_MeanFiberLength;
float m_MedianFiberLength;
float m_LengthStDev;
int m_FiberSampling;
std::vector<int> m_PointsRoi; // this global variable needs to be refactored
};
} // namespace mitk
#endif /* _MITK_FiberBundleX_H */
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp
index d2b317c8a9..0aa3f82461 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp
@@ -1,88 +1,129 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
template< class ScalarType >
AstroStickModel< ScalarType >::AstroStickModel()
: m_Diffusivity(0.001)
, m_BValue(1000)
, m_NumSticks(42)
, m_RandomizeSticks(false)
{
m_RandGen = ItkRandGenType::New();
vnl_matrix_fixed<ScalarType,3,42>* sticks = itk::PointShell<42, vnl_matrix_fixed<ScalarType, 3, 42> >::DistributePointShell();
for (int i=0; i<m_NumSticks; i++)
{
GradientType stick;
stick[0] = sticks->get(0,i); stick[1] = sticks->get(1,i); stick[2] = sticks->get(2,i);
stick.Normalize();
m_Sticks.push_back(stick);
}
}
template< class ScalarType >
AstroStickModel< ScalarType >::~AstroStickModel()
{
}
+template< class ScalarType >
+void AstroStickModel< ScalarType >::SetSeed(int s)
+{
+ m_RandGen->SetSeed(s);
+}
+
+template< class ScalarType >
+ScalarType AstroStickModel< ScalarType >::SimulateMeasurement(int dir)
+{
+ ScalarType signal = 0;
+
+ if (dir>=this->m_GradientList.size())
+ return signal;
+
+ ScalarType b = -m_BValue*m_Diffusivity;
+
+ if (m_RandomizeSticks)
+ m_NumSticks = 30 + m_RandGen->GetIntegerVariate()%31;
+
+ GradientType g = this->m_GradientList[dir];
+ ScalarType bVal = g.GetNorm(); bVal *= bVal;
+
+ if (bVal>0.0001)
+ {
+ for (int j=0; j<m_NumSticks; j++)
+ {
+ ScalarType dot = 0;
+ if(m_RandomizeSticks)
+ dot = GetRandomDirection()*g;
+ else
+ dot = m_Sticks[j]*g;
+ signal += exp( b*bVal*dot*dot );
+ }
+ signal /= m_NumSticks;
+ }
+ else
+ signal = 1;
+
+ return signal;
+}
+
template< class ScalarType >
typename AstroStickModel< ScalarType >::GradientType AstroStickModel< ScalarType >::GetRandomDirection()
{
GradientType vec;
vec[0] = m_RandGen->GetNormalVariate();
vec[1] = m_RandGen->GetNormalVariate();
vec[2] = m_RandGen->GetNormalVariate();
vec.Normalize();
return vec;
}
template< class ScalarType >
typename AstroStickModel< ScalarType >::PixelType AstroStickModel< ScalarType >::SimulateMeasurement()
{
PixelType signal;
signal.SetSize(this->m_GradientList.size());
ScalarType b = -m_BValue*m_Diffusivity;
if (m_RandomizeSticks)
m_NumSticks = 30 + m_RandGen->GetIntegerVariate()%31;
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
{
GradientType g = this->m_GradientList[i];
ScalarType bVal = g.GetNorm(); bVal *= bVal;
if (bVal>0.0001)
{
for (int j=0; j<m_NumSticks; j++)
{
ScalarType dot = 0;
if(m_RandomizeSticks)
dot = GetRandomDirection()*g;
else
dot = m_Sticks[j]*g;
signal[i] += exp( b*bVal*dot*dot );
}
signal[i] /= m_NumSticks;
}
else
signal[i] = 1;
}
return signal;
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h
index 1affee007f..7766d2c36d 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h
@@ -1,104 +1,107 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_AstroStickModel_H
#define _MITK_AstroStickModel_H
#include <mitkDiffusionSignalModel.h>
#include <itkPointShell.h>
namespace mitk {
/**
* \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²)
*
*/
template< class ScalarType >
class AstroStickModel : public DiffusionSignalModel< ScalarType >
{
public:
AstroStickModel();
~AstroStickModel();
typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType;
/** Actual signal generation **/
PixelType SimulateMeasurement();
+ ScalarType SimulateMeasurement(int dir);
+
+ void SetSeed(int s); ///< set seed for random generator that creates the stick orientations
void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; }
void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal
void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant
void SetNumSticks(unsigned int order)
{
vnl_matrix<double> sticks;
switch (order)
{
case 1:
m_NumSticks = 12;
sticks = itk::PointShell<12, vnl_matrix_fixed<double, 3, 12> >::DistributePointShell()->as_matrix();
break;
case 2:
m_NumSticks = 42;
sticks = itk::PointShell<42, vnl_matrix_fixed<double, 3, 42> >::DistributePointShell()->as_matrix();
break;
case 3:
m_NumSticks = 92;
sticks = itk::PointShell<92, vnl_matrix_fixed<double, 3, 92> >::DistributePointShell()->as_matrix();
break;
case 4:
m_NumSticks = 162;
sticks = itk::PointShell<162, vnl_matrix_fixed<double, 3, 162> >::DistributePointShell()->as_matrix();
break;
case 5:
m_NumSticks = 252;
sticks = itk::PointShell<252, vnl_matrix_fixed<double, 3, 252> >::DistributePointShell()->as_matrix();
break;
default:
m_NumSticks = 42;
sticks = itk::PointShell<42, vnl_matrix_fixed<double, 3, 42> >::DistributePointShell()->as_matrix();
break;
}
for (int i=0; i<m_NumSticks; i++)
{
GradientType stick;
stick[0] = sticks.get(0,i); stick[1] = sticks.get(1,i); stick[2] = sticks.get(2,i);
stick.Normalize();
m_Sticks.push_back(stick);
}
}
protected:
GradientType GetRandomDirection();
ScalarType m_BValue; ///< b-value used to generate the artificial signal
ScalarType m_Diffusivity; ///< Scalar diffusion constant
GradientListType m_Sticks;
unsigned int m_NumSticks;
bool m_RandomizeSticks;
ItkRandGenType::Pointer m_RandGen; // random generator
};
}
#include "mitkAstroStickModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.cpp
index d60f990511..8ca92bdf4a 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.cpp
@@ -1,51 +1,70 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
template< class ScalarType >
BallModel< ScalarType >::BallModel()
: m_Diffusivity(0.001)
, m_BValue(1000)
{
}
template< class ScalarType >
BallModel< ScalarType >::~BallModel()
{
}
+template< class ScalarType >
+ScalarType BallModel< ScalarType >::SimulateMeasurement(int dir)
+{
+ ScalarType signal = 0;
+
+ if (dir>=this->m_GradientList.size())
+ return signal;
+
+ GradientType g = this->m_GradientList[dir];
+ ScalarType bVal = g.GetNorm(); bVal *= bVal;
+
+ if (bVal>0.0001)
+ signal = exp( -m_BValue * bVal * m_Diffusivity );
+ else
+ signal = 1;
+
+ return signal;
+}
+
template< class ScalarType >
typename BallModel< ScalarType >::PixelType BallModel< ScalarType >::SimulateMeasurement()
{
PixelType signal;
signal.SetSize(this->m_GradientList.size());
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
{
GradientType g = this->m_GradientList[i];
ScalarType bVal = g.GetNorm(); bVal *= bVal;
if (bVal>0.0001)
signal[i] = exp( -m_BValue * bVal * m_Diffusivity );
else
signal[i] = 1;
}
return signal;
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h
index a2a832740c..37d8c21e6e 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h
@@ -1,58 +1,59 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_BallModel_H
#define _MITK_BallModel_H
#include <mitkDiffusionSignalModel.h>
namespace mitk {
/**
* \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd)
*
*/
template< class ScalarType >
class BallModel : public DiffusionSignalModel< ScalarType >
{
public:
BallModel();
~BallModel();
typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
/** Actual signal generation **/
PixelType SimulateMeasurement();
+ ScalarType SimulateMeasurement(int dir);
void SetDiffusivity(ScalarType D) { m_Diffusivity = D; }
void SetBvalue(ScalarType bValue) { m_BValue = bValue; }
protected:
ScalarType m_Diffusivity; ///< Scalar diffusion constant
ScalarType m_BValue; ///< b-value used to generate the artificial signal
};
}
#include "mitkBallModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp
similarity index 64%
copy from Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
copy to Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp
index c1759751e0..d1977bc9a4 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.cpp
@@ -1,38 +1,39 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
+#include <mitkChiSquareNoiseModel.h>
+
+using namespace mitk;
template< class ScalarType >
-DotModel< ScalarType >::DotModel()
+ChiSquareNoiseModel< ScalarType >::ChiSquareNoiseModel()
{
}
template< class ScalarType >
-DotModel< ScalarType >::~DotModel()
+ChiSquareNoiseModel< ScalarType >::~ChiSquareNoiseModel()
{
}
template< class ScalarType >
-typename DotModel< ScalarType >::PixelType DotModel< ScalarType >::SimulateMeasurement()
+void ChiSquareNoiseModel< ScalarType >::AddNoise(PixelType& pixel)
{
- PixelType signal;
- signal.SetSize(this->m_GradientList.size());
- signal.Fill(1);
- return signal;
+ for( unsigned int i=0; i<pixel.Size(); i++)
+ pixel[i] += (ScalarType)(m_Distribution(m_Randgen)-m_Distribution.n());
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.h
similarity index 64%
copy from Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
copy to Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.h
index 5fc1260ed4..3bc5c8ddaa 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChiSquareNoiseModel.h
@@ -1,54 +1,57 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
-#ifndef _MITK_RicianNoiseModel_H
-#define _MITK_RicianNoiseModel_H
+#ifndef _MITK_ChiSquareNoiseModel_H
+#define _MITK_ChiSquareNoiseModel_H
#include <mitkDiffusionNoiseModel.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>
namespace mitk {
/**
* \brief Implementation of noise following a rician distribution
*
*/
template< class ScalarType >
-class RicianNoiseModel : public DiffusionNoiseModel< ScalarType >
+class ChiSquareNoiseModel : public DiffusionNoiseModel< ScalarType >
{
public:
- RicianNoiseModel();
- ~RicianNoiseModel();
+ ChiSquareNoiseModel();
+ ~ChiSquareNoiseModel();
typedef typename DiffusionNoiseModel< ScalarType >::PixelType PixelType;
/** Adds rician noise to the input pixel **/
void AddNoise(PixelType& pixel);
-protected:
+ void SetDOF(double var){ m_Distribution = boost::random::chi_squared_distribution<double>(var); }
+ double GetNoiseVariance(){ return m_Distribution.n(); }
- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
+protected:
+ boost::random::mt19937 m_Randgen;
+ boost::random::chi_squared_distribution<double> m_Distribution;
};
}
-#include "mitkRicianNoiseModel.cpp"
+#include "mitkChiSquareNoiseModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.cpp
similarity index 59%
copy from Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
copy to Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.cpp
index c1759751e0..675e240773 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.cpp
@@ -1,38 +1,42 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
+#include <mitkChisquareNoiseModel.h>
+
+using namespace mitk;
template< class ScalarType >
-DotModel< ScalarType >::DotModel()
+ChisquareNoiseModel< ScalarType >::ChisquareNoiseModel()
{
-
+ this->m_NoiseVariance = 0;
+ m_Distribution = std::chi_squared_distribution<double>(4.0);
}
template< class ScalarType >
-DotModel< ScalarType >::~DotModel()
+ChisquareNoiseModel< ScalarType >::~ChisquareNoiseModel()
{
}
template< class ScalarType >
-typename DotModel< ScalarType >::PixelType DotModel< ScalarType >::SimulateMeasurement()
+void ChisquareNoiseModel< ScalarType >::AddNoise(PixelType& pixel)
{
- PixelType signal;
- signal.SetSize(this->m_GradientList.size());
- signal.Fill(1);
- return signal;
+ for( unsigned int i=0; i<pixel.Size(); i++)
+ {
+ pixel[i] += m_Distribution(m_RandGen);
+ }
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.h
similarity index 71%
copy from Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
copy to Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.h
index 5fc1260ed4..b0c3ab42b7 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkChisquareNoiseModel.h
@@ -1,54 +1,55 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
-#ifndef _MITK_RicianNoiseModel_H
-#define _MITK_RicianNoiseModel_H
+#ifndef _MITK_ChisquareNoiseModel_H
+#define _MITK_ChisquareNoiseModel_H
#include <mitkDiffusionNoiseModel.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>
+#include <random>
namespace mitk {
/**
* \brief Implementation of noise following a rician distribution
*
*/
template< class ScalarType >
-class RicianNoiseModel : public DiffusionNoiseModel< ScalarType >
+class ChisquareNoiseModel : public DiffusionNoiseModel< ScalarType >
{
public:
- RicianNoiseModel();
- ~RicianNoiseModel();
+ ChisquareNoiseModel();
+ ~ChisquareNoiseModel();
typedef typename DiffusionNoiseModel< ScalarType >::PixelType PixelType;
/** Adds rician noise to the input pixel **/
void AddNoise(PixelType& pixel);
protected:
- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
-
+ std::default_random_engine m_RandGen;
+ std::chi_squared_distribution<double> m_Distribution;
};
}
-#include "mitkRicianNoiseModel.cpp"
+#include "mitkChisquareNoiseModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionNoiseModel.h
index ef545d6511..695f1c312a 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionNoiseModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionNoiseModel.h
@@ -1,56 +1,53 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_DiffusionNoiseModel_H
#define _MITK_DiffusionNoiseModel_H
#include <FiberTrackingExports.h>
#include <itkVariableLengthVector.h>
#include <itkVector.h>
#include <vnl/vnl_vector_fixed.h>
+#include <boost/random.hpp>
namespace mitk {
/**
* \brief Abstract class for diffusion noise models
*
*/
template< class ScalarType >
class DiffusionNoiseModel
{
public:
DiffusionNoiseModel(){}
~DiffusionNoiseModel(){}
typedef itk::VariableLengthVector< ScalarType > PixelType;
/** Adds noise according to model to the input pixel. Has to be implemented in subclass. **/
virtual void AddNoise(PixelType& pixel) = 0;
- void SetNoiseVariance(double var){ m_NoiseVariance = var; }
- double GetNoiseVariance(){ return m_NoiseVariance; }
-
protected:
- double m_NoiseVariance; ///< variance of underlying distribution
};
}
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h
index ea818ecbe8..7fbdcf119f 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h
@@ -1,91 +1,93 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_DiffusionSignalModel_H
#define _MITK_DiffusionSignalModel_H
#include <FiberTrackingExports.h>
#include <itkVariableLengthVector.h>
#include <itkVector.h>
#include <vnl/vnl_vector_fixed.h>
namespace mitk {
/**
* \brief Abstract class for diffusion signal models
*
*/
template< class ScalarType >
class DiffusionSignalModel
{
public:
DiffusionSignalModel()
: m_T2(100)
, m_Weight(1)
{}
~DiffusionSignalModel(){}
typedef itk::VariableLengthVector< ScalarType > PixelType;
typedef itk::Vector<double,3> GradientType;
typedef std::vector<GradientType> GradientListType;
/** Realizes actual signal generation. Has to be implemented in subclass. **/
virtual PixelType SimulateMeasurement() = 0;
+ virtual ScalarType SimulateMeasurement(int dir) = 0;
+
GradientType GetGradientDirection(int i) { return m_GradientList.at(i); }
void SetFiberDirection(GradientType fiberDirection){ m_FiberDirection = fiberDirection; }
void SetGradientList(GradientListType gradientList) { m_GradientList = gradientList; }
void SetT2(double T2) { m_T2 = T2; }
void SetWeight(double Weight) { m_Weight = Weight; }
double GetWeight() { return m_Weight; }
double GetT2() { return m_T2; }
int GetNumGradients(){ return m_GradientList.size(); }
std::vector< int > GetBaselineIndices()
{
std::vector< int > result;
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
if (m_GradientList.at(i).GetNorm()<0.0001)
result.push_back(i);
return result;
}
int GetFirstBaselineIndex()
{
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
if (m_GradientList.at(i).GetNorm()<0.0001)
return i;
return -1;
}
bool IsBaselineIndex(int idx)
{
if (m_GradientList.size()>idx && m_GradientList.at(idx).GetNorm()<0.0001)
return true;
return false;
}
protected:
GradientType m_FiberDirection; ///< Needed to generate anisotropc signal to determin direction of anisotropy
GradientListType m_GradientList; ///< Diffusion gradient direction container
double m_T2; ///< Tissue specific relaxation time
double m_Weight;
};
}
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
index c1759751e0..2d030faf78 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.cpp
@@ -1,38 +1,44 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
template< class ScalarType >
DotModel< ScalarType >::DotModel()
{
}
template< class ScalarType >
DotModel< ScalarType >::~DotModel()
{
}
+template< class ScalarType >
+ScalarType DotModel< ScalarType >::SimulateMeasurement(int dir)
+{
+ return 1;
+}
+
template< class ScalarType >
typename DotModel< ScalarType >::PixelType DotModel< ScalarType >::SimulateMeasurement()
{
PixelType signal;
signal.SetSize(this->m_GradientList.size());
signal.Fill(1);
return signal;
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h
index 5a4cc038f0..7b05c51f60 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h
@@ -1,52 +1,53 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_DotModel_H
#define _MITK_DotModel_H
#include <mitkDiffusionSignalModel.h>
namespace mitk {
/**
* \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd)
*
*/
template< class ScalarType >
class DotModel : public DiffusionSignalModel< ScalarType >
{
public:
DotModel();
~DotModel();
typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
/** Actual signal generation **/
PixelType SimulateMeasurement();
+ ScalarType SimulateMeasurement(int dir);
protected:
};
}
#include "mitkDotModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkKspaceArtifact.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkKspaceArtifact.h
deleted file mode 100644
index 42d575de35..0000000000
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkKspaceArtifact.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*===================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center,
-Division of Medical and Biological Informatics.
-All rights reserved.
-
-This software is distributed WITHOUT ANY WARRANTY; without
-even the implied warranty of MERCHANTABILITY or FITNESS FOR
-A PARTICULAR PURPOSE.
-
-See LICENSE.txt or http://www.mitk.org for details.
-
-===================================================================*/
-
-#ifndef _MITK_KspaceArtifact_H
-#define _MITK_KspaceArtifact_H
-
-#include <FiberTrackingExports.h>
-#include <itkImage.h>
-#include <itkVnlForwardFFTImageFilter.h>
-
-namespace mitk {
-
-/**
- * \brief Abstract class for diffusion noise models
- *
- */
-
-template< class ScalarType >
-class KspaceArtifact
-{
-public:
-
- KspaceArtifact()
- : m_TE(100)
- , m_Tinhom(50)
- , m_LineReadoutTime(1)
- {
- }
- ~KspaceArtifact(){}
-
- typedef itk::Image< ScalarType, 2 > WorkImageType;
- typedef typename itk::VnlForwardFFTImageFilter< WorkImageType >::OutputImageType ComplexSliceType;
-
- /** Adds artifact according to model to the input slice. Has to be implemented in subclass. **/
- virtual typename ComplexSliceType::Pointer AddArtifact(typename ComplexSliceType::Pointer slice) = 0;
-
- void SetTline(double LineReadoutTime){ m_LineReadoutTime=LineReadoutTime; }
- void SetTE(double TE){ m_TE=TE; }
- void SetTinhom(unsigned int Tinhom){ m_Tinhom=Tinhom; }
-
-protected:
-
- double m_Tinhom;
- double m_TE;
- double m_LineReadoutTime;
-};
-
-}
-
-#endif
-
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
index 5fc1260ed4..ae7b9fc82e 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRicianNoiseModel.h
@@ -1,54 +1,58 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_RicianNoiseModel_H
#define _MITK_RicianNoiseModel_H
#include <mitkDiffusionNoiseModel.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>
namespace mitk {
/**
* \brief Implementation of noise following a rician distribution
*
*/
template< class ScalarType >
class RicianNoiseModel : public DiffusionNoiseModel< ScalarType >
{
public:
RicianNoiseModel();
~RicianNoiseModel();
typedef typename DiffusionNoiseModel< ScalarType >::PixelType PixelType;
/** Adds rician noise to the input pixel **/
void AddNoise(PixelType& pixel);
+ void SetNoiseVariance(double var){ m_NoiseVariance = var; }
+ double GetNoiseVariance(){ return m_NoiseVariance; }
+
protected:
itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
+ double m_NoiseVariance; ///< variance of underlying distribution
};
}
#include "mitkRicianNoiseModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp
index 4bd3a68891..f33b803332 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp
@@ -1,55 +1,79 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
template< class ScalarType >
StickModel< ScalarType >::StickModel()
: m_Diffusivity(0.001)
, m_BValue(1000)
{
}
template< class ScalarType >
StickModel< ScalarType >::~StickModel()
{
}
+template< class ScalarType >
+ScalarType StickModel< ScalarType >::SimulateMeasurement(int dir)
+{
+ ScalarType signal = 0;
+
+ if (dir>=this->m_GradientList.size())
+ return signal;
+
+ this->m_FiberDirection.Normalize();
+
+ GradientType g = this->m_GradientList[dir];
+ ScalarType bVal = g.GetNorm(); bVal *= bVal;
+
+ if (bVal>0.0001)
+ {
+ ScalarType dot = this->m_FiberDirection*g;
+ signal = exp( -m_BValue * bVal * m_Diffusivity*dot*dot );
+ }
+ else
+ signal = 1;
+
+ return signal;
+}
+
template< class ScalarType >
typename StickModel< ScalarType >::PixelType StickModel< ScalarType >::SimulateMeasurement()
{
this->m_FiberDirection.Normalize();
PixelType signal;
signal.SetSize(this->m_GradientList.size());
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
{
GradientType g = this->m_GradientList[i];
ScalarType bVal = g.GetNorm(); bVal *= bVal;
if (bVal>0.0001)
{
ScalarType dot = this->m_FiberDirection*g;
signal[i] = exp( -m_BValue * bVal * m_Diffusivity*dot*dot );
}
else
signal[i] = 1;
}
return signal;
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h
index 7452b65f3d..72625e03c4 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h
@@ -1,57 +1,58 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_StickModel_H
#define _MITK_StickModel_H
#include <mitkDiffusionSignalModel.h>
namespace mitk {
/**
* \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²)
*
*/
template< class ScalarType >
class StickModel : public DiffusionSignalModel< ScalarType >
{
public:
StickModel();
~StickModel();
typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
/** Actual signal generation **/
PixelType SimulateMeasurement();
+ ScalarType SimulateMeasurement(int dir);
void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal
void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant
protected:
ScalarType m_BValue; ///< b-value used to generate the artificial signal
ScalarType m_Diffusivity; ///< Scalar diffusion constant
};
}
#include "mitkStickModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp
index 67a1662cf4..00667f83bc 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp
@@ -1,80 +1,126 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vnl/vnl_cross.h>
#include <vnl/vnl_quaternion.h>
template< class ScalarType >
TensorModel< ScalarType >::TensorModel()
: m_BValue(1000)
{
m_KernelDirection[0]=1; m_KernelDirection[1]=0; m_KernelDirection[2]=0;
m_KernelTensorMatrix.fill(0.0);
m_KernelTensorMatrix[0][0] = 0.002;
m_KernelTensorMatrix[1][1] = 0.0005;
m_KernelTensorMatrix[2][2] = 0.0005;
}
template< class ScalarType >
TensorModel< ScalarType >::~TensorModel()
{
}
+template< class ScalarType >
+ScalarType TensorModel< ScalarType >::SimulateMeasurement(int dir)
+{
+ ScalarType signal = 0;
+
+ if (dir>=this->m_GradientList.size())
+ return signal;
+
+ ItkTensorType tensor; tensor.Fill(0.0);
+ this->m_FiberDirection.Normalize();
+ vnl_vector_fixed<double, 3> axis = itk::CrossProduct(m_KernelDirection, this->m_FiberDirection).GetVnlVector(); axis.normalize();
+ vnl_quaternion<double> rotation(axis, acos(m_KernelDirection*this->m_FiberDirection));
+ rotation.normalize();
+ vnl_matrix_fixed<double, 3, 3> matrix = rotation.rotation_matrix_transpose();
+
+ vnl_matrix_fixed<double, 3, 3> tensorMatrix = matrix.transpose()*m_KernelTensorMatrix*matrix;
+ tensor[0] = tensorMatrix[0][0]; tensor[1] = tensorMatrix[0][1]; tensor[2] = tensorMatrix[0][2];
+ tensor[3] = tensorMatrix[1][1]; tensor[4] = tensorMatrix[1][2]; tensor[5] = tensorMatrix[2][2];
+
+ GradientType g = this->m_GradientList[dir];
+ ScalarType bVal = g.GetNorm(); bVal *= bVal;
+
+ if (bVal>0.0001)
+ {
+ itk::DiffusionTensor3D< ScalarType > S;
+ S[0] = g[0]*g[0];
+ S[1] = g[1]*g[0];
+ S[2] = g[2]*g[0];
+ S[3] = g[1]*g[1];
+ S[4] = g[2]*g[1];
+ S[5] = g[2]*g[2];
+
+ ScalarType D = tensor[0]*S[0] + tensor[1]*S[1] + tensor[2]*S[2] +
+ tensor[1]*S[1] + tensor[3]*S[3] + tensor[4]*S[4] +
+ tensor[2]*S[2] + tensor[4]*S[4] + tensor[5]*S[5];
+
+ // check for corrupted tensor and generate signal
+ if (D>=0)
+ signal = exp ( -m_BValue * bVal * D );
+ }
+ else
+ signal = 1;
+
+ return signal;
+}
+
template< class ScalarType >
typename TensorModel< ScalarType >::PixelType TensorModel< ScalarType >::SimulateMeasurement()
{
PixelType signal; signal.SetSize(this->m_GradientList.size()); signal.Fill(0.0);
ItkTensorType tensor; tensor.Fill(0.0);
this->m_FiberDirection.Normalize();
vnl_vector_fixed<double, 3> axis = itk::CrossProduct(m_KernelDirection, this->m_FiberDirection).GetVnlVector(); axis.normalize();
vnl_quaternion<double> rotation(axis, acos(m_KernelDirection*this->m_FiberDirection));
rotation.normalize();
vnl_matrix_fixed<double, 3, 3> matrix = rotation.rotation_matrix_transpose();
vnl_matrix_fixed<double, 3, 3> tensorMatrix = matrix.transpose()*m_KernelTensorMatrix*matrix;
tensor[0] = tensorMatrix[0][0]; tensor[1] = tensorMatrix[0][1]; tensor[2] = tensorMatrix[0][2];
tensor[3] = tensorMatrix[1][1]; tensor[4] = tensorMatrix[1][2]; tensor[5] = tensorMatrix[2][2];
for( unsigned int i=0; i<this->m_GradientList.size(); i++)
{
GradientType g = this->m_GradientList[i];
ScalarType bVal = g.GetNorm(); bVal *= bVal;
if (bVal>0.0001)
{
itk::DiffusionTensor3D< ScalarType > S;
S[0] = g[0]*g[0];
S[1] = g[1]*g[0];
S[2] = g[2]*g[0];
S[3] = g[1]*g[1];
S[4] = g[2]*g[1];
S[5] = g[2]*g[2];
ScalarType D = tensor[0]*S[0] + tensor[1]*S[1] + tensor[2]*S[2] +
tensor[1]*S[1] + tensor[3]*S[3] + tensor[4]*S[4] +
tensor[2]*S[2] + tensor[4]*S[4] + tensor[5]*S[5];
// check for corrupted tensor and generate signal
if (D>=0)
signal[i] = exp ( -m_BValue * bVal * D );
}
else
signal[i] = 1;
}
return signal;
}
diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h
index fba519de02..000dcdddaf 100644
--- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h
+++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h
@@ -1,64 +1,65 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef _MITK_TensorModel_H
#define _MITK_TensorModel_H
#include <mitkDiffusionSignalModel.h>
#include <itkDiffusionTensor3D.h>
namespace mitk {
/**
* \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg)
*
*/
template< class ScalarType >
class TensorModel : public DiffusionSignalModel< ScalarType >
{
public:
TensorModel();
~TensorModel();
typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType;
typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
/** Actual signal generation **/
PixelType SimulateMeasurement();
+ ScalarType SimulateMeasurement(int dir);
void SetBvalue(ScalarType bValue) { m_BValue = bValue; }
void SetDiffusivity1(ScalarType d1){ m_KernelTensorMatrix[0][0] = d1; }
void SetDiffusivity2(ScalarType d2){ m_KernelTensorMatrix[1][1] = d2; }
void SetDiffusivity3(ScalarType d3){ m_KernelTensorMatrix[2][2] = d3; }
protected:
/** Calculates tensor matrix from FA and ADC **/
void UpdateKernelTensor();
GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector
vnl_matrix_fixed<ScalarType, 3, 3> m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values
ScalarType m_BValue; ///< b-value used to generate the artificial signal
};
}
#include "mitkTensorModel.cpp"
#endif
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt
index 2cec1f80ae..5fbb85bdd8 100644
--- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt
@@ -1,5 +1,11 @@
MITK_CREATE_MODULE_TESTS()
mitkAddCustomModuleTest(mitkFiberBundleXReaderWriterTest mitkFiberBundleXReaderWriterTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib)
-#mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib)
-#mitkAddCustomModuleTest(mitkFiberBundleXTest mitkFiberBundleXTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib)
+mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/gibbsTractogram.fib)
+mitkAddCustomModuleTest(mitkStreamlineTrackingTest mitkStreamlineTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/tensorImage.dti ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogram.fib)
+mitkAddCustomModuleTest(mitkPeakExtractionTest mitkPeakExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_SHCoeffs.nrrd ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_VectorField.fib)
+mitkAddCustomModuleTest(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogram.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_NUM_DIRECTIONS.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_VECTOR_FIELD.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_2.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE_IGNORE.nrrd)
+mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib)
+mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX-fiberBundleX_extracted.fib)
+mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib)
+# TODO: fiberfox signalgen
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake
index b5d52ea256..64863cfc8f 100644
--- a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake
@@ -1,7 +1,12 @@
SET(MODULE_CUSTOM_TESTS
mitkFiberBundleXReaderWriterTest.cpp
- mitkFiberBundleXTest.cpp
mitkGibbsTrackingTest.cpp
+ mitkStreamlineTrackingTest.cpp
+ mitkPeakExtractionTest.cpp
+ mitkLocalFiberPlausibilityTest.cpp
+ mitkFiberTransformationTest.cpp
+ mitkFiberExtractionTest.cpp
+ mitkFiberGenerationTest.cpp
)
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXTest.cpp
deleted file mode 100644
index 7d14539dbb..0000000000
--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXTest.cpp
+++ /dev/null
@@ -1,100 +0,0 @@
-/*===================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center,
-Division of Medical and Biological Informatics.
-All rights reserved.
-
-This software is distributed WITHOUT ANY WARRANTY; without
-even the implied warranty of MERCHANTABILITY or FITNESS FOR
-A PARTICULAR PURPOSE.
-
-See LICENSE.txt or http://www.mitk.org for details.
-
-===================================================================*/
-
-#include "mitkTestingMacros.h"
-
-#include <mitkFiberTrackingObjectFactory.h>
-#include <mitkFiberBundleX.h>
-#include <mitkFiberBundleXReader.h>
-#include <mitkBaseDataIOFactory.h>
-#include <mitkBaseData.h>
-#include <itksys/SystemTools.hxx>
-#include <mitkTestingConfig.h>
-#include <math.h>
-
-/**Documentation
- * Test for fiber bundle reader and writer
- */
-int mitkFiberBundleXTest(int argc, char* argv[])
-{
- MITK_TEST_BEGIN("mitkFiberBundleXTest");
-
- MITK_TEST_CONDITION_REQUIRED(argc>1,"check for filename")
-
- mitk::FiberBundleXReader::Pointer reader = mitk::FiberBundleXReader::New();
- mitk::FiberBundleX::Pointer fib1, fib2;
-
- // first test: did this work?
- // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since
- // it makes no sense to continue without an object.
- MITK_TEST_CONDITION_REQUIRED(reader.IsNotNull(),"reader instantiation")
-
- try{
- RegisterFiberTrackingObjectFactory();
-
- // test if fib1 can be read
- const std::string s1="", s2="";
- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false );
- mitk::BaseData::Pointer baseData = fibInfile.at(0);
- fib1 = dynamic_cast<mitk::FiberBundleX*>(baseData.GetPointer());
- MITK_TEST_CONDITION_REQUIRED(fib1.IsNotNull(),"check if reader 1 returned null")
-
- fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false );
- baseData = fibInfile.at(0);
- fib2 = dynamic_cast<mitk::FiberBundleX*>(baseData.GetPointer());
- MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(),"check if reader 2 returned null")
-
- MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2),"check if equals method is working");
-
- int randNum = rand()%20;
- MITK_INFO << "DoFiberSmoothing(" << randNum << ")" << randNum; fib2->DoFiberSmoothing(randNum);
- MITK_TEST_CONDITION_REQUIRED(!fib1->Equals(fib2),"check if fiber resampling method does something");
-
- mitk::FiberBundleX::Pointer fib3 = fib1->AddBundle(fib2);
- MITK_TEST_CONDITION_REQUIRED(!fib1->Equals(fib3),"check if A+B!=A");
-// fib3 = fib3->SubtractBundle(fib2);
-// MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib3),"check if A+B-B==A");
-
- fib1->AddBundle(NULL);
- MITK_INFO << "GenerateFiberIds"; fib1->GenerateFiberIds();
- MITK_INFO << "GetFiberPolyData"; fib1->GetFiberPolyData();
- MITK_INFO << "GetAvailableColorCodings"; fib1->GetAvailableColorCodings();
- MITK_INFO << "GetCurrentColorCoding"; fib1->GetCurrentColorCoding();
- MITK_INFO << "SetFiberPolyData"; fib1->SetFiberPolyData(NULL);
- MITK_INFO << "ExtractFiberSubset"; fib1->ExtractFiberSubset(NULL);
- MITK_INFO << "ExtractFiberIdSubset"; fib1->ExtractFiberIdSubset(NULL);
- std::vector< long > tmp;
- MITK_INFO << "GeneratePolyDataByIds"; fib1->GeneratePolyDataByIds(tmp);
- MITK_INFO << "SetColorCoding"; fib1->SetColorCoding(NULL);
- MITK_INFO << "SetFAMap"; fib1->SetFAMap(NULL);
- MITK_INFO << "DoColorCodingOrientationBased"; fib1->DoColorCodingOrientationBased();
- MITK_INFO << "DoColorCodingFaBased"; fib1->DoColorCodingFaBased();
- MITK_INFO << "DoUseFaFiberOpacity"; fib1->DoUseFaFiberOpacity();
- MITK_INFO << "ResetFiberOpacity"; fib1->ResetFiberOpacity();
-
- float randFloat = rand()%300;
- MITK_INFO << "RemoveShortFibers(" << randFloat << ")"; fib1->RemoveShortFibers(randFloat);
- }
- catch(...)
- {
- //this means that a wrong exception (i.e. no itk:Exception) has been thrown
- std::cout << "Wrong exception (i.e. no itk:Exception) caught during write [FAILED]" << std::endl;
- return EXIT_FAILURE;
- }
-
- // always end with this!
- MITK_TEST_END();
-}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp
new file mode 100644
index 0000000000..80fdb0a633
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp
@@ -0,0 +1,94 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkTestingMacros.h>
+#include <mitkIOUtil.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberBundleX.h>
+#include <mitkPlanarFigure.h>
+#include <mitkPlanarFigureComposite.h>
+#include <mitkImageCast.h>
+
+/**Documentation
+ * Test if fiber transfortaiom methods work correctly
+ */
+int mitkFiberExtractionTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkFiberExtractionTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc==13,"check for input data")
+
+ try{
+ RegisterFiberTrackingObjectFactory();
+
+ mitk::FiberBundleX::Pointer groundTruthFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData());
+ mitk::FiberBundleX::Pointer testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData());
+
+ // test planar figure based extraction
+ mitk::PlanarFigure::Pointer pf1 = dynamic_cast<mitk::PlanarFigure*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData());
+ mitk::PlanarFigure::Pointer pf2 = dynamic_cast<mitk::PlanarFigure*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData());
+ mitk::PlanarFigure::Pointer pf3 = dynamic_cast<mitk::PlanarFigure*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData());
+ mitk::PlanarFigureComposite::Pointer pfc1 = mitk::PlanarFigureComposite::New();
+ pfc1->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION);
+ pfc1->addPlanarFigure(pf2);
+ pfc1->addPlanarFigure(pf3);
+ mitk::PlanarFigureComposite::Pointer pfc2 = mitk::PlanarFigureComposite::New();
+ pfc2->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION);
+ pfc2->addPlanarFigure(pf1);
+ pfc2->addPlanarFigure(dynamic_cast<mitk::PlanarFigure*>(pfc1.GetPointer()));
+ mitk::FiberBundleX::Pointer extractedFibs = groundTruthFibs->ExtractFiberSubset(pfc2);
+ MITK_TEST_CONDITION_REQUIRED(extractedFibs->Equals(testFibs),"check planar figure extraction")
+
+ // test subtraction and addition
+ mitk::FiberBundleX::Pointer notExtractedFibs = groundTruthFibs->SubtractBundle(extractedFibs);
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(notExtractedFibs->Equals(testFibs),"check bundle subtraction")
+
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData());
+ mitk::FiberBundleX::Pointer joinded = extractedFibs->AddBundle(notExtractedFibs);
+ MITK_TEST_CONDITION_REQUIRED(joinded->Equals(testFibs),"check bundle addition")
+
+ // test binary image based extraction
+ mitk::Image::Pointer mitkRoiImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData());
+ typedef itk::Image< unsigned char, 3 > itkUCharImageType;
+ itkUCharImageType::Pointer itkRoiImage = itkUCharImageType::New();
+ mitk::CastToItkImage<itkUCharImageType>(mitkRoiImage, itkRoiImage);
+
+ mitk::FiberBundleX::Pointer inside = groundTruthFibs->RemoveFibersOutside(itkRoiImage, false);
+ mitk::FiberBundleX::Pointer outside = groundTruthFibs->RemoveFibersOutside(itkRoiImage, true);
+ mitk::FiberBundleX::Pointer passing = groundTruthFibs->ExtractFiberSubset(itkRoiImage, true);
+ mitk::FiberBundleX::Pointer ending = groundTruthFibs->ExtractFiberSubset(itkRoiImage, false);
+
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(inside->Equals(testFibs),"check inside mask extraction")
+
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(outside->Equals(testFibs),"check outside mask extraction")
+
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(passing->Equals(testFibs),"check passing mask extraction")
+
+ testFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(ending->Equals(testFibs),"check ending in mask extraction")
+ }
+ catch(...) {
+ return EXIT_FAILURE;
+ }
+
+ // always end with this!
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp
new file mode 100644
index 0000000000..65634e700e
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp
@@ -0,0 +1,89 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkTestingMacros.h>
+#include <mitkIOUtil.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberBundleX.h>
+#include <mitkPlanarEllipse.h>
+#include <itkFibersFromPlanarFiguresFilter.h>
+
+/**Documentation
+ * Test if fiber transfortaiom methods work correctly
+ */
+int mitkFiberGenerationTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkFiberGenerationTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc==6,"check for input data")
+
+ try{
+ RegisterFiberTrackingObjectFactory();
+
+ mitk::PlanarEllipse::Pointer pf1 = dynamic_cast<mitk::PlanarEllipse*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData());
+ mitk::PlanarEllipse::Pointer pf2 = dynamic_cast<mitk::PlanarEllipse*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData());
+ mitk::PlanarEllipse::Pointer pf3 = dynamic_cast<mitk::PlanarEllipse*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData());
+ mitk::FiberBundleX::Pointer uniform = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData());
+ mitk::FiberBundleX::Pointer gaussian = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData());
+
+
+ vector< mitk::PlanarEllipse::Pointer > fid; fid.push_back(pf1); fid.push_back(pf2); fid.push_back(pf3);
+ vector< unsigned int > flip; flip.push_back(0); flip.push_back(0); flip.push_back(0);
+ vector< vector< mitk::PlanarEllipse::Pointer > > fiducials;
+ vector< vector< unsigned int > > fliplist;
+ fiducials.push_back(fid); fliplist.push_back(flip);
+
+ // check uniform fiber distribution
+ {
+ itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
+ filter->SetFiducials(fiducials);
+ filter->SetFlipList(fliplist);
+ filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM);
+ filter->SetDensity(50);
+ filter->SetTension(0);
+ filter->SetContinuity(0);
+ filter->SetBias(0);
+ filter->SetFiberSampling(1);
+ filter->Update();
+ vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles();
+ MITK_TEST_CONDITION_REQUIRED(uniform->Equals(fiberBundles.at(0)),"check uniform bundle")
+ }
+
+ // check gaussian fiber distribution
+ {
+ itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
+ filter->SetFiducials(fiducials);
+ filter->SetFlipList(fliplist);
+ filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN);
+ filter->SetVariance(0.1);
+ filter->SetDensity(50);
+ filter->SetTension(0);
+ filter->SetContinuity(0);
+ filter->SetBias(0);
+ filter->SetFiberSampling(1);
+ filter->Update();
+ vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles();
+ MITK_TEST_CONDITION_REQUIRED(gaussian->Equals(fiberBundles.at(0)),"check gaussian bundle")
+ }
+ }
+ catch(...) {
+ return EXIT_FAILURE;
+ }
+
+ // always end with this!
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp
new file mode 100644
index 0000000000..956872c9a9
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp
@@ -0,0 +1,57 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkTestingMacros.h>
+#include <mitkIOUtil.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberBundleX.h>
+
+/**Documentation
+ * Test if fiber transfortaiom methods work correctly
+ */
+int mitkFiberTransformationTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkFiberTransformationTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc==3,"check for input data")
+
+ try{
+ RegisterFiberTrackingObjectFactory();
+
+ mitk::FiberBundleX::Pointer groundTruthFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData());
+ mitk::FiberBundleX::Pointer transformedFibs = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData());
+
+ groundTruthFibs->RotateAroundAxis(90, 45, 10);
+ groundTruthFibs->TranslateFibers(2, 3, 5);
+ groundTruthFibs->ScaleFibers(1, 0.1, 1.3);
+ groundTruthFibs->RemoveLongFibers(150);
+ groundTruthFibs->RemoveShortFibers(20);
+ groundTruthFibs->DoFiberSmoothing(1.0);
+ groundTruthFibs->ApplyCurvatureThreshold(3.0, true);
+ groundTruthFibs->MirrorFibers(0);
+ groundTruthFibs->MirrorFibers(1);
+ groundTruthFibs->MirrorFibers(2);
+
+ MITK_TEST_CONDITION_REQUIRED(groundTruthFibs->Equals(transformedFibs),"check transformation")
+ }
+ catch(...) {
+ return EXIT_FAILURE;
+ }
+
+ // always end with this!
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp
new file mode 100755
index 0000000000..223e67136a
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp
@@ -0,0 +1,175 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkBaseDataIOFactory.h>
+#include <mitkBaseData.h>
+#include <mitkImageCast.h>
+#include <mitkImageToItk.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <itkEvaluateDirectionImagesFilter.h>
+#include <itkTractsToVectorImageFilter.h>
+#include <usAny.h>
+#include <itkImageFileWriter.h>
+#include <mitkIOUtil.h>
+#include <boost/lexical_cast.hpp>
+#include <iostream>
+#include <fstream>
+#include <itksys/SystemTools.hxx>
+#include <mitkTestingMacros.h>
+#include <mitkCompareImageDataFilter.h>
+
+#define _USE_MATH_DEFINES
+#include <math.h>
+
+using namespace std;
+
+int mitkLocalFiberPlausibilityTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkLocalFiberPlausibilityTest");
+ MITK_TEST_CONDITION_REQUIRED(argc==11,"check for input data")
+
+ string fibFile = argv[1];
+ vector< string > referenceImages; referenceImages.push_back(argv[2]); referenceImages.push_back(argv[3]);
+ string LDFP_ERROR_IMAGE = argv[4];
+ string LDFP_NUM_DIRECTIONS = argv[5];
+ string LDFP_VECTOR_FIELD = argv[6];
+
+ float angularThreshold = 25;
+
+ try
+ {
+ RegisterDiffusionCoreObjectFactory();
+ RegisterFiberTrackingObjectFactory();
+
+ typedef itk::Image<unsigned char, 3> ItkUcharImgType;
+ typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType;
+ typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType;
+ typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType;
+
+ // load fiber bundle
+ mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
+
+ // load reference directions
+ ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
+ for (int i=0; i<referenceImages.size(); i++)
+ {
+ try
+ {
+ mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData());
+ typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType;
+ CasterType::Pointer caster = CasterType::New();
+ caster->SetInput(img);
+ caster->Update();
+ ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput();
+ referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg);
+ }
+ catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); }
+ }
+
+ ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
+ ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
+ itkMaskImage->SetSpacing( dirImg->GetSpacing() );
+ itkMaskImage->SetOrigin( dirImg->GetOrigin() );
+ itkMaskImage->SetDirection( dirImg->GetDirection() );
+ itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->Allocate();
+ itkMaskImage->FillBuffer(1);
+
+ // extract directions from fiber bundle
+ itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
+ fOdfFilter->SetFiberBundle(inputTractogram);
+ fOdfFilter->SetMaskImage(itkMaskImage);
+ fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180));
+ fOdfFilter->SetNormalizeVectors(true);
+ fOdfFilter->SetUseWorkingCopy(false);
+ fOdfFilter->Update();
+ ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer();
+
+ // evaluate directions
+ EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
+ evaluationFilter->SetImageSet(directionImageContainer);
+ evaluationFilter->SetReferenceImageSet(referenceImageContainer);
+ evaluationFilter->SetMaskImage(itkMaskImage);
+ evaluationFilter->SetIgnoreMissingDirections(false);
+ evaluationFilter->Update();
+
+ EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
+ ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage();
+ mitk::FiberBundleX::Pointer testDirections = fOdfFilter->GetOutputFiberBundle();
+
+ mitk::Image::Pointer mitkAngularErrorImage = mitk::Image::New();
+ mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() );
+ mitkAngularErrorImage->SetVolume( angularErrorImage->GetBufferPointer() );
+
+ mitk::Image::Pointer mitkNumDirImage = mitk::Image::New();
+ mitkNumDirImage->InitializeByItk( numDirImage.GetPointer() );
+ mitkNumDirImage->SetVolume( numDirImage->GetBufferPointer() );
+
+ mitk::Image::Pointer gtAngularErrorImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE)->GetData());
+ mitk::Image::Pointer gtNumTestDirImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_NUM_DIRECTIONS)->GetData());
+ mitk::FiberBundleX::Pointer gtTestDirections = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(LDFP_VECTOR_FIELD)->GetData());
+
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImage, mitkAngularErrorImage, 0.0001, true), "Check if error images are equal.");
+ MITK_TEST_CONDITION_REQUIRED(testDirections->Equals(gtTestDirections), "Check if vector fields are equal.");
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtNumTestDirImage, mitkNumDirImage, 0.0001, true), "Check if num direction images are equal.");
+
+ evaluationFilter = EvaluationFilterType::New();
+ evaluationFilter->SetImageSet(directionImageContainer);
+ evaluationFilter->SetReferenceImageSet(referenceImageContainer);
+ //evaluationFilter->SetMaskImage(itkMaskImage);
+ evaluationFilter->SetIgnoreMissingDirections(true);
+ evaluationFilter->Update();
+ angularErrorImage = evaluationFilter->GetOutput(0);
+ mitkAngularErrorImage = mitk::Image::New();
+ mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() );
+ mitkAngularErrorImage->SetVolume( angularErrorImage->GetBufferPointer() );
+ mitk::IOUtil::SaveImage(mitkAngularErrorImage, "test.nrrd");
+ gtAngularErrorImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImage, mitkAngularErrorImage, 0.0001, true), "Check if error images with ignored missing directions are equal.");
+
+
+ for (int i=0; i<directionImageContainer->Size(); i++)
+ {
+ MITK_INFO << "Checking direction image " << i;
+ itk::TractsToVectorImageFilter<float>::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i);
+ mitk::Image::Pointer dirImage = mitk::Image::New();
+ dirImage->InitializeByItk( itkImg.GetPointer() );
+ dirImage->SetVolume( itkImg->GetBufferPointer() );
+
+ mitk::Image::Pointer refDirImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(argv[7+i])->GetData());
+ MITK_TEST_CONDITION_REQUIRED(mitk::Equal(dirImage, refDirImage, 0.0001, true), "Check if direction images are equal.");
+ }
+ }
+ catch (itk::ExceptionObject e)
+ {
+ MITK_INFO << e;
+ return EXIT_FAILURE;
+ }
+ catch (std::exception e)
+ {
+ MITK_INFO << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_INFO << "ERROR!?!";
+ return EXIT_FAILURE;
+ }
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp
new file mode 100755
index 0000000000..b17b6f9864
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp
@@ -0,0 +1,114 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <itkImageFileWriter.h>
+#include <itkResampleImageFilter.h>
+#include <itkFiniteDiffOdfMaximaExtractionFilter.h>
+
+#include <mitkBaseDataIOFactory.h>
+#include <mitkDiffusionImage.h>
+#include <mitkQBallImage.h>
+#include <mitkImageCast.h>
+#include <mitkImageToItk.h>
+#include <mitkTensorImage.h>
+
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <mitkCoreObjectFactory.h>
+#include <mitkFiberBundleXWriter.h>
+#include <itkShCoefficientImageImporter.h>
+#include <mitkNrrdQBallImageWriter.h>
+#include <itkFlipImageFilter.h>
+#include <boost/lexical_cast.hpp>
+#include <boost/algorithm/string.hpp>
+#include <mitkTestingMacros.h>
+#include <mitkIOUtil.h>
+
+using namespace std;
+
+int mitkPeakExtractionTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkStreamlineTrackingTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data")
+
+ string shCoeffFileName = argv[1];
+ string maskFileName = argv[2];
+ string referenceFileName = argv[3];
+
+ MITK_INFO << "SH-coefficient file: " << shCoeffFileName;
+ MITK_INFO << "Mask file: " << maskFileName;
+ MITK_INFO << "Reference fiber file: " << referenceFileName;
+
+ try
+ {
+ mitk::CoreObjectFactory::GetInstance();
+
+ RegisterDiffusionCoreObjectFactory();
+ RegisterFiberTrackingObjectFactory();
+
+ mitk::Image::Pointer image = mitk::IOUtil::LoadImage(shCoeffFileName);
+ mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName);
+
+ typedef itk::Image<unsigned char, 3> ItkUcharImgType;
+ typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, 4, 20242 > MaximaExtractionFilterType;
+ typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
+
+ MITK_INFO << "Casting mask image ...";
+ ItkUcharImgType::Pointer itkMask = ItkUcharImgType::New();
+ mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMask);
+ filter->SetMaskImage(itkMask);
+
+ MITK_INFO << "Casting SH image ...";
+ typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
+ typename CasterType::Pointer caster = CasterType::New();
+ caster->SetInput(image);
+ caster->Update();
+ filter->SetInput(caster->GetOutput());
+ filter->SetMaxNumPeaks(2);
+ filter->SetPeakThreshold(0.4);
+ filter->SetAbsolutePeakThreshold(0.01);
+ filter->SetAngularThreshold(25);
+ filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
+ MITK_INFO << "Starting extraction ...";
+ filter->Update();
+ mitk::FiberBundleX::Pointer fib1 = filter->GetOutputFiberBundle();
+
+ MITK_INFO << "Loading reference ...";
+ const std::string s1="", s2="";
+ std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false );
+ mitk::FiberBundleX::Pointer fib2 = dynamic_cast<mitk::FiberBundleX*>(infile.at(0).GetPointer());
+
+ MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "Check if tractograms are equal.");
+ }
+ catch (itk::ExceptionObject e)
+ {
+ MITK_INFO << e;
+ return EXIT_FAILURE;
+ }
+ catch (std::exception e)
+ {
+ MITK_INFO << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_INFO << "ERROR!?!";
+ return EXIT_FAILURE;
+ }
+
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp
new file mode 100755
index 0000000000..14c6008ed0
--- /dev/null
+++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp
@@ -0,0 +1,129 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkImageCast.h>
+#include <mitkTensorImage.h>
+#include <mitkIOUtil.h>
+#include <mitkBaseDataIOFactory.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <mitkFiberTrackingObjectFactory.h>
+#include <mitkFiberBundleX.h>
+#include <itkStreamlineTrackingFilter.h>
+#include <itkDiffusionTensor3D.h>
+#include <mitkTestingMacros.h>
+
+using namespace std;
+
+int mitkStreamlineTrackingTest(int argc, char* argv[])
+{
+ MITK_TEST_BEGIN("mitkStreamlineTrackingTest");
+
+ MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data")
+
+ string dtiFileName = argv[1];
+ string maskFileName = argv[2];
+ string referenceFileName = argv[3];
+
+ MITK_INFO << "DTI file: " << dtiFileName;
+ MITK_INFO << "Mask file: " << maskFileName;
+ MITK_INFO << "Reference fiber file: " << referenceFileName;
+
+ float minFA = 0.05;
+ float minCurv = -1;
+ float stepSize = -1;
+ float tendf = 1;
+ float tendg = 0;
+ float minLength = 20;
+ int numSeeds = 1;
+ bool interpolate = false;
+
+ try
+ {
+ RegisterDiffusionCoreObjectFactory();
+ RegisterFiberTrackingObjectFactory();
+
+ // load input image
+ const std::string s1="", s2="";
+ std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( dtiFileName, s1, s2, false );
+
+ MITK_INFO << "Loading tensor image ...";
+ typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
+ mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(infile.at(0).GetPointer());
+ ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
+ mitk::CastToItkImage<ItkTensorImage>(mitkTensorImage, itk_dti);
+
+ MITK_INFO << "Loading seed image ...";
+ typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
+ mitk::Image::Pointer mitkSeedImage = mitk::IOUtil::LoadImage(maskFileName);
+
+ MITK_INFO << "Loading mask image ...";
+ mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName);
+
+ // instantiate tracker
+ typedef itk::StreamlineTrackingFilter< float > FilterType;
+ FilterType::Pointer filter = FilterType::New();
+ filter->SetInput(itk_dti);
+ filter->SetSeedsPerVoxel(numSeeds);
+ filter->SetFaThreshold(minFA);
+ filter->SetMinCurvatureRadius(minCurv);
+ filter->SetStepSize(stepSize);
+ filter->SetF(tendf);
+ filter->SetG(tendg);
+ filter->SetInterpolate(interpolate);
+ filter->SetMinTractLength(minLength);
+
+ if (mitkSeedImage.IsNotNull())
+ {
+ ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
+ mitk::CastToItkImage<ItkUCharImageType>(mitkSeedImage, mask);
+ filter->SetSeedImage(mask);
+ }
+
+ if (mitkMaskImage.IsNotNull())
+ {
+ ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
+ mitk::CastToItkImage<ItkUCharImageType>(mitkMaskImage, mask);
+ filter->SetMaskImage(mask);
+ }
+
+ filter->Update();
+
+ vtkSmartPointer<vtkPolyData> fiberBundle = filter->GetFiberPolyData();
+ mitk::FiberBundleX::Pointer fib1 = mitk::FiberBundleX::New(fiberBundle);
+
+ infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false );
+ mitk::FiberBundleX::Pointer fib2 = dynamic_cast<mitk::FiberBundleX*>(infile.at(0).GetPointer());
+ MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(), "Check if reference tractogram is not null.");
+ MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "Check if tractograms are equal.");
+ }
+ catch (itk::ExceptionObject e)
+ {
+ MITK_INFO << e;
+ return EXIT_FAILURE;
+ }
+ catch (std::exception e)
+ {
+ MITK_INFO << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_INFO << "ERROR!?!";
+ return EXIT_FAILURE;
+ }
+
+ MITK_TEST_END();
+}
diff --git a/Modules/DiffusionImaging/FiberTracking/files.cmake b/Modules/DiffusionImaging/FiberTracking/files.cmake
index 8ea747434e..56a3dfe386 100644
--- a/Modules/DiffusionImaging/FiberTracking/files.cmake
+++ b/Modules/DiffusionImaging/FiberTracking/files.cmake
@@ -1,103 +1,103 @@
set(CPP_FILES
# DataStructures -> FiberBundleX
IODataStructures/FiberBundleX/mitkFiberBundleX.cpp
IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp
IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp
IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp
IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp
IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp
IODataStructures/FiberBundleX/mitkTrackvis.cpp
# IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp
# DataStructures -> PlanarFigureComposite
IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp
# DataStructures
IODataStructures/mitkFiberTrackingObjectFactory.cpp
# Rendering
Rendering/mitkFiberBundleXMapper2D.cpp
Rendering/mitkFiberBundleXMapper3D.cpp
# Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp
#Rendering/mitkPlanarFigureMapper3D.cpp
# Interactions
Interactions/mitkFiberBundleInteractor.cpp
# Tractography
Algorithms/GibbsTracking/mitkParticleGrid.cpp
Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp
Algorithms/GibbsTracking/mitkEnergyComputer.cpp
Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp
Algorithms/GibbsTracking/mitkFiberBuilder.cpp
Algorithms/GibbsTracking/mitkSphereInterpolator.cpp
)
set(H_FILES
# Rendering
Rendering/mitkFiberBundleXMapper3D.h
Rendering/mitkFiberBundleXMapper2D.h
# Rendering/mitkFiberBundleXThreadMonitorMapper3D.h
#Rendering/mitkPlanarFigureMapper3D.h
# DataStructures -> FiberBundleX
IODataStructures/FiberBundleX/mitkFiberBundleX.h
IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h
IODataStructures/FiberBundleX/mitkFiberBundleXReader.h
IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h
IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h
IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h
# IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h
IODataStructures/FiberBundleX/mitkTrackvis.h
IODataStructures/mitkFiberTrackingObjectFactory.h
# Algorithms
Algorithms/itkTractDensityImageFilter.h
Algorithms/itkTractsToFiberEndingsImageFilter.h
Algorithms/itkTractsToRgbaImageFilter.h
Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h
Algorithms/itkFibersFromPlanarFiguresFilter.h
Algorithms/itkTractsToDWIImageFilter.h
Algorithms/itkTractsToVectorImageFilter.h
Algorithms/itkKspaceImageFilter.h
Algorithms/itkDftImageFilter.h
Algorithms/itkAddArtifactsToDwiImageFilter.h
Algorithms/itkFieldmapGeneratorFilter.h
Algorithms/itkEvaluateDirectionImagesFilter.h
Algorithms/itkEvaluateTractogramDirectionsFilter.h
# (old) Tractography
Algorithms/itkGibbsTrackingFilter.h
Algorithms/itkStochasticTractographyFilter.h
Algorithms/itkStreamlineTrackingFilter.h
Algorithms/GibbsTracking/mitkParticle.h
Algorithms/GibbsTracking/mitkParticleGrid.h
Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h
Algorithms/GibbsTracking/mitkSimpSamp.h
Algorithms/GibbsTracking/mitkEnergyComputer.h
Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h
Algorithms/GibbsTracking/mitkSphereInterpolator.h
Algorithms/GibbsTracking/mitkFiberBuilder.h
# Signal Models
SignalModels/mitkDiffusionSignalModel.h
SignalModels/mitkTensorModel.h
SignalModels/mitkBallModel.h
SignalModels/mitkDotModel.h
SignalModels/mitkAstroStickModel.h
SignalModels/mitkStickModel.h
SignalModels/mitkDiffusionNoiseModel.h
SignalModels/mitkRicianNoiseModel.h
- SignalModels/mitkKspaceArtifact.h
+ SignalModels/mitkChiSquareNoiseModel.h
)
set(RESOURCE_FILES
# Binary directory resources
FiberTrackingLUTBaryCoords.bin
FiberTrackingLUTIndices.bin
# Shaders
Shaders/mitkShaderFiberClipping.xml
)
diff --git a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt
index 11da805e7b..372d6a5ee3 100755
--- a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt
+++ b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt
@@ -1,61 +1,67 @@
OPTION(BUILD_DiffusionMiniApps "Build commandline tools for diffusion" OFF)
IF(BUILD_DiffusionMiniApps)
# include necessary modules here
MITK_CHECK_MODULE(_RESULT DiffusionCore FiberTracking )
IF(_RESULT)
MESSAGE("Warning: DiffusionMiniApps is missing ${_RESULT}")
ELSE(_RESULT)
MITK_USE_MODULE( DiffusionCore FiberTracking )
# needed include directories
INCLUDE_DIRECTORIES(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
${ALL_INCLUDE_DIRECTORIES})
PROJECT( mitkDiffusionMiniApps )
# fill in the standalone executables here
SET(DIFFUSIONMINIAPPS
mitkDiffusionMiniApps
)
# set additional files here
SET(DIFFUSIONCORE_ADDITIONAL_FILES
MiniAppManager.cpp
FileFormatConverter.cpp
TensorReconstruction.cpp
QballReconstruction.cpp
DiffusionIndices.cpp
CopyGeometry.cpp
GibbsTracking.cpp
StreamlineTracking.cpp
FiberProcessing.cpp
- TractometerAngularErrorTool.cpp
- TractogramAngularError.cpp
+ LocalDirectionalFiberPlausibility.cpp
+ #TractogramAngularError.cpp
FiberDirectionExtraction.cpp
PeakExtraction.cpp
PeaksAngularError.cpp
MultishellMethods.cpp
FiberFoxProcessing.cpp
+ ExportShImage.cpp
+ )
+
+ # deprecated
+# FOREACH(tool ${DIFFUSIONMINIAPPS})
+# ADD_EXECUTABLE(
+# ${tool}
+# ${tool}.cpp
+# ${DIFFUSIONCORE_ADDITIONAL_FILES}
+# )
+
+# TARGET_LINK_LIBRARIES(
+# ${tool}
+# ${ALL_LIBRARIES} )
+# ENDFOREACH(tool)
+
+ mitk_create_executable(mitkDiffusionMiniApps
+ DEPENDS DiffusionCore FiberTracking
)
- # create an executable foreach tool (only one at the moment)
- FOREACH(tool ${DIFFUSIONMINIAPPS})
- ADD_EXECUTABLE(
- ${tool}
- ${tool}.cpp
- ${DIFFUSIONCORE_ADDITIONAL_FILES}
- )
-
- TARGET_LINK_LIBRARIES(
- ${tool}
- ${ALL_LIBRARIES} )
- ENDFOREACH(tool)
ENDIF()
MITK_INSTALL_TARGETS(EXECUTABLES mitkDiffusionMiniApps )
ENDIF(BUILD_DiffusionMiniApps)
diff --git a/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp
new file mode 100755
index 0000000000..e99592b7e6
--- /dev/null
+++ b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp
@@ -0,0 +1,131 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include "MiniAppManager.h"
+#include <mitkBaseDataIOFactory.h>
+#include <mitkBaseData.h>
+#include <mitkImageCast.h>
+#include <mitkImageToItk.h>
+#include <mitkDiffusionCoreObjectFactory.h>
+#include <metaCommand.h>
+#include "ctkCommandLineParser.h"
+#include <usAny.h>
+#include <itkImageFileWriter.h>
+#include <itkImageFileReader.h>
+#include <mitkIOUtil.h>
+#include <boost/lexical_cast.hpp>
+#include <itkShCoefficientImageExporter.h>
+#include <itkFlipImageFilter.h>
+
+#define _USE_MATH_DEFINES
+#include <math.h>
+
+template<int shOrder>
+int StartShConversion(int argc, char* argv[])
+{
+ ctkCommandLineParser parser;
+ parser.setArgumentPrefix("--", "-");
+ parser.addArgument("input", "i", ctkCommandLineParser::String, "MITK SH image", us::Any(), false);
+ parser.addArgument("output", "o", ctkCommandLineParser::String, "MRtrix SH image", us::Any(), false);
+ parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "spherical harmonics order");
+
+ map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
+ if (parsedArgs.size()==0)
+ return EXIT_FAILURE;
+
+ string inFile = us::any_cast<string>(parsedArgs["input"]);
+ string outFile = us::any_cast<string>(parsedArgs["output"]);
+
+ try
+ {
+ RegisterDiffusionCoreObjectFactory();
+
+ typedef itk::Image< float, 4 > OutImageType;
+ typedef itk::Image< itk::Vector< float, (shOrder*shOrder + shOrder + 2)/2 + shOrder >, 3 > InputImageType;
+
+ typename InputImageType::Pointer itkInImage = InputImageType::New();
+ typedef itk::ImageFileReader< InputImageType > ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ MITK_INFO << "reading " << inFile;
+ reader->SetFileName(inFile.c_str());
+ reader->Update();
+ itkInImage = reader->GetOutput();
+
+ // extract directions from fiber bundle
+ typename itk::ShCoefficientImageExporter<float, shOrder>::Pointer filter = itk::ShCoefficientImageExporter<float,shOrder>::New();
+ filter->SetInputImage(itkInImage);
+ filter->GenerateData();
+ OutImageType::Pointer outImage = filter->GetOutputImage();
+
+ typedef itk::ImageFileWriter< OutImageType > WriterType;
+ WriterType::Pointer writer = WriterType::New();
+ MITK_INFO << "writing " << outFile;
+ writer->SetFileName(outFile.c_str());
+ writer->SetInput(outImage);
+ writer->Update();
+
+ MITK_INFO << "DONE";
+ }
+ catch (itk::ExceptionObject e)
+ {
+ MITK_INFO << e;
+ return EXIT_FAILURE;
+ }
+ catch (std::exception e)
+ {
+ MITK_INFO << e.what();
+ return EXIT_FAILURE;
+ }
+ catch (...)
+ {
+ MITK_INFO << "ERROR!?!";
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
+}
+
+int ExportShImage(int argc, char* argv[])
+{
+ ctkCommandLineParser parser;
+ parser.setArgumentPrefix("--", "-");
+ parser.addArgument("input", "i", ctkCommandLineParser::String, "MITK SH image", us::Any(), false);
+ parser.addArgument("output", "o", ctkCommandLineParser::String, "MRtrix SH image", us::Any(), false);
+ parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "spherical harmonics order");
+
+ map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
+ if (parsedArgs.size()==0)
+ return EXIT_FAILURE;
+
+ int shOrder = -1;
+ if (parsedArgs.count("shOrder"))
+ shOrder = us::any_cast<int>(parsedArgs["shOrder"]);
+
+ switch (shOrder)
+ {
+ case 4:
+ return StartShConversion<4>(argc, argv);
+ case 6:
+ return StartShConversion<6>(argc, argv);
+ case 8:
+ return StartShConversion<8>(argc, argv);
+ case 10:
+ return StartShConversion<10>(argc, argv);
+ case 12:
+ return StartShConversion<12>(argc, argv);
+ }
+ return EXIT_FAILURE;
+}
+RegisterDiffusionMiniApp(ExportShImage);
diff --git a/Modules/DiffusionImaging/MiniApps/FiberFoxProcessing.cpp b/Modules/DiffusionImaging/MiniApps/FiberFoxProcessing.cpp
index 48464741b2..f202e2f69b 100755
--- a/Modules/DiffusionImaging/MiniApps/FiberFoxProcessing.cpp
+++ b/Modules/DiffusionImaging/MiniApps/FiberFoxProcessing.cpp
@@ -1,550 +1,547 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <mitkImageCast.h>
#include <mitkDiffusionImage.h>
#include <mitkBaseDataIOFactory.h>
#include <mitkDiffusionCoreObjectFactory.h>
#include <mitkFiberTrackingObjectFactory.h>
#include <mitkIOUtil.h>
#include <mitkNrrdDiffusionImageWriter.h>
#include <mitkFiberBundleX.h>
//#include "ctkCommandLineParser.h"
#include "ctkCommandLineParser.h"
#include <mitkRicianNoiseModel.h>
#include <itkAddArtifactsToDwiImageFilter.h>
#include <itkTractsToDWIImageFilter.h>
#include "boost/property_tree/ptree.hpp"
#include "boost/property_tree/xml_parser.hpp"
#include "boost/foreach.hpp"
#include <mitkStickModel.h>
#include <mitkTensorModel.h>
#include <mitkAstroStickModel.h>
#include <mitkBallModel.h>
#include <mitkDotModel.h>
using namespace mitk;
struct ImageParameters {
itk::ImageRegion<3> imageRegion;
itk::Vector<double,3> imageSpacing;
itk::Point<double,3> imageOrigin;
itk::Matrix<double, 3, 3> imageDirection;
unsigned int numGradients;
double b_value;
unsigned int repetitions;
double signalScale;
double tEcho;
double tLine;
double tInhom;
double axonRadius;
unsigned int interpolationShrink;
double kspaceLineOffset;
double upsampling;
double eddyStrength;
double comp3Weight;
double comp4Weight;
int spikes;
double spikeAmplitude;
bool doSimulateRelaxation;
bool doSimulateEddyCurrents;
bool doDisablePartialVolume;
mitk::RicianNoiseModel<double> ricianNoiseModel;
mitk::DiffusionSignalModel<double>::GradientListType gradientDirections;
itk::TractsToDWIImageFilter< short >::DiffusionModelList fiberModelList, nonFiberModelList;
- itk::TractsToDWIImageFilter< short >::KspaceArtifactList artifactList;
std::string signalModelString, artifactModelString;
itk::Image<double, 3>::Pointer frequencyMap;
itk::Image<unsigned char, 3>::Pointer tissueMaskImage;
mitk::DataNode::Pointer resultNode;
};
void LoadParameters(const std::string & filename,
ImageParameters & m_ImageGenParameters,
mitk::Image::Pointer m_fImage,
mitk::Image::Pointer m_maskImage,
mitk::StickModel<double> * m_StickModel1,
mitk::StickModel<double> * m_StickModel2,
mitk::TensorModel<double> * m_ZeppelinModel1,
mitk::TensorModel<double> * m_ZeppelinModel2,
mitk::TensorModel<double> * m_TensorModel1,
mitk::TensorModel<double> * m_TensorModel2,
// extra axonal compartment models
mitk::BallModel<double> * m_BallModel1,
mitk::BallModel<double> * m_BallModel2,
mitk::AstroStickModel<double> * m_AstrosticksModel1,
mitk::AstroStickModel<double> * m_AstrosticksModel2,
mitk::DotModel<double> * m_DotModel1,
mitk::DotModel<double> * m_DotModel2)
{
MITK_INFO << "Initialize Diffusion Models";
boost::property_tree::ptree parameters;
boost::property_tree::xml_parser::read_xml(filename, parameters);
- m_ImageGenParameters.artifactList.clear();
m_ImageGenParameters.nonFiberModelList.clear();
m_ImageGenParameters.fiberModelList.clear();
m_ImageGenParameters.signalModelString = "";
m_ImageGenParameters.artifactModelString = "";
m_ImageGenParameters.resultNode = mitk::DataNode::New();
//m_ImageGenParameters.tissueMaskImage = NULL;
//m_ImageGenParameters.frequencyMap = NULL;
//m_ImageGenParameters.gradientDirections.clear();
m_ImageGenParameters.spikes = 0;
m_ImageGenParameters.spikeAmplitude = 1;
MITK_INFO << "reset params";
BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") )
{
if( v1.first == "image" )
{
MITK_INFO << "Load image params";
m_ImageGenParameters.tEcho = v1.second.get<double>("tEcho");
m_ImageGenParameters.tLine = v1.second.get<double>("tLine");
m_ImageGenParameters.doSimulateEddyCurrents = v1.second.get<bool>("artifacts.addeddy");
m_ImageGenParameters.eddyStrength = 0;
if (m_ImageGenParameters.doSimulateEddyCurrents)
{
m_ImageGenParameters.eddyStrength = v1.second.get<double>("artifacts.eddyStrength");
}
// signal relaxation
m_ImageGenParameters.doSimulateRelaxation = v1.second.get<bool>("doSimulateRelaxation");
if (m_ImageGenParameters.doSimulateRelaxation)
// N/2 ghosts
if (v1.second.get<bool>("artifacts.addghost"))
{
m_ImageGenParameters.kspaceLineOffset = v1.second.get<double>("artifacts.kspaceLineOffset");
}
else
{
m_ImageGenParameters.kspaceLineOffset = 0;
}
if (v1.second.get<bool>("artifacts.addspikes"))
{
m_ImageGenParameters.spikes = v1.second.get<int>("artifacts.spikesnum");
m_ImageGenParameters.spikeAmplitude = v1.second.get<double>("artifacts.spikesscale");
}
// add distortions
if (v1.second.get<bool>("artifacts.distortions") && m_fImage)
{
itk::Image<double,3>::Pointer itkImg = itk::Image<double,3>::New();
mitk::CastToItkImage< itk::Image<double,3> >(m_fImage, itkImg);
if (m_ImageGenParameters.imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) &&
m_ImageGenParameters.imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) &&
m_ImageGenParameters.imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2))
{
m_ImageGenParameters.frequencyMap = itkImg;
}
}
// rician noise
if (v1.second.get<bool>("artifacts.addnoise"))
m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(v1.second.get<double>("artifacts.noisevariance"));
else
m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(0);
// gibbs ringing
m_ImageGenParameters.upsampling = 1;
if (v1.second.get<bool>("artifacts.addringing"))
m_ImageGenParameters.upsampling = v1.second.get<double>("artifacts.ringingupsampling");
// adjusting line readout time to the adapted image size needed for the DFT
int y = m_ImageGenParameters.imageRegion.GetSize(1);
if ( y%2 == 1 )
y += 1;
if ( y>m_ImageGenParameters.imageRegion.GetSize(1) )
m_ImageGenParameters.tLine *= (double)m_ImageGenParameters.imageRegion.GetSize(1)/y;
// check tissue mask
if (m_maskImage.IsNotNull())
{
m_ImageGenParameters.tissueMaskImage = itk::Image<unsigned char,3>::New();
mitk::CastToItkImage<itk::Image<unsigned char,3> >(m_maskImage.GetPointer(), m_ImageGenParameters.tissueMaskImage);
}
// signal models
m_ImageGenParameters.comp3Weight = 1;
m_ImageGenParameters.comp4Weight = 0;
if (v1.second.get<int>("compartment4.index") > 0)
{
m_ImageGenParameters.comp4Weight = v1.second.get<double>("compartment4.weight");
m_ImageGenParameters.comp3Weight -= m_ImageGenParameters.comp4Weight;
}
// compartment 1
switch(v1.second.get<int>("compartment1.index")){
case 0:
m_StickModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_StickModel1->SetBvalue(m_ImageGenParameters.b_value);
m_StickModel1->SetDiffusivity(v1.second.get<double>("compartment1.stick.d"));
m_StickModel1->SetT2(v1.second.get<double>("compartment1.stick.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_StickModel1);
break;
case 1:
m_ZeppelinModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_ZeppelinModel1->SetBvalue(m_ImageGenParameters.b_value);
m_ZeppelinModel1->SetDiffusivity1(v1.second.get<double>("compartment1.zeppelin.d1"));
m_ZeppelinModel1->SetDiffusivity2(v1.second.get<double>("compartment1.zeppelin.d2"));
m_ZeppelinModel1->SetDiffusivity3(v1.second.get<double>("compartment1.zeppelin.d2"));
m_ZeppelinModel1->SetT2(v1.second.get<double>("compartment1.zeppelin.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_ZeppelinModel1);
break;
case 2:
m_TensorModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_TensorModel1->SetBvalue(m_ImageGenParameters.b_value);
m_TensorModel1->SetDiffusivity1(v1.second.get<double>("compartment1.tensor.d1"));
m_TensorModel1->SetDiffusivity2(v1.second.get<double>("compartment1.tensor.d2"));
m_TensorModel1->SetDiffusivity3(v1.second.get<double>("compartment1.tensor.d3"));
m_TensorModel1->SetT2(v1.second.get<double>("compartment1.tensor.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_TensorModel1);
break;
}
// compartment 2
switch(v1.second.get<int>("compartment2.index")){
case 0:
m_StickModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_StickModel2->SetBvalue(m_ImageGenParameters.b_value);
m_StickModel2->SetDiffusivity(v1.second.get<double>("compartment2.stick.d"));
m_StickModel2->SetT2(v1.second.get<double>("compartment2.stick.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_StickModel2);
break;
case 1:
m_ZeppelinModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_ZeppelinModel2->SetBvalue(m_ImageGenParameters.b_value);
m_ZeppelinModel2->SetDiffusivity1(v1.second.get<double>("compartment2.zeppelin.d1"));
m_ZeppelinModel2->SetDiffusivity2(v1.second.get<double>("compartment2.zeppelin.d2"));
m_ZeppelinModel2->SetDiffusivity3(v1.second.get<double>("compartment2.zeppelin.d2"));
m_ZeppelinModel2->SetT2(v1.second.get<double>("compartment2.zeppelin.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_ZeppelinModel2);
break;
case 2:
m_TensorModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_TensorModel2->SetBvalue(m_ImageGenParameters.b_value);
m_TensorModel2->SetDiffusivity1(v1.second.get<double>("compartment2.tensor.d1"));
m_TensorModel2->SetDiffusivity2(v1.second.get<double>("compartment2.tensor.d2"));
m_TensorModel2->SetDiffusivity3(v1.second.get<double>("compartment2.tensor.d3"));
m_TensorModel2->SetT2(v1.second.get<double>("compartment2.tensor.t2"));
m_ImageGenParameters.fiberModelList.push_back(m_TensorModel2);
break;
}
// compartment 3
switch(v1.second.get<int>("compartment3.index")){
case 0:
m_BallModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_BallModel1->SetBvalue(m_ImageGenParameters.b_value);
m_BallModel1->SetDiffusivity(v1.second.get<double>("compartment3.ball.d"));
m_BallModel1->SetT2(v1.second.get<double>("compartment3.ball.t2"));
m_BallModel1->SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_BallModel1);
break;
case 1:
m_AstrosticksModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_AstrosticksModel1->SetBvalue(m_ImageGenParameters.b_value);
m_AstrosticksModel1->SetDiffusivity(v1.second.get<double>("compartment3.astrosticks.d"));
m_AstrosticksModel1->SetT2(v1.second.get<double>("compartment3.astrosticks.t2"));
m_AstrosticksModel1->SetRandomizeSticks(v1.second.get<bool>("compartment3.astrosticks.randomize"));
m_AstrosticksModel1->SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_AstrosticksModel1);
break;
case 2:
m_DotModel1->SetGradientList(m_ImageGenParameters.gradientDirections);
m_DotModel1->SetT2(v1.second.get<double>("compartment3.dot.t2"));
m_DotModel1->SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_DotModel1);
break;
}
// compartment 4
switch(v1.second.get<int>("compartment4.index")){
case 0:
m_BallModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_BallModel2->SetBvalue(m_ImageGenParameters.b_value);
m_BallModel2->SetDiffusivity(v1.second.get<double>("compartment4.ball.d"));
m_BallModel2->SetT2(v1.second.get<double>("compartment4.ball.t2"));
m_BallModel2->SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_BallModel2);
break;
case 1:
m_AstrosticksModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_AstrosticksModel2->SetBvalue(m_ImageGenParameters.b_value);
m_AstrosticksModel2->SetDiffusivity(v1.second.get<double>("compartment4.astrosticks.d"));
m_AstrosticksModel2->SetT2(v1.second.get<double>("compartment4.astrosticks.t2"));
m_AstrosticksModel2->SetRandomizeSticks(v1.second.get<bool>("compartment4.astrosticks.randomize"));
m_AstrosticksModel2->SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_AstrosticksModel2);
break;
case 2:
m_DotModel2->SetGradientList(m_ImageGenParameters.gradientDirections);
m_DotModel2->SetT2(v1.second.get<double>("compartment4.dot.t2"));
m_DotModel2->SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(m_DotModel2);
break;
}
m_ImageGenParameters.signalScale = v1.second.get<int>("signalScale");
m_ImageGenParameters.repetitions = v1.second.get<int>("repetitions");
m_ImageGenParameters.tInhom = v1.second.get<double>("tInhom");
m_ImageGenParameters.doDisablePartialVolume = v1.second.get<bool>("doDisablePartialVolume");
m_ImageGenParameters.interpolationShrink = v1.second.get<int>("interpolationShrink");
m_ImageGenParameters.axonRadius = v1.second.get<double>("axonRadius");
}
/*
m_Controls->m_VarianceBox->setValue(v1.second.get<double>("variance"));
m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get<bool>("showadvanced"));
m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get<bool>("showadvanced"));
m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get<bool>("outputvolumefractions"));
m_Controls->m_RealTimeFibers->setChecked(v1.second.get<bool>("realtime"));
m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get<int>("distribution"));
m_Controls->m_FiberDensityBox->setValue(v1.second.get<int>("density"));
m_Controls->m_IncludeFiducials->setChecked(v1.second.get<bool>("includeFiducials"));
m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get<bool>("constantradius"));
BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second )
{
if( v2.first == "spline" )
{
m_Controls->m_FiberSamplingBox->setValue(v2.second.get<double>("sampling"));
m_Controls->m_TensionBox->setValue(v2.second.get<double>("tension"));
m_Controls->m_ContinuityBox->setValue(v2.second.get<double>("continuity"));
m_Controls->m_BiasBox->setValue(v2.second.get<double>("bias"));
}
if( v2.first == "rotation" )
{
m_Controls->m_XrotBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YrotBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZrotBox->setValue(v2.second.get<double>("z"));
}
if( v2.first == "translation" )
{
m_Controls->m_XtransBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YtransBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZtransBox->setValue(v2.second.get<double>("z"));
}
if( v2.first == "scale" )
{
m_Controls->m_XscaleBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YscaleBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZscaleBox->setValue(v2.second.get<double>("z"));
}
}
}
if( v1.first == "image" )
{
m_Controls->m_SizeX->setValue(v1.second.get<int>("basic.size.x"));
m_Controls->m_SizeY->setValue(v1.second.get<int>("basic.size.y"));
m_Controls->m_SizeZ->setValue(v1.second.get<int>("basic.size.z"));
m_Controls->m_SpacingX->setValue(v1.second.get<double>("basic.spacing.x"));
m_Controls->m_SpacingY->setValue(v1.second.get<double>("basic.spacing.y"));
m_Controls->m_SpacingZ->setValue(v1.second.get<double>("basic.spacing.z"));
m_Controls->m_NumGradientsBox->setValue(v1.second.get<int>("basic.numgradients"));
m_Controls->m_BvalueBox->setValue(v1.second.get<int>("basic.bvalue"));
*/
}
}
int FiberFoxProcessing(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("in", "i", ctkCommandLineParser::String, "input file", us::Any(), false);
parser.addArgument("out", "o", ctkCommandLineParser::String, "output file", us::Any(), false);
parser.addArgument("fiberbundle", "f", ctkCommandLineParser::String, "defined fiber bundle for signal generation", us::Any(), false);
parser.addArgument("loadparameters", "l", ctkCommandLineParser::String, "load fiber fox signal parameter file", us::Any(), false);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
// mandatory arguments
string inName = us::any_cast<string>(parsedArgs["in"]);
string outName = us::any_cast<string>(parsedArgs["out"]);
string fbName = us::any_cast<string>(parsedArgs["fiberbundle"]);
string paramName = us::any_cast<string>(parsedArgs["loadparameters"]);
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
ImageParameters m_ImageGenParameters;
mitk::Image::Pointer m_maskImage = 0;
mitk::Image::Pointer m_fImage = 0;
MITK_INFO << "Loading " << inName;
const std::string s1="", s2="";
std::vector<BaseData::Pointer> infile = BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false );
mitk::BaseData::Pointer baseData = infile.at(0);
MITK_INFO << "Loading " << fbName;
std::vector<BaseData::Pointer> infile2 = BaseDataIO::LoadBaseDataFromFile( fbName, s1, s2, false );
mitk::BaseData::Pointer baseData2 = infile2.at(0);
DiffusionImage<short>::Pointer dwi;
FiberBundleX::Pointer fbi;
if ( dynamic_cast<DiffusionImage<short>*>(baseData.GetPointer()) )
dwi = dynamic_cast<DiffusionImage<short>*>(baseData.GetPointer());
else
MITK_ERROR << "LOADING DWI FAILD: " << inName;
if ( dynamic_cast<FiberBundleX*>(baseData2.GetPointer()) )
fbi = dynamic_cast<FiberBundleX*>(baseData2.GetPointer());
else
MITK_ERROR << "LOADING FBI FAILD: " << fbName;
m_ImageGenParameters.imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion();
m_ImageGenParameters.imageSpacing = dwi->GetVectorImage()->GetSpacing();
m_ImageGenParameters.imageOrigin = dwi->GetVectorImage()->GetOrigin();
m_ImageGenParameters.imageDirection = dwi->GetVectorImage()->GetDirection();
m_ImageGenParameters.b_value = dwi->GetB_Value();
mitk::DiffusionImage<short>::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections();
m_ImageGenParameters.numGradients = 0;
for (int i=0; i<dirs->Size(); i++)
{
DiffusionSignalModel<double>::GradientType g;
g[0] = dirs->at(i)[0];
g[1] = dirs->at(i)[1];
g[2] = dirs->at(i)[2];
m_ImageGenParameters.gradientDirections.push_back(g);
if (dirs->at(i).magnitude()>0.0001)
m_ImageGenParameters.numGradients++;
}
mitk::StickModel<double> m_StickModel1;
mitk::StickModel<double> m_StickModel2;
mitk::TensorModel<double> m_ZeppelinModel1;
mitk::TensorModel<double> m_ZeppelinModel2;
mitk::TensorModel<double> m_TensorModel1;
mitk::TensorModel<double> m_TensorModel2;
// extra axonal compartment models
mitk::BallModel<double> m_BallModel1;
mitk::BallModel<double> m_BallModel2;
mitk::AstroStickModel<double> m_AstrosticksModel1;
mitk::AstroStickModel<double> m_AstrosticksModel2;
mitk::DotModel<double> m_DotModel1;
mitk::DotModel<double> m_DotModel2;
LoadParameters(paramName,m_ImageGenParameters,NULL, NULL,
&m_StickModel1,
&m_StickModel2,
&m_ZeppelinModel1,
&m_ZeppelinModel2,
&m_TensorModel1,
&m_TensorModel2,
&m_BallModel1,
&m_BallModel2,
&m_AstrosticksModel1,
&m_AstrosticksModel2,
&m_DotModel1,
&m_DotModel2);
MITK_INFO << "Parameter loaded";
itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
tractsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.doSimulateEddyCurrents);
tractsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.eddyStrength);
//tractsToDwiFilter->SetUpsampling(m_ImageGenParameters.upsampling);
tractsToDwiFilter->SetSimulateRelaxation(m_ImageGenParameters.doSimulateRelaxation);
tractsToDwiFilter->SetImageRegion(m_ImageGenParameters.imageRegion);
tractsToDwiFilter->SetSpacing(m_ImageGenParameters.imageSpacing);
tractsToDwiFilter->SetOrigin(m_ImageGenParameters.imageOrigin);
tractsToDwiFilter->SetDirectionMatrix(m_ImageGenParameters.imageDirection);
tractsToDwiFilter->SetFiberBundle(fbi);
tractsToDwiFilter->SetFiberModels(m_ImageGenParameters.fiberModelList);
tractsToDwiFilter->SetNonFiberModels(m_ImageGenParameters.nonFiberModelList);
tractsToDwiFilter->SetNoiseModel(&m_ImageGenParameters.ricianNoiseModel);
- tractsToDwiFilter->SetKspaceArtifacts(m_ImageGenParameters.artifactList);
tractsToDwiFilter->SetkOffset(m_ImageGenParameters.kspaceLineOffset);
tractsToDwiFilter->SettLine(m_ImageGenParameters.tLine);
tractsToDwiFilter->SettInhom(m_ImageGenParameters.tInhom);
tractsToDwiFilter->SetTE(m_ImageGenParameters.tEcho);
tractsToDwiFilter->SetNumberOfRepetitions(m_ImageGenParameters.repetitions);
tractsToDwiFilter->SetEnforcePureFiberVoxels(m_ImageGenParameters.doDisablePartialVolume);
tractsToDwiFilter->SetInterpolationShrink(m_ImageGenParameters.interpolationShrink);
tractsToDwiFilter->SetFiberRadius(m_ImageGenParameters.axonRadius);
tractsToDwiFilter->SetSignalScale(m_ImageGenParameters.signalScale);
if (m_ImageGenParameters.interpolationShrink>0)
tractsToDwiFilter->SetUseInterpolation(true);
tractsToDwiFilter->SetTissueMask(m_ImageGenParameters.tissueMaskImage);
tractsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.frequencyMap);
tractsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.spikeAmplitude);
tractsToDwiFilter->SetSpikes(m_ImageGenParameters.spikes);
tractsToDwiFilter->Update();
mitk::DiffusionImage<short>::Pointer image = mitk::DiffusionImage<short>::New();
image->SetVectorImage( tractsToDwiFilter->GetOutput() );
image->SetB_Value(dwi->GetB_Value());
image->SetDirections(dwi->GetDirections());
image->InitializeFromVectorImage();
MITK_INFO << "Writing " << outName;
NrrdDiffusionImageWriter<short>::Pointer writer = NrrdDiffusionImageWriter<short>::New();
writer->SetFileName(outName);
writer->SetInput(image);
writer->Update();
}
MITK_INFO << "DONE";
return EXIT_SUCCESS;
}
RegisterDiffusionMiniApp(FiberFoxProcessing);
diff --git a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp
index 6d6129c9f3..8a6e2b1b88 100755
--- a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp
+++ b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp
@@ -1,215 +1,248 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <mitkImageCast.h>
#include <mitkQBallImage.h>
#include <mitkTensorImage.h>
#include <mitkBaseDataIOFactory.h>
#include <mitkDiffusionCoreObjectFactory.h>
#include <mitkFiberTrackingObjectFactory.h>
#include <mitkFiberBundleX.h>
#include <itkGibbsTrackingFilter.h>
#include <itkDiffusionTensor3D.h>
#include <itkShCoefficientImageImporter.h>
#include <mitkImageToItk.h>
#include <mitkIOUtil.h>
#include "ctkCommandLineParser.h"
#include <boost/algorithm/string.hpp>
+#include <itkFlipImageFilter.h>
template<int shOrder>
-typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit)
+typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit, bool noFlip = false)
{
typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
-
+ itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();
typename FilterType::Pointer filter = FilterType::New();
+
+ if (noFlip)
+ {
+ filter->SetInputImage(itkImage);
+ }
+ else
+ {
+ MITK_INFO << "Flipping image";
+ itk::FixedArray<bool, 4> flipAxes;
+ flipAxes[0] = true;
+ flipAxes[1] = true;
+ flipAxes[2] = false;
+ flipAxes[3] = false;
+ itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
+ flipper->SetInput(itkImage);
+ flipper->SetFlipAxes(flipAxes);
+ flipper->Update();
+ itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
+ itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
+ flipped->SetDirection(m);
+
+ itk::Point< float, 4 > o = itkImage->GetOrigin();
+ o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
+ o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
+ flipped->SetOrigin(o);
+ filter->SetInputImage(flipped);
+ }
+
switch (toolkit)
{
case 0:
filter->SetToolkit(FilterType::FSL);
break;
case 1:
filter->SetToolkit(FilterType::MRTRIX);
break;
default:
filter->SetToolkit(FilterType::FSL);
}
- filter->SetInputImage(caster->GetOutput());
filter->GenerateData();
return filter->GetQballImage();
}
int GibbsTracking(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false);
parser.addArgument("parameters", "p", ctkCommandLineParser::String, "parameter file (.gtp)", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::String, "binary mask image");
parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "sh coefficient convention (FSL, MRtrix)", string("FSL"), true);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", us::Any(), false);
+ parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "do not flip input image to match MITK coordinate convention");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
string inFileName = us::any_cast<string>(parsedArgs["input"]);
string paramFileName = us::any_cast<string>(parsedArgs["parameters"]);
string outFileName = us::any_cast<string>(parsedArgs["outFile"]);
+ bool noFlip = false;
+ if (parsedArgs.count("noFlip"))
+ noFlip = us::any_cast<bool>(parsedArgs["noFlip"]);
+
try
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
// instantiate gibbs tracker
typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType;
typedef itk::Image<OdfVectorType,3> ItkQballImageType;
typedef itk::GibbsTrackingFilter<ItkQballImageType> GibbsTrackingFilterType;
GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New();
// load input image
const std::string s1="", s2="";
std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false );
// try to cast to qball image
if( boost::algorithm::ends_with(inFileName, ".qbi") )
{
MITK_INFO << "Loading qball image ...";
mitk::QBallImage::Pointer mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer());
ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New();
mitk::CastToItkImage<ItkQballImageType>(mitkQballImage, itk_qbi);
gibbsTracker->SetQBallImage(itk_qbi.GetPointer());
}
else if( boost::algorithm::ends_with(inFileName, ".dti") )
{
MITK_INFO << "Loading tensor image ...";
typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(infile.at(0).GetPointer());
ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
mitk::CastToItkImage<ItkTensorImage>(mitkTensorImage, itk_dti);
gibbsTracker->SetTensorImage(itk_dti);
}
else if ( boost::algorithm::ends_with(inFileName, ".nii") )
{
MITK_INFO << "Loading sh-coefficient image ...";
mitk::Image::Pointer mitkImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer());
int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3];
int c=3, d=2-2*nrCoeffs;
double D = c*c-4*d;
int shOrder;
if (D>0)
{
shOrder = (-c+sqrt(D))/2.0;
if (shOrder<0)
shOrder = (-c-sqrt(D))/2.0;
}
else if (D==0)
shOrder = -c/2.0;
MITK_INFO << "using SH-order " << shOrder;
int toolkitConvention = 0;
if (parsedArgs.count("shConvention"))
{
string convention = us::any_cast<string>(parsedArgs["shConvention"]).c_str();
if ( boost::algorithm::equals(convention, "MRtrix") )
{
toolkitConvention = 1;
MITK_INFO << "Using MRtrix style sh-coefficient convention";
}
else
MITK_INFO << "Using FSL style sh-coefficient convention";
}
else
MITK_INFO << "Using FSL style sh-coefficient convention";
switch (shOrder)
{
case 4:
- gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention));
+ gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention, noFlip));
break;
case 6:
- gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention));
+ gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention, noFlip));
break;
case 8:
- gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention));
+ gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention, noFlip));
break;
case 10:
- gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention));
+ gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention, noFlip));
break;
case 12:
- gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention));
+ gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention, noFlip));
break;
default:
MITK_INFO << "SH-order " << shOrder << " not supported";
}
}
else
return EXIT_FAILURE;
// global tracking
if (parsedArgs.count("mask"))
{
typedef itk::Image<float,3> MaskImgType;
mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["mask"]));
MaskImgType::Pointer itk_mask = MaskImgType::New();
mitk::CastToItkImage<MaskImgType>(mitkMaskImage, itk_mask);
gibbsTracker->SetMaskImage(itk_mask);
}
gibbsTracker->SetDuplicateImage(false);
gibbsTracker->SetLoadParameterFile( paramFileName );
// gibbsTracker->SetLutPath( "" );
gibbsTracker->Update();
mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle());
mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters();
for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it)
{
if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) {
(*it)->SetFileName( outFileName.c_str() );
(*it)->DoWrite( mitkFiberBundle.GetPointer() );
}
}
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
RegisterDiffusionMiniApp(GibbsTracking);
diff --git a/Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp
similarity index 59%
rename from Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp
rename to Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp
index 294bb67ea9..e444ed3349 100755
--- a/Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp
+++ b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp
@@ -1,263 +1,302 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <mitkBaseDataIOFactory.h>
#include <mitkBaseData.h>
#include <mitkImageCast.h>
#include <mitkImageToItk.h>
#include <mitkDiffusionCoreObjectFactory.h>
#include <mitkFiberTrackingObjectFactory.h>
#include <itkEvaluateDirectionImagesFilter.h>
#include <metaCommand.h>
#include "ctkCommandLineParser.h"
#include <itkTractsToVectorImageFilter.h>
#include <usAny.h>
#include <itkImageFileWriter.h>
#include <mitkIOUtil.h>
#include <boost/lexical_cast.hpp>
#include <iostream>
#include <fstream>
+#include <itksys/SystemTools.hxx>
#define _USE_MATH_DEFINES
#include <math.h>
-int TractometerAngularErrorTool(int argc, char* argv[])
+int LocalDirectionalFiberPlausibility(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", us::Any(), false);
parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", us::Any(), false);
parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", us::Any(), false);
- parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image");
+ parser.addArgument("mask", "m", ctkCommandLineParser::StringList, "mask images");
parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true);
parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results");
parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "don't increase error for missing or too many directions");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
ctkCommandLineParser::StringContainerType referenceImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
+ ctkCommandLineParser::StringContainerType maskImages;
+ if (parsedArgs.count("mask"))
+ maskImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["mask"]);
string fibFile = us::any_cast<string>(parsedArgs["input"]);
- string maskImage("");
- if (parsedArgs.count("mask"))
- maskImage = us::any_cast<string>(parsedArgs["mask"]);
-
float angularThreshold = 25;
if (parsedArgs.count("athresh"))
angularThreshold = us::any_cast<float>(parsedArgs["athresh"]);
string outRoot = us::any_cast<string>(parsedArgs["out"]);
bool verbose = false;
if (parsedArgs.count("verbose"))
verbose = us::any_cast<bool>(parsedArgs["verbose"]);
bool ignore = false;
if (parsedArgs.count("ignore"))
ignore = us::any_cast<bool>(parsedArgs["ignore"]);
try
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType;
typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType;
typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType;
// load fiber bundle
mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
// load reference directions
ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
for (int i=0; i<referenceImages.size(); i++)
{
try
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData());
typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput();
referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg);
}
catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); }
}
- // load/create mask image
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
- if (maskImage.compare("")==0)
- {
- ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
- itkMaskImage->SetSpacing( dirImg->GetSpacing() );
- itkMaskImage->SetOrigin( dirImg->GetOrigin() );
- itkMaskImage->SetDirection( dirImg->GetDirection() );
- itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
- itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
- itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
- itkMaskImage->Allocate();
- itkMaskImage->FillBuffer(1);
- }
- else
- {
- mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(maskImage)->GetData());
- mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMaskImage);
- }
-
+ ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0);
+ itkMaskImage->SetSpacing( dirImg->GetSpacing() );
+ itkMaskImage->SetOrigin( dirImg->GetOrigin() );
+ itkMaskImage->SetDirection( dirImg->GetDirection() );
+ itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() );
+ itkMaskImage->Allocate();
+ itkMaskImage->FillBuffer(1);
// extract directions from fiber bundle
itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
fOdfFilter->SetFiberBundle(inputTractogram);
fOdfFilter->SetMaskImage(itkMaskImage);
fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180));
fOdfFilter->SetNormalizeVectors(true);
fOdfFilter->SetUseWorkingCopy(false);
fOdfFilter->Update();
ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer();
if (verbose)
{
// write vector field
mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle();
mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters();
for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it)
{
if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) {
string outfilename = outRoot;
outfilename.append("_VECTOR_FIELD.fib");
(*it)->SetFileName( outfilename.c_str() );
(*it)->DoWrite( directions.GetPointer() );
}
}
// write direction images
for (int i=0; i<directionImageContainer->Size(); i++)
{
itk::TractsToVectorImageFilter<float>::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i);
typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter<float>::ItkDirectionImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_DIRECTION_");
outfilename.append(boost::lexical_cast<string>(i));
outfilename.append(".nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(itkImg);
writer->Update();
}
// write num direction image
{
ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage();
typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outfilename = outRoot;
outfilename.append("_NUM_DIRECTIONS.nrrd");
MITK_INFO << "writing " << outfilename;
writer->SetFileName(outfilename.c_str());
writer->SetInput(numDirImage);
writer->Update();
}
}
- // evaluate directions
- EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
- evaluationFilter->SetImageSet(directionImageContainer);
- evaluationFilter->SetReferenceImageSet(referenceImageContainer);
- evaluationFilter->SetMaskImage(itkMaskImage);
- evaluationFilter->SetIgnoreMissingDirections(ignore);
- evaluationFilter->Update();
+ string logFile = outRoot;
+ logFile.append("_ANGULAR_ERROR.csv");
+ ofstream file;
+ file.open (logFile.c_str());
- if (verbose)
+ if (maskImages.size()>0)
{
- EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
- typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
- WriterType::Pointer writer = WriterType::New();
+ for (int i=0; i<maskImages.size(); i++)
+ {
+ mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(maskImages.at(i))->GetData());
+ mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMaskImage);
+
+ // evaluate directions
+ EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
+ evaluationFilter->SetImageSet(directionImageContainer);
+ evaluationFilter->SetReferenceImageSet(referenceImageContainer);
+ evaluationFilter->SetMaskImage(itkMaskImage);
+ evaluationFilter->SetIgnoreMissingDirections(ignore);
+ evaluationFilter->Update();
+
+ if (verbose)
+ {
+ EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
+ typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
+ WriterType::Pointer writer = WriterType::New();
+
+ string outfilename = outRoot;
+ outfilename.append("_ERROR_IMAGE.nrrd");
+
+ MITK_INFO << "writing " << outfilename;
+ writer->SetFileName(outfilename.c_str());
+ writer->SetInput(angularErrorImage);
+ writer->Update();
+ }
+
+ string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile));
+ sens.append(",");
- string outfilename = outRoot;
- outfilename.append("_ERROR_IMAGE.nrrd");
+ sens.append(itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(maskImages.at(i))));
+ sens.append(",");
- MITK_INFO << "writing " << outfilename;
- writer->SetFileName(outfilename.c_str());
- writer->SetInput(angularErrorImage);
- writer->Update();
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
+ sens.append(",");
+
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
+ sens.append(",");
+
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
+ sens.append(",");
+
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
+ sens.append(",");
+
+ sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
+ sens.append(";\n");
+ file << sens;
+ }
}
+ else
+ {
+ // evaluate directions
+ EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
+ evaluationFilter->SetImageSet(directionImageContainer);
+ evaluationFilter->SetReferenceImageSet(referenceImageContainer);
+ evaluationFilter->SetMaskImage(itkMaskImage);
+ evaluationFilter->SetIgnoreMissingDirections(ignore);
+ evaluationFilter->Update();
+
+ if (verbose)
+ {
+ EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
+ typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
+ WriterType::Pointer writer = WriterType::New();
- string logFile = outRoot;
- logFile.append("_ANGULAR_ERROR.csv");
+ string outfilename = outRoot;
+ outfilename.append("_ERROR_IMAGE.nrrd");
- ofstream file;
- file.open (logFile.c_str());
+ MITK_INFO << "writing " << outfilename;
+ writer->SetFileName(outfilename.c_str());
+ writer->SetInput(angularErrorImage);
+ writer->Update();
+ }
- string sens = "Mean:";
- sens.append(",");
- sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
- sens.append(";\n");
+ string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile));
+ sens.append(",");
- sens.append("Median:");
- sens.append(",");
- sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
- sens.append(";\n");
+ sens.append("FULL");
+ sens.append(",");
- sens.append("Maximum:");
- sens.append(",");
- sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
- sens.append(";\n");
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMeanAngularError()));
+ sens.append(",");
- sens.append("Minimum:");
- sens.append(",");
- sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
- sens.append(";\n");
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMedianAngularError()));
+ sens.append(",");
- sens.append("STDEV:");
- sens.append(",");
- sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
- sens.append(";\n");
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMaxAngularError()));
+ sens.append(",");
- file << sens;
+ sens.append(boost::lexical_cast<string>(evaluationFilter->GetMinAngularError()));
+ sens.append(",");
+ sens.append(boost::lexical_cast<string>(std::sqrt(evaluationFilter->GetVarAngularError())));
+ sens.append(";\n");
+ file << sens;
+ }
file.close();
MITK_INFO << "DONE";
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
-RegisterDiffusionMiniApp(TractometerAngularErrorTool);
+RegisterDiffusionMiniApp(LocalDirectionalFiberPlausibility);
diff --git a/Modules/DiffusionImaging/MiniApps/MiniAppManager.cpp b/Modules/DiffusionImaging/MiniApps/MiniAppManager.cpp
index 77e6724914..c78d95d9d7 100755
--- a/Modules/DiffusionImaging/MiniApps/MiniAppManager.cpp
+++ b/Modules/DiffusionImaging/MiniApps/MiniAppManager.cpp
@@ -1,93 +1,96 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <itkMultiThreader.h>
MiniAppManager* MiniAppManager::GetInstance()
{
static MiniAppManager instance;
return &instance;
}
// Attention: Name of the miniApp must be the last argument!!!
// it will be cut off from the rest of the arguments and then
// the app will be run
int MiniAppManager::RunMiniApp(int argc, char* argv[])
{
- itk::MultiThreader::SetGlobalDefaultNumberOfThreads(itk::MultiThreader::GetGlobalMaximumNumberOfThreads());
+ int threadNum = itk::MultiThreader::GetGlobalMaximumNumberOfThreads();
+ if (threadNum>12)
+ threadNum = 12;
+ itk::MultiThreader::SetGlobalDefaultNumberOfThreads(threadNum);
try
{
std::string nameOfMiniApp;
std::map< std::string, MiniAppFunction >::iterator it = m_Functions.begin();
if( argc < 2)
{
std::cout << "Please choose the mini app to execute: " << std::endl;
for(int i=0; it != m_Functions.end(); ++i,++it)
{
std::cout << "(" << i << ")" << " " << it->first << std::endl;
}
std::cout << "Please select: ";
int choose;
std::cin >> choose;
it = m_Functions.begin();
std::advance(it, choose);
if( it != m_Functions.end() )
nameOfMiniApp = it->first;
}
else
{
nameOfMiniApp = argv[1];
//--argc;
}
it = m_Functions.find(nameOfMiniApp);
if(it == m_Functions.end())
{
std::ostringstream s; s << "MiniApp (" << nameOfMiniApp << ") not found!";
throw std::invalid_argument(s.str().c_str());
}
MITK_INFO << "Start " << nameOfMiniApp << " ..";
MiniAppFunction func = it->second;
return func( argc, argv );
}
catch(std::exception& e)
{
MITK_ERROR << e.what();
}
catch(...)
{
MITK_ERROR << "Unknown error occurred";
}
return EXIT_FAILURE;
}
/////////////////////
// MiniAppFunction //
/////////////////////
MiniAppManager::MiniAppFunction
MiniAppManager::AddFunction(const std::string& name, MiniAppFunction func)
{
m_Functions.insert( std::pair<std::string, MiniAppFunction>(name, func) );
return func;
}
diff --git a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp
index 9201e7f0b0..ca72cc996a 100755
--- a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp
+++ b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp
@@ -1,379 +1,378 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <itkImageFileWriter.h>
#include <itkResampleImageFilter.h>
#include <itkFiniteDiffOdfMaximaExtractionFilter.h>
#include <mitkBaseDataIOFactory.h>
#include <mitkDiffusionImage.h>
#include <mitkQBallImage.h>
#include <mitkImageCast.h>
#include <mitkImageToItk.h>
#include <mitkTensorImage.h>
#include <mitkDiffusionCoreObjectFactory.h>
-#include <mitkCoreExtObjectFactory.h>
#include <mitkCoreObjectFactory.h>
#include "ctkCommandLineParser.h"
#include <mitkFiberBundleXWriter.h>
#include <itkShCoefficientImageImporter.h>
#include <mitkNrrdQBallImageWriter.h>
#include <itkFlipImageFilter.h>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
mitk::Image::Pointer LoadData(std::string filename)
{
if( filename.empty() )
return NULL;
const std::string s1="", s2="";
std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false );
if( infile.empty() )
{
MITK_INFO << "File " << filename << " could not be read!";
return NULL;
}
mitk::BaseData::Pointer baseData = infile.at(0);
return dynamic_cast<mitk::Image*>(baseData.GetPointer());
}
template<int shOrder>
-int Start(int argc, char* argv[])
+int StartPeakExtraction(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("image", "i", ctkCommandLineParser::String, "sh coefficient image", us::Any(), false);
parser.addArgument("outroot", "o", ctkCommandLineParser::String, "output root", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image");
parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "0=no norm, 1=max norm, 2=single vec norm", 1, true);
parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "maximum number of extracted peaks", 2, true);
parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "peak threshold relative to largest peak", 0.4, true);
parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "absolute peak threshold weighted with local GFA value", 0.06, true);
parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true);
parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "do not flip input image to match MITK coordinate convention");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
// mandatory arguments
string imageName = us::any_cast<string>(parsedArgs["image"]);
string outRoot = us::any_cast<string>(parsedArgs["outroot"]);
// optional arguments
string maskImageName("");
if (parsedArgs.count("mask"))
maskImageName = us::any_cast<string>(parsedArgs["mask"]);
int normalization = 1;
if (parsedArgs.count("normalization"))
normalization = us::any_cast<int>(parsedArgs["normalization"]);
int numPeaks = 2;
if (parsedArgs.count("numpeaks"))
numPeaks = us::any_cast<int>(parsedArgs["numpeaks"]);
float peakThres = 0.4;
if (parsedArgs.count("peakthres"))
peakThres = us::any_cast<float>(parsedArgs["peakthres"]);
float absPeakThres = 0.06;
if (parsedArgs.count("abspeakthres"))
absPeakThres = us::any_cast<float>(parsedArgs["abspeakthres"]);
bool noFlip = false;
if (parsedArgs.count("noFlip"))
noFlip = us::any_cast<bool>(parsedArgs["noFlip"]);
MITK_INFO << "image: " << imageName;
MITK_INFO << "outroot: " << outRoot;
if (!maskImageName.empty())
MITK_INFO << "mask: " << maskImageName;
else
MITK_INFO << "no mask image selected";
MITK_INFO << "numpeaks: " << numPeaks;
MITK_INFO << "peakthres: " << peakThres;
MITK_INFO << "abspeakthres: " << absPeakThres;
MITK_INFO << "shOrder: " << shOrder;
try
{
mitk::CoreObjectFactory::GetInstance();
RegisterDiffusionCoreObjectFactory();
mitk::Image::Pointer image = LoadData(imageName);
mitk::Image::Pointer mask = LoadData(maskImageName);
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType;
typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
int toolkitConvention = 0;
if (parsedArgs.count("shConvention"))
{
string convention = us::any_cast<string>(parsedArgs["shConvention"]).c_str();
if ( boost::algorithm::equals(convention, "FSL") )
{
toolkitConvention = 1;
MITK_INFO << "Using FSL SH-basis";
}
else if ( boost::algorithm::equals(convention, "MRtrix") )
{
toolkitConvention = 2;
MITK_INFO << "Using MRtrix SH-basis";
}
else
MITK_INFO << "Using MITK SH-basis";
}
else
MITK_INFO << "Using MITK SH-basis";
ItkUcharImgType::Pointer itkMaskImage = NULL;
if (mask.IsNotNull())
{
try{
itkMaskImage = ItkUcharImgType::New();
mitk::CastToItkImage<ItkUcharImgType>(mask, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
catch(...)
{
}
}
if (toolkitConvention>0)
{
MITK_INFO << "Converting coefficient image to MITK format";
typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(image);
caster->Update();
itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();
typename ConverterType::Pointer converter = ConverterType::New();
if (noFlip)
{
converter->SetInputImage(itkImage);
}
else
{
MITK_INFO << "Flipping image";
itk::FixedArray<bool, 4> flipAxes;
flipAxes[0] = true;
flipAxes[1] = true;
flipAxes[2] = false;
flipAxes[3] = false;
itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
flipper->SetInput(itkImage);
flipper->SetFlipAxes(flipAxes);
flipper->Update();
itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
flipped->SetDirection(m);
itk::Point< float, 4 > o = itkImage->GetOrigin();
o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
flipped->SetOrigin(o);
converter->SetInputImage(flipped);
}
MITK_INFO << "Starting conversion";
switch (toolkitConvention)
{
case 1:
converter->SetToolkit(ConverterType::FSL);
filter->SetToolkit(MaximaExtractionFilterType::FSL);
break;
case 2:
converter->SetToolkit(ConverterType::MRTRIX);
filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
break;
default:
converter->SetToolkit(ConverterType::FSL);
filter->SetToolkit(MaximaExtractionFilterType::FSL);
break;
}
converter->GenerateData();
filter->SetInput(converter->GetCoefficientImage());
}
else
{
try{
typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
typename CasterType::Pointer caster = CasterType::New();
caster->SetInput(image);
caster->Update();
filter->SetInput(caster->GetOutput());
}
catch(...)
{
MITK_INFO << "wrong image type";
return EXIT_FAILURE;
}
}
filter->SetMaxNumPeaks(numPeaks);
filter->SetPeakThreshold(peakThres);
filter->SetAbsolutePeakThreshold(absPeakThres);
filter->SetAngularThreshold(1);
switch (normalization)
{
case 0:
filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
break;
case 1:
filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
break;
case 2:
filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
break;
}
MITK_INFO << "Starting extraction";
filter->Update();
// write direction images
{
typedef typename MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
typename ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
typename MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
if (itkMaskImage.IsNotNull())
{
itkImg->SetDirection(itkMaskImage->GetDirection());
itkImg->SetOrigin(itkMaskImage->GetOrigin());
}
string outfilename = outRoot;
outfilename.append("_DIRECTION_");
outfilename.append(boost::lexical_cast<string>(i));
outfilename.append(".nrrd");
MITK_INFO << "writing " << outfilename;
typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::ItkDirectionImage > WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outfilename);
writer->SetInput(itkImg);
writer->Update();
}
}
// write num directions image
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
if (itkMaskImage.IsNotNull())
{
numDirImage->SetDirection(itkMaskImage->GetDirection());
numDirImage->SetOrigin(itkMaskImage->GetOrigin());
}
string outfilename = outRoot.c_str();
outfilename.append("_NUM_DIRECTIONS.nrrd");
MITK_INFO << "writing " << outfilename;
typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outfilename);
writer->SetInput(numDirImage);
writer->Update();
}
// write vector field
{
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
string outfilename = outRoot.c_str();
outfilename.append("_VECTOR_FIELD.fib");
mitk::FiberBundleXWriter::Pointer fibWriter = mitk::FiberBundleXWriter::New();
fibWriter->SetFileName(outfilename.c_str());
fibWriter->DoWrite(directions.GetPointer());
}
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
MITK_INFO << "DONE";
return EXIT_SUCCESS;
}
int PeakExtraction(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("image", "i", ctkCommandLineParser::String, "sh coefficient image", us::Any(), false);
parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "spherical harmonics order");
parser.addArgument("outroot", "o", ctkCommandLineParser::String, "output root", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image");
parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "0=no norm, 1=max norm, 2=single vec norm", 1, true);
parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "maximum number of extracted peaks", 2, true);
parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "peak threshold relative to largest peak", 0.4, true);
parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "absolute peak threshold weighted with local GFA value", 0.06, true);
parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true);
parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "do not flip input image to match MITK coordinate convention");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
int shOrder = -1;
if (parsedArgs.count("shOrder"))
shOrder = us::any_cast<int>(parsedArgs["shOrder"]);
switch (shOrder)
{
case 4:
- return Start<4>(argc, argv);
+ return StartPeakExtraction<4>(argc, argv);
case 6:
- return Start<6>(argc, argv);
+ return StartPeakExtraction<6>(argc, argv);
case 8:
- return Start<8>(argc, argv);
+ return StartPeakExtraction<8>(argc, argv);
case 10:
- return Start<10>(argc, argv);
+ return StartPeakExtraction<10>(argc, argv);
case 12:
- return Start<12>(argc, argv);
+ return StartPeakExtraction<12>(argc, argv);
}
return EXIT_FAILURE;
}
RegisterDiffusionMiniApp(PeakExtraction);
diff --git a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp
index 98a593cff9..de754ffb21 100644
--- a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp
+++ b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp
@@ -1,234 +1,245 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include "mitkBaseDataIOFactory.h"
#include "mitkDiffusionImage.h"
#include "mitkDiffusionCoreObjectFactory.h"
#include "itkAnalyticalDiffusionQballReconstructionImageFilter.h"
#include <boost/lexical_cast.hpp>
#include <mitkNrrdQBallImageWriter.h>
#include "ctkCommandLineParser.h"
#include <mitkIOUtil.h>
#include <itksys/SystemTools.hxx>
using namespace mitk;
+
/**
* Perform Q-ball reconstruction using a spherical harmonics basis
*/
int QballReconstruction(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output file", us::Any(), false);
parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "spherical harmonics order", 4, true);
parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "baseline image intensity threshold", 0, true);
parser.addArgument("lambda", "r", ctkCommandLineParser::Float, "ragularization factor lambda", 0.006, true);
parser.addArgument("csa", "csa", ctkCommandLineParser::Bool, "use constant solid angle consideration");
parser.addArgument("outputCoeffs", "shc", ctkCommandLineParser::Bool, "output file containing the SH coefficients");
+ parser.addArgument("mrtrix", "mb", ctkCommandLineParser::Bool, "use MRtrix compatible spherical harmonics definition");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
std::string inFileName = us::any_cast<string>(parsedArgs["input"]);
std::string outfilename = us::any_cast<string>(parsedArgs["outFile"]);
- outfilename = itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
+ outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
int threshold = 0;
if (parsedArgs.count("b0Threshold"))
threshold = us::any_cast<int>(parsedArgs["b0Threshold"]);
int shOrder = 4;
if (parsedArgs.count("shOrder"))
shOrder = us::any_cast<int>(parsedArgs["shOrder"]);
float lambda = 0.006;
if (parsedArgs.count("lambda"))
lambda = us::any_cast<float>(parsedArgs["lambda"]);
int normalization = 0;
if (parsedArgs.count("csa") && us::any_cast<bool>(parsedArgs["csa"]))
normalization = 6;
bool outCoeffs = false;
if (parsedArgs.count("outputCoeffs"))
outCoeffs = us::any_cast<bool>(parsedArgs["outputCoeffs"]);
+ bool mrTrix = false;
+ if (parsedArgs.count("mrtrix"))
+ mrTrix = us::any_cast<bool>(parsedArgs["mrtrix"]);
+
try
{
RegisterDiffusionCoreObjectFactory();
MITK_INFO << "Loading image ...";
const std::string s1="", s2="";
std::vector<BaseData::Pointer> infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false );
DiffusionImage<short>::Pointer dwi = dynamic_cast<DiffusionImage<short>*>(infile.at(0).GetPointer());
dwi->AverageRedundantGradients(0.001);
mitk::QBallImage::Pointer image = mitk::QBallImage::New();
mitk::Image::Pointer coeffsImage = mitk::Image::New();
MITK_INFO << "SH order: " << shOrder;
MITK_INFO << "lambda: " << lambda;
MITK_INFO << "B0 threshold: " << threshold;
switch ( shOrder )
{
case 4:
{
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
+ filter->SetUseMrtrixBasis(mrTrix);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
break;
}
case 6:
{
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,6,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
+ filter->SetUseMrtrixBasis(mrTrix);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
break;
}
case 8:
{
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,8,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
+ filter->SetUseMrtrixBasis(mrTrix);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
break;
}
case 10:
{
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,10,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
+ filter->SetUseMrtrixBasis(mrTrix);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
break;
}
case 12:
{
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,12,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
break;
}
default:
{
MITK_INFO << "Supplied SH order not supported. Using default order of 4.";
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold( threshold );
filter->SetLambda(lambda);
+ filter->SetUseMrtrixBasis(mrTrix);
if (normalization==0)
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
else
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
}
}
std::string coeffout = outfilename;
coeffout += "_shcoeffs.nrrd";
outfilename += ".qbi";
MITK_INFO << "writing image " << outfilename;
mitk::NrrdQBallImageWriter::Pointer writer = mitk::NrrdQBallImageWriter::New();
writer->SetInput(image.GetPointer());
writer->SetFileName(outfilename.c_str());
writer->Update();
if (outCoeffs)
mitk::IOUtil::SaveImage(coeffsImage, coeffout);
}
catch ( itk::ExceptionObject &err)
{
MITK_INFO << "Exception: " << err;
}
catch ( std::exception err)
{
MITK_INFO << "Exception: " << err.what();
}
catch ( ... )
{
MITK_INFO << "Exception!";
}
return EXIT_SUCCESS;
}
RegisterDiffusionMiniApp(QballReconstruction);
diff --git a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp
index 376205940d..6bec2facfd 100755
--- a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp
+++ b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp
@@ -1,174 +1,181 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include <mitkImageCast.h>
#include <mitkTensorImage.h>
#include <mitkIOUtil.h>
#include <mitkBaseDataIOFactory.h>
#include <mitkDiffusionCoreObjectFactory.h>
#include <mitkFiberTrackingObjectFactory.h>
#include <mitkFiberBundleX.h>
#include <itkStreamlineTrackingFilter.h>
#include <itkDiffusionTensor3D.h>
#include "ctkCommandLineParser.h"
int StreamlineTracking(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
- parser.addArgument("input", "i", ctkCommandLineParser::String, "input tensor image (.dti)", us::Any(), false);
- parser.addArgument("seed", "si", ctkCommandLineParser::String, "binary seed image");
- parser.addArgument("mask", "mi", ctkCommandLineParser::String, "binary mask image");
+ parser.addArgument("input", "i", ctkCommandLineParser::StringList, "input tensor image (.dti)", us::Any(), false);
+ parser.addArgument("seed", "si", ctkCommandLineParser::String, "binary seed image", us::Any(), true);
+ parser.addArgument("mask", "mi", ctkCommandLineParser::String, "binary mask image", us::Any(), true);
+ parser.addArgument("faImage", "fai", ctkCommandLineParser::String, "FA image", us::Any(), true);
parser.addArgument("minFA", "fa", ctkCommandLineParser::Float, "minimum fractional anisotropy threshold", 0.15, true);
parser.addArgument("minCurv", "c", ctkCommandLineParser::Float, "minimum curvature radius in mm (default = 0.5*minimum-spacing)");
parser.addArgument("stepSize", "s", ctkCommandLineParser::Float, "stepsize in mm (default = 0.1*minimum-spacing)");
parser.addArgument("tendf", "f", ctkCommandLineParser::Float, "Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).", 1.0, true);
parser.addArgument("tendg", "g", ctkCommandLineParser::Float, "Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0, true);
parser.addArgument("numSeeds", "n", ctkCommandLineParser::Int, "Number of seeds per voxel.", 1, true);
parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "minimum fiber length in mm", 20, true);
parser.addArgument("interpolate", "ip", ctkCommandLineParser::Bool, "Use linear interpolation", false, true);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", us::Any(), false);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
- string dtiFileName = us::any_cast<string>(parsedArgs["input"]);
+ ctkCommandLineParser::StringContainerType inputImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["input"]);
+ string dtiFileName;
string outFileName = us::any_cast<string>(parsedArgs["outFile"]);
float minFA = 0.15;
float minCurv = -1;
float stepSize = -1;
float tendf = 1;
float tendg = 0;
float minLength = 20;
int numSeeds = 1;
bool interpolate = false;
if (parsedArgs.count("minCurv"))
minCurv = us::any_cast<float>(parsedArgs["minCurv"]);
if (parsedArgs.count("minFA"))
minFA = us::any_cast<float>(parsedArgs["minFA"]);
if (parsedArgs.count("stepSize"))
stepSize = us::any_cast<float>(parsedArgs["stepSize"]);
if (parsedArgs.count("tendf"))
tendf = us::any_cast<float>(parsedArgs["tendf"]);
if (parsedArgs.count("tendg"))
tendg = us::any_cast<float>(parsedArgs["tendg"]);
if (parsedArgs.count("minLength"))
minLength = us::any_cast<float>(parsedArgs["minLength"]);
if (parsedArgs.count("numSeeds"))
numSeeds = us::any_cast<int>(parsedArgs["numSeeds"]);
if (parsedArgs.count("interpolate"))
interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);
try
{
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
- // load input image
- const std::string s1="", s2="";
- std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( dtiFileName, s1, s2, false );
+ typedef itk::StreamlineTrackingFilter< float > FilterType;
+ FilterType::Pointer filter = FilterType::New();
- MITK_INFO << "Loading tensor image ...";
+ MITK_INFO << "Loading tensor images ...";
typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
- mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(infile.at(0).GetPointer());
- ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
- mitk::CastToItkImage<ItkTensorImage>(mitkTensorImage, itk_dti);
+ dtiFileName = inputImages.at(0);
+ for (int i=0; i<inputImages.size(); i++)
+ {
+ try
+ {
+ mitk::TensorImage::Pointer img = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData());
+ ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
+ mitk::CastToItkImage<ItkTensorImage>(img, itk_dti);
+ filter->SetInput(i, itk_dti);
+ }
+ catch(...){ MITK_INFO << "could not load: " << inputImages.at(i); }
+ }
MITK_INFO << "Loading seed image ...";
typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
mitk::Image::Pointer mitkSeedImage = NULL;
if (parsedArgs.count("seed"))
mitkSeedImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["seed"]));
MITK_INFO << "Loading mask image ...";
mitk::Image::Pointer mitkMaskImage = NULL;
if (parsedArgs.count("mask"))
mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["mask"]));
// instantiate tracker
- typedef itk::StreamlineTrackingFilter< float > FilterType;
- FilterType::Pointer filter = FilterType::New();
- filter->SetInput(itk_dti);
filter->SetSeedsPerVoxel(numSeeds);
filter->SetFaThreshold(minFA);
filter->SetMinCurvatureRadius(minCurv);
filter->SetStepSize(stepSize);
filter->SetF(tendf);
filter->SetG(tendg);
filter->SetInterpolate(interpolate);
filter->SetMinTractLength(minLength);
if (mitkSeedImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(mitkSeedImage, mask);
filter->SetSeedImage(mask);
}
if (mitkMaskImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(mitkMaskImage, mask);
filter->SetMaskImage(mask);
}
filter->Update();
vtkSmartPointer<vtkPolyData> fiberBundle = filter->GetFiberPolyData();
if ( fiberBundle->GetNumberOfLines()==0 )
{
MITK_INFO << "No fibers reconstructed. Check parametrization.";
return EXIT_FAILURE;
}
mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle);
mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters();
for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it)
{
if ( (*it)->CanWriteBaseDataType(fib.GetPointer()) ) {
(*it)->SetFileName( outFileName.c_str() );
(*it)->DoWrite( fib.GetPointer() );
}
}
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
MITK_INFO << "DONE";
return EXIT_SUCCESS;
}
RegisterDiffusionMiniApp(StreamlineTracking);
diff --git a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp
index ac7701e4db..98db98975c 100644
--- a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp
+++ b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp
@@ -1,100 +1,100 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "MiniAppManager.h"
#include "mitkBaseDataIOFactory.h"
#include "mitkDiffusionImage.h"
#include "mitkBaseData.h"
#include "mitkDiffusionCoreObjectFactory.h"
#include <itkDiffusionTensor3DReconstructionImageFilter.h>
#include <itkDiffusionTensor3D.h>
#include <itkImageFileWriter.h>
#include <itkNrrdImageIO.h>
#include "ctkCommandLineParser.h"
#include <itksys/SystemTools.hxx>
using namespace mitk;
/**
* Convert files from one ending to the other
*/
int TensorReconstruction(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output file", us::Any(), false);
parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "baseline image intensity threshold", 0, true);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
std::string inFileName = us::any_cast<string>(parsedArgs["input"]);
std::string outfilename = us::any_cast<string>(parsedArgs["outFile"]);
- outfilename = itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
+ outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
outfilename += ".dti";
int threshold = 0;
if (parsedArgs.count("b0Threshold"))
threshold = us::any_cast<int>(parsedArgs["b0Threshold"]);
try
{
RegisterDiffusionCoreObjectFactory();
MITK_INFO << "Loading image ...";
const std::string s1="", s2="";
std::vector<BaseData::Pointer> infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false );
DiffusionImage<short>::Pointer dwi = dynamic_cast<DiffusionImage<short>*>(infile.at(0).GetPointer());
MITK_INFO << "B0 threshold: " << threshold;
typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetThreshold(threshold);
filter->Update();
// Save tensor image
MITK_INFO << "writing image " << outfilename;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
io->SetFileType( itk::ImageIOBase::Binary );
io->UseCompressionOn();
itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New();
writer->SetInput(filter->GetOutput());
writer->SetFileName(outfilename);
writer->SetImageIO(io);
writer->UseCompressionOn();
writer->Update();
}
catch ( itk::ExceptionObject &err)
{
MITK_INFO << "Exception: " << err;
}
catch ( std::exception err)
{
MITK_INFO << "Exception: " << err.what();
}
catch ( ... )
{
MITK_INFO << "Exception!";
}
return EXIT_SUCCESS;
}
RegisterDiffusionMiniApp(TensorReconstruction);
diff --git a/Modules/DiffusionImaging/MiniApps/files.cmake b/Modules/DiffusionImaging/MiniApps/files.cmake
new file mode 100644
index 0000000000..45b39388e7
--- /dev/null
+++ b/Modules/DiffusionImaging/MiniApps/files.cmake
@@ -0,0 +1,20 @@
+set(CPP_FILES
+ mitkDiffusionMiniApps.cpp
+ MiniAppManager.cpp
+ FileFormatConverter.cpp
+ TensorReconstruction.cpp
+ QballReconstruction.cpp
+ DiffusionIndices.cpp
+ CopyGeometry.cpp
+ GibbsTracking.cpp
+ StreamlineTracking.cpp
+ FiberProcessing.cpp
+ LocalDirectionalFiberPlausibility.cpp
+ #TractogramAngularError.cpp
+ FiberDirectionExtraction.cpp
+ PeakExtraction.cpp
+ PeaksAngularError.cpp
+ MultishellMethods.cpp
+ FiberFoxProcessing.cpp
+ ExportShImage.cpp
+)
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox
index 354d8f4784..30e1922e3a 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox
@@ -1,112 +1,116 @@
/**
\page org_mitk_views_fiberfoxview Fiberfox
-This view provides the user interface for Fiberfox [1,2], an interactive simulation tool for defining artificial white matter fibers and generating corresponding diffusion weighted images. Arbitrary fiber configurations like bent, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers. From these fibers a diffusion weighted signal is simulated using a flexible combination of various diffusion models. It can be modified using specified acquisition settings such as gradient direction, b-value, signal-to-noise ratio, image size, and resolution. Additionally it enables the simulation of magnetic resonance artifacts including thermal noise, Gibbs ringing, N/2 ghosting and susceptibility distortions. The employed parameters can be saved and loaded as xml file with the ending ".ffp" (Fiberfox parameters).
+This view provides the user interface for Fiberfox [1,2,3], an interactive simulation tool for defining artificial white matter fibers and generating corresponding diffusion weighted images. Arbitrary fiber configurations like bent, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers. From these fibers a diffusion weighted signal is simulated using a flexible combination of various diffusion models. It can be modified using specified acquisition settings such as gradient direction, b-value, signal-to-noise ratio, image size, and resolution. Additionally it enables the simulation of magnetic resonance artifacts including thermal noise, Gibbs ringing, N/2 ghosting, susceptibility distortions and motion artifacts. The employed parameters can be saved and loaded as xml file with the ending ".ffp" (Fiberfox parameters).
<b>Available sections:</b>
- \ref QmitkFiberfoxViewUserManualFiberDefinition
- \ref QmitkFiberfoxViewUserManualSignalGeneration
- \ref QmitkFiberfoxViewUserManualKnownIssues
- \ref QmitkFiberfoxViewUserManualReferences
\image html Fiberfox.png Fig. 1: Screenshot of the Fiberfox framework. The four render windows display an axial (top left), sagittal (top right) and coronal (bottom left) 2D cut as well as a 3D view of a synthetic fiber helix and the fiducials used to define its shape. In the 2D views the helix is superimposing the baseline volume of the corresponding diffusion weighted image. The sagittal render window shows a close-up view on one of the circular fiducials.
\section QmitkFiberfoxViewUserManualFiberDefinition Fiber Definition
Fiber strands are defined simply by placing markers in a 3D image volume. The fibers are then interpolated between these fiducials.
<b>Example:</b>
\li Chose an image volume to place the markers used to define the fiber pathway. If you don't have such an image available switch to the "Signal Generation" tab, define the size and spacing of the desired image and click "Generate Image". If no fiber bundle is selected, this will generate a dummy image that can be used to place the fiducials.
\li Start placing fiducials at the desired positions to define the fiber pathway. To do that, click on the button with the circle pictogram, then click at the desired position and plane in the image volume and drag your mouse while keeping the button pressed to generate a circular shape. Adjust the shape using the control points (Fig. 2). The position of control point D introduces a twist of the fibers between two successive fiducials. The actual fiber generation is triggered automatically as soon as you place the second control point.
\li In some cases the fibers are entangled in a way that can't be resolved by introducing an additional fiber twist. Fiberfox tries to avoid these situations, which arise from different normal orientations of succeeding fiducials, automatically. In rare cases this is not successful. Use the double-arrow button to flip the fiber positions of the selected fiducial in one dimension. Either the problem is resolved now or you can resolve it manually by adjusting the twist-control point.
\li To create non elliptical fiber profile shapes switch to the Fiber Extraction View. This view provides tools to extract subesets of fibers from fiber bundles and enables to cut out arbitrary polygonal fiber shapes from existing bundles.
\image html Fiberfox-Fiducial.png Fig. 2: Control points defining the actual shape of the fiducial. A specifies the fiducials position in space, B and C the two ellipse radii and D the twisting angle between two successive fiducials.
<b>Fiber Options:</b>
\li <b>Real Time Fibers</b>: If checked, each parameter adjustment (fiducial position, number of fibers, ...) will be directly applied to the selected fiber bundle. If unchecked, the fibers will only be generated if the corresponding button "Generate Fibers" is clicked.
\li <b>Advanced Options</b>: Show/hide advanced options
\li <b>#Fibers</b>: Specifies the number of fibers that will be generated for the selected bundle.
\li <b>Fiber Sampling</b>: Adjusts the distenace of the fiber sampling points (in mm). A higher sampling rate is needed if high curvatures are modeled.
\li <b>Tension, Continuity, Bias</b>: Parameters controlling the shape of the splines interpolation the fiducials. See <a href="http://en.wikipedia.org/wiki/Kochanek%E2%80%93Bartels_spline">Wikipedia</a> for details.
<b>Fiducial Options:</b>
\li <b>Use Constant Fiducial Radius</b>: If checked, all fiducials are treated as circles with the same radius. The first fiducial of the bundle defines the radius of all other fiducials.
\li <b>Align with grid</b>: Click to shift all fiducial center points to the next voxel center.
<b>Operations:</b>
\li <b>Rotation</b>: Define the rotation of the selected fiber bundle around each axis (in degree).
\li <b>Translation</b>: Define the translation of the selected fiber bundle along each axis (in mm).
\li <b>Scaling</b>: Define a scaling factor for the selected fiber bundle in each dimension.
\li <b>Transform Selection</b>: Apply specified rotation, translation and scaling to the selected Bundle/Fiducial
\li <b>Copy Bundles</b>: Add copies of the selected fiber bundles to the datamanager.
\li <b>Join Bundles</b>: Add new bundle to the datamanager that contains all fibers from the selected bundles.
\li <b>Include Fiducials</b>: If checked, the specified transformation is also applied to the fiducials belonging to the selected fiber bundle and the fiducials are also copied.
\image html FiberfoxExamples.png Fig. 3: Examples of artificial crossing (a,b), fanning (c,d), highly curved (e,f), kissing (g,h) and twisting (i,j) fibers as well as of the corresponding tensor images generated with Fiberfox.
\section QmitkFiberfoxViewUserManualSignalGeneration Signal Generation
To generate an artificial signal from the input fibers we follow the concepts recently presented by Panagiotaki et al. in a review and taxonomy of different compartment models: a flexible model combining multiple compartments is used to simulate the anisotropic diffusion inside (intra-axonal compartment) and between axons (inter-axonal compartment), isotropic diffusion outside of the axons (extra-axonal compartment 1) and the restricted diffusion in other cell types (extra-axonal compartment 2) weighted according to their respective volume fraction.
A diffusion weighted image is generated from the fibers by selecting the according fiber bundle in the datamanager and clicking "Generate Image". If some other diffusion weighted image is selected together with the fiber bundle, Fiberfox directly uses the parameters of the selected image (size, spacing, gradient directions, b-values) for the signal generation process. Additionally a binary image can be selected that defines the tissue area. Voxels outside of this mask will contain no signal, only noise.
<b>Basic Image Settings:</b>
\li <b>Image Dimensions</b>: Specifies actual image size (number of voxels in each dimension).
\li <b>Image Spacing</b>: Specifies voxel size in mm. Beware that changing the voxel size also changes the signal strength, e.g. increasing the resolution from <em>2x2x2</em> mm to <em>1x1x1</em> mm decreases the signal obtained for each voxel by a factor 8.
\li <b>Gradient Directions</b>: Number of gradients directions distributed equally over the half sphere. 10% baseline images are automatically added.
\li <b>b-Value</b>: Diffusion weighting in s/mm². If an existing diffusion weighted image is used to set the basic parameters, the b-value is defined by the gradient direction magnitudes of this image, which also enables the use of multiple b-values.
<b>Advanced Image Settings (activate checkbox "Advanced Options"):</b>
\li <b>Repetitions</b>: Specifies the number of averages used for the acquisition to reduce noise.
\li <b>Signal Scale</b>: Additional scaling factor for the signal in each voxel. The default value of 125 results in a maximum signal amplitude of 1000 for <em>2x2x2</em> mm voxels. Beware that changing this value without changing the noise variance results in a changed SNR. Adjustment of this value might be needed if the overall signal values are much too high or much too low (depends on a variety of factors like voxel size and relaxation times).
\li <b>Echo Time <em>TE</em></b>: Time between the 90° excitation pulse and the first spin echo. Increasing this time results in a stronger <em>T2</em>-relaxation effect (<a href="http://en.wikipedia.org/wiki/Relaxation_%28NMR%29">Wikipedia</a>).
\li <b>Line Readout Time</b>: Time to read one line in k-space. Increasing this time results in a stronger <em>T2*</em> effect which causes an attenuation of the higher frequencies in phase direction (here along y-axis) which again results in a blurring effect of sharp edges perpendicular to the phase direction.
\li <b><em>T<sub>inhom</sub></em> Relaxation</b>: Time constant specifying the signal decay due to magnetic field inhomogeneities (also called <em>T2'</em>). Together with the tissue specific relaxation time constant <em>T2</em> this defines the <em>T2*</em> decay constant: <em>T2*=(T2 T2')/(T2+T2')</em>
\li <b>Fiber Radius (in µm)</b>: Used to calculate the volume fractions of the used compartments (fiber, water, etc.). If set to 0 (default) the fiber radius is set automatically so that the voxel containing the most fibers is filled completely. A realistic axon radius ranges from about 5 to 20 microns. Using the automatic estimation the resulting value might very well be much larger or smaller than this range.
\li <b>Interpolation Shrink</b>: The signal generated at each position along the fibers is distributed on the surrounding voxels using an interpolation scheme shaped like an arctangent function. Large values result in a steeper interpolation scheme approximating a nearest neighbor interpolation. Very small values result in an almost linear interpolation.
\li <b>Simulate Signal Relaxation</b>: If checked, the relaxation induced signal decay is simulated, other wise the parameters <em>TE</em>, Line Readout Time, <em>T<sub>inhom</sub></em>, and <em>T2</em> are ignored.
\li <b>Disable Partial Volume Effects</b>: If checked, the actual volume fractions of the single compartments are ignored. A voxel will either be filled by the intra axonal compartment completely or will contain no fiber at all.
\li <b>Output Volume Fractions</b>: Output a double image for each compartment. The voxel values correspond to the volume fraction of the respective compartment.
<b>Compartment Settings:</b>
The group-boxes "Intra-axonal Compartment", "Inter-axonal Compartment" and "Extra-axonal Compartments" allow the specification which model to use and the corresponding model parameters. Currently the following models are implemented:
\li <b>Stick</b>: The “stick” model describes diffusion in an idealized cylinder with zero radius. Parameter: Diffusivity <em>d</em>
\li <b>Zeppelin</b>: Cylindrically symmetric diffusion tensor. Parameters: Parallel diffusivity <em>d<sub>||</sub></em> and perpendicular diffusivity <em>d<sub>⊥</sub></em>
\li <b>Tensor</b>: Full diffusion tensor. Parameters: Parallel diffusivity <em>d<sub>||</sub></em> and perpendicular diffusivity constants <em>d<sub>⊥1</sub></em> and <em>d<sub>⊥2</sub></em>
\li <b>Ball</b>: Isotropic compartment. Parameter: Diffusivity <em>d</em>
\li <b>Astrosticks</b>: Consists of multiple stick models pointing in different directions. The single stick orientations can either be distributed equally over the sphere or are sampled randomly. The model represents signal coming from a type of glial cell called astrocytes, or populations of axons with arbitrary orientation. Parameters: randomization of the stick orientations and diffusivity of the sticks <em>d</em>.
\li <b>Dot</b>: Isotropically restricted compartment. No parameter.
For a detailed description of the single models, please refer to Panagiotaki <em>et al.</em> "Compartment models of the diffusion MR signal in brain white matter: A taxonomy and comparison". Additionally to the model parameters, each compartment has its own <em>T2</em> signal relaxation constant (in <em>ms</em>).
<b>Noise and Artifacts:</b>
\li <b>Rician Noise</b>: Add Rician noise with the specified variance to the signal.
-\li <b>Rician Spikes</b>: Add signal spikes to the k-space signal resulting in stripe artifacts across the corresponding image slice.
+\li <b>Spikes</b>: Add signal spikes to the k-space signal resulting in stripe artifacts across the corresponding image slice.
+\li <b>Aliasing</b>: Aliasing artifacts occur if the FOV in phase direction is smaller than the imaged object. The parameter defines the percentage by which the FOV is shrunk.
\li <b>N/2 Ghosts</b>: Specify the offset between successive lines in k-space. This offset causes ghost images in distance N/2 in phase direction due to the alternating EPI readout directions.
\li <b>Distortions</b>: Simulate distortions due to magnetic field inhomogeneities. This is achieved by adding an additional phase during the readout process. The input is a frequency map specifying the inhomogeneities. The "Fieldmap Generator" view provides an interface to generate simple artificial frequency maps.
+\li <b>Motion Artifacts</b>: To simulate motion artifacts, the fiber configuration is moved between the signal simulation of the individual gradient volumes. The motion can be performed randomly, where the parameters are used to define the +/- maximum of the corresponding motion, or linearly, where the parameters define the maximum rotation/translation around/along the corresponding axis at the and of the simulated acquisition.
\li <b>Eddy Currents</b>: EXPERIMENTAL! This feature is currently being tested and might not yet behave as expected!
-\li <b>Gibbs Ringing</b>: Ringing artifacts occurring on edges in the image due to the frequency low-pass filtering caused by the limited size of the k-space. The higher the oversampling factor, the larger the distance from the corresponding edge in which the ringing is still visible. Keep in mind that increasing the oversampling factor results in a quadratic increase of computation time.
+\li <b>Gibbs Ringing</b>: Ringing artifacts occurring on edges in the image due to the frequency low-pass filtering caused by the limited size of the k-space.
\section QmitkFiberfoxViewUserManualKnownIssues Known Issues
\li If fiducials are created in one of the marginal slices of the underlying image, a position change of the fiducial can be observed upon selection/deselection. If the fiducial is created in any other slice this bug does not occur.
\li If a scaling factor is applied to the selcted fiber bundle, the corresponding fiducials are not scaled accordingly.
\li In some cases the automatic update of the selected fiber bundle is not triggered even if "Real Time Fibers" is checked, e.g. if a fiducial is deleted. If this happens on can always force an update by pressing the "Generate Fibers" button.
If any other issues or feature requests arises during the use of Fiberfox, please don't hesitate to send us an e-mail or directly report the issue in our bugtracker: http://bugs.mitk.org/
\section QmitkFiberfoxViewUserManualReferences References
-[1] Peter F. Neher, Bram Stieltjes, Frederik B. Laun, and Klaus H. Fritzsche: Fiberfox: An extensible system for generating realistic white matter software phantoms, MICCAI CDMRI Workshop, Nagoya; 09/2013
+[1] Peter F. Neher, Frederik B. Laun, Bram Stieltjes, and Klaus H. Fritzsche: Fiberfox: Facilitating the creation of realistic white matter software phantoms, Magn Reson Med, Accepted for publication.
-[2] Peter F. Neher, Bram Stieltjes, Frederik B. Laun, Hans-Peter Meinzer, and Klaus H. Fritzsche: Fiberfox: Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, ISMRM, Salt Lake City; 04/2013
+[2] Peter F. Neher, Frederik B. Laun, Bram Stieltjes, and Klaus H. Fritzsche: Fiberfox: An extensible system for generating realistic white matter software phantoms, MICCAI CDMRI Workshop, Nagoya; 09/2013
+
+[3] Peter F. Neher, Bram Stieltjes, Frederik B. Laun, Hans-Peter Meinzer, and Klaus H. Fritzsche: Fiberfox: Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, ISMRM, Salt Lake City; 04/2013
*/
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc
index 9caa2bf372..d4cc60c09a 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc
@@ -1,38 +1,62 @@
<RCC>
<qresource prefix="/QmitkDiffusionImaging">
<file>qball.png</file>
<file>tensor.png</file>
<file>dwi.png</file>
<file>dwiimport.png</file>
<file>quantification.png</file>
<file>reconodf.png</file>
<file>recontensor.png</file>
<file>texIntONIcon.png</file>
<file>texIntOFFIcon.png</file>
<file>vizControls.png</file>
<file>Refresh_48.png</file>
<file>QBallData24.png</file>
<file>glyphsoff_C.png</file>
<file>glyphsoff_S.png</file>
<file>glyphsoff_T.png</file>
<file>glyphson_C.png</file>
<file>glyphson_S.png</file>
<file>glyphson_T.png</file>
<file>FiberBundle.png</file>
<file>FiberBundleX.png</file>
<file>connectomics/ConnectomicsNetwork.png</file>
<file>rectangle.png</file>
<file>circle.png</file>
<file>polygon.png</file>
<file>color24.gif</file>
<file>color48.gif</file>
<file>color64.gif</file>
<file>crosshair.png</file>
<file>paint2.png</file>
<file>IVIM_48.png</file>
<file>reset.png</file>
<file>MapperEfx2D.png</file>
<file>refresh.xpm</file>
<file>odf.png</file>
+ <file>general_icons/download.ico</file>
+ <file>general_icons/play.ico</file>
+ <file>general_icons/plus.ico</file>
+ <file>general_icons/refresh.ico</file>
+ <file>general_icons/right.ico</file>
+ <file>general_icons/save.ico</file>
+ <file>general_icons/undo.ico</file>
+ <file>general_icons/upload.ico</file>
+ <file>general_icons/abort.ico</file>
+ <file>general_icons/copy1.ico</file>
+ <file>general_icons/copy2.ico</file>
+ <file>general_icons/cut.ico</file>
+ <file>general_icons/deny1.ico</file>
+ <file>general_icons/deny2.ico</file>
+ <file>general_icons/down.ico</file>
+ <file>general_icons/left.ico</file>
+ <file>general_icons/magn_minus.ico</file>
+ <file>general_icons/magn_plus.ico</file>
+ <file>general_icons/search.ico</file>
+ <file>general_icons/stop.ico</file>
+ <file>general_icons/up.ico</file>
+ <file>general_icons/help.ico</file>
+ <file>general_icons/pencil.ico</file>
+ <file>general_icons/edit.ico</file>
</qresource>
</RCC>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/abort.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/abort.ico
new file mode 100644
index 0000000000..b8edcbdc33
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/abort.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy1.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy1.ico
new file mode 100644
index 0000000000..22b77ce46a
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy1.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy2.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy2.ico
new file mode 100644
index 0000000000..f09778af37
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/copy2.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/cut.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/cut.ico
new file mode 100644
index 0000000000..bd757f5d10
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/cut.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny1.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny1.ico
new file mode 100644
index 0000000000..b3d67e68e9
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny1.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny2.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny2.ico
new file mode 100644
index 0000000000..1c70699dc8
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/deny2.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/down.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/down.ico
new file mode 100644
index 0000000000..5a85a4136a
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/down.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/download.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/download.ico
new file mode 100644
index 0000000000..a991a963c8
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/download.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/edit.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/edit.ico
new file mode 100644
index 0000000000..9f6951a514
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/edit.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/help.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/help.ico
new file mode 100644
index 0000000000..2a972dfbf8
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/help.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/left.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/left.ico
new file mode 100644
index 0000000000..964f60ad8e
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/left.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_minus.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_minus.ico
new file mode 100644
index 0000000000..10c7d311d0
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_minus.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_plus.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_plus.ico
new file mode 100644
index 0000000000..e520a689a0
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/magn_plus.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/pencil.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/pencil.ico
new file mode 100644
index 0000000000..0e58e1cc94
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/pencil.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/play.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/play.ico
new file mode 100644
index 0000000000..d6379ce139
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/play.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/plus.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/plus.ico
new file mode 100644
index 0000000000..a2b7a026b0
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/plus.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/refresh.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/refresh.ico
new file mode 100644
index 0000000000..d603e55ff2
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/refresh.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/right.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/right.ico
new file mode 100644
index 0000000000..6a06a666a4
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/right.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/save.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/save.ico
new file mode 100644
index 0000000000..80c7ecdbdf
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/save.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/search.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/search.ico
new file mode 100644
index 0000000000..25802edcc9
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/search.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/stop.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/stop.ico
new file mode 100644
index 0000000000..292166968c
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/stop.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/undo.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/undo.ico
new file mode 100644
index 0000000000..2b6a67a2cb
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/undo.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/up.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/up.ico
new file mode 100644
index 0000000000..e221d345e9
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/up.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/upload.ico b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/upload.ico
new file mode 100644
index 0000000000..9b85d6ed4b
Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/general_icons/upload.ico differ
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp
index 60d5040099..44f5efd51a 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp
@@ -1,825 +1,822 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "QmitkDiffusionDicomImportView.h"
// qt includes
#include <QFileDialog>
// itk includes
#include "itkTimeProbesCollectorBase.h"
#include "itkGDCMSeriesFileNames.h"
#include "itksys/SystemTools.hxx"
// mitk includes
#include "mitkProgressBar.h"
#include "mitkStatusBar.h"
#include "mitkProperties.h"
#include "mitkRenderingManager.h"
#include "mitkMemoryUtilities.h"
// diffusion module includes
#include "mitkDicomDiffusionImageHeaderReader.h"
#include "mitkDicomDiffusionImageReader.h"
#include "mitkDiffusionImage.h"
#include "mitkNrrdDiffusionImageWriter.h"
#include "gdcmDirectory.h"
#include "gdcmScanner.h"
#include "gdcmSorter.h"
#include "gdcmIPPSorter.h"
#include "gdcmAttribute.h"
#include "gdcmVersion.h"
#include <QMessageBox>
const std::string QmitkDiffusionDicomImport::VIEW_ID = "org.mitk.views.diffusiondicomimport";
QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(QObject* /*parent*/, const char* /*name*/)
: QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL),
m_OutputFolderName(""), m_OutputFolderNameSet(false)
{
}
QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other)
{
Q_UNUSED(other)
throw std::runtime_error("Copy constructor not implemented");
}
QmitkDiffusionDicomImport::~QmitkDiffusionDicomImport()
{}
void QmitkDiffusionDicomImport::CreateQtPartControl(QWidget *parent)
{
m_Parent = parent;
if (m_Controls == NULL)
{
m_Controls = new Ui::QmitkDiffusionDicomImportControls;
m_Controls->setupUi(parent);
this->CreateConnections();
m_Controls->m_DicomLoadRecursiveCheckbox->setChecked(true);
m_Controls->m_DicomLoadAverageDuplicatesCheckbox->setChecked(false);
m_Controls->m_DicomLoadRecursiveCheckbox->setVisible(false);
m_Controls->m_OverrideOptionCheckbox->setVisible(false);
AverageClicked();
}
}
void QmitkDiffusionDicomImport::CreateConnections()
{
if ( m_Controls )
{
connect( m_Controls->m_AddFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadAddFolderNames()) );
connect( m_Controls->m_DeleteFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadDeleteFolderNames()) );
connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(DicomLoadStartLoad()) );
connect( m_Controls->m_DicomLoadAverageDuplicatesCheckbox, SIGNAL(clicked()), this, SLOT(AverageClicked()) );
connect( m_Controls->m_OutputSetButton, SIGNAL(clicked()), this, SLOT(OutputSet()) );
connect( m_Controls->m_OutputClearButton, SIGNAL(clicked()), this, SLOT(OutputClear()) );
connect( m_Controls->m_Remove, SIGNAL(clicked()), this, SLOT(Remove()) );
}
}
void QmitkDiffusionDicomImport::Remove()
{
int i = m_Controls->listWidget->currentRow();
m_Controls->listWidget->takeItem(i);
}
void QmitkDiffusionDicomImport::OutputSet()
{
// SELECT FOLDER DIALOG
QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") );
w->setFileMode( QFileDialog::Directory );
// RETRIEVE SELECTION
if ( w->exec() != QDialog::Accepted )
return;
m_OutputFolderName = w->selectedFiles()[0];
m_OutputFolderNameSet = true;
m_Controls->m_OutputLabel->setText(m_OutputFolderName);
// show file override option checkbox
m_Controls->m_OverrideOptionCheckbox->setVisible(true);
}
void QmitkDiffusionDicomImport::OutputClear()
{
m_OutputFolderName = "";
m_OutputFolderNameSet = false;
m_Controls->m_OutputLabel->setText("... optional out-folder ...");
// hide file override option checkbox - no output specified
m_Controls->m_OverrideOptionCheckbox->setVisible(false);
}
void QmitkDiffusionDicomImport::AverageClicked()
{
m_Controls->m_Blur->setEnabled(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked());
}
void QmitkDiffusionDicomImport::Activated()
{
QmitkFunctionality::Activated();
}
void QmitkDiffusionDicomImport::DicomLoadDeleteFolderNames()
{
m_Controls->listWidget->clear();
}
void QmitkDiffusionDicomImport::DicomLoadAddFolderNames()
{
// SELECT FOLDER DIALOG
QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") );
w->setFileMode( QFileDialog::Directory );
// RETRIEVE SELECTION
if ( w->exec() != QDialog::Accepted )
return;
m_Controls->listWidget->addItems(w->selectedFiles());
}
bool SortBySeriesUID(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
{
gdcm::Attribute<0x0020,0x000e> at1;
at1.Set( ds1 );
gdcm::Attribute<0x0020,0x000e> at2;
at2.Set( ds2 );
return at1 < at2;
}
bool SortByAcquisitionNumber(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
{
gdcm::Attribute<0x0020,0x0012> at1;
at1.Set( ds1 );
gdcm::Attribute<0x0020,0x0012> at2;
at2.Set( ds2 );
return at1 < at2;
}
bool SortBySeqName(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
{
gdcm::Attribute<0x0018, 0x0024> at1;
at1.Set( ds1 );
gdcm::Attribute<0x0018, 0x0024> at2;
at2.Set( ds2 );
std::string str1 = at1.GetValue().Trim();
std::string str2 = at2.GetValue().Trim();
return std::lexicographical_compare(str1.begin(), str1.end(),
str2.begin(), str2.end() );
}
void QmitkDiffusionDicomImport::Status(QString status)
{
mitk::StatusBar::GetInstance()->DisplayText(status.toAscii());
MITK_INFO << status.toStdString().c_str();
}
void QmitkDiffusionDicomImport::Status(std::string status)
{
mitk::StatusBar::GetInstance()->DisplayText(status.c_str());
MITK_INFO << status.c_str();
}
void QmitkDiffusionDicomImport::Status(const char* status)
{
mitk::StatusBar::GetInstance()->DisplayText(status);
MITK_INFO << status;
}
void QmitkDiffusionDicomImport::Error(QString status)
{
mitk::StatusBar::GetInstance()->DisplayErrorText(status.toAscii());
MITK_ERROR << status.toStdString().c_str();
}
void QmitkDiffusionDicomImport::Error(std::string status)
{
mitk::StatusBar::GetInstance()->DisplayErrorText(status.c_str());
MITK_ERROR << status.c_str();
}
void QmitkDiffusionDicomImport::Error(const char* status)
{
mitk::StatusBar::GetInstance()->DisplayErrorText(status);
MITK_ERROR << status;
}
void QmitkDiffusionDicomImport::PrintMemoryUsage()
{
size_t processSize = mitk::MemoryUtilities::GetProcessMemoryUsage();
size_t totalSize = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam();
float percentage = ( (float) processSize / (float) totalSize ) * 100.0;
MITK_INFO << "Current memory usage: " << GetMemoryDescription( processSize, percentage );
}
std::string QmitkDiffusionDicomImport::FormatMemorySize( size_t size )
{
double val = size;
std::string descriptor("B");
if ( val >= 1000.0 )
{
val /= 1024.0;
descriptor = "KB";
}
if ( val >= 1000.0 )
{
val /= 1024.0;
descriptor = "MB";
}
if ( val >= 1000.0 )
{
val /= 1024.0;
descriptor = "GB";
}
std::ostringstream str;
str << std::fixed << std::setprecision(2) << val << " " << descriptor;
return str.str();
}
std::string QmitkDiffusionDicomImport::FormatPercentage( double val )
{
std::ostringstream str;
str << std::fixed << std::setprecision(2) << val << " " << "%";
return str.str();
}
std::string QmitkDiffusionDicomImport::GetMemoryDescription( size_t processSize, float percentage )
{
std::ostringstream str;
str << FormatMemorySize(processSize) << " (" << FormatPercentage( percentage ) <<")" ;
return str.str();
}
void QmitkDiffusionDicomImport::DicomLoadStartLoad()
{
itk::TimeProbesCollectorBase clock;
bool imageSuccessfullySaved = true;
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, NULL) << " to '" << locale << "'";
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
int nrFolders = m_Controls->listWidget->count();
if(!nrFolders)
{
Error(QString("No input folders were selected. ABORTING."));
return;
}
Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion()));
PrintMemoryUsage();
QString status;
mitk::DataNode::Pointer node;
mitk::ProgressBar::GetInstance()->AddStepsToDo(2*nrFolders);
std::string folder = m_Controls->m_OutputLabel->text().toStdString();
if(berry::Platform::IsWindows())
{
folder.append("\\import.log");
}
else
{
folder.append("/import.log");
}
ofstream logfile;
if(m_OutputFolderNameSet) logfile.open(folder.c_str());
while(m_Controls->listWidget->count())
{
// RETREIVE FOLDERNAME
QListWidgetItem * item = m_Controls->listWidget->takeItem(0);
QString folderName = item->text();
if(m_OutputFolderNameSet) logfile << "Reading " << folderName.toStdString() << '\n';
// PARSING DIRECTORY
PrintMemoryUsage();
clock.Start(folderName.toAscii());
std::vector<std::string> seriesUIDs(0);
std::vector<std::vector<std::string> > seriesFilenames(0);
Status("== Initial Directory Scan ==");
if(m_OutputFolderNameSet) logfile << "== Initial Directory Scan ==\n";
gdcm::Directory d;
d.Load( folderName.toStdString().c_str(), true ); // recursive !
const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
const unsigned int ntotalfiles = l1.size();
Status(QString(" ... found %1 different files").arg(ntotalfiles));
if(m_OutputFolderNameSet)logfile << "...found " << ntotalfiles << " different files\n";
Status("Scanning Headers");
if(m_OutputFolderNameSet) logfile << "Scanning Headers\n";
gdcm::Scanner s;
const gdcm::Tag t1(0x0020,0x000d); // Study Instance UID
const gdcm::Tag t2(0x0020,0x000e); // Series Instance UID
const gdcm::Tag t5(0x0028, 0x0010); // number rows
const gdcm::Tag t6(0x0028, 0x0011); // number cols
s.AddTag( t1 );
s.AddTag( t2 );
s.AddTag( t5 );
s.AddTag( t6 );
bool b = s.Scan( d.GetFilenames() );
if( !b )
{
Error("Scanner failed");
if(m_OutputFolderNameSet )logfile << "ERROR: scanner failed\n";
continue;
}
// Only get the DICOM files:
gdcm::Directory::FilenamesType l2 = s.GetKeys();
gdcm::Directory::FilenamesType::iterator it;
for (it = l2.begin() ; it != l2.end(); ++it) {
MITK_INFO << "-------FN " << *it;
}
const int nfiles = l2.size();
if(nfiles < 1)
{
Error("No DICOM files found");
if(m_OutputFolderNameSet)logfile << "ERROR: No DICOM files found\n";
continue;
}
Status(QString(" ... successfully scanned %1 headers.").arg(nfiles));
if(m_OutputFolderNameSet) logfile << "...succesfully scanned " << nfiles << " headers\n";
Status("Sorting");
if(m_OutputFolderNameSet) logfile << "Sorting\n";
const gdcm::Scanner::ValuesType &values1 = s.GetValues(t1);
int nvalues;
if(m_Controls->m_DuplicateID->isChecked())
{
nvalues = 1;
}
else
{
nvalues = values1.size();
}
if(nvalues>1)
{
Error("Multiple sSeries tudies found. Please limit to 1 study per folder");
if(m_OutputFolderNameSet) logfile << "Multiple series found. Limit to one. If you are convinced this is an error use the merge duplicate study IDs option \n";
continue;
}
const gdcm::Scanner::ValuesType &values5 = s.GetValues(t5);
const gdcm::Scanner::ValuesType &values6 = s.GetValues(t6);
if(values5.size()>1 || values6.size()>1)
{
Error("Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING.");
if(m_OutputFolderNameSet) logfile << "Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING\n.";
continue;
}
const gdcm::Scanner::ValuesType &values2 = s.GetValues(t2);
int nSeries;
if(m_Controls->m_DuplicateID->isChecked())
{
nSeries = 1;
}
else
{
nSeries = values2.size();
}
gdcm::Directory::FilenamesType files;
if(nSeries > 1)
{
gdcm::Sorter sorter;
sorter.SetSortFunction( SortBySeriesUID );
if (sorter.StableSort( l2 ))
{
files = sorter.GetFilenames();
}
else
{
Error("Loading of at least one DICOM file not successfull!");
return;
}
}
else
{
files = l2;
}
unsigned int nTotalAcquis = 0;
if(nfiles % nSeries != 0)
{
Error("Number of files in series not equal, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files in series not equal, Some volumes are probably incomplete. ABORTING \n";
continue;
}
int filesPerSeries = nfiles / nSeries;
gdcm::Scanner::ValuesType::const_iterator it2 = values2.begin();
for(int i=0; i<nSeries; i++)
{
gdcm::Directory::FilenamesType sub( files.begin() + i*filesPerSeries, files.begin() + (i+1)*filesPerSeries);
gdcm::Scanner s;
const gdcm::Tag t3(0x0020,0x0012); // Acquisition ID
const gdcm::Tag t4(0x0018,0x0024); // Sequence Name (in case acquisitions are equal for all)
// const gdcm::Tag t5(0x20,0x32) ); // Image Position (Patient)
s.AddTag(t3);
s.AddTag(t4);
// s.AddTag(t5);
bool b = s.Scan( sub );
if( !b )
{
Error("Scanner failed");
if(m_OutputFolderNameSet) logfile << "Scanner failed\n";
continue;
}
gdcm::Sorter subsorter;
gdcm::Scanner::ValuesType::const_iterator it;
const gdcm::Scanner::ValuesType &values3 = s.GetValues(t3);
const gdcm::Scanner::ValuesType &values4 = s.GetValues(t4);
unsigned int nAcquis = values3.size();
if(nAcquis > 1) // More than one element must have this tag (Not != )
{
subsorter.SetSortFunction( SortByAcquisitionNumber );
it = values3.begin();
}
else if (values4.size() > 1)
{
nAcquis = values4.size();
subsorter.SetSortFunction( SortBySeqName );
it = values4.begin();
}
// Hotfix for Bug 14758, better fix by selecting always availible tags.
if( nAcquis == 0 || values4.size() == 0)
{
std::string err_msg = "Sorting tag (0x0020,0x0012) [Acquisition ID] or (0x0018,0x0024) [Sequence Name] missing, ABORTING";
Error(err_msg);
if(m_OutputFolderNameSet) logfile << err_msg << "\n";
continue;
}
nTotalAcquis += nAcquis;
subsorter.Sort( sub );
if(filesPerSeries % nAcquis != 0)
{
Error("Number of files per acquisition not equal, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files per acquisition not equal, ABORTING \n";
continue;
}
int filesPerAcqu = filesPerSeries / nAcquis;
gdcm::Directory::FilenamesType subfiles = subsorter.GetFilenames();
for ( unsigned int j = 0 ; j < nAcquis ; ++j )
{
std::string identifier = "serie_" + *it2 + "_acquis_" + *it++;
gdcm::IPPSorter ippsorter;
gdcm::Directory::FilenamesType ipplist((j)*filesPerAcqu+subfiles.begin(),(j+1)*filesPerAcqu+subfiles.begin());
ippsorter.SetComputeZSpacing( true );
if( !ippsorter.Sort( ipplist ) )
{
Error(QString("Failed to sort acquisition %1, ABORTING").arg(identifier.c_str()));
if(m_OutputFolderNameSet) logfile << "Failed to sort acquisition " << identifier.c_str() << " , Aborting\n";
continue;
}
const std::vector<std::string> & list = ippsorter.GetFilenames();
seriesFilenames.push_back(list);
seriesUIDs.push_back(identifier.c_str());
}
++it2;
}
// Hot Fix for Bug 14758, checking if no file is acuired.
if (nTotalAcquis < 1) // Test if zero, if true than error because no file was selected
{
Error("Nno files in acquisitions, ABORTING");
if(m_OutputFolderNameSet) logfile << "Nno files in acquisitions, ABORTING \n";
continue;
}
if(nfiles % nTotalAcquis != 0)
{
Error("Number of files per acquisition differs between series, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files per acquisition differs between series, ABORTING \n";
continue;
}
int slices = nfiles/nTotalAcquis;
Status(QString("Series is composed of %1 different 3D volumes with %2 slices.").arg(nTotalAcquis).arg(slices));
if(m_OutputFolderNameSet) logfile << "Series is composed of " << nTotalAcquis << " different 3D volumes with " << slices << " slices\n";
// READING HEADER-INFOS
PrintMemoryUsage();
Status(QString("Reading Headers %1").arg(folderName));
if(m_OutputFolderNameSet) logfile << "Reading Headers "<< folderName.toStdString() << "\n";
mitk::DicomDiffusionImageHeaderReader::Pointer headerReader;
typedef short PixelValueType;
typedef mitk::DicomDiffusionImageReader< PixelValueType, 3 > VolumesReader;
VolumesReader::HeaderContainer inHeaders;
unsigned int size2 = seriesUIDs.size();
for ( unsigned int i = 0 ; i < size2 ; ++i )
{
// Hot Fix for Bug 14459, catching if no valid data in datafile.
try
{
Status(QString("Reading header image #%1/%2").arg(i+1).arg(size2));
headerReader = mitk::DicomDiffusionImageHeaderReader::New();
headerReader->SetSeriesDicomFilenames(seriesFilenames[i]);
headerReader->Update();
inHeaders.push_back(headerReader->GetOutput());
}
catch (mitk::Exception e)
{
Error("Could not read file header, ABORTING");
if(m_OutputFolderNameSet) logfile << e;
continue;
}
//Status(std::endl;
}
mitk::ProgressBar::GetInstance()->Progress();
// // GROUP HEADERS
// mitk::GroupDiffusionHeadersFilter::Pointer grouper
// = mitk::GroupDiffusionHeadersFilter::New();
// mitk::GroupDiffusionHeadersFilter::OutputType outHeaders;
// grouper->SetInput(inHeaders);
// grouper->Update();
// outHeaders = grouper->GetOutput();
// READ VOLUMES
PrintMemoryUsage();
if(m_OutputFolderNameSet) logfile << "Loading volumes\n";
Status(QString("Loading Volumes %1").arg(folderName));
VolumesReader::Pointer vReader = VolumesReader::New();
VolumesReader::HeaderContainer hc = inHeaders;
// hc.insert(hc.end(), outHeaders[1].begin(), outHeaders[1].end() );
// hc.insert(hc.end(), outHeaders[2].begin(), outHeaders[2].end() );
if(hc.size()>1)
{
vReader->SetHeaders(hc);
vReader->Update();
VolumesReader::OutputImageType::Pointer vecImage;
vecImage = vReader->GetOutput();
Status(QString("Volumes Loaded (%1)").arg(folderName));
// CONSTRUCT CONTAINER WITH DIRECTIONS
typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
typedef itk::VectorContainer< unsigned int,
GradientDirectionType > GradientDirectionContainerType;
GradientDirectionContainerType::Pointer directions =
GradientDirectionContainerType::New();
std::vector<double> b_vals;
double maxb = 0;
for(unsigned int i=0; i<hc.size(); i++)
{
double bv = hc[i]->bValue;
if(maxb<bv)
{
maxb = bv;
}
b_vals.push_back(bv);
}
for(unsigned int i=0; i<hc.size(); i++)
{
vnl_vector_fixed<double, 3> vect = hc[i]->DiffusionVector;
- // since some protocols provide a gradient direction of (0,0,0) in their dicom files when isotropic diffusion is assumed,
- // the nrrd compatible way of storing b-values is not possible, so in this case we overwrite
- // the gradient direction to (1,1,1)
- if (b_vals[i] > 0 && vect[0] == 0.0 && vect[1] == 0.0 && vect[2] ==0.0)
+ if (vect.magnitude()<0.0001 && b_vals[i]>0)
{
- vect.fill(1.0);
+ vect.fill(0.0);
+ vect[0] = 1;
}
-
vect.normalize();
vect *= sqrt(b_vals[i]/maxb);
directions->push_back(vect);
}
// DWI TO DATATREE
PrintMemoryUsage();
Status(QString("Initializing Diffusion Image"));
if(m_OutputFolderNameSet) logfile << "Initializing Diffusion Image\n";
typedef mitk::DiffusionImage<PixelValueType> DiffVolumesType;
DiffVolumesType::Pointer diffImage = DiffVolumesType::New();
diffImage->SetDirections(directions);
diffImage->SetVectorImage(vecImage);
diffImage->SetB_Value(maxb);
diffImage->InitializeFromVectorImage();
diffImage->UpdateBValueMap();
Status(QString("Diffusion Image initialized"));
if(m_OutputFolderNameSet) logfile << "Diffusion Image initialized\n";
if(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked())
{
PrintMemoryUsage();
Status(QString("Averaging gradient directions"));
logfile << "Averaging gradient directions\n";
diffImage->AverageRedundantGradients(m_Controls->m_Blur->value());
}
QString descr = QString("%1_%2_%3")
.arg(((inHeaders)[0])->seriesDescription.c_str())
.arg(((inHeaders)[0])->seriesNumber)
.arg(((inHeaders)[0])->patientName.c_str());
descr = descr.trimmed();
descr = descr.replace(" ", "_");
if(!m_OutputFolderNameSet)
{
node=mitk::DataNode::New();
node->SetData( diffImage );
GetDefaultDataStorage()->Add(node);
SetDwiNodeProperties(node, descr.toStdString().c_str());
Status(QString("Image %1 added to datastorage").arg(descr));
}
else
{
typedef mitk::NrrdDiffusionImageWriter<PixelValueType> WriterType;
WriterType::Pointer writer = WriterType::New();
QString fullpath = QString("%1/%2.dwi")
.arg(m_OutputFolderName)
.arg(descr);
// if the override option is not checked, we need to make sure that the current filepath
// does not point to an existing file
if( !(m_Controls->m_OverrideOptionCheckbox->isChecked()) )
{
QFile outputFile( fullpath );
// generate new filename if file exists
int file_counter = 0;
while( outputFile.exists() )
{
// copy base name
QString newdescr = descr;
file_counter++;
MITK_WARN << "The file "<< fullpath.toStdString() << " exists already.";
QString appendix = QString("_%1").arg( QString::number(file_counter) );
newdescr.append(appendix);
fullpath = QString("%1/%2.dwi")
.arg(m_OutputFolderName)
.arg(newdescr);
// set the new generated filename for next check
outputFile.setFileName( fullpath );
}
}
writer->SetFileName(fullpath.toStdString());
writer->SetInput(diffImage);
try
{
writer->Update();
}
catch (itk::ExceptionObject &ex)
{
imageSuccessfullySaved = false;
Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
logfile << QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()).toStdString() << "\n";
node=mitk::DataNode::New();
node->SetData( diffImage );
GetDefaultDataStorage()->Add(node);
SetDwiNodeProperties(node, descr.toStdString().c_str());
Status(QString("Image %1 added to datastorage").arg(descr));
logfile << "Image " << descr.toStdString() << " added to datastorage\n";
continue ;
}
Status(QString("Image %1 written to disc (%1)").arg(fullpath.toStdString().c_str()));
logfile << "Image " << fullpath.toStdString() << "\n";
}
}
else
{
Status(QString("No diffusion information found (%1)").arg(folderName));
if(m_OutputFolderNameSet) logfile << "No diffusion information found "<< folderName.toStdString();
}
Status(QString("Finished processing %1 with memory:").arg(folderName));
if(m_OutputFolderNameSet) logfile << "Finished processing " << folderName.toStdString() << "\n";
PrintMemoryUsage();
clock.Stop(folderName.toAscii());
mitk::ProgressBar::GetInstance()->Progress();
int lwidget = m_Controls->listWidget->count();
std::cout << lwidget <<std::endl;
logfile << "\n";
}
logfile.close();
Status("Timing information");
clock.Report();
if(!m_OutputFolderNameSet && node.IsNotNull())
{
mitk::BaseData::Pointer basedata = node->GetData();
if (basedata.IsNotNull())
{
mitk::RenderingManager::GetInstance()->InitializeViews(
basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
}
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
try
{
MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, NULL) << " to '" << currLocale << "'";
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch (itk::ExceptionObject &ex)
{
Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
return ;
}
if (!imageSuccessfullySaved)
QMessageBox::warning(NULL,"WARNING","One or more files could not be saved! The according files where moved to the datastorage.");
Status(QString("Finished import with memory:"));
PrintMemoryUsage();
}
void QmitkDiffusionDicomImport::SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name)
{
node->SetProperty( "IsDWIRawVolume", mitk::BoolProperty::New( true ) );
// set foldername as string property
mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name );
node->SetProperty( "name", nameProp );
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp
index 5be77a4ac4..b28a792da4 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp
@@ -1,1445 +1,1498 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Qmitk
#include "QmitkFiberExtractionView.h"
#include <QmitkStdMultiWidget.h>
// Qt
#include <QMessageBox>
// MITK
#include <mitkNodePredicateProperty.h>
#include <mitkImageCast.h>
#include <mitkPointSet.h>
#include <mitkPlanarCircle.h>
#include <mitkPlanarPolygon.h>
#include <mitkPlanarRectangle.h>
#include <mitkPlanarFigureInteractor.h>
#include <mitkGlobalInteraction.h>
#include <mitkImageAccessByItk.h>
#include <mitkDataNodeObject.h>
#include <mitkDiffusionImage.h>
#include <mitkTensorImage.h>
#include "usModuleRegistry.h"
// ITK
#include <itkResampleImageFilter.h>
#include <itkGaussianInterpolateImageFunction.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <itkTractsToFiberEndingsImageFilter.h>
#include <itkTractDensityImageFilter.h>
#include <itkImageRegion.h>
#include <itkTractsToRgbaImageFilter.h>
#include <math.h>
const std::string QmitkFiberExtractionView::VIEW_ID = "org.mitk.views.fiberextraction";
const std::string id_DataManager = "org.mitk.views.datamanager";
using namespace mitk;
QmitkFiberExtractionView::QmitkFiberExtractionView()
: QmitkFunctionality()
, m_Controls( 0 )
, m_MultiWidget( NULL )
, m_CircleCounter(0)
, m_PolygonCounter(0)
, m_UpsamplingFactor(1)
+ , m_LastAddedPf(NULL)
{
}
// Destructor
QmitkFiberExtractionView::~QmitkFiberExtractionView()
{
}
void QmitkFiberExtractionView::CreateQtPartControl( QWidget *parent )
{
// build up qt view, unless already done
if ( !m_Controls )
{
// create GUI widgets from the Qt Designer's .ui file
m_Controls = new Ui::QmitkFiberExtractionViewControls;
m_Controls->setupUi( parent );
m_Controls->doExtractFibersButton->setDisabled(true);
m_Controls->PFCompoANDButton->setDisabled(true);
m_Controls->PFCompoORButton->setDisabled(true);
m_Controls->PFCompoNOTButton->setDisabled(true);
m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false);
m_Controls->m_RectangleButton->setVisible(false);
connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) );
connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) );
connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) );
connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) );
connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) );
connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) );
connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) );
connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) );
connect(m_Controls->m_Extract3dButton, SIGNAL(clicked()), this, SLOT(ExtractPassingMask()));
connect( m_Controls->m_ExtractMask, SIGNAL(clicked()), this, SLOT(ExtractEndingInMask()) );
connect( m_Controls->doExtractFibersButton, SIGNAL(clicked()), this, SLOT(DoFiberExtraction()) );
connect( m_Controls->m_RemoveOutsideMaskButton, SIGNAL(clicked()), this, SLOT(DoRemoveOutsideMask()));
connect( m_Controls->m_RemoveInsideMaskButton, SIGNAL(clicked()), this, SLOT(DoRemoveInsideMask()));
}
}
void QmitkFiberExtractionView::DoRemoveInsideMask()
{
if (m_MaskImageNode.IsNull())
return;
mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData());
for (int i=0; i<m_SelectedFB.size(); i++)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData());
QString name(m_SelectedFB.at(i)->GetName().c_str());
itkUCharImageType::Pointer mask = itkUCharImageType::New();
mitk::CastToItkImage<itkUCharImageType>(mitkMask, mask);
mitk::FiberBundleX::Pointer newFib = fib->RemoveFibersOutside(mask, true);
if (newFib->GetNumFibers()<=0)
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers.");
continue;
}
DataNode::Pointer newNode = DataNode::New();
newNode->SetData(newFib);
name += "_Cut";
newNode->SetName(name.toStdString());
GetDefaultDataStorage()->Add(newNode);
m_SelectedFB.at(i)->SetVisibility(false);
}
}
void QmitkFiberExtractionView::DoRemoveOutsideMask()
{
if (m_MaskImageNode.IsNull())
return;
mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData());
for (int i=0; i<m_SelectedFB.size(); i++)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData());
QString name(m_SelectedFB.at(i)->GetName().c_str());
itkUCharImageType::Pointer mask = itkUCharImageType::New();
mitk::CastToItkImage<itkUCharImageType>(mitkMask, mask);
mitk::FiberBundleX::Pointer newFib = fib->RemoveFibersOutside(mask);
if (newFib->GetNumFibers()<=0)
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers.");
continue;
}
DataNode::Pointer newNode = DataNode::New();
newNode->SetData(newFib);
name += "_Cut";
newNode->SetName(name.toStdString());
GetDefaultDataStorage()->Add(newNode);
m_SelectedFB.at(i)->SetVisibility(false);
}
}
void QmitkFiberExtractionView::ExtractEndingInMask()
{
if (m_MaskImageNode.IsNull())
return;
mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData());
for (int i=0; i<m_SelectedFB.size(); i++)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData());
QString name(m_SelectedFB.at(i)->GetName().c_str());
itkUCharImageType::Pointer mask = itkUCharImageType::New();
mitk::CastToItkImage<itkUCharImageType>(mitkMask, mask);
mitk::FiberBundleX::Pointer newFib = fib->ExtractFiberSubset(mask, false);
if (newFib->GetNumFibers()<=0)
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers.");
continue;
}
DataNode::Pointer newNode = DataNode::New();
newNode->SetData(newFib);
name += "_ending-in-mask";
newNode->SetName(name.toStdString());
GetDefaultDataStorage()->Add(newNode);
m_SelectedFB.at(i)->SetVisibility(false);
}
}
void QmitkFiberExtractionView::ExtractPassingMask()
{
if (m_MaskImageNode.IsNull())
return;
mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData());
for (int i=0; i<m_SelectedFB.size(); i++)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData());
QString name(m_SelectedFB.at(i)->GetName().c_str());
itkUCharImageType::Pointer mask = itkUCharImageType::New();
mitk::CastToItkImage<itkUCharImageType>(mitkMask, mask);
mitk::FiberBundleX::Pointer newFib = fib->ExtractFiberSubset(mask, true);
if (newFib->GetNumFibers()<=0)
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers.");
continue;
}
DataNode::Pointer newNode = DataNode::New();
newNode->SetData(newFib);
name += "_passing-mask";
newNode->SetName(name.toStdString());
GetDefaultDataStorage()->Add(newNode);
m_SelectedFB.at(i)->SetVisibility(false);
}
}
void QmitkFiberExtractionView::GenerateRoiImage(){
if (m_SelectedPF.empty())
return;
mitk::Geometry3D::Pointer geometry;
if (!m_SelectedFB.empty())
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.front()->GetData());
geometry = fib->GetGeometry();
}
else if (m_SelectedImage)
geometry = m_SelectedImage->GetGeometry();
else
return;
itk::Vector<double,3> spacing = geometry->GetSpacing();
spacing /= m_UpsamplingFactor;
mitk::Point3D newOrigin = geometry->GetOrigin();
mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
newOrigin[0] += bounds.GetElement(0);
newOrigin[1] += bounds.GetElement(2);
newOrigin[2] += bounds.GetElement(4);
itk::Matrix<double, 3, 3> direction;
itk::ImageRegion<3> imageRegion;
for (int i=0; i<3; i++)
for (int j=0; j<3; j++)
direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j];
imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
m_PlanarFigureImage = itkUCharImageType::New();
m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing
m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin
m_PlanarFigureImage->SetDirection( direction ); // Set the image direction
m_PlanarFigureImage->SetRegions( imageRegion );
m_PlanarFigureImage->Allocate();
m_PlanarFigureImage->FillBuffer( 0 );
Image::Pointer tmpImage = Image::New();
tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
for (int i=0; i<m_SelectedPF.size(); i++)
CompositeExtraction(m_SelectedPF.at(i), tmpImage);
DataNode::Pointer node = DataNode::New();
tmpImage = Image::New();
tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
node->SetData(tmpImage);
node->SetName("ROI Image");
this->GetDefaultDataStorage()->Add(node);
}
void QmitkFiberExtractionView::CompositeExtraction(mitk::DataNode::Pointer node, mitk::Image* image)
{
if (dynamic_cast<mitk::PlanarFigure*>(node.GetPointer()->GetData()) && !dynamic_cast<mitk::PlanarFigureComposite*>(node.GetPointer()->GetData()))
{
m_PlanarFigure = dynamic_cast<mitk::PlanarFigure*>(node.GetPointer()->GetData());
AccessFixedDimensionByItk_2(
image,
InternalReorientImagePlane, 3,
m_PlanarFigure->GetGeometry(), -1);
AccessFixedDimensionByItk_2(
m_InternalImage,
InternalCalculateMaskFromPlanarFigure,
3, 2, node->GetName() );
}
}
template < typename TPixel, unsigned int VImageDimension >
void QmitkFiberExtractionView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex )
{
MITK_DEBUG << "InternalReorientImagePlane() start";
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef itk::Image< float, VImageDimension > FloatImageType;
typedef itk::ResampleImageFilter<ImageType, FloatImageType, double> ResamplerType;
typename ResamplerType::Pointer resampler = ResamplerType::New();
mitk::PlaneGeometry* planegeo = dynamic_cast<mitk::PlaneGeometry*>(planegeo3D);
float upsamp = m_UpsamplingFactor;
float gausssigma = 0.5;
// Spacing
typename ResamplerType::SpacingType spacing = planegeo->GetSpacing();
spacing[0] = image->GetSpacing()[0] / upsamp;
spacing[1] = image->GetSpacing()[1] / upsamp;
spacing[2] = image->GetSpacing()[2];
resampler->SetOutputSpacing( spacing );
// Size
typename ResamplerType::SizeType size;
size[0] = planegeo->GetParametricExtentInMM(0) / spacing[0];
size[1] = planegeo->GetParametricExtentInMM(1) / spacing[1];
size[2] = 1;
resampler->SetSize( size );
// Origin
typename mitk::Point3D orig = planegeo->GetOrigin();
typename mitk::Point3D corrorig;
planegeo3D->WorldToIndex(orig,corrorig);
corrorig[0] += 0.5/upsamp;
corrorig[1] += 0.5/upsamp;
corrorig[2] += 0;
planegeo3D->IndexToWorld(corrorig,corrorig);
resampler->SetOutputOrigin(corrorig );
// Direction
typename ResamplerType::DirectionType direction;
typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix();
for(int c=0; c<matrix.ColumnDimensions; c++)
{
double sum = 0;
for(int r=0; r<matrix.RowDimensions; r++)
{
sum += matrix(r,c)*matrix(r,c);
}
for(int r=0; r<matrix.RowDimensions; r++)
{
direction(r,c) = matrix(r,c)/sqrt(sum);
}
}
resampler->SetOutputDirection( direction );
// Gaussian interpolation
if(gausssigma != 0)
{
double sigma[3];
for( unsigned int d = 0; d < 3; d++ )
{
sigma[d] = gausssigma * image->GetSpacing()[d];
}
double alpha = 2.0;
typedef itk::GaussianInterpolateImageFunction<ImageType, double>
GaussianInterpolatorType;
typename GaussianInterpolatorType::Pointer interpolator
= GaussianInterpolatorType::New();
interpolator->SetInputImage( image );
interpolator->SetParameters( sigma, alpha );
resampler->SetInterpolator( interpolator );
}
else
{
// typedef typename itk::BSplineInterpolateImageFunction<ImageType, double>
// InterpolatorType;
typedef typename itk::LinearInterpolateImageFunction<ImageType, double> InterpolatorType;
typename InterpolatorType::Pointer interpolator
= InterpolatorType::New();
interpolator->SetInputImage( image );
resampler->SetInterpolator( interpolator );
}
// Other resampling options
resampler->SetInput( image );
resampler->SetDefaultPixelValue(0);
MITK_DEBUG << "Resampling requested image plane ... ";
resampler->Update();
MITK_DEBUG << " ... done";
if(additionalIndex < 0)
{
this->m_InternalImage = mitk::Image::New();
this->m_InternalImage->InitializeByItk( resampler->GetOutput() );
this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() );
}
}
template < typename TPixel, unsigned int VImageDimension >
void QmitkFiberExtractionView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName )
{
MITK_DEBUG << "InternalCalculateMaskFromPlanarFigure() start";
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef itk::CastImageFilter< ImageType, itkUCharImageType > CastFilterType;
// Generate mask image as new image with same header as input image and
// initialize with "1".
itkUCharImageType::Pointer newMaskImage = itkUCharImageType::New();
newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing
newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin
newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction
newMaskImage->SetRegions( image->GetLargestPossibleRegion() );
newMaskImage->Allocate();
newMaskImage->FillBuffer( 1 );
// Generate VTK polygon from (closed) PlanarFigure polyline
// (The polyline points are shifted by -0.5 in z-direction to make sure
// that the extrusion filter, which afterwards elevates all points by +0.5
// in z-direction, creates a 3D object which is cut by the the plane z=0)
const Geometry2D *planarFigureGeometry2D = m_PlanarFigure->GetGeometry2D();
const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 );
const Geometry3D *imageGeometry3D = m_InternalImage->GetGeometry( 0 );
vtkPolyData *polyline = vtkPolyData::New();
polyline->Allocate( 1, 1 );
// Determine x- and y-dimensions depending on principal axis
int i0, i1;
switch ( axis )
{
case 0:
i0 = 1;
i1 = 2;
break;
case 1:
i0 = 0;
i1 = 2;
break;
case 2:
default:
i0 = 0;
i1 = 1;
break;
}
// Create VTK polydata object of polyline contour
vtkPoints *points = vtkPoints::New();
PlanarFigure::PolyLineType::const_iterator it;
std::vector<vtkIdType> indices;
unsigned int numberOfPoints = 0;
for ( it = planarFigurePolyline.begin();
it != planarFigurePolyline.end();
++it )
{
Point3D point3D;
// Convert 2D point back to the local index coordinates of the selected
// image
Point2D point2D = it->Point;
planarFigureGeometry2D->WorldToIndex(point2D, point2D);
point2D[0] -= 0.5/m_UpsamplingFactor;
point2D[1] -= 0.5/m_UpsamplingFactor;
planarFigureGeometry2D->IndexToWorld(point2D, point2D);
planarFigureGeometry2D->Map( point2D, point3D );
// Polygons (partially) outside of the image bounds can not be processed
// further due to a bug in vtkPolyDataToImageStencil
if ( !imageGeometry3D->IsInside( point3D ) )
{
float bounds[2] = {0,0};
bounds[0] =
this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0);
bounds[1] =
this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1);
imageGeometry3D->WorldToIndex( point3D, point3D );
// if (point3D[i0]<0)
// point3D[i0] = 0.5;
// else if (point3D[i0]>bounds[0])
// point3D[i0] = bounds[0]-0.5;
// if (point3D[i1]<0)
// point3D[i1] = 0.5;
// else if (point3D[i1]>bounds[1])
// point3D[i1] = bounds[1]-0.5;
if (point3D[i0]<0)
point3D[i0] = 0.0;
else if (point3D[i0]>bounds[0])
point3D[i0] = bounds[0]-0.001;
if (point3D[i1]<0)
point3D[i1] = 0.0;
else if (point3D[i1]>bounds[1])
point3D[i1] = bounds[1]-0.001;
points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
numberOfPoints++;
}
else
{
imageGeometry3D->WorldToIndex( point3D, point3D );
// Add point to polyline array
points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
numberOfPoints++;
}
}
polyline->SetPoints( points );
points->Delete();
vtkIdType *ptIds = new vtkIdType[numberOfPoints];
for ( vtkIdType i = 0; i < numberOfPoints; ++i )
{
ptIds[i] = i;
}
polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds );
// Extrude the generated contour polygon
vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New();
extrudeFilter->SetInputData( polyline );
extrudeFilter->SetScaleFactor( 1 );
extrudeFilter->SetExtrusionTypeToNormalExtrusion();
extrudeFilter->SetVector( 0.0, 0.0, 1.0 );
// Make a stencil from the extruded polygon
vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New();
polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() );
// Export from ITK to VTK (to use a VTK filter)
typedef itk::VTKImageImport< itkUCharImageType > ImageImportType;
typedef itk::VTKImageExport< itkUCharImageType > ImageExportType;
typename ImageExportType::Pointer itkExporter = ImageExportType::New();
itkExporter->SetInput( newMaskImage );
vtkImageImport *vtkImporter = vtkImageImport::New();
this->ConnectPipelines( itkExporter, vtkImporter );
vtkImporter->Update();
// Apply the generated image stencil to the input image
vtkImageStencil *imageStencilFilter = vtkImageStencil::New();
imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() );
imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() );
imageStencilFilter->ReverseStencilOff();
imageStencilFilter->SetBackgroundValue( 0 );
imageStencilFilter->Update();
// Export from VTK back to ITK
vtkImageExport *vtkExporter = vtkImageExport::New();
vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() );
vtkExporter->Update();
typename ImageImportType::Pointer itkImporter = ImageImportType::New();
this->ConnectPipelines( vtkExporter, itkImporter );
itkImporter->Update();
// calculate cropping bounding box
m_InternalImageMask3D = itkImporter->GetOutput();
m_InternalImageMask3D->SetDirection(image->GetDirection());
itk::ImageRegionConstIterator<itkUCharImageType>
itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType>
itimage(image, image->GetLargestPossibleRegion());
itmask = itmask.Begin();
itimage = itimage.Begin();
typename ImageType::SizeType lowersize = {{9999999999,9999999999,9999999999}};
typename ImageType::SizeType uppersize = {{0,0,0}};
while( !itmask.IsAtEnd() )
{
if(itmask.Get() == 0)
{
itimage.Set(0);
}
else
{
typename ImageType::IndexType index = itimage.GetIndex();
typename ImageType::SizeType signedindex;
signedindex[0] = index[0];
signedindex[1] = index[1];
signedindex[2] = index[2];
lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0];
lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1];
lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2];
uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0];
uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1];
uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2];
}
++itmask;
++itimage;
}
typename ImageType::IndexType index;
index[0] = lowersize[0];
index[1] = lowersize[1];
index[2] = lowersize[2];
typename ImageType::SizeType size;
size[0] = uppersize[0] - lowersize[0] + 1;
size[1] = uppersize[1] - lowersize[1] + 1;
size[2] = uppersize[2] - lowersize[2] + 1;
itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size);
// crop internal mask
typedef itk::RegionOfInterestImageFilter< itkUCharImageType, itkUCharImageType > ROIMaskFilterType;
typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New();
roi2->SetRegionOfInterest(cropRegion);
roi2->SetInput(m_InternalImageMask3D);
roi2->Update();
m_InternalImageMask3D = roi2->GetOutput();
Image::Pointer tmpImage = Image::New();
tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer());
tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer());
Image::Pointer tmpImage2 = Image::New();
tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer());
const Geometry3D *pfImageGeometry3D = tmpImage2->GetGeometry( 0 );
const Geometry3D *intImageGeometry3D = tmpImage->GetGeometry( 0 );
typedef itk::ImageRegionIteratorWithIndex<itkUCharImageType> IteratorType;
IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion());
imageIterator.GoToBegin();
while ( !imageIterator.IsAtEnd() )
{
unsigned char val = imageIterator.Value();
if (val>0)
{
itk::Index<3> index = imageIterator.GetIndex();
Point3D point;
point[0] = index[0];
point[1] = index[1];
point[2] = index[2];
intImageGeometry3D->IndexToWorld(point, point);
pfImageGeometry3D->WorldToIndex(point, point);
point[i0] += 0.5;
point[i1] += 0.5;
index[0] = point[0];
index[1] = point[1];
index[2] = point[2];
if (pfImageGeometry3D->IsIndexInside(index))
m_PlanarFigureImage->SetPixel(index, 1);
}
++imageIterator;
}
// Clean up VTK objects
polyline->Delete();
extrudeFilter->Delete();
polyDataToImageStencil->Delete();
vtkImporter->Delete();
imageStencilFilter->Delete();
//vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak??
delete[] ptIds;
}
void QmitkFiberExtractionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
{
m_MultiWidget = &stdMultiWidget;
}
void QmitkFiberExtractionView::StdMultiWidgetNotAvailable()
{
m_MultiWidget = NULL;
}
/* OnSelectionChanged is registered to SelectionService, therefore no need to
implement SelectionService Listener explicitly */
void QmitkFiberExtractionView::UpdateGui()
{
m_Controls->m_Extract3dButton->setEnabled(false);
m_Controls->m_ExtractMask->setEnabled(false);
m_Controls->m_RemoveOutsideMaskButton->setEnabled(false);
m_Controls->m_RemoveInsideMaskButton->setEnabled(false);
// are fiber bundles selected?
if ( m_SelectedFB.empty() )
{
m_Controls->m_InputData->setTitle("Please Select Input Data");
m_Controls->m_JoinBundles->setEnabled(false);
m_Controls->m_SubstractBundles->setEnabled(false);
m_Controls->doExtractFibersButton->setEnabled(false);
m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false);
}
else
{
m_Controls->m_InputData->setTitle("Input Data");
m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
// one bundle and one planar figure needed to extract fibers
if (!m_SelectedPF.empty())
m_Controls->doExtractFibersButton->setEnabled(true);
// more than two bundles needed to join/subtract
if (m_SelectedFB.size() > 1)
{
m_Controls->m_JoinBundles->setEnabled(true);
m_Controls->m_SubstractBundles->setEnabled(true);
}
else
{
m_Controls->m_JoinBundles->setEnabled(false);
m_Controls->m_SubstractBundles->setEnabled(false);
}
if (m_MaskImageNode.IsNotNull())
{
m_Controls->m_Extract3dButton->setEnabled(true);
m_Controls->m_ExtractMask->setEnabled(true);
m_Controls->m_RemoveOutsideMaskButton->setEnabled(true);
m_Controls->m_RemoveInsideMaskButton->setEnabled(true);
}
}
// are planar figures selected?
if ( m_SelectedPF.empty() )
{
m_Controls->doExtractFibersButton->setEnabled(false);
m_Controls->PFCompoANDButton->setEnabled(false);
m_Controls->PFCompoORButton->setEnabled(false);
m_Controls->PFCompoNOTButton->setEnabled(false);
m_Controls->m_GenerateRoiImage->setEnabled(false);
}
else
{
if ( !m_SelectedFB.empty() || m_SelectedImage.IsNotNull())
m_Controls->m_GenerateRoiImage->setEnabled(true);
else
m_Controls->m_GenerateRoiImage->setEnabled(false);
if (m_SelectedPF.size() > 1)
{
m_Controls->PFCompoANDButton->setEnabled(true);
m_Controls->PFCompoORButton->setEnabled(true);
m_Controls->PFCompoNOTButton->setEnabled(false);
}
else
{
m_Controls->PFCompoANDButton->setEnabled(false);
m_Controls->PFCompoORButton->setEnabled(false);
m_Controls->PFCompoNOTButton->setEnabled(true);
}
}
}
void QmitkFiberExtractionView::OnSelectionChanged( std::vector<mitk::DataNode*> nodes )
{
//reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection
m_SelectedFB.clear();
m_SelectedPF.clear();
m_SelectedSurfaces.clear();
m_SelectedImage = NULL;
m_MaskImageNode = NULL;
m_Controls->m_FibLabel->setText("<font color='red'>mandatory</font>");
m_Controls->m_PfLabel->setText("<font color='grey'>needed for extraction</font>");
for( std::vector<mitk::DataNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it )
{
mitk::DataNode::Pointer node = *it;
if ( dynamic_cast<mitk::FiberBundleX*>(node->GetData()) )
{
m_Controls->m_FibLabel->setText(node->GetName().c_str());
m_SelectedFB.push_back(node);
}
else if (dynamic_cast<mitk::PlanarFigure*>(node->GetData()))
{
m_Controls->m_PfLabel->setText(node->GetName().c_str());
m_SelectedPF.push_back(node);
}
else if (dynamic_cast<mitk::Image*>(node->GetData()))
{
m_SelectedImage = dynamic_cast<mitk::Image*>(node->GetData());
bool isBinary = false;
node->GetPropertyValue<bool>("binary", isBinary);
if (isBinary)
{
m_MaskImageNode = node;
m_Controls->m_PfLabel->setText(node->GetName().c_str());
}
}
else if (dynamic_cast<mitk::Surface*>(node->GetData()))
{
m_Controls->m_PfLabel->setText(node->GetName().c_str());
m_SelectedSurfaces.push_back(dynamic_cast<mitk::Surface*>(node->GetData()));
}
}
+
+ if (m_SelectedFB.empty())
+ {
+ int maxLayer = 0;
+ itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll();
+ for (unsigned int i=0; i<nodes->Size(); i++)
+ if (dynamic_cast<mitk::FiberBundleX*>(nodes->at(i)->GetData()))
+ {
+ int layer = 0;
+ nodes->at(i)->GetPropertyValue("layer", layer);
+ if (layer>=maxLayer)
+ {
+ maxLayer = layer;
+ m_Controls->m_FibLabel->setText(nodes->at(i)->GetName().c_str());
+ m_SelectedFB.clear();
+ m_SelectedFB.push_back(nodes->at(i));
+ }
+ }
+ }
+
+ if (m_SelectedPF.empty() && m_LastAddedPf.IsNotNull())
+ {
+ m_Controls->m_PfLabel->setText(m_LastAddedPf->GetName().c_str());
+ m_SelectedPF.push_back(m_LastAddedPf);
+
+// int maxLayer = 0;
+// itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll();
+// for (unsigned int i=0; i<nodes->Size(); i++)
+// if (dynamic_cast<mitk::PlanarFigure*>(nodes->at(i)->GetData()))
+// {
+// int layer;
+// nodes->at(i)->GetPropertyValue("layer", layer);
+// if (layer>=maxLayer)
+// {
+// maxLayer = layer;
+// m_Controls->m_PfLabel->setText(nodes->at(i)->GetName().c_str());
+// m_SelectedPF.clear();
+// m_SelectedPF.push_back(nodes->at(i));
+// }
+// }
+ }
+
UpdateGui();
GenerateStats();
}
void QmitkFiberExtractionView::OnDrawPolygon()
{
// bool checked = m_Controls->m_PolygonButton->isChecked();
// if(!this->AssertDrawingIsPossible(checked))
// return;
mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New();
figure->ClosedOn();
this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter));
MITK_DEBUG << "PlanarPolygon created ...";
mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll();
mitk::DataNode* node = 0;
mitk::PlanarFigureInteractor::Pointer figureInteractor = 0;
mitk::PlanarFigure* figureP = 0;
for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End()
; it++)
{
node = const_cast<mitk::DataNode*>(it->Value().GetPointer());
figureP = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
if(figureP)
{
- figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
-
- if(figureInteractor.IsNull())
- {
- figureInteractor = mitk::PlanarFigureInteractor::New();
- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
- figureInteractor->SetDataNode( node );
- }
+ figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
+
+ if(figureInteractor.IsNull())
+ {
+ figureInteractor = mitk::PlanarFigureInteractor::New();
+ us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
+ figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
+ figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
+ figureInteractor->SetDataNode( node );
+ }
}
}
}
void QmitkFiberExtractionView::OnDrawCircle()
{
mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New();
this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter));
this->GetDataStorage()->Modified();
mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll();
mitk::DataNode* node = 0;
mitk::PlanarFigureInteractor::Pointer figureInteractor = 0;
mitk::PlanarFigure* figureP = 0;
for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End(); it++)
{
node = const_cast<mitk::DataNode*>(it->Value().GetPointer());
figureP = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
if(figureP)
{
figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
if(figureInteractor.IsNull())
- {
- figureInteractor = mitk::PlanarFigureInteractor::New();
- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
- figureInteractor->SetDataNode( node );
- }
+ {
+ figureInteractor = mitk::PlanarFigureInteractor::New();
+ us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
+ figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
+ figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
+ figureInteractor->SetDataNode( node );
+ }
}
}
}
void QmitkFiberExtractionView::Activated()
{
}
void QmitkFiberExtractionView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name,
const char *propertyKey, mitk::BaseProperty *property )
{
// initialize figure's geometry with empty geometry
mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New();
figure->SetGeometry2D( emptygeometry );
//set desired data to DataNode where Planarfigure is stored
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
newNode->SetName(name.toStdString());
newNode->SetData(figure);
newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,0.0,0.0));
newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(2.0));
newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true));
newNode->AddProperty( "selected", mitk::BoolProperty::New(true) );
newNode->AddProperty( "planarfigure.ishovering", mitk::BoolProperty::New(true) );
newNode->AddProperty( "planarfigure.drawoutline", mitk::BoolProperty::New(true) );
newNode->AddProperty( "planarfigure.drawquantities", mitk::BoolProperty::New(false) );
newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true) );
newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(3.0) );
newNode->AddProperty( "planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.outline.width", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.helperline.width", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,1.0,1.0) );
newNode->AddProperty( "planarfigure.default.line.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.default.outline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.default.helperline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(0.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.default.markerline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(1.0,1.0,1.0) );
newNode->AddProperty( "planarfigure.default.marker.opacity",mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.hover.line.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.hover.outline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.hover.helperline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.hover.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.hover.markerline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.hover.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.hover.marker.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.selected.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.selected.line.opacity",mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.selected.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.selected.outline.opacity", mitk::FloatProperty::New(2.0));
newNode->AddProperty( "planarfigure.selected.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.selected.helperline.opacity",mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.selected.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.selected.markerline.opacity", mitk::FloatProperty::New(2.0) );
newNode->AddProperty( "planarfigure.selected.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) );
newNode->AddProperty( "planarfigure.selected.marker.opacity",mitk::FloatProperty::New(2.0));
// figure drawn on the topmost layer / image
newNode->SetColor(1.0,1.0,1.0);
newNode->SetOpacity(0.8);
GetDataStorage()->Add(newNode );
- std::vector<mitk::DataNode*> selectedNodes = GetDataManagerSelection();
- for(unsigned int i = 0; i < selectedNodes.size(); i++)
- {
- selectedNodes[i]->SetSelected(false);
- }
+ for(unsigned int i = 0; i < m_SelectedPF.size(); i++)
+ m_SelectedPF[i]->SetSelected(false);
newNode->SetSelected(true);
+ m_SelectedPF.clear();
+ m_SelectedPF.push_back(newNode);
+ m_LastAddedPf = newNode;
+ m_Controls->m_PfLabel->setText(newNode->GetName().c_str());
}
void QmitkFiberExtractionView::DoFiberExtraction()
{
if ( m_SelectedFB.empty() ){
QMessageBox::information( NULL, "Warning", "No fibe bundle selected!");
MITK_WARN("QmitkFiberExtractionView") << "no fibe bundle selected";
return;
}
- for (int i=0; i<m_SelectedFB.size(); i++)
+ for (unsigned int i=0; i<m_SelectedFB.size(); i++)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData());
mitk::PlanarFigure::Pointer roi = dynamic_cast<mitk::PlanarFigure*> (m_SelectedPF.at(0)->GetData());
mitk::FiberBundleX::Pointer extFB = fib->ExtractFiberSubset(roi);
if (extFB->GetNumFibers()<=0)
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers.");
continue;
}
mitk::DataNode::Pointer node;
node = mitk::DataNode::New();
node->SetData(extFB);
QString name(m_SelectedFB.at(i)->GetName().c_str());
name += "_";
name += m_SelectedPF.at(0)->GetName().c_str();
node->SetName(name.toStdString());
GetDataStorage()->Add(node);
m_SelectedFB.at(i)->SetVisibility(false);
}
}
void QmitkFiberExtractionView::GenerateAndComposite()
{
mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New();
mitk::PlaneGeometry* currentGeometry2D = dynamic_cast<mitk::PlaneGeometry*>( const_cast<mitk::Geometry2D*>(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D()));
PFCAnd->SetGeometry2D(currentGeometry2D);
PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION);
for( std::vector<mitk::DataNode::Pointer>::iterator it = m_SelectedPF.begin();
it != m_SelectedPF.end(); ++it )
{
mitk::DataNode::Pointer nodePF = *it;
mitk::PlanarFigure::Pointer tmpPF = dynamic_cast<mitk::PlanarFigure*>( nodePF->GetData() );
PFCAnd->addPlanarFigure( tmpPF );
PFCAnd->addDataNode( nodePF );
PFCAnd->setDisplayName("AND_COMPO");
}
AddCompositeToDatastorage(PFCAnd, NULL);
}
void QmitkFiberExtractionView::GenerateOrComposite()
{
mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New();
mitk::PlaneGeometry* currentGeometry2D = dynamic_cast<mitk::PlaneGeometry*>( const_cast<mitk::Geometry2D*>(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D()));
PFCOr->SetGeometry2D(currentGeometry2D);
PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION);
for( std::vector<mitk::DataNode::Pointer>::iterator it = m_SelectedPF.begin();
it != m_SelectedPF.end(); ++it )
{
mitk::DataNode::Pointer nodePF = *it;
mitk::PlanarFigure::Pointer tmpPF = dynamic_cast<mitk::PlanarFigure*>( nodePF->GetData() );
PFCOr->addPlanarFigure( tmpPF );
PFCOr->addDataNode( nodePF );
PFCOr->setDisplayName("OR_COMPO");
}
AddCompositeToDatastorage(PFCOr, NULL);
}
void QmitkFiberExtractionView::GenerateNotComposite()
{
mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New();
mitk::PlaneGeometry* currentGeometry2D = dynamic_cast<mitk::PlaneGeometry*>( const_cast<mitk::Geometry2D*>(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D()));
PFCNot->SetGeometry2D(currentGeometry2D);
PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION);
for( std::vector<mitk::DataNode::Pointer>::iterator it = m_SelectedPF.begin();
it != m_SelectedPF.end(); ++it )
{
mitk::DataNode::Pointer nodePF = *it;
mitk::PlanarFigure::Pointer tmpPF = dynamic_cast<mitk::PlanarFigure*>( nodePF->GetData() );
PFCNot->addPlanarFigure( tmpPF );
PFCNot->addDataNode( nodePF );
PFCNot->setDisplayName("NOT_COMPO");
}
AddCompositeToDatastorage(PFCNot, NULL);
}
/* CLEANUP NEEDED */
void QmitkFiberExtractionView::AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer pfcomp, mitk::DataNode::Pointer parentDataNode )
{
mitk::DataNode::Pointer newPFCNode;
newPFCNode = mitk::DataNode::New();
newPFCNode->SetName( pfcomp->getDisplayName() );
newPFCNode->SetData(pfcomp);
newPFCNode->SetVisibility(true);
+ for(unsigned int i = 0; i < m_SelectedPF.size(); i++)
+ m_SelectedPF[i]->SetSelected(false);
+
+ newPFCNode->SetSelected(true);
+ m_LastAddedPf = newPFCNode;
+ m_SelectedPF.clear();
+ m_SelectedPF.push_back(newPFCNode);
+ m_Controls->m_PfLabel->setText(newPFCNode->GetName().c_str());
+
switch (pfcomp->getOperationType()) {
case 0:
{
if (!parentDataNode.IsNull()) {
GetDataStorage()->Add(newPFCNode, parentDataNode);
} else {
GetDataStorage()->Add(newPFCNode);
}
//iterate through its childs
for(int i=0; i<pfcomp->getNumberOfChildren(); ++i)
{
mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i);
mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i);
mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast<mitk::PlanarFigureComposite*>(tmpPFchild.GetPointer());
if ( !pfcompcast.IsNull() )
{
// child is of type planar Figure composite
// make new node of the child, cuz later the child has to be removed of its old position in datamanager
// feed new dataNode with information of the savedDataNode, which is gonna be removed soon
mitk::DataNode::Pointer newChildPFCNode;
newChildPFCNode = mitk::DataNode::New();
newChildPFCNode->SetData(tmpPFchild);
newChildPFCNode->SetName( savedPFchildNode->GetName() );
pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user
//update inside vector the dataNodePointer
pfcomp->replaceDataNodeAt(i, newChildPFCNode);
AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent
// remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager
// without having its parent anymore
//GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}else{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
}
else
{
// child is not of type PlanarFigureComposite, so its one of the planarFigures
// create new dataNode containing the data of the old dataNode, but position in dataManager will be
// modified cuz we re setting a (new) parent.
mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New();
newPFchildNode->SetName(savedPFchildNode->GetName() );
newPFchildNode->SetData(tmpPFchild);
newPFchildNode->SetVisibility(true);
// replace the dataNode in PFComp DataNodeVector
pfcomp->replaceDataNodeAt(i, newPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}
else
{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode))
{
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName();
//add new child to datamanager with its new position as child of newPFCNode parent
GetDataStorage()->Add(newPFchildNode, newPFCNode);
}
}
GetDataStorage()->Modified();
break;
}
case 1:
{
if (!parentDataNode.IsNull()) {
MITK_DEBUG << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ;
GetDataStorage()->Add(newPFCNode, parentDataNode);
} else {
MITK_DEBUG << "adding " << newPFCNode->GetName();
GetDataStorage()->Add(newPFCNode);
}
for(int i=0; i<pfcomp->getNumberOfChildren(); ++i)
{
mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i);
mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i);
mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast<mitk::PlanarFigureComposite*>(tmpPFchild.GetPointer());
if ( !pfcompcast.IsNull() )
{ // child is of type planar Figure composite
// make new node of the child, cuz later the child has to be removed of its old position in datamanager
// feed new dataNode with information of the savedDataNode, which is gonna be removed soon
mitk::DataNode::Pointer newChildPFCNode;
newChildPFCNode = mitk::DataNode::New();
newChildPFCNode->SetData(tmpPFchild);
newChildPFCNode->SetName( savedPFchildNode->GetName() );
pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user
//update inside vector the dataNodePointer
pfcomp->replaceDataNodeAt(i, newChildPFCNode);
AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent
// remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager
// without having its parent anymore
//GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}else{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
} else {
// child is not of type PlanarFigureComposite, so its one of the planarFigures
// create new dataNode containing the data of the old dataNode, but position in dataManager will be
// modified cuz we re setting a (new) parent.
mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New();
newPFchildNode->SetName(savedPFchildNode->GetName() );
newPFchildNode->SetData(tmpPFchild);
newPFchildNode->SetVisibility(true);
// replace the dataNode in PFComp DataNodeVector
pfcomp->replaceDataNodeAt(i, newPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}else{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName();
//add new child to datamanager with its new position as child of newPFCNode parent
GetDataStorage()->Add(newPFchildNode, newPFCNode);
}
}
GetDataStorage()->Modified();
break;
}
case 2:
{
if (!parentDataNode.IsNull()) {
MITK_DEBUG << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ;
GetDataStorage()->Add(newPFCNode, parentDataNode);
}
else
{
MITK_DEBUG << "adding " << newPFCNode->GetName();
GetDataStorage()->Add(newPFCNode);
}
//iterate through its childs
for(int i=0; i<pfcomp->getNumberOfChildren(); ++i)
{
mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i);
mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i);
mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast<mitk::PlanarFigureComposite*>(tmpPFchild.GetPointer());
if ( !pfcompcast.IsNull() )
{ // child is of type planar Figure composite
// makeRemoveBundle new node of the child, cuz later the child has to be removed of its old position in datamanager
// feed new dataNode with information of the savedDataNode, which is gonna be removed soon
mitk::DataNode::Pointer newChildPFCNode;
newChildPFCNode = mitk::DataNode::New();
newChildPFCNode->SetData(tmpPFchild);
newChildPFCNode->SetName( savedPFchildNode->GetName() );
pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user
//update inside vector the dataNodePointer
pfcomp->replaceDataNodeAt(i, newChildPFCNode);
AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent
// remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager
// without having its parent anymore
//GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}else{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
} else {
// child is not of type PlanarFigureComposite, so its one of the planarFigures
// create new dataNode containing the data of the old dataNode, but position in dataManager will be
// modified cuz we re setting a (new) parent.
mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New();
newPFchildNode->SetName(savedPFchildNode->GetName() );
newPFchildNode->SetData(tmpPFchild);
newPFchildNode->SetVisibility(true);
// replace the dataNode in PFComp DataNodeVector
pfcomp->replaceDataNodeAt(i, newPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it";
}else{
MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName();
}
// remove old child position in dataStorage
GetDataStorage()->Remove(savedPFchildNode);
if ( GetDataStorage()->Exists(savedPFchildNode)) {
MITK_DEBUG << savedPFchildNode->GetName() << " still exists";
}
MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName();
//add new child to datamanager with its new position as child of newPFCNode parent
GetDataStorage()->Add(newPFchildNode, newPFCNode);
}
}
GetDataStorage()->Modified();
break;
}
default:
MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ;
break;
}
}
void QmitkFiberExtractionView::JoinBundles()
{
if ( m_SelectedFB.size()<2 ){
QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!");
MITK_WARN("QmitkFiberExtractionView") << "Select at least two fiber bundles!";
return;
}
mitk::FiberBundleX::Pointer newBundle = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(0)->GetData());
m_SelectedFB.at(0)->SetVisibility(false);
QString name("");
name += QString(m_SelectedFB.at(0)->GetName().c_str());
for (int i=1; i<m_SelectedFB.size(); i++)
{
newBundle = newBundle->AddBundle(dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData()));
name += "+"+QString(m_SelectedFB.at(i)->GetName().c_str());
m_SelectedFB.at(i)->SetVisibility(false);
}
mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
fbNode->SetData(newBundle);
fbNode->SetName(name.toStdString());
fbNode->SetVisibility(true);
GetDataStorage()->Add(fbNode);
}
void QmitkFiberExtractionView::SubstractBundles()
{
if ( m_SelectedFB.size()<2 ){
QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!");
MITK_WARN("QmitkFiberExtractionView") << "Select at least two fiber bundles!";
return;
}
mitk::FiberBundleX::Pointer newBundle = dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(0)->GetData());
m_SelectedFB.at(0)->SetVisibility(false);
QString name("");
name += QString(m_SelectedFB.at(0)->GetName().c_str());
for (int i=1; i<m_SelectedFB.size(); i++)
{
newBundle = newBundle->SubtractBundle(dynamic_cast<mitk::FiberBundleX*>(m_SelectedFB.at(i)->GetData()));
if (newBundle.IsNull())
break;
name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str());
m_SelectedFB.at(i)->SetVisibility(false);
}
if (newBundle.IsNull())
{
QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!");
return;
}
mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
fbNode->SetData(newBundle);
fbNode->SetName(name.toStdString());
fbNode->SetVisibility(true);
GetDataStorage()->Add(fbNode);
}
void QmitkFiberExtractionView::GenerateStats()
{
if ( m_SelectedFB.empty() )
return;
QString stats("");
for( int i=0; i<m_SelectedFB.size(); i++ )
{
mitk::DataNode::Pointer node = m_SelectedFB[i];
if (node.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(node->GetData()))
{
if (i>0)
stats += "\n-----------------------------\n";
stats += QString(node->GetName().c_str()) + "\n";
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>(node->GetData());
stats += "Number of fibers: "+ QString::number(fib->GetNumFibers()) + "\n";
stats += "Min. length: "+ QString::number(fib->GetMinFiberLength(),'f',1) + " mm\n";
stats += "Max. length: "+ QString::number(fib->GetMaxFiberLength(),'f',1) + " mm\n";
stats += "Mean length: "+ QString::number(fib->GetMeanFiberLength(),'f',1) + " mm\n";
stats += "Median length: "+ QString::number(fib->GetMedianFiberLength(),'f',1) + " mm\n";
stats += "Standard deviation: "+ QString::number(fib->GetLengthStDev(),'f',1) + " mm\n";
}
}
this->m_Controls->m_StatsTextEdit->setText(stats);
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h
index d1f7913143..b0544e16f6 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h
@@ -1,174 +1,175 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef QmitkFiberExtractionView_h
#define QmitkFiberExtractionView_h
#include <QmitkFunctionality.h>
#include "ui_QmitkFiberExtractionViewControls.h"
#include <mitkPlanarFigureComposite.h>
#include <mitkFiberBundleX.h>
#include <mitkSurface.h>
#include <itkCastImageFilter.h>
#include <itkVTKImageImport.h>
#include <itkVTKImageExport.h>
#include <itkRegionOfInterestImageFilter.h>
#include <vtkLinearExtrusionFilter.h>
#include <vtkPolyDataToImageStencil.h>
#include <vtkSelectEnclosedPoints.h>
#include <vtkImageImport.h>
#include <vtkImageExport.h>
#include <vtkImageStencil.h>
#include <vtkSmartPointer.h>
#include <vtkSelection.h>
#include <vtkSelectionNode.h>
#include <vtkExtractSelectedThresholds.h>
#include <vtkFloatArray.h>
/*!
\brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, join and subtract bundles, generate images from the selected bundle and much more.
\sa QmitkFunctionality
\ingroup Functionalities
*/
class QmitkFiberExtractionView : public QmitkFunctionality
{
// this is needed for all Qt objects that should have a Qt meta-object
// (everything that derives from QObject and wants to have signal/slots)
Q_OBJECT
public:
typedef itk::Image< unsigned char, 3 > itkUCharImageType;
static const std::string VIEW_ID;
QmitkFiberExtractionView();
virtual ~QmitkFiberExtractionView();
virtual void CreateQtPartControl(QWidget *parent);
virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget);
virtual void StdMultiWidgetNotAvailable();
virtual void Activated();
protected slots:
void OnDrawCircle(); ///< add circle interactors etc.
void OnDrawPolygon(); ///< add circle interactors etc.
void DoFiberExtraction(); ///< Extract fibers from selected bundle
void GenerateAndComposite();
void GenerateOrComposite();
void GenerateNotComposite();
void DoRemoveOutsideMask();
void DoRemoveInsideMask();
void JoinBundles(); ///< merge selected fiber bundles
void SubstractBundles(); ///< subtract bundle A from bundle B. Not commutative! Defined by order of selection.
void GenerateRoiImage(); ///< generate binary image of selected planar figures.
void ExtractPassingMask(); ///< extract all fibers passing the selected surface mesh
void ExtractEndingInMask(); ///< extract all fibers passing the selected surface mesh
virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey = NULL, mitk::BaseProperty *property = NULL );
protected:
/// \brief called by QmitkFunctionality when DataManager's selection has changed
virtual void OnSelectionChanged( std::vector<mitk::DataNode*> nodes );
Ui::QmitkFiberExtractionViewControls* m_Controls;
QmitkStdMultiWidget* m_MultiWidget;
/** Connection from VTK to ITK */
template <typename VTK_Exporter, typename ITK_Importer>
void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
{
importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
importer->SetCallbackUserData(exporter->GetCallbackUserData());
}
template <typename ITK_Exporter, typename VTK_Importer>
void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
{
importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
importer->SetCallbackUserData(exporter->GetCallbackUserData());
}
template < typename TPixel, unsigned int VImageDimension >
void InternalCalculateMaskFromPlanarFigure(
itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName );
template < typename TPixel, unsigned int VImageDimension >
void InternalReorientImagePlane(
const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex );
void GenerateStats(); ///< generate statistics of selected fiber bundles
void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection
int m_CircleCounter; ///< used for data node naming
int m_PolygonCounter; ///< used for data node naming
std::vector<mitk::DataNode::Pointer> m_SelectedFB; ///< selected fiber bundle nodes
std::vector<mitk::DataNode::Pointer> m_SelectedPF; ///< selected planar figure nodes
std::vector<mitk::Surface::Pointer> m_SelectedSurfaces;
mitk::Image::Pointer m_SelectedImage;
mitk::Image::Pointer m_InternalImage;
mitk::PlanarFigure::Pointer m_PlanarFigure;
itkUCharImageType::Pointer m_InternalImageMask3D;
itkUCharImageType::Pointer m_PlanarFigureImage;
float m_UpsamplingFactor; ///< upsampling factor for all image generations
mitk::DataNode::Pointer m_MaskImageNode;
+ mitk::DataNode::Pointer m_LastAddedPf;
void AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer, mitk::DataNode::Pointer);
void debugPFComposition(mitk::PlanarFigureComposite::Pointer , int );
void CompositeExtraction(mitk::DataNode::Pointer node, mitk::Image* image);
mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute);
mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib);
mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib);
mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib);
};
#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp
index b9c9bcbca0..ee4363664a 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp
@@ -1,2035 +1,2336 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
//misc
#define _USE_MATH_DEFINES
#include <math.h>
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Qmitk
#include "QmitkFiberfoxView.h"
// MITK
#include <mitkImage.h>
#include <mitkDiffusionImage.h>
#include <mitkImageToItk.h>
#include <mitkImageCast.h>
#include <mitkProperties.h>
#include <mitkPlanarFigureInteractor.h>
#include <mitkDataStorage.h>
#include <itkFibersFromPlanarFiguresFilter.h>
#include <itkTractsToDWIImageFilter.h>
#include <mitkTensorImage.h>
#include <mitkILinkedRenderWindowPart.h>
#include <mitkGlobalInteraction.h>
#include <mitkImageToItk.h>
#include <mitkImageCast.h>
#include <mitkImageGenerator.h>
#include <mitkNodePredicateDataType.h>
#include <itkScalableAffineTransform.h>
#include <mitkLevelWindowProperty.h>
#include <mitkNodePredicateOr.h>
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateNot.h>
-#include <itkAddArtifactsToDwiImageFilter.h>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/xml_parser.hpp>
#include <boost/foreach.hpp>
#include <QFileDialog>
#include <QMessageBox>
#include "usModuleRegistry.h"
+#include <mitkChiSquareNoiseModel.h>
+#include <itksys/SystemTools.hxx>
+#include <mitkNrrdDiffusionImageWriter.h>
#define _USE_MATH_DEFINES
#include <math.h>
+QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view)
+ : m_View(view)
+{
+
+}
+
+void QmitkFiberfoxWorker::run()
+{
+ try{
+ switch (m_FilterType)
+ {
+ case 0:
+ m_View->m_TractsToDwiFilter->Update();
+ break;
+ case 1:
+ m_View->m_ArtifactsToDwiFilter->Update();
+ break;
+ }
+ }
+ catch( ... )
+ {
+
+ }
+ m_View->m_Thread.quit();
+}
+
const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview";
QmitkFiberfoxView::QmitkFiberfoxView()
: QmitkAbstractView()
, m_Controls( 0 )
, m_SelectedImage( NULL )
+ , m_OutputPath("")
+ , m_Worker(this)
+ , m_ThreadIsRunning(false)
+{
+ m_ImageGenParameters.noiseModel = NULL;
+ m_ImageGenParameters.noiseModelShort = NULL;
+
+ m_Worker.moveToThread(&m_Thread);
+ connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread()));
+ connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run()));
+ connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread()));
+ connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread()));
+ m_SimulationTimer = new QTimer(this);
+}
+
+void QmitkFiberfoxView::KillThread()
{
+ MITK_INFO << "Aborting DWI simulation.";
+ switch (m_Worker.m_FilterType)
+ {
+ case 0:
+ m_TractsToDwiFilter->SetAbortGenerateData(true);
+ break;
+ case 1:
+ m_ArtifactsToDwiFilter->SetAbortGenerateData(true);
+ break;
+ }
+}
+void QmitkFiberfoxView::BeforeThread()
+{
+ m_SimulationTime = QTime::currentTime();
+ m_SimulationTimer->start(100);
+ m_ImageGenParametersBackup = m_ImageGenParameters;
+ m_Controls->m_AbortSimulationButton->setVisible(true);
+ m_Controls->m_GenerateImageButton->setVisible(false);
+ m_Controls->m_SimulationStatusText->setVisible(true);
+ m_ThreadIsRunning = true;
+}
+
+void QmitkFiberfoxView::AfterThread()
+{
+ UpdateSimulationStatus();
+ m_SimulationTimer->stop();
+ m_Controls->m_AbortSimulationButton->setVisible(false);
+ m_Controls->m_GenerateImageButton->setVisible(true);
+ //m_Controls->m_SimulationStatusText->setVisible(false);
+ m_ThreadIsRunning = false;
+
+ mitk::DiffusionImage<short>::Pointer mitkImage = mitk::DiffusionImage<short>::New();
+ switch (m_Worker.m_FilterType)
+ {
+ case 0:
+ {
+ if (m_TractsToDwiFilter->GetAbortGenerateData())
+ {
+ MITK_INFO << "Simulation aborted.";
+ return;
+ }
+
+ mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() );
+ mitkImage->SetB_Value(m_ImageGenParametersBackup.b_value);
+ mitkImage->SetDirections(m_ImageGenParametersBackup.gradientDirections);
+ mitkImage->InitializeFromVectorImage();
+ m_ImageGenParametersBackup.resultNode->SetData( mitkImage );
+
+ m_ImageGenParametersBackup.resultNode->SetName(m_ImageGenParametersBackup.parentNode->GetName()
+ +"_D"+QString::number(m_ImageGenParametersBackup.imageRegion.GetSize(0)).toStdString()
+ +"-"+QString::number(m_ImageGenParametersBackup.imageRegion.GetSize(1)).toStdString()
+ +"-"+QString::number(m_ImageGenParametersBackup.imageRegion.GetSize(2)).toStdString()
+ +"_S"+QString::number(m_ImageGenParametersBackup.imageSpacing[0]).toStdString()
+ +"-"+QString::number(m_ImageGenParametersBackup.imageSpacing[1]).toStdString()
+ +"-"+QString::number(m_ImageGenParametersBackup.imageSpacing[2]).toStdString()
+ +"_b"+QString::number(m_ImageGenParametersBackup.b_value).toStdString()
+ +"_"+m_ImageGenParametersBackup.signalModelString.toStdString()
+ +m_ImageGenParametersBackup.artifactModelString.toStdString());
+
+ GetDataStorage()->Add(m_ImageGenParametersBackup.resultNode, m_ImageGenParametersBackup.parentNode);
+
+ m_ImageGenParametersBackup.resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) );
+
+ if (m_Controls->m_VolumeFractionsBox->isChecked())
+ {
+ std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions();
+ for (int k=0; k<volumeFractions.size(); k++)
+ {
+ mitk::Image::Pointer image = mitk::Image::New();
+ image->InitializeByItk(volumeFractions.at(k).GetPointer());
+ image->SetVolume(volumeFractions.at(k)->GetBufferPointer());
+
+ mitk::DataNode::Pointer node = mitk::DataNode::New();
+ node->SetData( image );
+ node->SetName(m_ImageGenParametersBackup.parentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString());
+ GetDataStorage()->Add(node, m_ImageGenParametersBackup.parentNode);
+ }
+ }
+ break;
+ }
+ case 1:
+ {
+ if (m_ArtifactsToDwiFilter->GetAbortGenerateData())
+ {
+ MITK_INFO << "Simulation aborted.";
+ return;
+ }
+
+ mitk::DiffusionImage<short>::Pointer diffImg = dynamic_cast<mitk::DiffusionImage<short>*>(m_ImageGenParametersBackup.parentNode->GetData());
+ mitkImage = mitk::DiffusionImage<short>::New();
+ mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() );
+ mitkImage->SetB_Value(diffImg->GetB_Value());
+ mitkImage->SetDirections(diffImg->GetDirections());
+ mitkImage->InitializeFromVectorImage();
+ m_ImageGenParametersBackup.resultNode->SetData( mitkImage );
+ m_ImageGenParametersBackup.resultNode->SetName(m_ImageGenParametersBackup.parentNode->GetName()+m_ImageGenParameters.artifactModelString.toStdString());
+ GetDataStorage()->Add(m_ImageGenParametersBackup.resultNode, m_ImageGenParametersBackup.parentNode);
+ break;
+ }
+ }
+
+ mitk::BaseData::Pointer basedata = m_ImageGenParametersBackup.resultNode->GetData();
+ if (basedata.IsNotNull())
+ {
+ mitk::RenderingManager::GetInstance()->InitializeViews(
+ basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
+ mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+ }
+
+ if (!m_ImageGenParametersBackup.outputPath.isEmpty())
+ {
+ try{
+ QString status("Saving output image to ");
+ status += m_ImageGenParametersBackup.outputPath;
+ status += m_ImageGenParametersBackup.resultNode->GetName().c_str();
+ status += ".dwi";
+ m_Controls->m_SimulationStatusText->append(status);
+ mitk::NrrdDiffusionImageWriter<short>::Pointer writer = NrrdDiffusionImageWriter<short>::New();
+ writer->SetFileName(m_ImageGenParametersBackup.outputPath.toStdString()+m_ImageGenParametersBackup.resultNode->GetName()+".dwi");
+ writer->SetInput(mitkImage);
+ writer->Update();
+ m_Controls->m_SimulationStatusText->append("File saved successfully.");
+ }
+ catch (itk::ExceptionObject &e)
+ {
+ QString status("Exception during DWI writing: ");
+ status += e.GetDescription();
+ m_Controls->m_SimulationStatusText->append(status);
+ }
+ catch (...)
+ {
+ m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!");
+ }
+ }
+}
+
+void QmitkFiberfoxView::UpdateSimulationStatus()
+{
+ QString statusText;
+ switch (m_Worker.m_FilterType)
+ {
+ case 0:
+ statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str());
+ break;
+ case 1:
+ statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str());
+ break;
+ }
+
+ if (QString::compare(m_SimulationStatusText,statusText)!=0)
+ {
+ m_Controls->m_SimulationStatusText->clear();
+ statusText = "<pre>"+statusText+"</pre>";
+ m_Controls->m_SimulationStatusText->setText(statusText);
+ }
}
// Destructor
QmitkFiberfoxView::~QmitkFiberfoxView()
{
-
+ if (m_ImageGenParameters.noiseModel!=NULL)
+ delete m_ImageGenParameters.noiseModel;
+ if (m_ImageGenParameters.noiseModelShort!=NULL)
+ delete m_ImageGenParameters.noiseModelShort;
+ delete m_SimulationTimer;
}
void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent )
{
// build up qt view, unless already done
if ( !m_Controls )
{
// create GUI widgets from the Qt Designer's .ui file
m_Controls = new Ui::QmitkFiberfoxViewControls;
m_Controls->setupUi( parent );
m_Controls->m_StickWidget1->setVisible(true);
m_Controls->m_StickWidget2->setVisible(false);
m_Controls->m_ZeppelinWidget1->setVisible(false);
m_Controls->m_ZeppelinWidget2->setVisible(false);
m_Controls->m_TensorWidget1->setVisible(false);
m_Controls->m_TensorWidget2->setVisible(false);
m_Controls->m_BallWidget1->setVisible(true);
m_Controls->m_BallWidget2->setVisible(false);
m_Controls->m_AstrosticksWidget1->setVisible(false);
m_Controls->m_AstrosticksWidget2->setVisible(false);
m_Controls->m_DotWidget1->setVisible(false);
m_Controls->m_DotWidget2->setVisible(false);
m_Controls->m_Comp4FractionFrame->setVisible(false);
m_Controls->m_DiffusionPropsMessage->setVisible(false);
m_Controls->m_GeometryMessage->setVisible(false);
m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false);
m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false);
m_Controls->m_VarianceBox->setVisible(false);
m_Controls->m_NoiseFrame->setVisible(false);
m_Controls->m_GhostFrame->setVisible(false);
m_Controls->m_DistortionsFrame->setVisible(false);
m_Controls->m_EddyFrame->setVisible(false);
m_Controls->m_SpikeFrame->setVisible(false);
m_Controls->m_AliasingFrame->setVisible(false);
+ m_Controls->m_MotionArtifactFrame->setVisible(false);
+ m_ParameterFile = QDir::currentPath()+"/param.ffp";
+
+ m_Controls->m_AbortSimulationButton->setVisible(false);
+ m_Controls->m_SimulationStatusText->setVisible(false);
m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage());
mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage");
mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti);
isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi);
mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage);
mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage);
m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate);
+ connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) );
+ connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread()));
connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage()));
connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers()));
connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI()));
connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton()));
connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles()));
connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double)));
connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int)));
connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int)));
connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double)));
connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double)));
connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double)));
connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double)));
- connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGibbsRinging(int)));
connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int)));
connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int)));
connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int)));
connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int)));
connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int)));
connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int)));
+ connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int)));
connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int)));
connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles()));
connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform()));
connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid()));
connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int)));
connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int)));
connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int)));
connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int)));
connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int)));
connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int)));
connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters()));
connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters()));
+ connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath()));
+
}
}
void QmitkFiberfoxView::UpdateImageParameters()
{
- m_ImageGenParameters.artifactList.clear();
m_ImageGenParameters.nonFiberModelList.clear();
m_ImageGenParameters.fiberModelList.clear();
m_ImageGenParameters.signalModelString = "";
m_ImageGenParameters.artifactModelString = "";
m_ImageGenParameters.resultNode = mitk::DataNode::New();
- m_ImageGenParameters.tissueMaskImage = NULL;
m_ImageGenParameters.frequencyMap = NULL;
m_ImageGenParameters.gradientDirections.clear();
m_ImageGenParameters.spikes = 0;
m_ImageGenParameters.spikeAmplitude = 1;
m_ImageGenParameters.wrap = 1;
+ m_ImageGenParameters.outputPath = m_OutputPath;
if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI
{
mitk::DiffusionImage<short>::Pointer dwi = dynamic_cast<mitk::DiffusionImage<short>*>(m_SelectedDWI->GetData());
m_ImageGenParameters.imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion();
m_ImageGenParameters.imageSpacing = dwi->GetVectorImage()->GetSpacing();
m_ImageGenParameters.imageOrigin = dwi->GetVectorImage()->GetOrigin();
m_ImageGenParameters.imageDirection = dwi->GetVectorImage()->GetDirection();
m_ImageGenParameters.b_value = dwi->GetB_Value();
mitk::DiffusionImage<short>::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections();
m_ImageGenParameters.numGradients = 0;
for (int i=0; i<dirs->Size(); i++)
{
DiffusionSignalModel<double>::GradientType g;
g[0] = dirs->at(i)[0];
g[1] = dirs->at(i)[1];
g[2] = dirs->at(i)[2];
m_ImageGenParameters.gradientDirections.push_back(g);
if (dirs->at(i).magnitude()>0.0001)
m_ImageGenParameters.numGradients++;
}
}
else if (m_SelectedImage.IsNotNull()) // use geometry of selected image
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_SelectedImage->GetData());
itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New();
CastToItkImage< itk::Image< float, 3 > >(img, itkImg);
m_ImageGenParameters.imageRegion = itkImg->GetLargestPossibleRegion();
m_ImageGenParameters.imageSpacing = itkImg->GetSpacing();
m_ImageGenParameters.imageOrigin = itkImg->GetOrigin();
m_ImageGenParameters.imageDirection = itkImg->GetDirection();
m_ImageGenParameters.numGradients = m_Controls->m_NumGradientsBox->value();
m_ImageGenParameters.gradientDirections = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());
m_ImageGenParameters.b_value = m_Controls->m_BvalueBox->value();
}
else // use GUI parameters
{
m_ImageGenParameters.imageRegion.SetSize(0, m_Controls->m_SizeX->value());
m_ImageGenParameters.imageRegion.SetSize(1, m_Controls->m_SizeY->value());
m_ImageGenParameters.imageRegion.SetSize(2, m_Controls->m_SizeZ->value());
m_ImageGenParameters.imageSpacing[0] = m_Controls->m_SpacingX->value();
m_ImageGenParameters.imageSpacing[1] = m_Controls->m_SpacingY->value();
m_ImageGenParameters.imageSpacing[2] = m_Controls->m_SpacingZ->value();
m_ImageGenParameters.imageOrigin[0] = m_ImageGenParameters.imageSpacing[0]/2;
m_ImageGenParameters.imageOrigin[1] = m_ImageGenParameters.imageSpacing[1]/2;
m_ImageGenParameters.imageOrigin[2] = m_ImageGenParameters.imageSpacing[2]/2;
m_ImageGenParameters.imageDirection.SetIdentity();
m_ImageGenParameters.numGradients = m_Controls->m_NumGradientsBox->value();
m_ImageGenParameters.gradientDirections = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());;
m_ImageGenParameters.b_value = m_Controls->m_BvalueBox->value();
}
// signal relaxation
m_ImageGenParameters.doSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked();
- if (m_ImageGenParameters.doSimulateRelaxation)
+ if (m_ImageGenParameters.doSimulateRelaxation && m_SelectedBundles.size()>0 )
m_ImageGenParameters.artifactModelString += "_RELAX";
// N/2 ghosts
if (m_Controls->m_AddGhosts->isChecked())
{
m_ImageGenParameters.artifactModelString += "_GHOST";
m_ImageGenParameters.kspaceLineOffset = m_Controls->m_kOffsetBox->value();
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_ImageGenParameters.kspaceLineOffset));
}
else
m_ImageGenParameters.kspaceLineOffset = 0;
// Aliasing
if (m_Controls->m_AddAliasing->isChecked())
{
m_ImageGenParameters.artifactModelString += "_ALIASING";
- m_ImageGenParameters.wrap = 1/m_Controls->m_WrapBox->value();
+ m_ImageGenParameters.wrap = (100-m_Controls->m_WrapBox->value())/100;
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value()));
+ }
+
+ // Motion
+ m_ImageGenParameters.doAddMotion = m_Controls->m_AddMotion->isChecked();
+ m_ImageGenParameters.randomMotion = m_Controls->m_RandomMotion->isChecked();
+ m_ImageGenParameters.translation[0] = m_Controls->m_MaxTranslationBoxX->value();
+ m_ImageGenParameters.translation[1] = m_Controls->m_MaxTranslationBoxY->value();
+ m_ImageGenParameters.translation[2] = m_Controls->m_MaxTranslationBoxZ->value();
+ m_ImageGenParameters.rotation[0] = m_Controls->m_MaxRotationBoxX->value();
+ m_ImageGenParameters.rotation[1] = m_Controls->m_MaxRotationBoxY->value();
+ m_ImageGenParameters.rotation[2] = m_Controls->m_MaxRotationBoxZ->value();
+ if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 )
+ {
+ m_ImageGenParameters.artifactModelString += "_MOTION";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_ImageGenParameters.randomMotion));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_ImageGenParameters.translation[0]));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_ImageGenParameters.translation[1]));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_ImageGenParameters.translation[2]));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_ImageGenParameters.rotation[0]));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_ImageGenParameters.rotation[1]));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_ImageGenParameters.rotation[2]));
}
+ // other imaging parameters
m_ImageGenParameters.tLine = m_Controls->m_LineReadoutTimeBox->value();
m_ImageGenParameters.tInhom = m_Controls->m_T2starBox->value();
m_ImageGenParameters.tEcho = m_Controls->m_TEbox->value();
m_ImageGenParameters.repetitions = m_Controls->m_RepetitionsBox->value();
m_ImageGenParameters.doDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked();
m_ImageGenParameters.interpolationShrink = m_Controls->m_InterpolationShrink->value();
m_ImageGenParameters.axonRadius = m_Controls->m_FiberRadius->value();
m_ImageGenParameters.signalScale = m_Controls->m_SignalScaleBox->value();
if (m_Controls->m_AddSpikes->isChecked())
{
m_ImageGenParameters.spikes = m_Controls->m_SpikeNumBox->value();
m_ImageGenParameters.spikeAmplitude = m_Controls->m_SpikeScaleBox->value();
m_ImageGenParameters.artifactModelString += "_SPIKES";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_ImageGenParameters.spikes));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_ImageGenParameters.spikeAmplitude));
+
}
// adjust echo time if needed
if ( m_ImageGenParameters.tEcho < m_ImageGenParameters.imageRegion.GetSize(1)*m_ImageGenParameters.tLine )
{
this->m_Controls->m_TEbox->setValue( m_ImageGenParameters.imageRegion.GetSize(1)*m_ImageGenParameters.tLine );
m_ImageGenParameters.tEcho = m_Controls->m_TEbox->value();
QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(m_ImageGenParameters.tEcho)+" ms");
}
- // check tissue mask
- if (m_TissueMask.IsNotNull())
- {
- m_ImageGenParameters.tissueMaskImage = ItkUcharImgType::New();
- mitk::CastToItkImage<ItkUcharImgType>(m_TissueMask, m_ImageGenParameters.tissueMaskImage);
- }
-
// rician noise
if (m_Controls->m_AddNoise->isChecked())
{
+ if (m_ImageGenParameters.noiseModel!=NULL)
+ delete m_ImageGenParameters.noiseModel;
+ if (m_ImageGenParameters.noiseModelShort!=NULL)
+ delete m_ImageGenParameters.noiseModelShort;
+
double noiseVariance = m_Controls->m_NoiseLevel->value();
- m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(noiseVariance);
- m_ImageGenParameters.artifactModelString += "_NOISE";
+ {
+ switch (m_Controls->m_NoiseDistributionBox->currentIndex())
+ {
+ case 0:
+ {
+ mitk::RicianNoiseModel<double>* rician = new mitk::RicianNoiseModel<double>();
+ rician->SetNoiseVariance(noiseVariance);
+ m_ImageGenParameters.noiseModel = rician;
+ m_ImageGenParameters.artifactModelString += "_RICIAN-";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician"));
+ break;
+ }
+ case 1:
+ {
+ mitk::ChiSquareNoiseModel<double>* chiSquare = new mitk::ChiSquareNoiseModel<double>();
+ chiSquare->SetDOF(noiseVariance/2);
+ m_ImageGenParameters.noiseModel = chiSquare;
+ m_ImageGenParameters.artifactModelString += "_CHISQUARED-";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared"));
+ break;
+ }
+ default:
+ {
+ mitk::RicianNoiseModel<double>* rician = new mitk::RicianNoiseModel<double>();
+ rician->SetNoiseVariance(noiseVariance);
+ m_ImageGenParameters.noiseModel = rician;
+ m_ImageGenParameters.artifactModelString += "_RICIAN-";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician"));
+ }
+ }
+ }
+ {
+ switch (m_Controls->m_NoiseDistributionBox->currentIndex())
+ {
+ case 0:
+ {
+ mitk::RicianNoiseModel<short>* rician = new mitk::RicianNoiseModel<short>();
+ rician->SetNoiseVariance(noiseVariance);
+ m_ImageGenParameters.noiseModelShort = rician;
+ break;
+ }
+ case 1:
+ {
+ mitk::ChiSquareNoiseModel<short>* chiSquare = new mitk::ChiSquareNoiseModel<short>();
+ chiSquare->SetDOF(noiseVariance/2);
+ m_ImageGenParameters.noiseModelShort = chiSquare;
+ break;
+ }
+ default:
+ {
+ mitk::RicianNoiseModel<short>* rician = new mitk::RicianNoiseModel<short>();
+ rician->SetNoiseVariance(noiseVariance);
+ m_ImageGenParameters.noiseModelShort = rician;
+ }
+ }
+ }
m_ImageGenParameters.artifactModelString += QString::number(noiseVariance);
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance));
}
else
- m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(0);
+ {
+ if (m_ImageGenParameters.noiseModel!=NULL)
+ {
+ delete m_ImageGenParameters.noiseModel;
+ m_ImageGenParameters.noiseModel = NULL;
+ }
+ if (m_ImageGenParameters.noiseModelShort!=NULL)
+ {
+ delete m_ImageGenParameters.noiseModelShort;
+ m_ImageGenParameters.noiseModelShort = NULL;
+ }
+ }
// gibbs ringing
m_ImageGenParameters.addGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked();
if (m_Controls->m_AddGibbsRinging->isChecked())
+ {
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true));
m_ImageGenParameters.artifactModelString += "_RINGING";
+ }
// adjusting line readout time to the adapted image size needed for the DFT
int y = m_ImageGenParameters.imageRegion.GetSize(1);
if ( y%2 == 1 )
y += 1;
if ( y>m_ImageGenParameters.imageRegion.GetSize(1) )
m_ImageGenParameters.tLine *= (double)m_ImageGenParameters.imageRegion.GetSize(1)/y;
// add distortions
if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull())
{
mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode();
mitk::Image* img = dynamic_cast<mitk::Image*>(fMapNode->GetData());
ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New();
CastToItkImage< ItkDoubleImgType >(img, itkImg);
if (m_ImageGenParameters.imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) &&
m_ImageGenParameters.imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) &&
m_ImageGenParameters.imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2))
{
m_ImageGenParameters.frequencyMap = itkImg;
m_ImageGenParameters.artifactModelString += "_DISTORTED";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true));
}
}
m_ImageGenParameters.doSimulateEddyCurrents = m_Controls->m_AddEddy->isChecked();
m_ImageGenParameters.eddyStrength = 0;
if (m_Controls->m_AddEddy->isChecked())
{
m_ImageGenParameters.eddyStrength = m_Controls->m_EddyGradientStrength->value();
m_ImageGenParameters.artifactModelString += "_EDDY";
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_ImageGenParameters.eddyStrength));
}
// signal models
m_ImageGenParameters.comp3Weight = 1;
m_ImageGenParameters.comp4Weight = 0;
if (m_Controls->m_Compartment4Box->currentIndex()>0)
{
m_ImageGenParameters.comp4Weight = m_Controls->m_Comp4FractionBox->value();
m_ImageGenParameters.comp3Weight -= m_ImageGenParameters.comp4Weight;
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.weight", DoubleProperty::New(m_ImageGenParameters.comp3Weight));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.weight", DoubleProperty::New(m_ImageGenParameters.comp4Weight));
}
// compartment 1
switch (m_Controls->m_Compartment1Box->currentIndex())
{
case 0:
m_StickModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_StickModel1.SetBvalue(m_ImageGenParameters.b_value);
m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD());
m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_StickModel1);
m_ImageGenParameters.signalModelString += "Stick";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) );
break;
case 1:
m_ZeppelinModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_ZeppelinModel1.SetBvalue(m_ImageGenParameters.b_value);
m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1());
m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2());
m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2());
m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_ZeppelinModel1);
m_ImageGenParameters.signalModelString += "Zeppelin";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) );
break;
case 2:
m_TensorModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_TensorModel1.SetBvalue(m_ImageGenParameters.b_value);
m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1());
m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2());
m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3());
m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_TensorModel1);
m_ImageGenParameters.signalModelString += "Tensor";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) );
break;
}
// compartment 2
switch (m_Controls->m_Compartment2Box->currentIndex())
{
case 0:
break;
case 1:
m_StickModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_StickModel2.SetBvalue(m_ImageGenParameters.b_value);
m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD());
m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_StickModel2);
m_ImageGenParameters.signalModelString += "Stick";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) );
break;
case 2:
m_ZeppelinModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_ZeppelinModel2.SetBvalue(m_ImageGenParameters.b_value);
m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1());
m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2());
m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2());
m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_ZeppelinModel2);
m_ImageGenParameters.signalModelString += "Zeppelin";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) );
break;
case 3:
m_TensorModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_TensorModel2.SetBvalue(m_ImageGenParameters.b_value);
m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1());
m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2());
m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3());
m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2());
m_ImageGenParameters.fiberModelList.push_back(&m_TensorModel2);
m_ImageGenParameters.signalModelString += "Tensor";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) );
break;
}
// compartment 3
switch (m_Controls->m_Compartment3Box->currentIndex())
{
case 0:
m_BallModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_BallModel1.SetBvalue(m_ImageGenParameters.b_value);
m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD());
m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2());
m_BallModel1.SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_BallModel1);
m_ImageGenParameters.signalModelString += "Ball";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) );
break;
case 1:
m_AstrosticksModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_AstrosticksModel1.SetBvalue(m_ImageGenParameters.b_value);
m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD());
m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2());
m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks());
m_AstrosticksModel1.SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_AstrosticksModel1);
m_ImageGenParameters.signalModelString += "Astrosticks";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) );
break;
case 2:
m_DotModel1.SetGradientList(m_ImageGenParameters.gradientDirections);
m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2());
m_DotModel1.SetWeight(m_ImageGenParameters.comp3Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_DotModel1);
m_ImageGenParameters.signalModelString += "Dot";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) );
break;
}
// compartment 4
switch (m_Controls->m_Compartment4Box->currentIndex())
{
case 0:
break;
case 1:
m_BallModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_BallModel2.SetBvalue(m_ImageGenParameters.b_value);
m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD());
m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2());
m_BallModel2.SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_BallModel2);
m_ImageGenParameters.signalModelString += "Ball";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) );
break;
case 2:
m_AstrosticksModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_AstrosticksModel2.SetBvalue(m_ImageGenParameters.b_value);
m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD());
m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2());
m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks());
m_AstrosticksModel2.SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_AstrosticksModel2);
m_ImageGenParameters.signalModelString += "Astrosticks";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) );
break;
case 3:
m_DotModel2.SetGradientList(m_ImageGenParameters.gradientDirections);
m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2());
m_DotModel2.SetWeight(m_ImageGenParameters.comp4Weight);
m_ImageGenParameters.nonFiberModelList.push_back(&m_DotModel2);
m_ImageGenParameters.signalModelString += "Dot";
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") );
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) );
break;
}
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.InterpolationShrink", IntProperty::New(m_ImageGenParameters.interpolationShrink));
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_ImageGenParameters.signalScale));
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_ImageGenParameters.axonRadius));
- m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_ImageGenParameters.tInhom));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_ImageGenParameters.tInhom));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_ImageGenParameters.tLine));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_ImageGenParameters.tEcho));
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_ImageGenParameters.repetitions));
m_ImageGenParameters.resultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_ImageGenParameters.b_value));
- m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Model", StringProperty::New(m_ImageGenParameters.signalModelString.toStdString()));
- m_ImageGenParameters.resultNode->AddProperty("Fiberfox.PureFiberVoxels", BoolProperty::New(m_ImageGenParameters.doDisablePartialVolume));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_ImageGenParameters.doDisablePartialVolume));
+ m_ImageGenParameters.resultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_ImageGenParameters.doSimulateRelaxation));
m_ImageGenParameters.resultNode->AddProperty("binary", BoolProperty::New(false));
}
void QmitkFiberfoxView::SaveParameters()
{
UpdateImageParameters();
QString filename = QFileDialog::getSaveFileName(
0,
tr("Save Parameters"),
- QDir::currentPath()+"/param.ffp",
+ m_ParameterFile,
tr("Fiberfox Parameters (*.ffp)") );
if(filename.isEmpty() || filename.isNull())
return;
if(!filename.endsWith(".ffp"))
filename += ".ffp";
+ m_ParameterFile = filename;
+
boost::property_tree::ptree parameters;
// fiber generation parameters
parameters.put("fiberfox.fibers.realtime", m_Controls->m_RealTimeFibers->isChecked());
parameters.put("fiberfox.fibers.showadvanced", m_Controls->m_AdvancedOptionsBox->isChecked());
parameters.put("fiberfox.fibers.distribution", m_Controls->m_DistributionBox->currentIndex());
parameters.put("fiberfox.fibers.variance", m_Controls->m_VarianceBox->value());
parameters.put("fiberfox.fibers.density", m_Controls->m_FiberDensityBox->value());
parameters.put("fiberfox.fibers.spline.sampling", m_Controls->m_FiberSamplingBox->value());
parameters.put("fiberfox.fibers.spline.tension", m_Controls->m_TensionBox->value());
parameters.put("fiberfox.fibers.spline.continuity", m_Controls->m_ContinuityBox->value());
parameters.put("fiberfox.fibers.spline.bias", m_Controls->m_BiasBox->value());
parameters.put("fiberfox.fibers.constantradius", m_Controls->m_ConstantRadiusBox->isChecked());
parameters.put("fiberfox.fibers.rotation.x", m_Controls->m_XrotBox->value());
parameters.put("fiberfox.fibers.rotation.y", m_Controls->m_YrotBox->value());
parameters.put("fiberfox.fibers.rotation.z", m_Controls->m_ZrotBox->value());
parameters.put("fiberfox.fibers.translation.x", m_Controls->m_XtransBox->value());
parameters.put("fiberfox.fibers.translation.y", m_Controls->m_YtransBox->value());
parameters.put("fiberfox.fibers.translation.z", m_Controls->m_ZtransBox->value());
parameters.put("fiberfox.fibers.scale.x", m_Controls->m_XscaleBox->value());
parameters.put("fiberfox.fibers.scale.y", m_Controls->m_YscaleBox->value());
parameters.put("fiberfox.fibers.scale.z", m_Controls->m_ZscaleBox->value());
parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked());
parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked());
// image generation parameters
parameters.put("fiberfox.image.basic.size.x", m_ImageGenParameters.imageRegion.GetSize(0));
parameters.put("fiberfox.image.basic.size.y", m_ImageGenParameters.imageRegion.GetSize(1));
parameters.put("fiberfox.image.basic.size.z", m_ImageGenParameters.imageRegion.GetSize(2));
parameters.put("fiberfox.image.basic.spacing.x", m_ImageGenParameters.imageSpacing[0]);
parameters.put("fiberfox.image.basic.spacing.y", m_ImageGenParameters.imageSpacing[1]);
parameters.put("fiberfox.image.basic.spacing.z", m_ImageGenParameters.imageSpacing[2]);
parameters.put("fiberfox.image.basic.numgradients", m_ImageGenParameters.numGradients);
parameters.put("fiberfox.image.basic.bvalue", m_ImageGenParameters.b_value);
parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked());
parameters.put("fiberfox.image.repetitions", m_ImageGenParameters.repetitions);
parameters.put("fiberfox.image.signalScale", m_ImageGenParameters.signalScale);
parameters.put("fiberfox.image.tEcho", m_ImageGenParameters.tEcho);
parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value());
parameters.put("fiberfox.image.tInhom", m_ImageGenParameters.tInhom);
parameters.put("fiberfox.image.axonRadius", m_ImageGenParameters.axonRadius);
parameters.put("fiberfox.image.interpolationShrink", m_ImageGenParameters.interpolationShrink);
parameters.put("fiberfox.image.doSimulateRelaxation", m_ImageGenParameters.doSimulateRelaxation);
parameters.put("fiberfox.image.doDisablePartialVolume", m_ImageGenParameters.doDisablePartialVolume);
parameters.put("fiberfox.image.outputvolumefractions", m_Controls->m_VolumeFractionsBox->isChecked());
parameters.put("fiberfox.image.artifacts.addnoise", m_Controls->m_AddNoise->isChecked());
+ parameters.put("fiberfox.image.artifacts.noisedistribution", m_Controls->m_NoiseDistributionBox->currentIndex());
parameters.put("fiberfox.image.artifacts.noisevariance", m_Controls->m_NoiseLevel->value());
parameters.put("fiberfox.image.artifacts.addghost", m_Controls->m_AddGhosts->isChecked());
parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_Controls->m_kOffsetBox->value());
parameters.put("fiberfox.image.artifacts.distortions", m_Controls->m_AddDistortions->isChecked());
parameters.put("fiberfox.image.artifacts.addeddy", m_Controls->m_AddEddy->isChecked());
parameters.put("fiberfox.image.artifacts.eddyStrength", m_Controls->m_EddyGradientStrength->value());
parameters.put("fiberfox.image.artifacts.addringing", m_Controls->m_AddGibbsRinging->isChecked());
parameters.put("fiberfox.image.artifacts.addspikes", m_Controls->m_AddSpikes->isChecked());
parameters.put("fiberfox.image.artifacts.spikesnum", m_Controls->m_SpikeNumBox->value());
parameters.put("fiberfox.image.artifacts.spikesscale", m_Controls->m_SpikeScaleBox->value());
parameters.put("fiberfox.image.artifacts.addaliasing", m_Controls->m_AddAliasing->isChecked());
parameters.put("fiberfox.image.artifacts.aliasingfactor", m_Controls->m_WrapBox->value());
+ parameters.put("fiberfox.image.artifacts.doAddMotion", m_Controls->m_AddMotion->isChecked());
+ parameters.put("fiberfox.image.artifacts.randomMotion", m_Controls->m_RandomMotion->isChecked());
+ parameters.put("fiberfox.image.artifacts.translation0", m_Controls->m_MaxTranslationBoxX->value());
+ parameters.put("fiberfox.image.artifacts.translation1", m_Controls->m_MaxTranslationBoxY->value());
+ parameters.put("fiberfox.image.artifacts.translation2", m_Controls->m_MaxTranslationBoxZ->value());
+ parameters.put("fiberfox.image.artifacts.rotation0", m_Controls->m_MaxRotationBoxX->value());
+ parameters.put("fiberfox.image.artifacts.rotation1", m_Controls->m_MaxRotationBoxY->value());
+ parameters.put("fiberfox.image.artifacts.rotation2", m_Controls->m_MaxRotationBoxZ->value());
parameters.put("fiberfox.image.compartment1.index", m_Controls->m_Compartment1Box->currentIndex());
parameters.put("fiberfox.image.compartment2.index", m_Controls->m_Compartment2Box->currentIndex());
parameters.put("fiberfox.image.compartment3.index", m_Controls->m_Compartment3Box->currentIndex());
parameters.put("fiberfox.image.compartment4.index", m_Controls->m_Compartment4Box->currentIndex());
parameters.put("fiberfox.image.compartment1.stick.d", m_Controls->m_StickWidget1->GetD());
parameters.put("fiberfox.image.compartment1.stick.t2", m_Controls->m_StickWidget1->GetT2());
parameters.put("fiberfox.image.compartment1.zeppelin.d1", m_Controls->m_ZeppelinWidget1->GetD1());
parameters.put("fiberfox.image.compartment1.zeppelin.d2", m_Controls->m_ZeppelinWidget1->GetD2());
parameters.put("fiberfox.image.compartment1.zeppelin.t2", m_Controls->m_ZeppelinWidget1->GetT2());
parameters.put("fiberfox.image.compartment1.tensor.d1", m_Controls->m_TensorWidget1->GetD1());
parameters.put("fiberfox.image.compartment1.tensor.d2", m_Controls->m_TensorWidget1->GetD2());
parameters.put("fiberfox.image.compartment1.tensor.d3", m_Controls->m_TensorWidget1->GetD3());
parameters.put("fiberfox.image.compartment1.tensor.t2", m_Controls->m_TensorWidget1->GetT2());
parameters.put("fiberfox.image.compartment2.stick.d", m_Controls->m_StickWidget2->GetD());
parameters.put("fiberfox.image.compartment2.stick.t2", m_Controls->m_StickWidget2->GetT2());
parameters.put("fiberfox.image.compartment2.zeppelin.d1", m_Controls->m_ZeppelinWidget2->GetD1());
parameters.put("fiberfox.image.compartment2.zeppelin.d2", m_Controls->m_ZeppelinWidget2->GetD2());
parameters.put("fiberfox.image.compartment2.zeppelin.t2", m_Controls->m_ZeppelinWidget2->GetT2());
parameters.put("fiberfox.image.compartment2.tensor.d1", m_Controls->m_TensorWidget2->GetD1());
parameters.put("fiberfox.image.compartment2.tensor.d2", m_Controls->m_TensorWidget2->GetD2());
parameters.put("fiberfox.image.compartment2.tensor.d3", m_Controls->m_TensorWidget2->GetD3());
parameters.put("fiberfox.image.compartment2.tensor.t2", m_Controls->m_TensorWidget2->GetT2());
parameters.put("fiberfox.image.compartment3.ball.d", m_Controls->m_BallWidget1->GetD());
parameters.put("fiberfox.image.compartment3.ball.t2", m_Controls->m_BallWidget1->GetT2());
parameters.put("fiberfox.image.compartment3.astrosticks.d", m_Controls->m_AstrosticksWidget1->GetD());
parameters.put("fiberfox.image.compartment3.astrosticks.t2", m_Controls->m_AstrosticksWidget1->GetT2());
parameters.put("fiberfox.image.compartment3.astrosticks.randomize", m_Controls->m_AstrosticksWidget1->GetRandomizeSticks());
parameters.put("fiberfox.image.compartment3.dot.t2", m_Controls->m_DotWidget1->GetT2());
parameters.put("fiberfox.image.compartment4.ball.d", m_Controls->m_BallWidget2->GetD());
parameters.put("fiberfox.image.compartment4.ball.t2", m_Controls->m_BallWidget2->GetT2());
parameters.put("fiberfox.image.compartment4.astrosticks.d", m_Controls->m_AstrosticksWidget2->GetD());
parameters.put("fiberfox.image.compartment4.astrosticks.t2", m_Controls->m_AstrosticksWidget2->GetT2());
parameters.put("fiberfox.image.compartment4.astrosticks.randomize", m_Controls->m_AstrosticksWidget2->GetRandomizeSticks());
parameters.put("fiberfox.image.compartment4.dot.t2", m_Controls->m_DotWidget2->GetT2());
parameters.put("fiberfox.image.compartment4.weight", m_Controls->m_Comp4FractionBox->value());
boost::property_tree::xml_parser::write_xml(filename.toStdString(), parameters);
}
void QmitkFiberfoxView::LoadParameters()
{
- QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QDir::currentPath(), tr("Fiberfox Parameters (*.ffp)") );
+ QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") );
if(filename.isEmpty() || filename.isNull())
return;
+ m_ParameterFile = filename;
+
boost::property_tree::ptree parameters;
boost::property_tree::xml_parser::read_xml(filename.toStdString(), parameters);
BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") )
{
if( v1.first == "fibers" )
{
m_Controls->m_RealTimeFibers->setChecked(v1.second.get<bool>("realtime"));
m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get<bool>("showadvanced"));
m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get<int>("distribution"));
m_Controls->m_VarianceBox->setValue(v1.second.get<double>("variance"));
m_Controls->m_FiberDensityBox->setValue(v1.second.get<int>("density"));
m_Controls->m_IncludeFiducials->setChecked(v1.second.get<bool>("includeFiducials"));
m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get<bool>("constantradius"));
BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second )
{
if( v2.first == "spline" )
{
m_Controls->m_FiberSamplingBox->setValue(v2.second.get<double>("sampling"));
m_Controls->m_TensionBox->setValue(v2.second.get<double>("tension"));
m_Controls->m_ContinuityBox->setValue(v2.second.get<double>("continuity"));
m_Controls->m_BiasBox->setValue(v2.second.get<double>("bias"));
}
if( v2.first == "rotation" )
{
m_Controls->m_XrotBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YrotBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZrotBox->setValue(v2.second.get<double>("z"));
}
if( v2.first == "translation" )
{
m_Controls->m_XtransBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YtransBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZtransBox->setValue(v2.second.get<double>("z"));
}
if( v2.first == "scale" )
{
m_Controls->m_XscaleBox->setValue(v2.second.get<double>("x"));
m_Controls->m_YscaleBox->setValue(v2.second.get<double>("y"));
m_Controls->m_ZscaleBox->setValue(v2.second.get<double>("z"));
}
}
}
if( v1.first == "image" )
{
m_Controls->m_SizeX->setValue(v1.second.get<int>("basic.size.x"));
m_Controls->m_SizeY->setValue(v1.second.get<int>("basic.size.y"));
m_Controls->m_SizeZ->setValue(v1.second.get<int>("basic.size.z"));
m_Controls->m_SpacingX->setValue(v1.second.get<double>("basic.spacing.x"));
m_Controls->m_SpacingY->setValue(v1.second.get<double>("basic.spacing.y"));
m_Controls->m_SpacingZ->setValue(v1.second.get<double>("basic.spacing.z"));
m_Controls->m_NumGradientsBox->setValue(v1.second.get<int>("basic.numgradients"));
m_Controls->m_BvalueBox->setValue(v1.second.get<int>("basic.bvalue"));
m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get<bool>("showadvanced"));
m_Controls->m_RepetitionsBox->setValue(v1.second.get<int>("repetitions"));
m_Controls->m_SignalScaleBox->setValue(v1.second.get<int>("signalScale"));
m_Controls->m_TEbox->setValue(v1.second.get<double>("tEcho"));
m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get<double>("tLine"));
m_Controls->m_T2starBox->setValue(v1.second.get<double>("tInhom"));
m_Controls->m_FiberRadius->setValue(v1.second.get<double>("axonRadius"));
m_Controls->m_InterpolationShrink->setValue(v1.second.get<int>("interpolationShrink"));
m_Controls->m_RelaxationBox->setChecked(v1.second.get<bool>("doSimulateRelaxation"));
m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get<bool>("doDisablePartialVolume"));
m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get<bool>("outputvolumefractions"));
m_Controls->m_AddNoise->setChecked(v1.second.get<bool>("artifacts.addnoise"));
+ m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get<int>("artifacts.noisedistribution"));
m_Controls->m_NoiseLevel->setValue(v1.second.get<double>("artifacts.noisevariance"));
m_Controls->m_AddGhosts->setChecked(v1.second.get<bool>("artifacts.addghost"));
m_Controls->m_kOffsetBox->setValue(v1.second.get<double>("artifacts.kspaceLineOffset"));
m_Controls->m_AddAliasing->setChecked(v1.second.get<bool>("artifacts.addaliasing"));
m_Controls->m_WrapBox->setValue(v1.second.get<double>("artifacts.aliasingfactor"));
m_Controls->m_AddDistortions->setChecked(v1.second.get<bool>("artifacts.distortions"));
-
m_Controls->m_AddSpikes->setChecked(v1.second.get<bool>("artifacts.addspikes"));
m_Controls->m_SpikeNumBox->setValue(v1.second.get<int>("artifacts.spikesnum"));
m_Controls->m_SpikeScaleBox->setValue(v1.second.get<double>("artifacts.spikesscale"));
m_Controls->m_AddEddy->setChecked(v1.second.get<bool>("artifacts.addeddy"));
m_Controls->m_EddyGradientStrength->setValue(v1.second.get<double>("artifacts.eddyStrength"));
m_Controls->m_AddGibbsRinging->setChecked(v1.second.get<bool>("artifacts.addringing"));
+ m_Controls->m_AddMotion->setChecked(v1.second.get<bool>("artifacts.doAddMotion"));
+ m_Controls->m_RandomMotion->setChecked(v1.second.get<bool>("artifacts.randomMotion"));
+ m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get<double>("artifacts.translation0"));
+ m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get<double>("artifacts.translation1"));
+ m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get<double>("artifacts.translation2"));
+ m_Controls->m_MaxRotationBoxX->setValue(v1.second.get<double>("artifacts.rotation0"));
+ m_Controls->m_MaxRotationBoxY->setValue(v1.second.get<double>("artifacts.rotation1"));
+ m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get<double>("artifacts.rotation2"));
m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get<int>("compartment1.index"));
m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get<int>("compartment2.index"));
m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get<int>("compartment3.index"));
m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get<int>("compartment4.index"));
-
m_Controls->m_StickWidget1->SetD(v1.second.get<double>("compartment1.stick.d"));
m_Controls->m_StickWidget1->SetT2(v1.second.get<double>("compartment1.stick.t2"));
m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get<double>("compartment1.zeppelin.d1"));
m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get<double>("compartment1.zeppelin.d2"));
m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get<double>("compartment1.zeppelin.t2"));
m_Controls->m_TensorWidget1->SetD1(v1.second.get<double>("compartment1.tensor.d1"));
m_Controls->m_TensorWidget1->SetD2(v1.second.get<double>("compartment1.tensor.d2"));
m_Controls->m_TensorWidget1->SetD3(v1.second.get<double>("compartment1.tensor.d3"));
m_Controls->m_TensorWidget1->SetT2(v1.second.get<double>("compartment1.tensor.t2"));
m_Controls->m_StickWidget2->SetD(v1.second.get<double>("compartment2.stick.d"));
m_Controls->m_StickWidget2->SetT2(v1.second.get<double>("compartment2.stick.t2"));
m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get<double>("compartment2.zeppelin.d1"));
m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get<double>("compartment2.zeppelin.d2"));
m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get<double>("compartment2.zeppelin.t2"));
m_Controls->m_TensorWidget2->SetD1(v1.second.get<double>("compartment2.tensor.d1"));
m_Controls->m_TensorWidget2->SetD2(v1.second.get<double>("compartment2.tensor.d2"));
m_Controls->m_TensorWidget2->SetD3(v1.second.get<double>("compartment2.tensor.d3"));
m_Controls->m_TensorWidget2->SetT2(v1.second.get<double>("compartment2.tensor.t2"));
m_Controls->m_BallWidget1->SetD(v1.second.get<double>("compartment3.ball.d"));
m_Controls->m_BallWidget1->SetT2(v1.second.get<double>("compartment3.ball.t2"));
m_Controls->m_AstrosticksWidget1->SetD(v1.second.get<double>("compartment3.astrosticks.d"));
m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get<double>("compartment3.astrosticks.t2"));
m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get<bool>("compartment3.astrosticks.randomize"));
m_Controls->m_DotWidget1->SetT2(v1.second.get<double>("compartment3.dot.t2"));
m_Controls->m_BallWidget2->SetD(v1.second.get<double>("compartment4.ball.d"));
m_Controls->m_BallWidget2->SetT2(v1.second.get<double>("compartment4.ball.t2"));
m_Controls->m_AstrosticksWidget2->SetD(v1.second.get<double>("compartment4.astrosticks.d"));
m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get<double>("compartment4.astrosticks.t2"));
m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get<bool>("compartment4.astrosticks.randomize"));
m_Controls->m_DotWidget2->SetT2(v1.second.get<double>("compartment4.dot.t2"));
m_Controls->m_Comp4FractionBox->setValue(v1.second.get<double>("compartment4.weight"));
}
}
UpdateImageParameters();
}
void QmitkFiberfoxView::ShowAdvancedOptions(int state)
{
if (state)
{
m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true);
m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true);
m_Controls->m_AdvancedOptionsBox->setChecked(true);
m_Controls->m_AdvancedOptionsBox_2->setChecked(true);
}
else
{
m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false);
m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false);
m_Controls->m_AdvancedOptionsBox->setChecked(false);
m_Controls->m_AdvancedOptionsBox_2->setChecked(false);
}
}
void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index)
{
m_Controls->m_StickWidget1->setVisible(false);
m_Controls->m_ZeppelinWidget1->setVisible(false);
m_Controls->m_TensorWidget1->setVisible(false);
switch (index)
{
case 0:
m_Controls->m_StickWidget1->setVisible(true);
break;
case 1:
m_Controls->m_ZeppelinWidget1->setVisible(true);
break;
case 2:
m_Controls->m_TensorWidget1->setVisible(true);
break;
}
}
void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index)
{
m_Controls->m_StickWidget2->setVisible(false);
m_Controls->m_ZeppelinWidget2->setVisible(false);
m_Controls->m_TensorWidget2->setVisible(false);
switch (index)
{
case 0:
break;
case 1:
m_Controls->m_StickWidget2->setVisible(true);
break;
case 2:
m_Controls->m_ZeppelinWidget2->setVisible(true);
break;
case 3:
m_Controls->m_TensorWidget2->setVisible(true);
break;
}
}
void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index)
{
m_Controls->m_BallWidget1->setVisible(false);
m_Controls->m_AstrosticksWidget1->setVisible(false);
m_Controls->m_DotWidget1->setVisible(false);
switch (index)
{
case 0:
m_Controls->m_BallWidget1->setVisible(true);
break;
case 1:
m_Controls->m_AstrosticksWidget1->setVisible(true);
break;
case 2:
m_Controls->m_DotWidget1->setVisible(true);
break;
}
}
void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index)
{
m_Controls->m_BallWidget2->setVisible(false);
m_Controls->m_AstrosticksWidget2->setVisible(false);
m_Controls->m_DotWidget2->setVisible(false);
m_Controls->m_Comp4FractionFrame->setVisible(false);
switch (index)
{
case 0:
break;
case 1:
m_Controls->m_BallWidget2->setVisible(true);
m_Controls->m_Comp4FractionFrame->setVisible(true);
break;
case 2:
m_Controls->m_AstrosticksWidget2->setVisible(true);
m_Controls->m_Comp4FractionFrame->setVisible(true);
break;
case 3:
m_Controls->m_DotWidget2->setVisible(true);
m_Controls->m_Comp4FractionFrame->setVisible(true);
break;
}
}
void QmitkFiberfoxView::OnConstantRadius(int value)
{
if (value>0 && m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
+void QmitkFiberfoxView::OnAddMotion(int value)
+{
+ if (value>0)
+ m_Controls->m_MotionArtifactFrame->setVisible(true);
+ else
+ m_Controls->m_MotionArtifactFrame->setVisible(false);
+}
+
void QmitkFiberfoxView::OnAddAliasing(int value)
{
if (value>0)
m_Controls->m_AliasingFrame->setVisible(true);
else
m_Controls->m_AliasingFrame->setVisible(false);
}
void QmitkFiberfoxView::OnAddSpikes(int value)
{
if (value>0)
m_Controls->m_SpikeFrame->setVisible(true);
else
m_Controls->m_SpikeFrame->setVisible(false);
}
void QmitkFiberfoxView::OnAddEddy(int value)
{
if (value>0)
m_Controls->m_EddyFrame->setVisible(true);
else
m_Controls->m_EddyFrame->setVisible(false);
}
void QmitkFiberfoxView::OnAddDistortions(int value)
{
if (value>0)
m_Controls->m_DistortionsFrame->setVisible(true);
else
m_Controls->m_DistortionsFrame->setVisible(false);
}
void QmitkFiberfoxView::OnAddGhosts(int value)
{
if (value>0)
m_Controls->m_GhostFrame->setVisible(true);
else
m_Controls->m_GhostFrame->setVisible(false);
}
void QmitkFiberfoxView::OnAddNoise(int value)
{
if (value>0)
m_Controls->m_NoiseFrame->setVisible(true);
else
m_Controls->m_NoiseFrame->setVisible(false);
}
void QmitkFiberfoxView::OnDistributionChanged(int value)
{
if (value==1)
m_Controls->m_VarianceBox->setVisible(true);
else
m_Controls->m_VarianceBox->setVisible(false);
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnVarianceChanged(double value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnFiberDensityChanged(int value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnFiberSamplingChanged(double value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnTensionChanged(double value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnContinuityChanged(double value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnBiasChanged(double value)
{
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::AlignOnGrid()
{
for (int i=0; i<m_SelectedFiducials.size(); i++)
{
mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(i)->GetData());
mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i));
for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it )
{
mitk::DataNode::Pointer pFibNode = *it;
if ( pFibNode.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(pFibNode->GetData()) )
{
mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 )
{
mitk::DataNode::Pointer pImgNode = *it2;
if ( pImgNode.IsNotNull() && dynamic_cast<mitk::Image*>(pImgNode->GetData()) )
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(pImgNode->GetData());
mitk::Geometry3D::Pointer geom = img->GetGeometry();
itk::Index<3> idx;
geom->WorldToIndex(wc0, idx);
mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
mitk::Point3D world;
geom->IndexToWorld(cIdx,world);
mitk::Vector3D trans = world - wc0;
pe->GetGeometry()->Translate(trans);
break;
}
}
break;
}
}
}
for( int i=0; i<m_SelectedBundles2.size(); i++ )
{
mitk::DataNode::Pointer fibNode = m_SelectedBundles2.at(i);
mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(fibNode);
for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it )
{
mitk::DataNode::Pointer imgNode = *it;
if ( imgNode.IsNotNull() && dynamic_cast<mitk::Image*>(imgNode->GetData()) )
{
mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
{
mitk::DataNode::Pointer fiducialNode = *it2;
if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
{
mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(imgNode->GetData());
mitk::Geometry3D::Pointer geom = img->GetGeometry();
itk::Index<3> idx;
geom->WorldToIndex(wc0, idx);
mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
mitk::Point3D world;
geom->IndexToWorld(cIdx,world);
mitk::Vector3D trans = world - wc0;
pe->GetGeometry()->Translate(trans);
}
}
break;
}
}
}
for( int i=0; i<m_SelectedImages.size(); i++ )
{
mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_SelectedImages.at(i)->GetData());
mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i));
for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it )
{
mitk::DataNode::Pointer fibNode = *it;
if ( fibNode.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(fibNode->GetData()) )
{
mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 )
{
mitk::DataNode::Pointer fiducialNode = *it2;
if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
{
mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
mitk::Geometry3D::Pointer geom = img->GetGeometry();
itk::Index<3> idx;
geom->WorldToIndex(wc0, idx);
mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
mitk::Point3D world;
geom->IndexToWorld(cIdx,world);
mitk::Vector3D trans = world - wc0;
pe->GetGeometry()->Translate(trans);
}
}
}
}
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::OnFlipButton()
{
if (m_SelectedFiducial.IsNull())
return;
std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer());
if( it != m_DataNodeToPlanarFigureData.end() )
{
QmitkPlanarFigureData& data = it->second;
data.m_Flipped += 1;
data.m_Flipped %= 2;
}
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints)
{
NPoints *= 2;
GradientListType pointshell;
int numB0 = NPoints/20;
if (numB0==0)
numB0=1;
GradientType g;
g.Fill(0.0);
for (int i=0; i<numB0; i++)
pointshell.push_back(g);
if (NPoints==0)
return pointshell;
vnl_vector<double> theta; theta.set_size(NPoints);
vnl_vector<double> phi; phi.set_size(NPoints);
double C = sqrt(4*M_PI);
phi(0) = 0.0;
phi(NPoints-1) = 0.0;
for(int i=0; i<NPoints; i++)
{
theta(i) = acos(-1.0+2.0*i/(NPoints-1.0)) - M_PI / 2.0;
if( i>0 && i<NPoints-1)
{
phi(i) = (phi(i-1) + C /
sqrt(NPoints*(1-(-1.0+2.0*i/(NPoints-1.0))*(-1.0+2.0*i/(NPoints-1.0)))));
// % (2*DIST_POINTSHELL_PI);
}
}
for(int i=0; i<NPoints; i++)
{
g[2] = sin(theta(i));
if (g[2]<0)
continue;
g[0] = cos(theta(i)) * cos(phi(i));
g[1] = cos(theta(i)) * sin(phi(i));
pointshell.push_back(g);
}
return pointshell;
}
template<int ndirs>
std::vector<itk::Vector<double,3> > QmitkFiberfoxView::MakeGradientList()
{
std::vector<itk::Vector<double,3> > retval;
vnl_matrix_fixed<double, 3, ndirs>* U =
itk::PointShell<ndirs, vnl_matrix_fixed<double, 3, ndirs> >::DistributePointShell();
// Add 0 vector for B0
int numB0 = ndirs/10;
if (numB0==0)
numB0=1;
itk::Vector<double,3> v;
v.Fill(0.0);
for (int i=0; i<numB0; i++)
{
retval.push_back(v);
}
for(int i=0; i<ndirs;i++)
{
itk::Vector<double,3> v;
v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i);
retval.push_back(v);
}
return retval;
}
void QmitkFiberfoxView::OnAddBundle()
{
if (m_SelectedImage.IsNull())
return;
mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage);
mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New();
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData( bundle );
QString name = QString("Bundle_%1").arg(children->size());
node->SetName(name.toStdString());
m_SelectedBundles.push_back(node);
UpdateGui();
GetDataStorage()->Add(node, m_SelectedImage);
}
void QmitkFiberfoxView::OnDrawROI()
{
if (m_SelectedBundles.empty())
OnAddBundle();
if (m_SelectedBundles.empty())
return;
mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0));
mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New();
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData( figure );
QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
for( int i=0; i<nodes.size(); i++)
nodes.at(i)->SetSelected(false);
m_SelectedFiducial = node;
QString name = QString("Fiducial_%1").arg(children->size());
node->SetName(name.toStdString());
node->SetSelected(true);
this->DisableCrosshairNavigation();
mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
if(figureInteractor.IsNull())
{
- figureInteractor = mitk::PlanarFigureInteractor::New();
- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
- figureInteractor->SetDataNode( node );
+ figureInteractor = mitk::PlanarFigureInteractor::New();
+ us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
+ figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
+ figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
+ figureInteractor->SetDataNode( node );
}
UpdateGui();
GetDataStorage()->Add(node, m_SelectedBundles.at(0));
}
bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j)
{
int li = -1;
i->GetPropertyValue("layer", li);
int lj = -1;
j->GetPropertyValue("layer", lj);
return li<lj;
}
void QmitkFiberfoxView::GenerateFibers()
{
if (m_SelectedBundles.empty())
{
if (m_SelectedFiducial.IsNull())
return;
mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(m_SelectedFiducial);
for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it )
if(dynamic_cast<mitk::FiberBundleX*>((*it)->GetData()))
m_SelectedBundles.push_back(*it);
if (m_SelectedBundles.empty())
return;
}
vector< vector< mitk::PlanarEllipse::Pointer > > fiducials;
vector< vector< unsigned int > > fliplist;
for (int i=0; i<m_SelectedBundles.size(); i++)
{
mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(i));
std::vector< mitk::DataNode::Pointer > childVector;
for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it )
childVector.push_back(*it);
sort(childVector.begin(), childVector.end(), CompareLayer);
vector< mitk::PlanarEllipse::Pointer > fib;
vector< unsigned int > flip;
float radius = 1;
int count = 0;
for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it )
{
mitk::DataNode::Pointer node = *it;
if ( node.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(node->GetData()) )
{
mitk::PlanarEllipse* ellipse = dynamic_cast<mitk::PlanarEllipse*>(node->GetData());
if (m_Controls->m_ConstantRadiusBox->isChecked())
{
ellipse->SetTreatAsCircle(true);
mitk::Point2D c = ellipse->GetControlPoint(0);
mitk::Point2D p = ellipse->GetControlPoint(1);
mitk::Vector2D v = p-c;
if (count==0)
{
radius = v.GetVnlVector().magnitude();
ellipse->SetControlPoint(1, p);
}
else
{
v.Normalize();
v *= radius;
ellipse->SetControlPoint(1, c+v);
}
}
fib.push_back(ellipse);
std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer());
if( it != m_DataNodeToPlanarFigureData.end() )
{
QmitkPlanarFigureData& data = it->second;
flip.push_back(data.m_Flipped);
}
else
flip.push_back(0);
}
count++;
}
if (fib.size()>1)
{
fiducials.push_back(fib);
fliplist.push_back(flip);
}
else if (fib.size()>0)
m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
filter->SetFiducials(fiducials);
filter->SetFlipList(fliplist);
switch(m_Controls->m_DistributionBox->currentIndex()){
case 0:
filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM);
break;
case 1:
filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN);
filter->SetVariance(m_Controls->m_VarianceBox->value());
break;
}
filter->SetDensity(m_Controls->m_FiberDensityBox->value());
filter->SetTension(m_Controls->m_TensionBox->value());
filter->SetContinuity(m_Controls->m_ContinuityBox->value());
filter->SetBias(m_Controls->m_BiasBox->value());
filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value());
filter->Update();
vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles();
for (unsigned int i=0; i<fiberBundles.size(); i++)
{
m_SelectedBundles.at(i)->SetData( fiberBundles.at(i) );
if (fiberBundles.at(i)->GetNumFibers()>50000)
m_SelectedBundles.at(i)->SetVisibility(false);
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkFiberfoxView::GenerateImage()
{
- UpdateImageParameters();
- if (m_SelectedBundles.empty())
+ if (m_SelectedBundles.empty() && m_SelectedDWI.IsNull())
{
- if (m_SelectedDWI.IsNotNull()) // add artifacts to existing diffusion weighted image
- {
- for (unsigned int i=0; i<m_SelectedImages.size(); i++)
- {
- if (!dynamic_cast<mitk::DiffusionImage<short>*>(m_SelectedImages.at(i)->GetData()))
- continue;
-
- m_SelectedDWI = m_SelectedImages.at(i);
- UpdateImageParameters();
-
- mitk::DiffusionImage<short>::Pointer diffImg = dynamic_cast<mitk::DiffusionImage<short>*>(m_SelectedImages.at(i)->GetData());
-
- mitk::RicianNoiseModel<short> noiseModel;
- noiseModel.SetNoiseVariance(m_ImageGenParameters.ricianNoiseModel.GetNoiseVariance());
-
- itk::AddArtifactsToDwiImageFilter< short >::Pointer filter = itk::AddArtifactsToDwiImageFilter< short >::New();
- filter->SetInput(diffImg->GetVectorImage());
- filter->SettLine(m_ImageGenParameters.tLine);
- filter->SetkOffset(m_ImageGenParameters.kspaceLineOffset);
- filter->SetNoiseModel(&noiseModel);
- filter->SetGradientList(m_ImageGenParameters.gradientDirections);
- filter->SetTE(m_ImageGenParameters.tEcho);
- filter->SetSimulateEddyCurrents(m_ImageGenParameters.doSimulateEddyCurrents);
- filter->SetEddyGradientStrength(m_ImageGenParameters.eddyStrength);
- filter->SetAddGibbsRinging(m_ImageGenParameters.addGibbsRinging);
- filter->SetFrequencyMap(m_ImageGenParameters.frequencyMap);
- filter->SetSpikeAmplitude(m_ImageGenParameters.spikeAmplitude);
- filter->SetSpikes(m_ImageGenParameters.spikes);
- filter->SetWrap(m_ImageGenParameters.wrap);
- filter->Update();
-
- mitk::DiffusionImage<short>::Pointer image = mitk::DiffusionImage<short>::New();
- image->SetVectorImage( filter->GetOutput() );
- image->SetB_Value(diffImg->GetB_Value());
- image->SetDirections(diffImg->GetDirections());
- image->InitializeFromVectorImage();
- m_ImageGenParameters.resultNode->SetData( image );
- m_ImageGenParameters.resultNode->SetName(m_SelectedImages.at(i)->GetName()+m_ImageGenParameters.artifactModelString.toStdString());
- GetDataStorage()->Add(m_ImageGenParameters.resultNode);
- }
- m_SelectedDWI = m_SelectedImages.front();
- return;
- }
-
mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage<unsigned int>(
m_Controls->m_SizeX->value(),
m_Controls->m_SizeY->value(),
m_Controls->m_SizeZ->value(),
m_Controls->m_SpacingX->value(),
m_Controls->m_SpacingY->value(),
m_Controls->m_SpacingZ->value());
mitk::Geometry3D* geom = image->GetGeometry();
geom->SetOrigin(m_ImageGenParameters.imageOrigin);
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData( image );
node->SetName("Dummy");
unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value();
unsigned int level = window/2;
mitk::LevelWindow lw; lw.SetLevelWindow(level, window);
node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
GetDataStorage()->Add(node);
m_SelectedImage = node;
mitk::BaseData::Pointer basedata = node->GetData();
if (basedata.IsNotNull())
{
- mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
+ mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
UpdateGui();
+ }
+ else if (!m_SelectedBundles.empty())
+ SimulateImageFromFibers(m_SelectedBundles.at(0));
+ else if (m_SelectedDWI.IsNotNull())
+ SimulateForExistingDwi(m_SelectedDWI);
+}
+void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode)
+{
+ if (!dynamic_cast<mitk::DiffusionImage<short>*>(imageNode->GetData()))
return;
- }
- for (int i=0; i<m_SelectedBundles.size(); i++)
- {
- mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast<mitk::FiberBundleX*>(m_SelectedBundles.at(i)->GetData());
- if (fiberBundle->GetNumFibers()<=0)
- continue;
+ MITK_INFO << "TEST";
+ UpdateImageParameters();
- itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
-
- tractsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.doSimulateEddyCurrents);
- tractsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.eddyStrength);
- tractsToDwiFilter->SetAddGibbsRinging(m_ImageGenParameters.addGibbsRinging);
- tractsToDwiFilter->SetSimulateRelaxation(m_ImageGenParameters.doSimulateRelaxation);
- tractsToDwiFilter->SetImageRegion(m_ImageGenParameters.imageRegion);
- tractsToDwiFilter->SetSpacing(m_ImageGenParameters.imageSpacing);
- tractsToDwiFilter->SetOrigin(m_ImageGenParameters.imageOrigin);
- tractsToDwiFilter->SetDirectionMatrix(m_ImageGenParameters.imageDirection);
- tractsToDwiFilter->SetFiberBundle(fiberBundle);
- tractsToDwiFilter->SetFiberModels(m_ImageGenParameters.fiberModelList);
- tractsToDwiFilter->SetNonFiberModels(m_ImageGenParameters.nonFiberModelList);
- tractsToDwiFilter->SetNoiseModel(&m_ImageGenParameters.ricianNoiseModel);
- tractsToDwiFilter->SetKspaceArtifacts(m_ImageGenParameters.artifactList);
- tractsToDwiFilter->SetkOffset(m_ImageGenParameters.kspaceLineOffset);
- tractsToDwiFilter->SettLine(m_ImageGenParameters.tLine);
- tractsToDwiFilter->SettInhom(m_ImageGenParameters.tInhom);
- tractsToDwiFilter->SetTE(m_ImageGenParameters.tEcho);
- tractsToDwiFilter->SetNumberOfRepetitions(m_ImageGenParameters.repetitions);
- tractsToDwiFilter->SetEnforcePureFiberVoxels(m_ImageGenParameters.doDisablePartialVolume);
- tractsToDwiFilter->SetInterpolationShrink(m_ImageGenParameters.interpolationShrink);
- tractsToDwiFilter->SetFiberRadius(m_ImageGenParameters.axonRadius);
- tractsToDwiFilter->SetSignalScale(m_ImageGenParameters.signalScale);
- if (m_ImageGenParameters.interpolationShrink>0)
- tractsToDwiFilter->SetUseInterpolation(true);
- tractsToDwiFilter->SetTissueMask(m_ImageGenParameters.tissueMaskImage);
- tractsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.frequencyMap);
- tractsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.spikeAmplitude);
- tractsToDwiFilter->SetSpikes(m_ImageGenParameters.spikes);
- tractsToDwiFilter->SetWrap(m_ImageGenParameters.wrap);
- tractsToDwiFilter->Update();
-
- mitk::DiffusionImage<short>::Pointer image = mitk::DiffusionImage<short>::New();
- image->SetVectorImage( tractsToDwiFilter->GetOutput() );
- image->SetB_Value(m_ImageGenParameters.b_value);
- image->SetDirections(m_ImageGenParameters.gradientDirections);
- image->InitializeFromVectorImage();
- m_ImageGenParameters.resultNode->SetData( image );
- m_ImageGenParameters.resultNode->SetName(m_SelectedBundles.at(i)->GetName()
- +"_D"+QString::number(m_ImageGenParameters.imageRegion.GetSize(0)).toStdString()
- +"-"+QString::number(m_ImageGenParameters.imageRegion.GetSize(1)).toStdString()
- +"-"+QString::number(m_ImageGenParameters.imageRegion.GetSize(2)).toStdString()
- +"_S"+QString::number(m_ImageGenParameters.imageSpacing[0]).toStdString()
- +"-"+QString::number(m_ImageGenParameters.imageSpacing[1]).toStdString()
- +"-"+QString::number(m_ImageGenParameters.imageSpacing[2]).toStdString()
- +"_b"+QString::number(m_ImageGenParameters.b_value).toStdString()
- +"_"+m_ImageGenParameters.signalModelString.toStdString()
- +m_ImageGenParameters.artifactModelString.toStdString());
-
- GetDataStorage()->Add(m_ImageGenParameters.resultNode, m_SelectedBundles.at(i));
-
- m_ImageGenParameters.resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(tractsToDwiFilter->GetLevelWindow()) );
+ mitk::DiffusionImage<short>::Pointer diffImg = dynamic_cast<mitk::DiffusionImage<short>*>(imageNode->GetData());
+ m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New();
+ m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage());
+ m_ArtifactsToDwiFilter->SettLine(m_ImageGenParameters.tLine);
+ m_ArtifactsToDwiFilter->SetkOffset(m_ImageGenParameters.kspaceLineOffset);
+ m_ArtifactsToDwiFilter->SetNoiseModel(m_ImageGenParameters.noiseModelShort);
+ m_ArtifactsToDwiFilter->SetGradientList(m_ImageGenParameters.gradientDirections);
+ m_ArtifactsToDwiFilter->SetTE(m_ImageGenParameters.tEcho);
+ m_ArtifactsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.doSimulateEddyCurrents);
+ m_ArtifactsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.eddyStrength);
+ m_ArtifactsToDwiFilter->SetAddGibbsRinging(m_ImageGenParameters.addGibbsRinging);
+ m_ArtifactsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.frequencyMap);
+ m_ArtifactsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.spikeAmplitude);
+ m_ArtifactsToDwiFilter->SetSpikes(m_ImageGenParameters.spikes);
+ m_ArtifactsToDwiFilter->SetWrap(m_ImageGenParameters.wrap);
+ m_ImageGenParameters.parentNode = imageNode;
+ m_Worker.m_FilterType = 1;
+ m_Thread.start(QThread::LowestPriority);
+}
- if (m_Controls->m_VolumeFractionsBox->isChecked())
- {
- std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions();
- for (int k=0; k<volumeFractions.size(); k++)
- {
- mitk::Image::Pointer image = mitk::Image::New();
- image->InitializeByItk(volumeFractions.at(k).GetPointer());
- image->SetVolume(volumeFractions.at(k)->GetBufferPointer());
+void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode)
+{
+ mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast<mitk::FiberBundleX*>(fiberNode->GetData());
+ if (fiberBundle->GetNumFibers()<=0)
+ return;
- mitk::DataNode::Pointer node = mitk::DataNode::New();
- node->SetData( image );
- node->SetName(m_SelectedBundles.at(i)->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString());
- GetDataStorage()->Add(node, m_SelectedBundles.at(i));
- }
- }
+ UpdateImageParameters();
- mitk::BaseData::Pointer basedata = m_ImageGenParameters.resultNode->GetData();
- if (basedata.IsNotNull())
- {
- mitk::RenderingManager::GetInstance()->InitializeViews(
- basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
- }
- }
+ m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
+ m_TractsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.doSimulateEddyCurrents);
+ m_TractsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.eddyStrength);
+ m_TractsToDwiFilter->SetAddGibbsRinging(m_ImageGenParameters.addGibbsRinging);
+ m_TractsToDwiFilter->SetSimulateRelaxation(m_ImageGenParameters.doSimulateRelaxation);
+ m_TractsToDwiFilter->SetImageRegion(m_ImageGenParameters.imageRegion);
+ m_TractsToDwiFilter->SetSpacing(m_ImageGenParameters.imageSpacing);
+ m_TractsToDwiFilter->SetOrigin(m_ImageGenParameters.imageOrigin);
+ m_TractsToDwiFilter->SetDirectionMatrix(m_ImageGenParameters.imageDirection);
+ m_TractsToDwiFilter->SetFiberBundle(fiberBundle);
+ m_TractsToDwiFilter->SetFiberModels(m_ImageGenParameters.fiberModelList);
+ m_TractsToDwiFilter->SetNonFiberModels(m_ImageGenParameters.nonFiberModelList);
+ m_TractsToDwiFilter->SetNoiseModel(m_ImageGenParameters.noiseModel);
+ m_TractsToDwiFilter->SetkOffset(m_ImageGenParameters.kspaceLineOffset);
+ m_TractsToDwiFilter->SettLine(m_ImageGenParameters.tLine);
+ m_TractsToDwiFilter->SettInhom(m_ImageGenParameters.tInhom);
+ m_TractsToDwiFilter->SetTE(m_ImageGenParameters.tEcho);
+ m_TractsToDwiFilter->SetNumberOfRepetitions(m_ImageGenParameters.repetitions);
+ m_TractsToDwiFilter->SetEnforcePureFiberVoxels(m_ImageGenParameters.doDisablePartialVolume);
+ m_TractsToDwiFilter->SetInterpolationShrink(m_ImageGenParameters.interpolationShrink);
+ m_TractsToDwiFilter->SetFiberRadius(m_ImageGenParameters.axonRadius);
+ m_TractsToDwiFilter->SetSignalScale(m_ImageGenParameters.signalScale);
+ if (m_ImageGenParameters.interpolationShrink>0)
+ m_TractsToDwiFilter->SetUseInterpolation(true);
+ m_TractsToDwiFilter->SetTissueMask(m_ImageGenParameters.maskImage);
+ m_TractsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.frequencyMap);
+ m_TractsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.spikeAmplitude);
+ m_TractsToDwiFilter->SetSpikes(m_ImageGenParameters.spikes);
+ m_TractsToDwiFilter->SetWrap(m_ImageGenParameters.wrap);
+ m_TractsToDwiFilter->SetAddMotionArtifact(m_ImageGenParameters.doAddMotion);
+ m_TractsToDwiFilter->SetMaxTranslation(m_ImageGenParameters.translation);
+ m_TractsToDwiFilter->SetMaxRotation(m_ImageGenParameters.rotation);
+ m_TractsToDwiFilter->SetRandomMotion(m_ImageGenParameters.randomMotion);
+ m_ImageGenParameters.parentNode = fiberNode;
+ m_Worker.m_FilterType = 0;
+ m_Thread.start(QThread::LowestPriority);
}
void QmitkFiberfoxView::ApplyTransform()
{
vector< mitk::DataNode::Pointer > selectedBundles;
for( int i=0; i<m_SelectedImages.size(); i++ )
{
mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i));
for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it )
{
mitk::DataNode::Pointer fibNode = *it;
if ( fibNode.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(fibNode->GetData()) )
selectedBundles.push_back(fibNode);
}
}
if (selectedBundles.empty())
selectedBundles = m_SelectedBundles2;
if (!selectedBundles.empty())
{
std::vector<mitk::DataNode::Pointer>::const_iterator it = selectedBundles.begin();
for (it; it!=selectedBundles.end(); ++it)
{
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>((*it)->GetData());
fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value());
fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value());
fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value());
// handle child fiducials
if (m_Controls->m_IncludeFiducials->isChecked())
{
mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
{
mitk::DataNode::Pointer fiducialNode = *it2;
if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
{
mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
mitk::Geometry3D* geom = pe->GetGeometry();
// translate
mitk::Vector3D world;
world[0] = m_Controls->m_XtransBox->value();
world[1] = m_Controls->m_YtransBox->value();
world[2] = m_Controls->m_ZtransBox->value();
geom->Translate(world);
// calculate rotation matrix
double x = m_Controls->m_XrotBox->value()*M_PI/180;
double y = m_Controls->m_YrotBox->value()*M_PI/180;
double z = m_Controls->m_ZrotBox->value()*M_PI/180;
itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
rotX[1][1] = cos(x);
rotX[2][2] = rotX[1][1];
rotX[1][2] = -sin(x);
rotX[2][1] = -rotX[1][2];
itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
rotY[0][0] = cos(y);
rotY[2][2] = rotY[0][0];
rotY[0][2] = sin(y);
rotY[2][0] = -rotY[0][2];
itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
rotZ[0][0] = cos(z);
rotZ[1][1] = rotZ[0][0];
rotZ[0][1] = -sin(z);
rotZ[1][0] = -rotZ[0][1];
itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX;
// transform control point coordinate into geometry translation
geom->SetOrigin(pe->GetWorldControlPoint(0));
mitk::Point2D cp; cp.Fill(0.0);
pe->SetControlPoint(0, cp);
// rotate fiducial
geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix());
// implicit translation
mitk::Vector3D trans;
trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0];
trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1];
trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2];
mitk::Vector3D newWc = rot*trans;
newWc = newWc-trans;
geom->Translate(newWc);
}
}
}
}
}
else
{
for (int i=0; i<m_SelectedFiducials.size(); i++)
{
mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(i)->GetData());
mitk::Geometry3D* geom = pe->GetGeometry();
// translate
mitk::Vector3D world;
world[0] = m_Controls->m_XtransBox->value();
world[1] = m_Controls->m_YtransBox->value();
world[2] = m_Controls->m_ZtransBox->value();
geom->Translate(world);
// calculate rotation matrix
double x = m_Controls->m_XrotBox->value()*M_PI/180;
double y = m_Controls->m_YrotBox->value()*M_PI/180;
double z = m_Controls->m_ZrotBox->value()*M_PI/180;
itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
rotX[1][1] = cos(x);
rotX[2][2] = rotX[1][1];
rotX[1][2] = -sin(x);
rotX[2][1] = -rotX[1][2];
itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
rotY[0][0] = cos(y);
rotY[2][2] = rotY[0][0];
rotY[0][2] = sin(y);
rotY[2][0] = -rotY[0][2];
itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
rotZ[0][0] = cos(z);
rotZ[1][1] = rotZ[0][0];
rotZ[0][1] = -sin(z);
rotZ[1][0] = -rotZ[0][1];
itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX;
// transform control point coordinate into geometry translation
geom->SetOrigin(pe->GetWorldControlPoint(0));
mitk::Point2D cp; cp.Fill(0.0);
pe->SetControlPoint(0, cp);
// rotate fiducial
geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix());
}
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkFiberfoxView::CopyBundles()
{
if ( m_SelectedBundles.size()<1 ){
QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!");
MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!";
return;
}
std::vector<mitk::DataNode::Pointer>::const_iterator it = m_SelectedBundles.begin();
for (it; it!=m_SelectedBundles.end(); ++it)
{
// find parent image
mitk::DataNode::Pointer parentNode;
mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 )
{
mitk::DataNode::Pointer pImgNode = *it2;
if ( pImgNode.IsNotNull() && dynamic_cast<mitk::Image*>(pImgNode->GetData()) )
{
parentNode = pImgNode;
break;
}
}
mitk::FiberBundleX::Pointer fib = dynamic_cast<mitk::FiberBundleX*>((*it)->GetData());
mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy();
QString name((*it)->GetName().c_str());
name += "_copy";
mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
fbNode->SetData(newBundle);
fbNode->SetName(name.toStdString());
fbNode->SetVisibility(true);
if (parentNode.IsNotNull())
GetDataStorage()->Add(fbNode, parentNode);
else
GetDataStorage()->Add(fbNode);
// copy child fiducials
if (m_Controls->m_IncludeFiducials->isChecked())
{
mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it);
for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
{
mitk::DataNode::Pointer fiducialNode = *it2;
if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
{
mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New();
pe->DeepCopy(dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()));
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
newNode->SetData(pe);
newNode->SetName(fiducialNode->GetName());
GetDataStorage()->Add(newNode, fbNode);
}
}
}
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkFiberfoxView::JoinBundles()
{
if ( m_SelectedBundles.size()<2 ){
QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!");
MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!";
return;
}
std::vector<mitk::DataNode::Pointer>::const_iterator it = m_SelectedBundles.begin();
mitk::FiberBundleX::Pointer newBundle = dynamic_cast<mitk::FiberBundleX*>((*it)->GetData());
QString name("");
name += QString((*it)->GetName().c_str());
++it;
for (it; it!=m_SelectedBundles.end(); ++it)
{
newBundle = newBundle->AddBundle(dynamic_cast<mitk::FiberBundleX*>((*it)->GetData()));
name += "+"+QString((*it)->GetName().c_str());
}
mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
fbNode->SetData(newBundle);
fbNode->SetName(name.toStdString());
fbNode->SetVisibility(true);
GetDataStorage()->Add(fbNode);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkFiberfoxView::UpdateGui()
{
m_Controls->m_FiberBundleLabel->setText("<font color='red'>mandatory</font>");
m_Controls->m_GeometryFrame->setEnabled(true);
m_Controls->m_GeometryMessage->setVisible(false);
m_Controls->m_DiffusionPropsMessage->setVisible(false);
m_Controls->m_FiberGenMessage->setVisible(true);
m_Controls->m_TransformBundlesButton->setEnabled(false);
m_Controls->m_CopyBundlesButton->setEnabled(false);
m_Controls->m_GenerateFibersButton->setEnabled(false);
m_Controls->m_FlipButton->setEnabled(false);
m_Controls->m_CircleButton->setEnabled(false);
m_Controls->m_BvalueBox->setEnabled(true);
m_Controls->m_NumGradientsBox->setEnabled(true);
m_Controls->m_JoinBundlesButton->setEnabled(false);
m_Controls->m_AlignOnGrid->setEnabled(false);
if (m_SelectedFiducial.IsNotNull())
{
m_Controls->m_TransformBundlesButton->setEnabled(true);
m_Controls->m_FlipButton->setEnabled(true);
m_Controls->m_AlignOnGrid->setEnabled(true);
}
if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty())
{
m_Controls->m_TransformBundlesButton->setEnabled(true);
m_Controls->m_CircleButton->setEnabled(true);
m_Controls->m_FiberGenMessage->setVisible(false);
m_Controls->m_AlignOnGrid->setEnabled(true);
}
- if (m_TissueMask.IsNotNull() || m_SelectedImage.IsNotNull())
+ if (m_ImageGenParameters.maskImage.IsNotNull() || m_SelectedImage.IsNotNull())
{
m_Controls->m_GeometryMessage->setVisible(true);
m_Controls->m_GeometryFrame->setEnabled(false);
}
if (m_SelectedDWI.IsNotNull())
{
m_Controls->m_DiffusionPropsMessage->setVisible(true);
m_Controls->m_BvalueBox->setEnabled(false);
m_Controls->m_NumGradientsBox->setEnabled(false);
m_Controls->m_GeometryMessage->setVisible(true);
m_Controls->m_GeometryFrame->setEnabled(false);
}
if (!m_SelectedBundles.empty())
{
m_Controls->m_CopyBundlesButton->setEnabled(true);
m_Controls->m_GenerateFibersButton->setEnabled(true);
m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str());
if (m_SelectedBundles.size()>1)
m_Controls->m_JoinBundlesButton->setEnabled(true);
}
}
void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& nodes )
{
m_SelectedBundles2.clear();
m_SelectedImages.clear();
m_SelectedFiducials.clear();
m_SelectedFiducial = NULL;
- m_TissueMask = NULL;
+ m_ImageGenParameters.maskImage = NULL;
m_SelectedBundles.clear();
m_SelectedImage = NULL;
m_SelectedDWI = NULL;
m_Controls->m_TissueMaskLabel->setText("<font color='grey'>optional</font>");
// iterate all selected objects, adjust warning visibility
for( int i=0; i<nodes.size(); i++)
{
mitk::DataNode::Pointer node = nodes.at(i);
if ( node.IsNotNull() && dynamic_cast<mitk::DiffusionImage<short>*>(node->GetData()) )
{
m_SelectedDWI = node;
m_SelectedImage = node;
m_SelectedImages.push_back(node);
}
else if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
{
m_SelectedImages.push_back(node);
m_SelectedImage = node;
- bool isBinary = false;
- node->GetPropertyValue<bool>("binary", isBinary);
- if (isBinary)
+ mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
+ bool isbinary = false;
+ node->GetPropertyValue<bool>("binary", isbinary);
+ if (isbinary)
{
- m_TissueMask = dynamic_cast<mitk::Image*>(node->GetData());
+ mitk::CastToItkImage<ItkUcharImgType>(image, m_ImageGenParameters.maskImage);
m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str());
}
}
else if ( node.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(node->GetData()) )
{
m_SelectedBundles2.push_back(node);
if (m_Controls->m_RealTimeFibers->isChecked())
{
m_SelectedBundles.push_back(node);
mitk::FiberBundleX::Pointer newFib = dynamic_cast<mitk::FiberBundleX*>(node->GetData());
if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value())
GenerateFibers();
}
else
m_SelectedBundles.push_back(node);
}
else if ( node.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(node->GetData()) )
{
m_SelectedFiducials.push_back(node);
m_SelectedFiducial = node;
m_SelectedBundles.clear();
mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node);
for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it )
{
mitk::DataNode::Pointer pNode = *it;
if ( pNode.IsNotNull() && dynamic_cast<mitk::FiberBundleX*>(pNode->GetData()) )
m_SelectedBundles.push_back(pNode);
}
}
}
UpdateGui();
}
void QmitkFiberfoxView::EnableCrosshairNavigation()
{
MITK_DEBUG << "EnableCrosshairNavigation";
// enable the crosshair navigation
if (mitk::ILinkedRenderWindowPart* linkedRenderWindow =
dynamic_cast<mitk::ILinkedRenderWindowPart*>(this->GetRenderWindowPart()))
{
MITK_DEBUG << "enabling linked navigation";
linkedRenderWindow->EnableLinkedNavigation(true);
// linkedRenderWindow->EnableSlicingPlanes(true);
}
if (m_Controls->m_RealTimeFibers->isChecked())
GenerateFibers();
}
void QmitkFiberfoxView::DisableCrosshairNavigation()
{
MITK_DEBUG << "DisableCrosshairNavigation";
// disable the crosshair navigation during the drawing
if (mitk::ILinkedRenderWindowPart* linkedRenderWindow =
dynamic_cast<mitk::ILinkedRenderWindowPart*>(this->GetRenderWindowPart()))
{
MITK_DEBUG << "disabling linked navigation";
linkedRenderWindow->EnableLinkedNavigation(false);
// linkedRenderWindow->EnableSlicingPlanes(false);
}
}
void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node)
{
mitk::DataNode* nonConstNode = const_cast<mitk::DataNode*>(node);
std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode);
if (dynamic_cast<FiberBundleX*>(node->GetData()))
{
m_SelectedBundles.clear();
m_SelectedBundles2.clear();
}
else if (dynamic_cast<Image*>(node->GetData()))
m_SelectedImages.clear();
if( it != m_DataNodeToPlanarFigureData.end() )
{
QmitkPlanarFigureData& data = it->second;
// remove observers
data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag );
data.m_Figure->RemoveObserver( data.m_SelectObserverTag );
data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag );
data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag );
m_DataNodeToPlanarFigureData.erase( it );
}
}
void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node )
{
// add observer for selection in renderwindow
mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
bool isPositionMarker (false);
node->GetBoolProperty("isContourMarker", isPositionMarker);
if( figure && !isPositionMarker )
{
MITK_DEBUG << "figure added. will add interactor if needed.";
mitk::PlanarFigureInteractor::Pointer figureInteractor
= dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
mitk::DataNode* nonConstNode = const_cast<mitk::DataNode*>( node );
if(figureInteractor.IsNull())
{
- figureInteractor = mitk::PlanarFigureInteractor::New();
- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
- figureInteractor->SetDataNode( nonConstNode );
+ figureInteractor = mitk::PlanarFigureInteractor::New();
+ us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "PlanarFigure" );
+ figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
+ figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
+ figureInteractor->SetDataNode( nonConstNode );
}
MITK_DEBUG << "will now add observers for planarfigure";
QmitkPlanarFigureData data;
data.m_Figure = figure;
// // add observer for event when figure has been placed
typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType;
// SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New();
// initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized );
// data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand );
// add observer for event when figure is picked (selected)
typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType;
MemberCommandType::Pointer selectCommand = MemberCommandType::New();
selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected );
data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand );
// add observer for event when interaction with figure starts
SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New();
startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation);
data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand );
// add observer for event when interaction with figure starts
SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New();
endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation);
data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand );
m_DataNodeToPlanarFigureData[nonConstNode] = data;
}
}
void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& )
{
mitk::TNodePredicateDataType<mitk::PlanarFigure>::Pointer isPf = mitk::TNodePredicateDataType<mitk::PlanarFigure>::New();
mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf );
for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it)
{
mitk::DataNode* node = *it;
if( node->GetData() == object )
{
node->SetSelected(true);
m_SelectedFiducial = node;
}
else
node->SetSelected(false);
}
UpdateGui();
this->RequestRenderWindowUpdate();
}
void QmitkFiberfoxView::SetFocus()
{
m_Controls->m_CircleButton->setFocus();
}
+
+
+void QmitkFiberfoxView::SetOutputPath()
+{
+ // SELECT FOLDER DIALOG
+
+ m_OutputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", m_OutputPath);
+
+ if (m_OutputPath.isEmpty())
+ m_Controls->m_SavePathEdit->setText("-");
+ else
+ {
+ m_OutputPath += "/";
+ m_Controls->m_SavePathEdit->setText(m_OutputPath);
+ }
+}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h
index 172b68f5ba..c63364d3aa 100755
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h
@@ -1,214 +1,266 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <berryISelectionListener.h>
#include <berryIStructuredSelection.h>
#include <QmitkAbstractView.h>
#include "ui_QmitkFiberfoxViewControls.h"
#include <itkVectorImage.h>
#include <itkVectorContainer.h>
#include <itkOrientationDistributionFunction.h>
#include <mitkFiberBundleX.h>
#include <mitkPlanarEllipse.h>
#include <mitkDiffusionNoiseModel.h>
#include <mitkDiffusionSignalModel.h>
#include <mitkRicianNoiseModel.h>
#include <itkTractsToDWIImageFilter.h>
+#include <itkAddArtifactsToDwiImageFilter.h>
#include <mitkTensorModel.h>
#include <mitkBallModel.h>
#include <mitkStickModel.h>
#include <mitkAstroStickModel.h>
#include <mitkDotModel.h>
+#include <QThread>
+#include <QObject>
+#include <QTimer>
+#include <QTime>
/*!
\brief View for fiber based diffusion software phantoms (Fiberfox).
\sa QmitkFunctionality
\ingroup Functionalities
*/
// Forward Qt class declarations
using namespace std;
+class QmitkFiberfoxView;
+
+class QmitkFiberfoxWorker : public QObject
+{
+ Q_OBJECT
+
+public:
+
+ QmitkFiberfoxWorker(QmitkFiberfoxView* view);
+ int m_FilterType;
+
+public slots:
+
+ void run();
+
+private:
+
+ QmitkFiberfoxView* m_View;
+};
+
class QmitkFiberfoxView : public QmitkAbstractView
{
// this is needed for all Qt objects that should have a Qt meta-object
// (everything that derives from QObject and wants to have signal/slots)
Q_OBJECT
public:
static const string VIEW_ID;
QmitkFiberfoxView();
virtual ~QmitkFiberfoxView();
virtual void CreateQtPartControl(QWidget *parent);
void SetFocus();
typedef itk::Image<double, 3> ItkDoubleImgType;
typedef itk::Image<unsigned char, 3> ItkUcharImgType;
typedef itk::Vector<double,3> GradientType;
typedef vector<GradientType> GradientListType;
template<int ndirs> vector<itk::Vector<double,3> > MakeGradientList();
protected slots:
+ void SetOutputPath();
void LoadParameters();
void SaveParameters();
+ void BeforeThread();
+ void AfterThread();
+ void KillThread();
+ void UpdateSimulationStatus();
+
void OnDrawROI(); ///< adds new ROI, handles interactors etc.
void OnAddBundle(); ///< adds new fiber bundle to datastorage
void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists
void GenerateFibers(); ///< generate fibers from the selected ROIs
void GenerateImage(); ///< generate artificial image from the selected fiber bundle
void JoinBundles(); ///< merges selcted fiber bundles into one
void CopyBundles(); ///< add copy of the selected bundle to the datamanager
void ApplyTransform(); ///< rotate and shift selected bundles
void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center
void Comp1ModelFrameVisibility(int index);///< only show parameters of selected fiber model type
void Comp2ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type
void Comp3ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type
void Comp4ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type
void ShowAdvancedOptions(int state);
/** update fibers if any parameter changes */
void OnFiberDensityChanged(int value);
void OnFiberSamplingChanged(double value);
void OnTensionChanged(double value);
void OnContinuityChanged(double value);
void OnBiasChanged(double value);
void OnVarianceChanged(double value);
void OnDistributionChanged(int value);
void OnAddNoise(int value);
void OnAddGhosts(int value);
void OnAddDistortions(int value);
void OnAddEddy(int value);
void OnAddSpikes(int value);
void OnAddAliasing(int value);
+ void OnAddMotion(int value);
void OnConstantRadius(int value);
protected:
/// \brief called by QmitkFunctionality when DataManager's selection has changed
virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>&);
GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere
Ui::QmitkFiberfoxViewControls* m_Controls;
+ void SimulateForExistingDwi(mitk::DataNode* imageNode);
+ void SimulateImageFromFibers(mitk::DataNode* fiberNode);
void UpdateImageParameters(); ///< update iamge generation paaremeter struct
void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection
void PlanarFigureSelected( itk::Object* object, const itk::EventObject& );
void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends
void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts
void NodeAdded( const mitk::DataNode* node ); ///< add observers
void NodeRemoved(const mitk::DataNode* node); ///< remove observers
/** structure to keep track of planar figures and observers */
struct QmitkPlanarFigureData
{
QmitkPlanarFigureData()
: m_Figure(0)
, m_EndPlacementObserverTag(0)
, m_SelectObserverTag(0)
, m_StartInteractionObserverTag(0)
, m_EndInteractionObserverTag(0)
, m_Flipped(0)
{
}
mitk::PlanarFigure* m_Figure;
unsigned int m_EndPlacementObserverTag;
unsigned int m_SelectObserverTag;
unsigned int m_StartInteractionObserverTag;
unsigned int m_EndInteractionObserverTag;
unsigned int m_Flipped;
};
/** structure storing the image generation parameters */
struct ImageParameters {
itk::ImageRegion<3> imageRegion;
itk::Vector<double,3> imageSpacing;
itk::Point<double,3> imageOrigin;
itk::Matrix<double, 3, 3> imageDirection;
unsigned int numGradients;
double b_value;
unsigned int repetitions;
double signalScale;
double tEcho;
double tLine;
double tInhom;
double axonRadius;
unsigned int interpolationShrink;
double kspaceLineOffset;
bool addGibbsRinging;
double eddyStrength;
double comp3Weight;
double comp4Weight;
int spikes;
double spikeAmplitude;
double wrap;
-
+ itk::Vector<double,3> translation;
+ itk::Vector<double,3> rotation;
bool doSimulateRelaxation;
bool doSimulateEddyCurrents;
bool doDisablePartialVolume;
+ bool doAddMotion;
+ bool randomMotion;
- mitk::RicianNoiseModel<double> ricianNoiseModel;
+ mitk::DiffusionNoiseModel<double>* noiseModel;
+ mitk::DiffusionNoiseModel<short>* noiseModelShort;
mitk::DiffusionSignalModel<double>::GradientListType gradientDirections;
itk::TractsToDWIImageFilter< short >::DiffusionModelList fiberModelList, nonFiberModelList;
- itk::TractsToDWIImageFilter< short >::KspaceArtifactList artifactList;
QString signalModelString, artifactModelString;
-
ItkDoubleImgType::Pointer frequencyMap;
- ItkUcharImgType::Pointer tissueMaskImage;
-
+ ItkUcharImgType::Pointer maskImage;
mitk::DataNode::Pointer resultNode;
+ mitk::DataNode::Pointer parentNode;
+ QString outputPath;
};
ImageParameters m_ImageGenParameters;
+ ImageParameters m_ImageGenParametersBackup;
std::map<mitk::DataNode*, QmitkPlanarFigureData> m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData
- mitk::Image::Pointer m_TissueMask; ///< mask defining which regions of the image should contain signal and which are containing only noise
mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse
mitk::DataNode::Pointer m_SelectedImage;
mitk::DataNode::Pointer m_SelectedDWI;
vector< mitk::DataNode::Pointer > m_SelectedBundles;
vector< mitk::DataNode::Pointer > m_SelectedBundles2;
vector< mitk::DataNode::Pointer > m_SelectedFiducials;
vector< mitk::DataNode::Pointer > m_SelectedImages;
// intra and inter axonal compartments
mitk::StickModel<double> m_StickModel1;
mitk::StickModel<double> m_StickModel2;
mitk::TensorModel<double> m_ZeppelinModel1;
mitk::TensorModel<double> m_ZeppelinModel2;
mitk::TensorModel<double> m_TensorModel1;
mitk::TensorModel<double> m_TensorModel2;
// extra axonal compartment models
mitk::BallModel<double> m_BallModel1;
mitk::BallModel<double> m_BallModel2;
mitk::AstroStickModel<double> m_AstrosticksModel1;
mitk::AstroStickModel<double> m_AstrosticksModel2;
mitk::DotModel<double> m_DotModel1;
mitk::DotModel<double> m_DotModel2;
+
+ QString m_ParameterFile;
+ QString m_OutputPath;
+
+ // GUI thread
+ QmitkFiberfoxWorker m_Worker; ///< runs filter
+ QThread m_Thread; ///< worker thread
+ itk::TractsToDWIImageFilter< short >::Pointer m_TractsToDwiFilter;
+ itk::AddArtifactsToDwiImageFilter< short >::Pointer m_ArtifactsToDwiFilter;
+ bool m_ThreadIsRunning;
+ QTimer* m_SimulationTimer;
+ QTime m_SimulationTime;
+ QString m_SimulationStatusText;
+
+ friend class QmitkFiberfoxWorker;
};
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
index fd6bb151c9..a706b5e9f1 100755
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui
@@ -1,2462 +1,3065 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkFiberfoxViewControls</class>
<widget class="QWidget" name="QmitkFiberfoxViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>435</width>
- <height>1792</height>
+ <height>2274</height>
</rect>
</property>
<property name="windowTitle">
<string>Form</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
- <item row="1" column="0">
- <widget class="QCommandLinkButton" name="m_SaveParametersButton">
+ <item row="3" column="0">
+ <widget class="QCommandLinkButton" name="m_LoadParametersButton">
<property name="text">
- <string>Save Parameters</string>
+ <string>Load Parameters</string>
+ </property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/upload.ico</normaloff>:/QmitkDiffusionImaging/general_icons/upload.ico</iconset>
</property>
</widget>
</item>
- <item row="0" column="0">
+ <item row="1" column="0">
<widget class="QTabWidget" name="tabWidget">
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="tab">
<attribute name="title">
<string>Fiber Definition</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_8">
<item row="7" column="0">
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_FiberGenMessage">
<property name="styleSheet">
<string notr="true">color: rgb(255, 0, 0);</string>
</property>
<property name="text">
<string>Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab.</string>
</property>
<property name="textFormat">
<enum>Qt::AutoText</enum>
</property>
<property name="alignment">
<set>Qt::AlignJustify|Qt::AlignVCenter</set>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
<item row="5" column="0">
<widget class="QGroupBox" name="groupBox_7">
<property name="title">
<string>Fiducial Options</string>
</property>
<layout class="QGridLayout" name="gridLayout_16">
<item row="0" column="0">
<widget class="QCheckBox" name="m_ConstantRadiusBox">
<property name="toolTip">
<string>All fiducials are treated as circles with the same radius as the first fiducial. </string>
</property>
<property name="text">
<string>Use Constant Fiducial Radius</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCommandLinkButton" name="m_AlignOnGrid">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center.</string>
</property>
<property name="text">
<string>Align With Grid</string>
</property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
+ </property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="6" column="0" colspan="2">
<widget class="QGroupBox" name="groupBox_4">
<property name="title">
<string>Operations</string>
</property>
<layout class="QGridLayout" name="gridLayout_11">
<item row="5" column="0">
<widget class="QCommandLinkButton" name="m_JoinBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Join Bundles</string>
</property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/plus.ico</normaloff>:/QmitkDiffusionImaging/general_icons/plus.ico</iconset>
+ </property>
</widget>
</item>
<item row="2" column="0">
<widget class="QFrame" name="frame_4">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_12">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="1" column="2">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_18">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Y</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="m_XrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around x-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_22">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Axis:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="2">
<widget class="QDoubleSpinBox" name="m_YrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around y-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_21">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Translation:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="3" column="3">
<widget class="QDoubleSpinBox" name="m_ZtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the z-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="2">
<widget class="QDoubleSpinBox" name="m_YtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the y-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_17">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>X</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_20">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Rotation:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="3">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_19">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Z</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="3">
<widget class="QDoubleSpinBox" name="m_ZrotBox">
<property name="toolTip">
<string>Rotation angle (in degree) around z-axis.</string>
</property>
<property name="minimum">
<double>-360.000000000000000</double>
</property>
<property name="maximum">
<double>360.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QDoubleSpinBox" name="m_XtransBox">
<property name="toolTip">
<string>Translation (in mm) in direction of the x-axis.</string>
</property>
<property name="minimum">
<double>-1000.000000000000000</double>
</property>
<property name="maximum">
<double>1000.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_24">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Scaling:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="4" column="1">
<widget class="QDoubleSpinBox" name="m_XscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the x-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
<item row="4" column="2">
<widget class="QDoubleSpinBox" name="m_YscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the y-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
<item row="4" column="3">
<widget class="QDoubleSpinBox" name="m_ZscaleBox">
<property name="toolTip">
<string>Scaling factor for selected fiber bundle along the z-axis.</string>
</property>
<property name="minimum">
<double>0.010000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="4" column="0">
<widget class="QCommandLinkButton" name="m_CopyBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Copy Bundles</string>
</property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/copy2.ico</normaloff>:/QmitkDiffusionImaging/general_icons/copy2.ico</iconset>
+ </property>
</widget>
</item>
<item row="3" column="0">
<widget class="QCommandLinkButton" name="m_TransformBundlesButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Transform Selection</string>
</property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/refresh.ico</normaloff>:/QmitkDiffusionImaging/general_icons/refresh.ico</iconset>
+ </property>
</widget>
</item>
<item row="6" column="0">
<widget class="QCheckBox" name="m_IncludeFiducials">
<property name="toolTip">
<string>If checked, the fiducials belonging to the modified bundle are also modified.</string>
</property>
<property name="text">
<string>Include Fiducials</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="4" column="0">
<widget class="QGroupBox" name="groupBox_8">
<property name="title">
<string>Fiber Options</string>
</property>
<layout class="QGridLayout" name="gridLayout_15">
<item row="2" column="0">
<widget class="QFrame" name="frame_5">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_9">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="2" column="0">
<widget class="QFrame" name="m_AdvancedFiberOptionsFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_21">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="1" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_5">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Tension:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_8">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Sampling:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QDoubleSpinBox" name="m_TensionBox">
<property name="toolTip">
<string/>
</property>
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QDoubleSpinBox" name="m_BiasBox">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_7">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Bias:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_6">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Continuity:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QDoubleSpinBox" name="m_ContinuityBox">
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>-1.000000000000000</double>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.000000000000000</double>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_FiberSamplingBox">
<property name="toolTip">
<string>Distance of fiber sampling points (in mm)</string>
</property>
<property name="decimals">
<number>1</number>
</property>
<property name="minimum">
<double>0.100000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>1.000000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="1" column="0">
<widget class="QFrame" name="frame_2">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_25">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<property name="verticalSpacing">
<number>6</number>
</property>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_4">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>#Fibers:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QSpinBox" name="m_FiberDensityBox">
<property name="toolTip">
<string>Specify number of fibers to generate for the selected bundle.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>1000000</number>
</property>
<property name="singleStep">
<number>100</number>
</property>
<property name="value">
<number>100</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QCommandLinkButton" name="m_GenerateFibersButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Generate Fibers</string>
</property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
+ </property>
</widget>
</item>
<item row="1" column="0">
<widget class="QFrame" name="frame_3">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_5">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="0" column="1">
<widget class="QComboBox" name="m_DistributionBox">
<property name="toolTip">
<string>Select fiber distribution inside of the fiducials.</string>
</property>
<item>
<property name="text">
<string>Uniform</string>
</property>
</item>
<item>
<property name="text">
<string>Gaussian</string>
</property>
</item>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_9">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Distribution:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="QDoubleSpinBox" name="m_VarianceBox">
<property name="toolTip">
<string>Variance of the gaussian</string>
</property>
<property name="decimals">
<number>3</number>
</property>
<property name="minimum">
<double>0.001000000000000</double>
</property>
<property name="maximum">
<double>10.000000000000000</double>
</property>
<property name="singleStep">
<double>0.010000000000000</double>
</property>
<property name="value">
<double>0.100000000000000</double>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="0" column="0">
<widget class="QFrame" name="frame_8">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_22">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QCheckBox" name="m_RealTimeFibers">
<property name="toolTip">
<string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
</property>
<property name="text">
<string>Real Time Fibers</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="m_AdvancedOptionsBox">
<property name="toolTip">
<string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
</property>
<property name="text">
<string>Advanced Options</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QFrame" name="frame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QPushButton" name="m_CircleButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="maximumSize">
<size>
<width>30</width>
<height>30</height>
</size>
</property>
<property name="toolTip">
<string>Draw elliptical fiducial.</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset resource="../../resources/QmitkDiffusionImaging.qrc">
<normaloff>:/QmitkDiffusionImaging/circle.png</normaloff>:/QmitkDiffusionImaging/circle.png</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>false</bool>
</property>
<property name="flat">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QPushButton" name="m_FlipButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="maximumSize">
<size>
<width>30</width>
<height>30</height>
</size>
</property>
<property name="toolTip">
<string>Flip fiber waypoints of selcted fiducial around one axis.</string>
</property>
<property name="text">
<string/>
</property>
<property name="icon">
<iconset resource="../../resources/QmitkDiffusionImaging.qrc">
<normaloff>:/QmitkDiffusionImaging/refresh.xpm</normaloff>:/QmitkDiffusionImaging/refresh.xpm</iconset>
</property>
<property name="iconSize">
<size>
<width>32</width>
<height>32</height>
</size>
</property>
<property name="checkable">
<bool>false</bool>
</property>
<property name="flat">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="2">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_2">
<attribute name="title">
<string>Signal Generation</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
+ <item row="0" column="0" rowspan="2">
<widget class="QGroupBox" name="groupBox_2">
<property name="title">
<string>Data</string>
</property>
<layout class="QGridLayout" name="gridLayout_10">
+ <item row="3" column="0" colspan="2">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_3">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>Tissue Mask:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QLabel" name="m_TissueMaskLabel">
+ <property name="text">
+ <string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
<item row="0" column="0" rowspan="2" colspan="2">
<widget class="QLabel" name="m_TensorsToDWIBValueLabel_16">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Fiber Bundle:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="2" rowspan="2">
<widget class="QLabel" name="m_FiberBundleLabel">
<property name="text">
<string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
- <item row="3" column="0" colspan="2">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_3">
+ <item row="4" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_10">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
- <string>Tissue Mask:</string>
+ <string>Save path:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
- <item row="3" column="2">
- <widget class="QLabel" name="m_TissueMaskLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
+ <item row="4" column="2">
+ <widget class="QFrame" name="frame_6">
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
</property>
- <property name="wordWrap">
- <bool>true</bool>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
</property>
+ <layout class="QGridLayout" name="gridLayout_20">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <property name="spacing">
+ <number>0</number>
+ </property>
+ <item row="0" column="0">
+ <widget class="QLineEdit" name="m_SavePathEdit">
+ <property name="text">
+ <string>-</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QToolButton" name="m_OutputPathButton">
+ <property name="text">
+ <string>...</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
</widget>
</item>
</layout>
</widget>
</item>
- <item row="4" column="0">
- <widget class="QGroupBox" name="groupBox">
+ <item row="13" column="0">
+ <widget class="QGroupBox" name="groupBox_3">
<property name="title">
- <string>Image Settings</string>
+ <string>Noise and other Artifacts</string>
</property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="7" column="0">
- <widget class="QFrame" name="m_AdvancedSignalOptionsFrame">
+ <layout class="QGridLayout" name="gridLayout_6">
+ <item row="20" column="0">
+ <widget class="Line" name="line">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QCheckBox" name="m_AddNoise">
+ <property name="text">
+ <string>Add Noise</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="21" column="0">
+ <widget class="QCheckBox" name="m_AddGibbsRinging">
+ <property name="toolTip">
+ <string>Add ringing artifacts occuring at strong edges in the image.</string>
+ </property>
+ <property name="text">
+ <string>Add Gibbs Ringing</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="10" column="0">
+ <widget class="QFrame" name="m_AliasingFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
- <layout class="QGridLayout" name="gridLayout_23">
+ <layout class="QFormLayout" name="formLayout_10">
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
- <property name="horizontalSpacing">
- <number>6</number>
- </property>
- <item row="7" column="0">
- <widget class="QCheckBox" name="m_RelaxationBox">
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_27">
<property name="toolTip">
- <string><html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html></string>
+ <string/>
</property>
- <property name="text">
- <string>Simulate Signal Relaxation</string>
+ <property name="statusTip">
+ <string/>
</property>
- <property name="checked">
- <bool>true</bool>
+ <property name="whatsThis">
+ <string/>
</property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_2">
<property name="text">
- <string>Repetitions:</string>
+ <string>Shrink FOV (%):</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="3" column="1">
- <widget class="QDoubleSpinBox" name="m_LineReadoutTimeBox">
+ <item row="0" column="1">
+ <widget class="QDoubleSpinBox" name="m_WrapBox">
<property name="toolTip">
- <string>T2* relaxation time (in milliseconds).</string>
+ <string>Shrink FOV by this percentage.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="minimum">
+ <double>0.000000000000000</double>
</property>
<property name="maximum">
- <double>100.000000000000000</double>
+ <double>90.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
- <double>1.000000000000000</double>
+ <double>25.000000000000000</double>
</property>
</widget>
</item>
- <item row="5" column="0">
- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_4">
+ </layout>
+ </widget>
+ </item>
+ <item row="17" column="0">
+ <widget class="Line" name="line_4">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QFrame" name="m_SpikeFrame">
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QFormLayout" name="formLayout_9">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_NoiseLabel_2">
<property name="text">
- <string>Fiber Radius:</string>
+ <string>Num. Spikes:</string>
</property>
</widget>
</item>
- <item row="5" column="1">
- <widget class="QSpinBox" name="m_FiberRadius">
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="m_SpikeNumBox">
<property name="toolTip">
- <string>Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation.</string>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="maximum">
- <number>1000</number>
+ <string>The number of randomly occurring signal spikes.</string>
</property>
<property name="value">
- <number>0</number>
+ <number>1</number>
</property>
</widget>
</item>
<item row="1" column="1">
- <widget class="QSpinBox" name="m_SignalScaleBox">
+ <widget class="QDoubleSpinBox" name="m_SpikeScaleBox">
<property name="toolTip">
- <string>TE in milliseconds</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>10000</number>
+ <string>Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice.</string>
</property>
<property name="singleStep">
- <number>1</number>
+ <double>0.100000000000000</double>
</property>
<property name="value">
- <number>100</number>
+ <double>0.100000000000000</double>
</property>
</widget>
</item>
- <item row="6" column="0">
- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_3">
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_NoiseLabel_4">
<property name="text">
- <string>Interpolation Shrink:</string>
+ <string>Scale:</string>
</property>
</widget>
</item>
- <item row="3" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_15">
- <property name="toolTip">
- <string/>
- </property>
- <property name="statusTip">
- <string/>
- </property>
- <property name="whatsThis">
- <string/>
- </property>
- <property name="text">
- <string>Line Readout Time: </string>
- </property>
- <property name="wordWrap">
- <bool>false</bool>
+ </layout>
+ </widget>
+ </item>
+ <item row="18" column="0">
+ <widget class="QCheckBox" name="m_AddEddy">
+ <property name="toolTip">
+ <string>!!!EXPERIMENTAL!!!</string>
+ </property>
+ <property name="text">
+ <string>Add Eddy Current Effects</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QCheckBox" name="m_AddSpikes">
+ <property name="text">
+ <string>Add Spikes</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QFrame" name="m_NoiseFrame">
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QFormLayout" name="formLayout_5">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_NoiseLabel">
+ <property name="text">
+ <string>Variance:</string>
</property>
</widget>
</item>
- <item row="2" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_13">
+ <item row="1" column="1">
+ <widget class="QDoubleSpinBox" name="m_NoiseLevel">
<property name="toolTip">
- <string/>
+ <string>Variance of selected noise distribution.</string>
</property>
- <property name="statusTip">
- <string/>
+ <property name="decimals">
+ <number>4</number>
</property>
- <property name="whatsThis">
- <string/>
+ <property name="minimum">
+ <double>0.000000000000000</double>
</property>
- <property name="text">
- <string><html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html></string>
+ <property name="maximum">
+ <double>100000.000000000000000</double>
</property>
- <property name="wordWrap">
- <bool>false</bool>
+ <property name="singleStep">
+ <double>0.001000000000000</double>
+ </property>
+ <property name="value">
+ <double>50.000000000000000</double>
</property>
</widget>
</item>
- <item row="8" column="0">
- <widget class="QCheckBox" name="m_EnforcePureFiberVoxelsBox">
- <property name="toolTip">
- <string>Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present.</string>
- </property>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_NoiseLabel_5">
<property name="text">
- <string>Disable Partial Volume Effects</string>
- </property>
- <property name="checked">
- <bool>false</bool>
+ <string>Distribution:</string>
</property>
</widget>
</item>
- <item row="9" column="0">
- <widget class="QCheckBox" name="m_VolumeFractionsBox">
+ <item row="0" column="1">
+ <widget class="QComboBox" name="m_NoiseDistributionBox">
<property name="toolTip">
- <string>Output one image per compartment containing the corresponding volume fractions per voxel.</string>
- </property>
- <property name="text">
- <string>Output Volume Fractions</string>
- </property>
- <property name="checked">
- <bool>false</bool>
+ <string>Noise distribution</string>
</property>
+ <item>
+ <property name="text">
+ <string>Rician</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>Chi-squared</string>
+ </property>
+ </item>
</widget>
</item>
- <item row="4" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_12">
+ </layout>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <widget class="QCheckBox" name="m_AddGhosts">
+ <property name="text">
+ <string>Add N/2 Ghosts</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="13" column="0">
+ <widget class="QFrame" name="m_DistortionsFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QFormLayout" name="formLayout_7">
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_25">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
- <string><html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html></string>
+ <string>Frequency Map:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
- <widget class="QSpinBox" name="m_RepetitionsBox">
+ <widget class="QmitkDataStorageComboBox" name="m_FrequencyMapBox">
<property name="toolTip">
- <string>Number of signal averages. Increase to reduce noise.</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>100</number>
- </property>
- <property name="singleStep">
- <number>1</number>
- </property>
- <property name="value">
- <number>1</number>
+ <string>Select image specifying the frequency inhomogeneities (in Hz).</string>
</property>
</widget>
</item>
- <item row="4" column="1">
- <widget class="QSpinBox" name="m_T2starBox">
+ </layout>
+ </widget>
+ </item>
+ <item row="14" column="0">
+ <widget class="Line" name="line_5">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="8" column="0">
+ <widget class="Line" name="line_7">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="0">
+ <widget class="Line" name="line_6">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="16" column="0">
+ <widget class="QFrame" name="m_MotionArtifactFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QFormLayout" name="formLayout_11">
+ <property name="fieldGrowthPolicy">
+ <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
+ </property>
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>6</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="0" column="0">
+ <widget class="QCheckBox" name="m_RandomMotion">
<property name="toolTip">
- <string>Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds).</string>
- </property>
- <property name="minimum">
- <number>1</number>
+ <string>Toggle between random movement and linear movement.</string>
</property>
- <property name="maximum">
- <number>10000</number>
- </property>
- <property name="singleStep">
- <number>1</number>
+ <property name="text">
+ <string>Randomize motion</string>
</property>
- <property name="value">
- <number>50</number>
+ <property name="checked">
+ <bool>true</bool>
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QSpinBox" name="m_TEbox">
- <property name="toolTip">
- <string>TE in milliseconds</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>10000</number>
- </property>
- <property name="singleStep">
- <number>1</number>
- </property>
- <property name="value">
- <number>100</number>
- </property>
- </widget>
- </item>
- <item row="6" column="1">
- <widget class="QSpinBox" name="m_InterpolationShrink">
- <property name="toolTip">
- <string><html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html></string>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="maximum">
- <number>10000</number>
- </property>
- <property name="value">
- <number>0</number>
+ <item row="1" column="0" colspan="2">
+ <widget class="QGroupBox" name="m_RotationArtifactFrame">
+ <property name="title">
+ <string>Rotation</string>
</property>
+ <layout class="QGridLayout" name="gridLayout_19">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>9</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_36">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>Degree:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_29">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>x</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_28">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>Axis:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QDoubleSpinBox" name="m_MaxRotationBoxX">
+ <property name="toolTip">
+ <string>Maximum rotation around x-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>360.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="3">
+ <widget class="QDoubleSpinBox" name="m_MaxRotationBoxZ">
+ <property name="toolTip">
+ <string>Maximum rotation around z-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>360.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>15.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_30">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>y</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_31">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>z</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QDoubleSpinBox" name="m_MaxRotationBoxY">
+ <property name="toolTip">
+ <string>Maximum rotation around y-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>360.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ </layout>
</widget>
</item>
- <item row="1" column="0">
- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_5">
- <property name="text">
- <string>Signal Scale:</string>
+ <item row="2" column="0" colspan="2">
+ <widget class="QGroupBox" name="m_TranslationArtifactFrame">
+ <property name="title">
+ <string>Translation</string>
</property>
+ <layout class="QGridLayout" name="gridLayout_28">
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_48">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>Distance:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_51">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>x</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_52">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>y</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_47">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>Axis:</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_53">
+ <property name="toolTip">
+ <string/>
+ </property>
+ <property name="statusTip">
+ <string/>
+ </property>
+ <property name="whatsThis">
+ <string/>
+ </property>
+ <property name="text">
+ <string>z</string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxX">
+ <property name="toolTip">
+ <string>Maximum translation along x-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>1000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxY">
+ <property name="toolTip">
+ <string>Maximum translation along y-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>1000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="3">
+ <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxZ">
+ <property name="toolTip">
+ <string>Maximum translation along z-axis.</string>
+ </property>
+ <property name="decimals">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <double>1000.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>1.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ </layout>
</widget>
</item>
</layout>
</widget>
</item>
- <item row="2" column="0">
- <widget class="QLabel" name="m_GeometryMessage">
- <property name="styleSheet">
- <string notr="true">color: rgb(255, 0, 0);</string>
- </property>
+ <item row="15" column="0">
+ <widget class="QCheckBox" name="m_AddMotion">
<property name="text">
- <string>Using geometry of selected image!</string>
+ <string>Add Motion Artifacts</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="4" column="0">
- <widget class="QLabel" name="m_DiffusionPropsMessage">
- <property name="styleSheet">
- <string notr="true">color: rgb(255, 0, 0);</string>
+ <item row="12" column="0">
+ <widget class="QCheckBox" name="m_AddDistortions">
+ <property name="text">
+ <string>Add Distortions</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
</property>
+ </widget>
+ </item>
+ <item row="9" column="0">
+ <widget class="QCheckBox" name="m_AddAliasing">
<property name="text">
- <string>Using gradients of selected DWI!</string>
+ <string>Add Aliasing</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="3" column="0">
- <widget class="QFrame" name="m_GeometryFrame">
+ <item row="7" column="0">
+ <widget class="QFrame" name="m_GhostFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
- <layout class="QGridLayout" name="gridLayout_7">
+ <layout class="QFormLayout" name="formLayout_6">
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
- <item row="2" column="2">
- <widget class="QDoubleSpinBox" name="m_SpacingY">
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>0.100000000000000</double>
- </property>
- <property name="maximum">
- <double>50.000000000000000</double>
+ <item row="0" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_23">
+ <property name="toolTip">
+ <string/>
</property>
- <property name="singleStep">
- <double>0.100000000000000</double>
+ <property name="statusTip">
+ <string/>
</property>
- <property name="value">
- <double>2.000000000000000</double>
+ <property name="whatsThis">
+ <string/>
</property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_2">
<property name="text">
- <string>Image Spacing:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="3">
- <widget class="QDoubleSpinBox" name="m_SpacingZ">
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>0.100000000000000</double>
- </property>
- <property name="maximum">
- <double>50.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
+ <string>K-Space Line Offset:</string>
</property>
- <property name="value">
- <double>2.000000000000000</double>
+ <property name="wordWrap">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QDoubleSpinBox" name="m_SpacingX">
+ <item row="0" column="1">
+ <widget class="QDoubleSpinBox" name="m_kOffsetBox">
+ <property name="toolTip">
+ <string>A larger offset increases the inensity of the ghost image.</string>
+ </property>
<property name="decimals">
<number>3</number>
</property>
- <property name="minimum">
- <double>0.100000000000000</double>
- </property>
<property name="maximum">
- <double>50.000000000000000</double>
+ <double>1.000000000000000</double>
</property>
<property name="singleStep">
- <double>0.100000000000000</double>
+ <double>0.010000000000000</double>
</property>
<property name="value">
- <double>2.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Image Dimensions:</string>
+ <double>0.250000000000000</double>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="m_SizeX">
+ </layout>
+ </widget>
+ </item>
+ <item row="19" column="0">
+ <widget class="QFrame" name="m_EddyFrame">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QFormLayout" name="formLayout_8">
+ <property name="fieldGrowthPolicy">
+ <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
+ </property>
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
+ <property name="leftMargin">
+ <number>0</number>
+ </property>
+ <property name="topMargin">
+ <number>0</number>
+ </property>
+ <property name="rightMargin">
+ <number>0</number>
+ </property>
+ <property name="bottomMargin">
+ <number>0</number>
+ </property>
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_26">
<property name="toolTip">
- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
+ <string/>
</property>
- <property name="minimum">
- <number>1</number>
+ <property name="statusTip">
+ <string/>
</property>
- <property name="maximum">
- <number>1000</number>
+ <property name="whatsThis">
+ <string/>
</property>
- <property name="singleStep">
- <number>1</number>
+ <property name="text">
+ <string>Magnitude:</string>
</property>
- <property name="value">
- <number>11</number>
+ <property name="wordWrap">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="0" column="2">
- <widget class="QSpinBox" name="m_SizeY">
+ <item row="1" column="1">
+ <widget class="QDoubleSpinBox" name="m_EddyGradientStrength">
<property name="toolTip">
- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
+ <string>Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT).</string>
</property>
- <property name="minimum">
- <number>1</number>
+ <property name="decimals">
+ <number>5</number>
</property>
<property name="maximum">
- <number>1000</number>
+ <double>1000.000000000000000</double>
</property>
<property name="singleStep">
- <number>1</number>
+ <double>0.001000000000000</double>
</property>
<property name="value">
- <number>11</number>
+ <double>0.005000000000000</double>
</property>
</widget>
</item>
- <item row="0" column="3">
- <widget class="QSpinBox" name="m_SizeZ">
- <property name="toolTip">
- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>1000</number>
- </property>
- <property name="singleStep">
- <number>1</number>
+ <item row="0" column="1">
+ <widget class="QLabel" name="m_DiffusionPropsMessage_2">
+ <property name="styleSheet">
+ <string notr="true">color: rgb(255, 0, 0);</string>
</property>
- <property name="value">
- <number>3</number>
+ <property name="text">
+ <string>Experimental!</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="5" column="0">
- <widget class="QFrame" name="m_TensorsToDWIFrame">
+ <widget class="Line" name="line_8">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="Line" name="line_9">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ <item row="7" column="0">
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>Image Settings</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout">
+ <item row="7" column="0">
+ <widget class="QFrame" name="m_AdvancedSignalOptionsFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
- <layout class="QGridLayout" name="gridLayout_24">
+ <layout class="QGridLayout" name="gridLayout_23">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
- <property name="spacing">
+ <property name="horizontalSpacing">
<number>6</number>
</property>
+ <item row="7" column="0">
+ <widget class="QCheckBox" name="m_RelaxationBox">
+ <property name="toolTip">
+ <string><html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html></string>
+ </property>
+ <property name="text">
+ <string>Simulate Signal Relaxation</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
<item row="0" column="0">
- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel">
+ <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_2">
<property name="text">
- <string>Gradient Directions:</string>
+ <string>Repetitions:</string>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="m_NumGradientsBox">
+ <item row="3" column="1">
+ <widget class="QDoubleSpinBox" name="m_LineReadoutTimeBox">
<property name="toolTip">
- <string>Number of gradient directions distributed over the half sphere.</string>
+ <string>T2* relaxation time (in milliseconds).</string>
+ </property>
+ <property name="maximum">
+ <double>100.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="value">
+ <double>1.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="5" column="0">
+ <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_4">
+ <property name="text">
+ <string>Fiber Radius:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="5" column="1">
+ <widget class="QSpinBox" name="m_FiberRadius">
+ <property name="toolTip">
+ <string>Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation.</string>
+ </property>
+ <property name="minimum">
+ <number>0</number>
+ </property>
+ <property name="maximum">
+ <number>1000</number>
+ </property>
+ <property name="value">
+ <number>0</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="m_SignalScaleBox">
+ <property name="toolTip">
+ <string>TE in milliseconds</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>10000</number>
</property>
<property name="singleStep">
<number>1</number>
</property>
<property name="value">
- <number>30</number>
+ <number>100</number>
</property>
</widget>
</item>
- <item row="1" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel">
+ <item row="6" column="0">
+ <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_3">
+ <property name="text">
+ <string>Interpolation Shrink:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_15">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
- <string>b-Value:</string>
+ <string>Line Readout Time: </string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
- <item row="1" column="1">
- <widget class="QSpinBox" name="m_BvalueBox">
+ <item row="2" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_13">
<property name="toolTip">
- <string>b-value in mm/s²</string>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="maximum">
- <number>10000</number>
+ <string/>
</property>
- <property name="singleStep">
- <number>100</number>
+ <property name="statusTip">
+ <string/>
</property>
- <property name="value">
- <number>1000</number>
+ <property name="whatsThis">
+ <string/>
</property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QCheckBox" name="m_AdvancedOptionsBox_2">
- <property name="text">
- <string>Advanced Options</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="11" column="0">
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="10" column="0">
- <widget class="QGroupBox" name="groupBox_3">
- <property name="title">
- <string>Noise and other Artifacts</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_6">
- <item row="8" column="0">
- <widget class="QCheckBox" name="m_AddDistortions">
- <property name="text">
- <string>Add Distortions</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QCheckBox" name="m_AddNoise">
- <property name="text">
- <string>Add Rician Noise</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QFrame" name="m_NoiseFrame">
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QFormLayout" name="formLayout_5">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="m_NoiseLabel">
<property name="text">
- <string>Variance:</string>
+ <string><html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html></string>
+ </property>
+ <property name="wordWrap">
+ <bool>false</bool>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QDoubleSpinBox" name="m_NoiseLevel">
+ <item row="8" column="0">
+ <widget class="QCheckBox" name="m_EnforcePureFiberVoxelsBox">
<property name="toolTip">
- <string>Variance of Rician noise model.</string>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="minimum">
- <double>0.000000000000000</double>
- </property>
- <property name="maximum">
- <double>100000.000000000000000</double>
+ <string>Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present.</string>
</property>
- <property name="singleStep">
- <double>0.001000000000000</double>
+ <property name="text">
+ <string>Disable Partial Volume Effects</string>
</property>
- <property name="value">
- <double>50.000000000000000</double>
+ <property name="checked">
+ <bool>false</bool>
</property>
</widget>
</item>
- </layout>
- </widget>
- </item>
- <item row="12" column="0">
- <widget class="QCheckBox" name="m_AddGibbsRinging">
- <property name="toolTip">
- <string>Add ringing artifacts occuring at strong edges in the image.</string>
- </property>
- <property name="text">
- <string>Add Gibbs Ringing</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QFrame" name="m_GhostFrame">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QFormLayout" name="formLayout_6">
- <property name="horizontalSpacing">
- <number>6</number>
- </property>
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_23">
+ <item row="9" column="0">
+ <widget class="QCheckBox" name="m_VolumeFractionsBox">
+ <property name="toolTip">
+ <string>Output one image per compartment containing the corresponding volume fractions per voxel.</string>
+ </property>
+ <property name="text">
+ <string>Output Volume Fractions</string>
+ </property>
+ <property name="checked">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel_12">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
- <string>K-Space Line Offset:</string>
+ <string><html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html></string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="1">
- <widget class="QDoubleSpinBox" name="m_kOffsetBox">
+ <widget class="QSpinBox" name="m_RepetitionsBox">
<property name="toolTip">
- <string>A larger offset increases the inensity of the ghost image.</string>
+ <string>Number of signal averages. Increase to reduce noise.</string>
</property>
- <property name="decimals">
- <number>3</number>
+ <property name="minimum">
+ <number>1</number>
</property>
<property name="maximum">
- <double>1.000000000000000</double>
+ <number>100</number>
</property>
<property name="singleStep">
- <double>0.010000000000000</double>
+ <number>1</number>
</property>
<property name="value">
- <double>0.250000000000000</double>
+ <number>1</number>
</property>
</widget>
</item>
- </layout>
- </widget>
- </item>
- <item row="10" column="0">
- <widget class="QCheckBox" name="m_AddEddy">
- <property name="toolTip">
- <string>!!!EXPERIMENTAL!!!</string>
- </property>
- <property name="text">
- <string>Add Eddy Current Effects</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
- <widget class="QFrame" name="m_DistortionsFrame">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QFormLayout" name="formLayout_7">
- <property name="horizontalSpacing">
- <number>6</number>
- </property>
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_25">
+ <item row="4" column="1">
+ <widget class="QSpinBox" name="m_T2starBox">
<property name="toolTip">
- <string/>
+ <string>Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds).</string>
</property>
- <property name="statusTip">
- <string/>
+ <property name="minimum">
+ <number>1</number>
</property>
- <property name="whatsThis">
- <string/>
+ <property name="maximum">
+ <number>10000</number>
</property>
- <property name="text">
- <string>Frequency Map:</string>
+ <property name="singleStep">
+ <number>1</number>
</property>
- <property name="wordWrap">
- <bool>false</bool>
+ <property name="value">
+ <number>50</number>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QmitkDataStorageComboBox" name="m_FrequencyMapBox">
+ <item row="2" column="1">
+ <widget class="QSpinBox" name="m_TEbox">
<property name="toolTip">
- <string>Select image specifying the frequency inhomogeneities (in Hz).</string>
+ <string>TE in milliseconds</string>
</property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QFrame" name="m_SpikeFrame">
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QFormLayout" name="formLayout_9">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item row="0" column="0">
- <widget class="QLabel" name="m_NoiseLabel_2">
- <property name="text">
- <string>Num. Spikes:</string>
+ <property name="minimum">
+ <number>1</number>
</property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QSpinBox" name="m_SpikeNumBox">
- <property name="toolTip">
- <string>The number of randomly occurring signal spikes.</string>
+ <property name="maximum">
+ <number>10000</number>
</property>
- <property name="value">
+ <property name="singleStep">
<number>1</number>
</property>
+ <property name="value">
+ <number>100</number>
+ </property>
</widget>
</item>
- <item row="1" column="1">
- <widget class="QDoubleSpinBox" name="m_SpikeScaleBox">
+ <item row="6" column="1">
+ <widget class="QSpinBox" name="m_InterpolationShrink">
<property name="toolTip">
- <string>Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice.</string>
+ <string><html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html></string>
</property>
- <property name="singleStep">
- <double>0.100000000000000</double>
+ <property name="minimum">
+ <number>0</number>
+ </property>
+ <property name="maximum">
+ <number>10000</number>
</property>
<property name="value">
- <double>0.100000000000000</double>
+ <number>0</number>
</property>
</widget>
</item>
<item row="1" column="0">
- <widget class="QLabel" name="m_NoiseLabel_4">
+ <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_5">
<property name="text">
- <string>Scale:</string>
+ <string>Signal Scale:</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="2" column="0">
- <widget class="QCheckBox" name="m_AddSpikes">
- <property name="text">
- <string>Add Spikes</string>
+ <widget class="QLabel" name="m_GeometryMessage">
+ <property name="styleSheet">
+ <string notr="true">color: rgb(255, 0, 0);</string>
</property>
- <property name="checked">
- <bool>false</bool>
+ <property name="text">
+ <string>Using geometry of selected image!</string>
</property>
</widget>
</item>
<item row="4" column="0">
- <widget class="QCheckBox" name="m_AddGhosts">
- <property name="text">
- <string>Add N/2 Ghosts</string>
+ <widget class="QLabel" name="m_DiffusionPropsMessage">
+ <property name="styleSheet">
+ <string notr="true">color: rgb(255, 0, 0);</string>
</property>
- <property name="checked">
- <bool>false</bool>
+ <property name="text">
+ <string>Using gradients of selected DWI!</string>
</property>
</widget>
</item>
- <item row="11" column="0">
- <widget class="QFrame" name="m_EddyFrame">
- <property name="enabled">
- <bool>true</bool>
- </property>
+ <item row="3" column="0">
+ <widget class="QFrame" name="m_GeometryFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
- <layout class="QFormLayout" name="formLayout_8">
- <property name="fieldGrowthPolicy">
- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
- </property>
- <property name="horizontalSpacing">
- <number>6</number>
- </property>
+ <layout class="QGridLayout" name="gridLayout_7">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
- <item row="1" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_26">
- <property name="toolTip">
- <string/>
+ <item row="2" column="2">
+ <widget class="QDoubleSpinBox" name="m_SpacingY">
+ <property name="decimals">
+ <number>3</number>
+ </property>
+ <property name="minimum">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="maximum">
+ <double>50.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="value">
+ <double>2.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_2">
+ <property name="text">
+ <string>Image Spacing:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <widget class="QDoubleSpinBox" name="m_SpacingZ">
+ <property name="decimals">
+ <number>3</number>
+ </property>
+ <property name="minimum">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="maximum">
+ <double>50.000000000000000</double>
+ </property>
+ <property name="singleStep">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="value">
+ <double>2.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="1">
+ <widget class="QDoubleSpinBox" name="m_SpacingX">
+ <property name="decimals">
+ <number>3</number>
+ </property>
+ <property name="minimum">
+ <double>0.100000000000000</double>
+ </property>
+ <property name="maximum">
+ <double>50.000000000000000</double>
</property>
- <property name="statusTip">
- <string/>
+ <property name="singleStep">
+ <double>0.100000000000000</double>
</property>
- <property name="whatsThis">
- <string/>
+ <property name="value">
+ <double>2.000000000000000</double>
</property>
+ </widget>
+ </item>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label">
<property name="text">
- <string>Magnitude:</string>
+ <string>Image Dimensions:</string>
</property>
- <property name="wordWrap">
- <bool>false</bool>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="m_SizeX">
+ <property name="toolTip">
+ <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
+ </property>
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>1000</number>
+ </property>
+ <property name="singleStep">
+ <number>1</number>
+ </property>
+ <property name="value">
+ <number>11</number>
</property>
</widget>
</item>
- <item row="1" column="1">
- <widget class="QDoubleSpinBox" name="m_EddyGradientStrength">
+ <item row="0" column="2">
+ <widget class="QSpinBox" name="m_SizeY">
<property name="toolTip">
- <string>Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT).</string>
+ <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
</property>
- <property name="decimals">
- <number>5</number>
+ <property name="minimum">
+ <number>1</number>
</property>
<property name="maximum">
- <double>1000.000000000000000</double>
+ <number>1000</number>
</property>
<property name="singleStep">
- <double>0.001000000000000</double>
+ <number>1</number>
</property>
<property name="value">
- <double>0.005000000000000</double>
+ <number>11</number>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QLabel" name="m_DiffusionPropsMessage_2">
- <property name="styleSheet">
- <string notr="true">color: rgb(255, 0, 0);</string>
+ <item row="0" column="3">
+ <widget class="QSpinBox" name="m_SizeZ">
+ <property name="toolTip">
+ <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
</property>
- <property name="text">
- <string>Experimental!</string>
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>1000</number>
+ </property>
+ <property name="singleStep">
+ <number>1</number>
+ </property>
+ <property name="value">
+ <number>3</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
- <item row="6" column="0">
- <widget class="QCheckBox" name="m_AddAliasing">
- <property name="text">
- <string>Add Aliasing</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QFrame" name="m_AliasingFrame">
- <property name="enabled">
- <bool>true</bool>
- </property>
+ <item row="5" column="0">
+ <widget class="QFrame" name="m_TensorsToDWIFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
- <layout class="QFormLayout" name="formLayout_10">
- <property name="horizontalSpacing">
- <number>6</number>
- </property>
+ <layout class="QGridLayout" name="gridLayout_24">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
+ <property name="spacing">
+ <number>6</number>
+ </property>
<item row="0" column="0">
- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_27">
+ <widget class="QLabel" name="m_TensorsToDWINumDirsLabel">
+ <property name="text">
+ <string>Gradient Directions:</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QSpinBox" name="m_NumGradientsBox">
+ <property name="toolTip">
+ <string>Number of gradient directions distributed over the half sphere.</string>
+ </property>
+ <property name="minimum">
+ <number>1</number>
+ </property>
+ <property name="maximum">
+ <number>10000</number>
+ </property>
+ <property name="singleStep">
+ <number>1</number>
+ </property>
+ <property name="value">
+ <number>30</number>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="0">
+ <widget class="QLabel" name="m_TensorsToDWIBValueLabel">
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
- <string>Undersampling:</string>
+ <string>b-Value:</string>
</property>
<property name="wordWrap">
<bool>false</bool>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QDoubleSpinBox" name="m_WrapBox">
+ <item row="1" column="1">
+ <widget class="QSpinBox" name="m_BvalueBox">
<property name="toolTip">
- <string>Shrink FOV by this factor.</string>
- </property>
- <property name="decimals">
- <number>3</number>
+ <string>b-value in mm/s²</string>
</property>
<property name="minimum">
- <double>1.000000000000000</double>
+ <number>0</number>
</property>
<property name="maximum">
- <double>10.000000000000000</double>
+ <number>10000</number>
</property>
<property name="singleStep">
- <double>0.100000000000000</double>
+ <number>100</number>
</property>
<property name="value">
- <double>1.300000000000000</double>
+ <number>1000</number>
</property>
</widget>
</item>
</layout>
</widget>
</item>
+ <item row="6" column="0">
+ <widget class="QCheckBox" name="m_AdvancedOptionsBox_2">
+ <property name="text">
+ <string>Advanced Options</string>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
</item>
- <item row="7" column="0">
- <widget class="QGroupBox" name="groupBox_5">
+ <item row="2" column="0">
+ <widget class="QCommandLinkButton" name="m_GenerateImageButton">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="toolTip">
+ <string>Start DWI generation from selected fiber bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated.</string>
+ </property>
+ <property name="text">
+ <string>Start Simulation</string>
+ </property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
+ </property>
+ </widget>
+ </item>
+ <item row="9" column="0">
+ <widget class="QGroupBox" name="m_IntraAxonalGroupBox">
<property name="title">
- <string>Inter-axonal Compartment</string>
+ <string>Intra-axonal Compartment</string>
</property>
- <layout class="QGridLayout" name="gridLayout_17">
- <item row="3" column="0">
- <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget2" native="true"/>
- </item>
- <item row="1" column="0">
- <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget2" native="true"/>
- </item>
+ <layout class="QGridLayout" name="gridLayout_13">
<item row="0" column="0">
- <widget class="QComboBox" name="m_Compartment2Box">
+ <widget class="QComboBox" name="m_Compartment1Box">
<property name="toolTip">
<string>Select signal model for intra-axonal compartment.</string>
</property>
- <item>
- <property name="text">
- <string>--</string>
- </property>
- </item>
<item>
<property name="text">
<string>Stick Model</string>
</property>
</item>
<item>
<property name="text">
<string>Zeppelin Model</string>
</property>
</item>
<item>
<property name="text">
<string>Tensor Model</string>
</property>
</item>
</widget>
</item>
+ <item row="1" column="0">
+ <widget class="QmitkStickModelParametersWidget" name="m_StickWidget1" native="true"/>
+ </item>
<item row="2" column="0">
- <widget class="QmitkStickModelParametersWidget" name="m_StickWidget2" native="true"/>
+ <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget1" native="true"/>
+ </item>
+ <item row="3" column="0">
+ <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget1" native="true"/>
</item>
</layout>
</widget>
</item>
- <item row="8" column="0">
+ <item row="3" column="0">
+ <widget class="QCommandLinkButton" name="m_AbortSimulationButton">
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="toolTip">
+ <string>Stop current simulation.</string>
+ </property>
+ <property name="text">
+ <string>Abort Simulation</string>
+ </property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/abort.ico</normaloff>:/QmitkDiffusionImaging/general_icons/abort.ico</iconset>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="0">
<widget class="QGroupBox" name="groupBox_6">
<property name="title">
<string>Extra-axonal Compartments</string>
</property>
<layout class="QGridLayout" name="gridLayout_14">
<item row="6" column="0">
<widget class="QComboBox" name="m_Compartment3Box">
<property name="toolTip">
<string>Select signal model for extra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>Ball Model</string>
</property>
</item>
<item>
<property name="text">
<string>Astrosticks Model</string>
</property>
</item>
<item>
<property name="text">
<string>Dot Model</string>
</property>
</item>
</widget>
</item>
<item row="8" column="0">
<widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget1" native="true"/>
</item>
<item row="14" column="0">
<widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget2" native="true"/>
</item>
<item row="13" column="0">
<widget class="QmitkBallModelParametersWidget" name="m_BallWidget2" native="true"/>
</item>
<item row="7" column="0">
<widget class="QmitkBallModelParametersWidget" name="m_BallWidget1" native="true"/>
</item>
<item row="12" column="0">
<widget class="QComboBox" name="m_Compartment4Box">
<property name="toolTip">
<string>Select signal model for extra-axonal compartment.</string>
</property>
<item>
<property name="text">
<string>--</string>
</property>
</item>
<item>
<property name="text">
<string>Ball Model</string>
</property>
</item>
<item>
<property name="text">
<string>Astrosticks Model</string>
</property>
</item>
<item>
<property name="text">
<string>Dot Model</string>
</property>
</item>
</widget>
</item>
<item row="11" column="0">
<widget class="Line" name="line_2">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="15" column="0">
<widget class="QmitkDotModelParametersWidget" name="m_DotWidget2" native="true"/>
</item>
<item row="16" column="0">
<widget class="QFrame" name="m_Comp4FractionFrame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QGridLayout" name="gridLayout_18">
<property name="leftMargin">
<number>0</number>
</property>
<property name="topMargin">
<number>0</number>
</property>
<property name="rightMargin">
<number>0</number>
</property>
<property name="bottomMargin">
<number>0</number>
</property>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_Comp4FractionBox">
<property name="toolTip">
<string>Weighting factor between the two extra-axonal compartments.</string>
</property>
<property name="maximum">
<double>1.000000000000000</double>
</property>
<property name="singleStep">
<double>0.100000000000000</double>
</property>
<property name="value">
<double>0.300000000000000</double>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="m_NoiseLabel_3">
<property name="text">
<string>Compartment Fraction:</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="9" column="0">
<widget class="QmitkDotModelParametersWidget" name="m_DotWidget1" native="true"/>
</item>
</layout>
</widget>
</item>
- <item row="2" column="0">
- <widget class="QCommandLinkButton" name="m_GenerateImageButton">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="toolTip">
- <string>Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated.</string>
+ <item row="14" column="0">
+ <spacer name="verticalSpacer_2">
+ <property name="orientation">
+ <enum>Qt::Vertical</enum>
</property>
- <property name="text">
- <string>Generate Image</string>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>20</width>
+ <height>40</height>
+ </size>
</property>
- </widget>
+ </spacer>
</item>
- <item row="6" column="0">
- <widget class="QGroupBox" name="m_IntraAxonalGroupBox">
+ <item row="10" column="0">
+ <widget class="QGroupBox" name="groupBox_5">
<property name="title">
- <string>Intra-axonal Compartment</string>
+ <string>Inter-axonal Compartment</string>
</property>
- <layout class="QGridLayout" name="gridLayout_13">
+ <layout class="QGridLayout" name="gridLayout_17">
+ <item row="3" column="0">
+ <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget2" native="true"/>
+ </item>
+ <item row="1" column="0">
+ <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget2" native="true"/>
+ </item>
<item row="0" column="0">
- <widget class="QComboBox" name="m_Compartment1Box">
+ <widget class="QComboBox" name="m_Compartment2Box">
<property name="toolTip">
<string>Select signal model for intra-axonal compartment.</string>
</property>
+ <item>
+ <property name="text">
+ <string>--</string>
+ </property>
+ </item>
<item>
<property name="text">
<string>Stick Model</string>
</property>
</item>
<item>
<property name="text">
<string>Zeppelin Model</string>
</property>
</item>
<item>
<property name="text">
<string>Tensor Model</string>
</property>
</item>
</widget>
</item>
- <item row="1" column="0">
- <widget class="QmitkStickModelParametersWidget" name="m_StickWidget1" native="true"/>
- </item>
<item row="2" column="0">
- <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget1" native="true"/>
- </item>
- <item row="3" column="0">
- <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget1" native="true"/>
+ <widget class="QmitkStickModelParametersWidget" name="m_StickWidget2" native="true"/>
</item>
</layout>
</widget>
</item>
+ <item row="4" column="0">
+ <widget class="QTextEdit" name="m_SimulationStatusText">
+ <property name="font">
+ <font>
+ <pointsize>8</pointsize>
+ </font>
+ </property>
+ <property name="readOnly">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
</widget>
</item>
<item row="2" column="0">
- <widget class="QCommandLinkButton" name="m_LoadParametersButton">
+ <widget class="QCommandLinkButton" name="m_SaveParametersButton">
<property name="text">
- <string>Load Parameters</string>
+ <string>Save Parameters</string>
+ </property>
+ <property name="icon">
+ <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
+ <normaloff>:/QmitkDiffusionImaging/general_icons/download.ico</normaloff>:/QmitkDiffusionImaging/general_icons/download.ico</iconset>
</property>
</widget>
</item>
</layout>
</widget>
<customwidgets>
<customwidget>
<class>QmitkDataStorageComboBox</class>
<extends>QComboBox</extends>
<header location="global">QmitkDataStorageComboBox.h</header>
</customwidget>
<customwidget>
<class>QmitkTensorModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkTensorModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkStickModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkStickModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkZeppelinModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkZeppelinModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkBallModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkBallModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkAstrosticksModelParametersWidget</class>
<extends>QWidget</extends>
<header location="global">QmitkAstrosticksModelParametersWidget.h</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QmitkDotModelParametersWidget</class>
<extends>QWidget</extends>
<header>QmitkDotModelParametersWidget.h</header>
<container>1</container>
</customwidget>
</customwidgets>
<tabstops>
<tabstop>m_CircleButton</tabstop>
<tabstop>m_FlipButton</tabstop>
<tabstop>m_RealTimeFibers</tabstop>
<tabstop>m_AdvancedOptionsBox</tabstop>
<tabstop>m_DistributionBox</tabstop>
<tabstop>m_VarianceBox</tabstop>
<tabstop>m_FiberDensityBox</tabstop>
<tabstop>m_FiberSamplingBox</tabstop>
<tabstop>m_TensionBox</tabstop>
<tabstop>m_ContinuityBox</tabstop>
<tabstop>m_BiasBox</tabstop>
<tabstop>m_GenerateFibersButton</tabstop>
<tabstop>m_ConstantRadiusBox</tabstop>
<tabstop>m_AlignOnGrid</tabstop>
<tabstop>m_XrotBox</tabstop>
<tabstop>m_YrotBox</tabstop>
<tabstop>m_ZrotBox</tabstop>
<tabstop>m_XtransBox</tabstop>
<tabstop>m_YtransBox</tabstop>
<tabstop>m_ZtransBox</tabstop>
<tabstop>m_XscaleBox</tabstop>
<tabstop>m_YscaleBox</tabstop>
<tabstop>m_ZscaleBox</tabstop>
<tabstop>m_TransformBundlesButton</tabstop>
<tabstop>m_CopyBundlesButton</tabstop>
<tabstop>m_JoinBundlesButton</tabstop>
<tabstop>m_IncludeFiducials</tabstop>
<tabstop>m_GenerateImageButton</tabstop>
<tabstop>m_SizeX</tabstop>
<tabstop>m_SizeY</tabstop>
<tabstop>m_SizeZ</tabstop>
<tabstop>m_SpacingX</tabstop>
<tabstop>m_SpacingY</tabstop>
<tabstop>m_SpacingZ</tabstop>
<tabstop>m_NumGradientsBox</tabstop>
<tabstop>m_BvalueBox</tabstop>
<tabstop>m_AdvancedOptionsBox_2</tabstop>
<tabstop>m_RepetitionsBox</tabstop>
<tabstop>m_SignalScaleBox</tabstop>
<tabstop>m_TEbox</tabstop>
<tabstop>m_LineReadoutTimeBox</tabstop>
<tabstop>m_T2starBox</tabstop>
<tabstop>m_FiberRadius</tabstop>
<tabstop>m_InterpolationShrink</tabstop>
<tabstop>m_RelaxationBox</tabstop>
<tabstop>m_EnforcePureFiberVoxelsBox</tabstop>
<tabstop>m_VolumeFractionsBox</tabstop>
<tabstop>m_Compartment1Box</tabstop>
<tabstop>m_Compartment2Box</tabstop>
<tabstop>m_Compartment3Box</tabstop>
<tabstop>m_Compartment4Box</tabstop>
<tabstop>m_Comp4FractionBox</tabstop>
<tabstop>m_AddNoise</tabstop>
<tabstop>m_NoiseLevel</tabstop>
<tabstop>m_AddSpikes</tabstop>
<tabstop>m_SpikeNumBox</tabstop>
<tabstop>m_SpikeScaleBox</tabstop>
<tabstop>m_AddGhosts</tabstop>
<tabstop>m_kOffsetBox</tabstop>
+ <tabstop>m_AddAliasing</tabstop>
+ <tabstop>m_WrapBox</tabstop>
<tabstop>m_AddDistortions</tabstop>
<tabstop>m_FrequencyMapBox</tabstop>
+ <tabstop>m_AddMotion</tabstop>
+ <tabstop>m_RandomMotion</tabstop>
+ <tabstop>m_MaxRotationBoxX</tabstop>
+ <tabstop>m_MaxRotationBoxY</tabstop>
+ <tabstop>m_MaxRotationBoxZ</tabstop>
+ <tabstop>m_MaxTranslationBoxX</tabstop>
+ <tabstop>m_MaxTranslationBoxY</tabstop>
+ <tabstop>m_MaxTranslationBoxZ</tabstop>
<tabstop>m_AddEddy</tabstop>
<tabstop>m_EddyGradientStrength</tabstop>
<tabstop>m_AddGibbsRinging</tabstop>
<tabstop>m_SaveParametersButton</tabstop>
<tabstop>m_LoadParametersButton</tabstop>
<tabstop>tabWidget</tabstop>
</tabstops>
<resources>
<include location="../../resources/QmitkDiffusionImaging.qrc"/>
</resources>
<connections/>
</ui>
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp
index 8e309d4abd..e1ba64bee3 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp
@@ -1,776 +1,779 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
//misc
#define _USE_MATH_DEFINES
#include <math.h>
#include <QFileDialog>
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
// Qmitk
#include "QmitkOdfMaximaExtractionView.h"
// MITK
#include <mitkImageCast.h>
#include <mitkFiberBundleX.h>
#include <mitkImage.h>
#include <mitkDiffusionImage.h>
#include <mitkImageToItk.h>
#include <mitkTensorImage.h>
// ITK
#include <itkVectorImage.h>
#include <itkOdfMaximaExtractionFilter.h>
#include <itkFiniteDiffOdfMaximaExtractionFilter.h>
#include <itkMrtrixPeakImageConverter.h>
#include <itkFslPeakImageConverter.h>
#include <itkShCoefficientImageImporter.h>
#include <itkDiffusionTensorPrincipalDirectionImageFilter.h>
// Qt
#include <QMessageBox>
const std::string QmitkOdfMaximaExtractionView::VIEW_ID = "org.mitk.views.odfmaximaextractionview";
using namespace mitk;
QmitkOdfMaximaExtractionView::QmitkOdfMaximaExtractionView()
: QmitkFunctionality()
, m_Controls( 0 )
, m_MultiWidget( NULL )
{
}
// Destructor
QmitkOdfMaximaExtractionView::~QmitkOdfMaximaExtractionView()
{
}
void QmitkOdfMaximaExtractionView::CreateQtPartControl( QWidget *parent )
{
// build up qt view, unless already done
if ( !m_Controls )
{
// create GUI widgets from the Qt Designer's .ui file
m_Controls = new Ui::QmitkOdfMaximaExtractionViewControls;
m_Controls->setupUi( parent );
connect((QObject*) m_Controls->m_StartTensor, SIGNAL(clicked()), (QObject*) this, SLOT(StartTensor()));
connect((QObject*) m_Controls->m_StartFiniteDiff, SIGNAL(clicked()), (QObject*) this, SLOT(StartFiniteDiff()));
connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage()));
connect((QObject*) m_Controls->m_ImportPeaks, SIGNAL(clicked()), (QObject*) this, SLOT(ConvertPeaks()));
connect((QObject*) m_Controls->m_ImportShCoeffs, SIGNAL(clicked()), (QObject*) this, SLOT(ConvertShCoeffs()));
}
}
void QmitkOdfMaximaExtractionView::UpdateGui()
{
m_Controls->m_GenerateImageButton->setEnabled(false);
m_Controls->m_StartFiniteDiff->setEnabled(false);
m_Controls->m_StartTensor->setEnabled(false);
m_Controls->m_CoeffImageFrame->setEnabled(false);
if (!m_ImageNodes.empty() || !m_TensorImageNodes.empty())
{
m_Controls->m_InputData->setTitle("Input Data");
if (!m_TensorImageNodes.empty())
{
m_Controls->m_DwiFibLabel->setText(m_TensorImageNodes.front()->GetName().c_str());
m_Controls->m_StartTensor->setEnabled(true);
}
else
{
m_Controls->m_DwiFibLabel->setText(m_ImageNodes.front()->GetName().c_str());
m_Controls->m_StartFiniteDiff->setEnabled(true);
m_Controls->m_GenerateImageButton->setEnabled(true);
m_Controls->m_CoeffImageFrame->setEnabled(true);
m_Controls->m_ShOrderBox->setEnabled(true);
m_Controls->m_MaxNumPeaksBox->setEnabled(true);
m_Controls->m_PeakThresholdBox->setEnabled(true);
m_Controls->m_AbsoluteThresholdBox->setEnabled(true);
}
}
else
m_Controls->m_DwiFibLabel->setText("<font color='red'>mandatory</font>");
if (m_ImageNodes.empty())
{
m_Controls->m_ImportPeaks->setEnabled(false);
m_Controls->m_ImportShCoeffs->setEnabled(false);
}
else
{
m_Controls->m_ImportPeaks->setEnabled(true);
m_Controls->m_ImportShCoeffs->setEnabled(true);
}
if (!m_BinaryImageNodes.empty())
{
m_Controls->m_MaskLabel->setText(m_BinaryImageNodes.front()->GetName().c_str());
}
else
{
m_Controls->m_MaskLabel->setText("<font color='grey'>optional</font>");
}
}
template<int shOrder>
void QmitkOdfMaximaExtractionView::TemplatedConvertShCoeffs(mitk::Image* mitkImg)
{
typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
typename FilterType::Pointer filter = FilterType::New();
switch (m_Controls->m_ToolkitBox->currentIndex())
{
case 0:
filter->SetToolkit(FilterType::FSL);
break;
case 1:
filter->SetToolkit(FilterType::MRTRIX);
break;
default:
filter->SetToolkit(FilterType::FSL);
}
filter->SetInputImage(caster->GetOutput());
filter->GenerateData();
typename FilterType::QballImageType::Pointer itkQbi = filter->GetQballImage();
typename FilterType::CoefficientImageType::Pointer itkCi = filter->GetCoefficientImage();
{
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkCi.GetPointer() );
img->SetVolume( itkCi->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
node->SetName("_ShCoefficientImage");
node->SetVisibility(false);
GetDataStorage()->Add(node);
}
{
mitk::QBallImage::Pointer img = mitk::QBallImage::New();
img->InitializeByItk( itkQbi.GetPointer() );
img->SetVolume( itkQbi->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
node->SetName("_QballImage");
GetDataStorage()->Add(node);
}
}
void QmitkOdfMaximaExtractionView::ConvertShCoeffs()
{
if (m_ImageNodes.empty())
return;
mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_ImageNodes.at(0)->GetData());
if (mitkImg->GetDimension()!=4)
{
MITK_INFO << "wrong image type (need 4 dimensions)";
return;
}
int nrCoeffs = mitkImg->GetLargestPossibleRegion().GetSize()[3];
// solve bx² + cx + d = 0 = shOrder² + 2*shOrder + 2-2*neededCoeffs;
int c=3, d=2-2*nrCoeffs;
double D = c*c-4*d;
int shOrder;
if (D>0)
{
shOrder = (-c+sqrt(D))/2.0;
if (shOrder<0)
shOrder = (-c-sqrt(D))/2.0;
}
else if (D==0)
shOrder = -c/2.0;
MITK_INFO << "using SH-order " << shOrder;
switch (shOrder)
{
+ case 2:
+ TemplatedConvertShCoeffs<2>(mitkImg);
+ break;
case 4:
TemplatedConvertShCoeffs<4>(mitkImg);
break;
case 6:
TemplatedConvertShCoeffs<6>(mitkImg);
break;
case 8:
TemplatedConvertShCoeffs<8>(mitkImg);
break;
case 10:
TemplatedConvertShCoeffs<10>(mitkImg);
break;
case 12:
TemplatedConvertShCoeffs<12>(mitkImg);
break;
default:
MITK_INFO << "SH-order " << shOrder << " not supported";
}
}
void QmitkOdfMaximaExtractionView::ConvertPeaks()
{
if (m_ImageNodes.empty())
return;
switch (m_Controls->m_ToolkitBox->currentIndex())
{
case 0:
{
typedef itk::Image< float, 4 > ItkImageType;
typedef itk::FslPeakImageConverter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
FilterType::InputType::Pointer inputVec = FilterType::InputType::New();
mitk::Geometry3D::Pointer geom;
for (int i=0; i<m_ImageNodes.size(); i++)
{
mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_ImageNodes.at(i)->GetData());
geom = mitkImg->GetGeometry();
typedef mitk::ImageToItk< FilterType::InputImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
FilterType::InputImageType::Pointer itkImg = caster->GetOutput();
inputVec->InsertElement(inputVec->Size(), itkImg);
}
filter->SetInputImages(inputVec);
filter->GenerateData();
mitk::Vector3D outImageSpacing = geom->GetSpacing();
float maxSpacing = 1;
if(outImageSpacing[0]>outImageSpacing[1] && outImageSpacing[0]>outImageSpacing[2])
maxSpacing = outImageSpacing[0];
else if (outImageSpacing[1] > outImageSpacing[2])
maxSpacing = outImageSpacing[1];
else
maxSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
// directions->SetGeometry(geom);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
node->SetName("_VectorField");
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(maxSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
typedef FilterType::DirectionImageContainerType DirectionImageContainerType;
DirectionImageContainerType::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
ItkDirectionImage3DType::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(i)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
node->SetVisibility(false);
GetDataStorage()->Add(node);
}
break;
}
case 1:
{
typedef itk::Image< float, 4 > ItkImageType;
typedef itk::MrtrixPeakImageConverter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
// cast to itk
mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_ImageNodes.at(0)->GetData());
mitk::Geometry3D::Pointer geom = mitkImg->GetGeometry();
typedef mitk::ImageToItk< FilterType::InputImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
FilterType::InputImageType::Pointer itkImg = caster->GetOutput();
filter->SetInputImage(itkImg);
filter->GenerateData();
mitk::Vector3D outImageSpacing = geom->GetSpacing();
float maxSpacing = 1;
if(outImageSpacing[0]>outImageSpacing[1] && outImageSpacing[0]>outImageSpacing[2])
maxSpacing = outImageSpacing[0];
else if (outImageSpacing[1] > outImageSpacing[2])
maxSpacing = outImageSpacing[1];
else
maxSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
//directions->SetGeometry(geom);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(maxSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node2 = DataNode::New();
node2->SetData(image2);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
typedef FilterType::DirectionImageContainerType DirectionImageContainerType;
DirectionImageContainerType::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
ItkDirectionImage3DType::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
node->SetVisibility(false);
GetDataStorage()->Add(node);
}
break;
}
}
}
void QmitkOdfMaximaExtractionView::GenerateImage()
{
if (!m_ImageNodes.empty())
GenerateDataFromDwi();
}
void QmitkOdfMaximaExtractionView::StartTensor()
{
if (m_TensorImageNodes.empty())
return;
typedef itk::DiffusionTensorPrincipalDirectionImageFilter< float, float > MaximaExtractionFilterType;
MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
mitk::Geometry3D::Pointer geometry;
try{
TensorImage::Pointer img = dynamic_cast<TensorImage*>(m_TensorImageNodes.at(0)->GetData());
ItkTensorImage::Pointer itkImage = ItkTensorImage::New();
CastToItkImage<ItkTensorImage>(img, itkImage);
filter->SetInput(itkImage);
geometry = img->GetGeometry();
}
catch(itk::ExceptionObject &e)
{
MITK_INFO << "wrong image type: " << e.what();
QMessageBox::warning( NULL, "Wrong pixel type", "Could not perform Tensor Principal Direction Extraction due to Image has wrong pixel type.", QMessageBox::Ok );
return;
//throw e;
}
if (!m_BinaryImageNodes.empty())
{
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_BinaryImageNodes.at(0)->GetData());
CastToItkImage<ItkUcharImgType>(mitkMaskImg, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
if (m_Controls->m_NormalizationBox->currentIndex()==0)
filter->SetNormalizeVectors(false);
filter->Update();
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
MaximaExtractionFilterType::OutputImageType::Pointer itkImg = filter->GetOutput();
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_TensorImageNodes.at(0)->GetName().c_str());
name += "_PrincipalDirection";
node->SetName(name.toStdString().c_str());
node->SetVisibility(false);
GetDataStorage()->Add(node);
}
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node2 = DataNode::New();
node2->SetData(image2);
QString name(m_TensorImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Vector3D outImageSpacing = geometry->GetSpacing();
float minSpacing = 1;
if(outImageSpacing[0]<outImageSpacing[1] && outImageSpacing[0]<outImageSpacing[2])
minSpacing = outImageSpacing[0];
else if (outImageSpacing[1] < outImageSpacing[2])
minSpacing = outImageSpacing[1];
else
minSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
// directions->SetGeometry(geometry);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_TensorImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
}
}
template<int shOrder>
void QmitkOdfMaximaExtractionView::StartMaximaExtraction()
{
typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType;
typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
switch (m_Controls->m_ToolkitBox->currentIndex())
{
case 0:
filter->SetToolkit(MaximaExtractionFilterType::FSL);
break;
case 1:
filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
break;
default:
filter->SetToolkit(MaximaExtractionFilterType::FSL);
}
mitk::Geometry3D::Pointer geometry;
try{
Image::Pointer img = dynamic_cast<Image*>(m_ImageNodes.at(0)->GetData());
typedef ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
typename CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
filter->SetInput(caster->GetOutput());
geometry = img->GetGeometry();
}
catch(itk::ExceptionObject &e)
{
MITK_INFO << "wrong image type: " << e.what();
QMessageBox::warning( NULL, "Wrong pixel type", "Could not perform Finite Differences Extraction due to Image has wrong pixel type.", QMessageBox::Ok );
return;
//throw;
}
filter->SetAngularThreshold(cos((float)m_Controls->m_AngularThreshold->value()*M_PI/180));
filter->SetClusteringThreshold(cos((float)m_Controls->m_ClusteringAngleBox->value()*M_PI/180));
filter->SetMaxNumPeaks(m_Controls->m_MaxNumPeaksBox->value());
filter->SetPeakThreshold(m_Controls->m_PeakThresholdBox->value());
filter->SetAbsolutePeakThreshold(m_Controls->m_AbsoluteThresholdBox->value());
if (!m_BinaryImageNodes.empty())
{
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_BinaryImageNodes.at(0)->GetData());
CastToItkImage<ItkUcharImgType>(mitkMaskImg, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
switch (m_Controls->m_NormalizationBox->currentIndex())
{
case 0:
filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
break;
case 1:
filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
break;
case 2:
filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
break;
}
filter->Update();
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
typedef typename MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
typename ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
typename MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
node->SetVisibility(false);
GetDataStorage()->Add(node);
}
}
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node2 = DataNode::New();
node2->SetData(image2);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Vector3D outImageSpacing = geometry->GetSpacing();
float minSpacing = 1;
if(outImageSpacing[0]<outImageSpacing[1] && outImageSpacing[0]<outImageSpacing[2])
minSpacing = outImageSpacing[0];
else if (outImageSpacing[1] < outImageSpacing[2])
minSpacing = outImageSpacing[1];
else
minSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
// directions->SetGeometry(geometry);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
}
}
void QmitkOdfMaximaExtractionView::StartFiniteDiff()
{
if (m_ImageNodes.empty())
return;
switch (m_Controls->m_ShOrderBox->currentIndex())
{
case 0:
StartMaximaExtraction<2>();
break;
case 1:
StartMaximaExtraction<4>();
break;
case 2:
StartMaximaExtraction<6>();
break;
case 3:
StartMaximaExtraction<8>();
break;
case 4:
StartMaximaExtraction<10>();
break;
case 5:
StartMaximaExtraction<12>();
break;
}
}
void QmitkOdfMaximaExtractionView::GenerateDataFromDwi()
{
typedef itk::OdfMaximaExtractionFilter< float > MaximaExtractionFilterType;
MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
mitk::Geometry3D::Pointer geometry;
if (!m_ImageNodes.empty())
{
try{
Image::Pointer img = dynamic_cast<Image*>(m_ImageNodes.at(0)->GetData());
typedef ImageToItk< MaximaExtractionFilterType::CoefficientImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(img);
caster->Update();
filter->SetShCoeffImage(caster->GetOutput());
geometry = img->GetGeometry();
}
catch(itk::ExceptionObject &e)
{
MITK_INFO << "wrong image type: " << e.what();
return;
}
}
else
return;
filter->SetMaxNumPeaks(m_Controls->m_MaxNumPeaksBox->value());
filter->SetPeakThreshold(m_Controls->m_PeakThresholdBox->value());
if (!m_BinaryImageNodes.empty())
{
ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_BinaryImageNodes.at(0)->GetData());
CastToItkImage<ItkUcharImgType>(mitkMaskImg, itkMaskImage);
filter->SetMaskImage(itkMaskImage);
}
switch (m_Controls->m_NormalizationBox->currentIndex())
{
case 0:
filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
break;
case 1:
filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
break;
case 2:
filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
break;
}
filter->GenerateData();
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
typedef MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(image2);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_NumDirections";
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Vector3D outImageSpacing = geometry->GetSpacing();
float minSpacing = 1;
if(outImageSpacing[0]<outImageSpacing[1] && outImageSpacing[0]<outImageSpacing[2])
minSpacing = outImageSpacing[0];
else if (outImageSpacing[1] < outImageSpacing[2])
minSpacing = outImageSpacing[1];
else
minSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
// directions->SetGeometry(geometry);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
}
}
void QmitkOdfMaximaExtractionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
{
m_MultiWidget = &stdMultiWidget;
}
void QmitkOdfMaximaExtractionView::StdMultiWidgetNotAvailable()
{
m_MultiWidget = NULL;
}
void QmitkOdfMaximaExtractionView::OnSelectionChanged( std::vector<mitk::DataNode*> nodes )
{
m_Controls->m_InputData->setTitle("Please Select Input Data");
m_Controls->m_DwiFibLabel->setText("<font color='red'>mandatory</font>");
m_Controls->m_MaskLabel->setText("<font color='grey'>optional</font>");
m_BinaryImageNodes.clear();
m_ImageNodes.clear();
m_TensorImageNodes.clear();
// iterate all selected objects, adjust warning visibility
for( std::vector<mitk::DataNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it )
{
mitk::DataNode::Pointer node = *it;
if ( node.IsNotNull() && dynamic_cast<mitk::TensorImage*>(node->GetData()) )
{
m_TensorImageNodes.push_back(node);
}
else if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
{
bool isBinary = false;
node->GetPropertyValue<bool>("binary", isBinary);
if (isBinary)
m_BinaryImageNodes.push_back(node);
else
m_ImageNodes.push_back(node);
}
}
UpdateGui();
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp
index ababe491f9..26034e87c6 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp
@@ -1,246 +1,276 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
// Blueberry
#include <berryISelectionService.h>
#include <berryIWorkbenchWindow.h>
#include <berryIStructuredSelection.h>
// Qmitk
#include "QmitkStreamlineTrackingView.h"
#include "QmitkStdMultiWidget.h"
// Qt
#include <QMessageBox>
// MITK
#include <mitkImageToItk.h>
#include <mitkFiberBundleX.h>
#include <mitkImageCast.h>
+#include <mitkNodePredicateDataType.h>
+#include <mitkNodePredicateNot.h>
+#include <mitkNodePredicateAnd.h>
+#include <mitkNodePredicateProperty.h>
+#include <mitkNodePredicateDimension.h>
// VTK
#include <vtkPolyData.h>
#include <vtkPoints.h>
#include <vtkCellArray.h>
#include <vtkSmartPointer.h>
#include <vtkPolyLine.h>
#include <vtkCellData.h>
const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking";
const std::string id_DataManager = "org.mitk.views.datamanager";
using namespace berry;
QmitkStreamlineTrackingView::QmitkStreamlineTrackingView()
: QmitkFunctionality()
, m_Controls( 0 )
, m_MultiWidget( NULL )
- , m_TensorImage( NULL )
, m_SeedRoi( NULL )
+ , m_MaskImage( NULL )
{
}
// Destructor
QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView()
{
}
void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent )
{
if ( !m_Controls )
{
// create GUI widgets from the Qt Designer's .ui file
m_Controls = new Ui::QmitkStreamlineTrackingViewControls;
m_Controls->setupUi( parent );
+ m_Controls->m_FaImageBox->SetDataStorage(this->GetDataStorage());
+
+ mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
+
+ mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
+ mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate );
+ mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate );
+ mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3);
+
+ m_Controls->m_FaImageBox->SetPredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) );
connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) );
connect( m_Controls->m_SeedsPerVoxelSlider, SIGNAL(valueChanged(int)), this, SLOT(OnSeedsPerVoxelChanged(int)) );
connect( m_Controls->m_MinTractLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMinTractLengthChanged(int)) );
connect( m_Controls->m_FaThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnFaThresholdChanged(int)) );
connect( m_Controls->m_AngularThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAngularThresholdChanged(int)) );
connect( m_Controls->m_StepsizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnStepsizeChanged(int)) );
connect( m_Controls->m_fSlider, SIGNAL(valueChanged(int)), this, SLOT(OnfChanged(int)) );
connect( m_Controls->m_gSlider, SIGNAL(valueChanged(int)), this, SLOT(OngChanged(int)) );
}
}
void QmitkStreamlineTrackingView::OnfChanged(int value)
{
m_Controls->m_fLabel->setText(QString("f: ")+QString::number((float)value/100));
}
void QmitkStreamlineTrackingView::OngChanged(int value)
{
m_Controls->m_gLabel->setText(QString("g: ")+QString::number((float)value/100));
}
void QmitkStreamlineTrackingView::OnAngularThresholdChanged(int value)
{
if (value<0)
m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: auto"));
else
m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: ")+QString::number((float)value/10)+QString("mm"));
}
void QmitkStreamlineTrackingView::OnSeedsPerVoxelChanged(int value)
{
m_Controls->m_SeedsPerVoxelLabel->setText(QString("Seeds per Voxel: ")+QString::number(value));
}
void QmitkStreamlineTrackingView::OnMinTractLengthChanged(int value)
{
m_Controls->m_MinTractLengthLabel->setText(QString("Min. Tract Length: ")+QString::number(value)+QString("mm"));
}
void QmitkStreamlineTrackingView::OnFaThresholdChanged(int value)
{
m_Controls->m_FaThresholdLabel->setText(QString("FA Threshold: ")+QString::number((float)value/100));
}
void QmitkStreamlineTrackingView::OnStepsizeChanged(int value)
{
if (value==0)
m_Controls->m_StepsizeLabel->setText(QString("Stepsize: auto"));
else
m_Controls->m_StepsizeLabel->setText(QString("Stepsize: ")+QString::number((float)value/10)+QString("mm"));
}
void QmitkStreamlineTrackingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
{
m_MultiWidget = &stdMultiWidget;
}
void QmitkStreamlineTrackingView::StdMultiWidgetNotAvailable()
{
m_MultiWidget = NULL;
}
void QmitkStreamlineTrackingView::OnSelectionChanged( std::vector<mitk::DataNode*> nodes )
{
- m_TensorImageNode = NULL;
- m_TensorImage = NULL;
+ m_TensorImageNodes.clear();
+ m_TensorImages.clear();
m_SeedRoi = NULL;
m_MaskImage = NULL;
m_Controls->m_TensorImageLabel->setText("<font color='red'>mandatory</font>");
m_Controls->m_RoiImageLabel->setText("<font color='grey'>optional</font>");
m_Controls->m_MaskImageLabel->setText("<font color='grey'>optional</font>");
for( std::vector<mitk::DataNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it )
{
mitk::DataNode::Pointer node = *it;
if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
{
if( dynamic_cast<mitk::TensorImage*>(node->GetData()) )
{
- m_TensorImageNode = node;
- m_TensorImage = dynamic_cast<mitk::TensorImage*>(node->GetData());
- m_Controls->m_TensorImageLabel->setText(node->GetName().c_str());
+ m_TensorImageNodes.push_back(node);
+ m_TensorImages.push_back(dynamic_cast<mitk::TensorImage*>(node->GetData()));
}
else
{
bool isBinary = false;
node->GetPropertyValue<bool>("binary", isBinary);
if (isBinary && m_SeedRoi.IsNull())
{
m_SeedRoi = dynamic_cast<mitk::Image*>(node->GetData());
m_Controls->m_RoiImageLabel->setText(node->GetName().c_str());
}
else if (isBinary)
{
m_MaskImage = dynamic_cast<mitk::Image*>(node->GetData());
m_Controls->m_MaskImageLabel->setText(node->GetName().c_str());
}
}
}
}
- if(m_TensorImageNode.IsNotNull())
+ if(!m_TensorImageNodes.empty())
{
+ if (m_TensorImageNodes.size()>1)
+ m_Controls->m_TensorImageLabel->setText(m_TensorImageNodes.size()+" tensor images selected");
+ else
+ m_Controls->m_TensorImageLabel->setText(m_TensorImageNodes.at(0)->GetName().c_str());
m_Controls->m_InputData->setTitle("Input Data");
m_Controls->commandLinkButton->setEnabled(true);
}
else
{
m_Controls->m_InputData->setTitle("Please Select Input Data");
m_Controls->commandLinkButton->setEnabled(false);
}
}
void QmitkStreamlineTrackingView::DoFiberTracking()
{
- if (m_TensorImage.IsNull())
+ if (m_TensorImages.empty())
return;
typedef itk::Image< itk::DiffusionTensor3D<float>, 3> TensorImageType;
typedef mitk::ImageToItk<TensorImageType> CastType;
typedef mitk::ImageToItk<ItkUCharImageType> CastType2;
- CastType::Pointer caster = CastType::New();
- caster->SetInput(m_TensorImage);
- caster->Update();
- TensorImageType::Pointer image = caster->GetOutput();
-
typedef itk::StreamlineTrackingFilter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
- filter->SetInput(image);
+
+ for (int i=0; i<(int)m_TensorImages.size(); i++)
+ {
+ CastType::Pointer caster = CastType::New();
+ caster->SetInput(m_TensorImages.at(i));
+ caster->Update();
+ filter->SetInput(i, caster->GetOutput());
+ }
+
+ if (m_Controls->m_UseFaImage->isChecked())
+ {
+ mitk::ImageToItk<ItkFloatImageType>::Pointer floatCast = mitk::ImageToItk<ItkFloatImageType>::New();
+ floatCast->SetInput(dynamic_cast<mitk::Image*>(m_Controls->m_FaImageBox->GetSelectedNode()->GetData()));
+ floatCast->Update();
+ filter->SetFaImage(floatCast->GetOutput());
+ }
+
+ //filter->SetNumberOfThreads(1);
filter->SetSeedsPerVoxel(m_Controls->m_SeedsPerVoxelSlider->value());
filter->SetFaThreshold((float)m_Controls->m_FaThresholdSlider->value()/100);
filter->SetMinCurvatureRadius((float)m_Controls->m_AngularThresholdSlider->value()/10);
filter->SetStepSize((float)m_Controls->m_StepsizeSlider->value()/10);
filter->SetF((float)m_Controls->m_fSlider->value()/100);
filter->SetG((float)m_Controls->m_gSlider->value()/100);
filter->SetInterpolate(m_Controls->m_InterpolationBox->isChecked());
filter->SetMinTractLength(m_Controls->m_MinTractLengthSlider->value());
filter->SetResampleFibers(m_Controls->m_ResampleFibersBox->isChecked());
if (m_SeedRoi.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(m_SeedRoi, mask);
filter->SetSeedImage(mask);
}
if (m_MaskImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(m_MaskImage, mask);
filter->SetMaskImage(mask);
}
filter->Update();
vtkSmartPointer<vtkPolyData> fiberBundle = filter->GetFiberPolyData();
if ( fiberBundle->GetNumberOfLines()==0 )
return;
mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle);
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(fib);
QString name("FiberBundle_");
- name += m_TensorImageNode->GetName().c_str();
+ name += m_TensorImageNodes.at(0)->GetName().c_str();
name += "_Streamline";
node->SetName(name.toStdString());
node->SetVisibility(true);
- GetDataStorage()->Add(node, m_TensorImageNode);
+ GetDataStorage()->Add(node, m_TensorImageNodes.at(0));
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.h
index ab725cdaab..118a270370 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.h
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.h
@@ -1,90 +1,90 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#ifndef QmitkStreamlineTrackingView_h
#define QmitkStreamlineTrackingView_h
#include <QmitkFunctionality.h>
#include "ui_QmitkStreamlineTrackingViewControls.h"
#include <mitkTensorImage.h>
#include <mitkDataStorage.h>
#include <mitkImage.h>
#include <itkImage.h>
#include <itkStreamlineTrackingFilter.h>
/*!
\brief View for deterministic streamline fiber tracking.
\sa QmitkFunctionality
\ingroup Functionalities
*/
class QmitkStreamlineTrackingView : public QmitkFunctionality
{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
+ // this is needed for all Qt objects that should have a Qt meta-object
+ // (everything that derives from QObject and wants to have signal/slots)
+ Q_OBJECT
public:
- static const std::string VIEW_ID;
+ static const std::string VIEW_ID;
- typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
+ typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
+ typedef itk::Image< float, 3 > ItkFloatImageType;
- QmitkStreamlineTrackingView();
- virtual ~QmitkStreamlineTrackingView();
+ QmitkStreamlineTrackingView();
+ virtual ~QmitkStreamlineTrackingView();
- virtual void CreateQtPartControl(QWidget *parent);
+ virtual void CreateQtPartControl(QWidget *parent);
- virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget);
- virtual void StdMultiWidgetNotAvailable();
+ virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget);
+ virtual void StdMultiWidgetNotAvailable();
- protected slots:
+protected slots:
- void DoFiberTracking(); ///< start fiber tracking
+ void DoFiberTracking(); ///< start fiber tracking
protected:
- /// \brief called by QmitkFunctionality when DataManager's selection has changed
- virtual void OnSelectionChanged( std::vector<mitk::DataNode*> nodes );
- Ui::QmitkStreamlineTrackingViewControls* m_Controls;
- QmitkStdMultiWidget* m_MultiWidget;
+ /// \brief called by QmitkFunctionality when DataManager's selection has changed
+ virtual void OnSelectionChanged( std::vector<mitk::DataNode*> nodes );
+ Ui::QmitkStreamlineTrackingViewControls* m_Controls;
+ QmitkStdMultiWidget* m_MultiWidget;
protected slots:
- /** update labels if parameters have changed */
- void OnSeedsPerVoxelChanged(int value);
- void OnMinTractLengthChanged(int value);
- void OnFaThresholdChanged(int value);
- void OnAngularThresholdChanged(int value);
- void OnfChanged(int value);
- void OngChanged(int value);
- void OnStepsizeChanged(int value);
+ /** update labels if parameters have changed */
+ void OnSeedsPerVoxelChanged(int value);
+ void OnMinTractLengthChanged(int value);
+ void OnFaThresholdChanged(int value);
+ void OnAngularThresholdChanged(int value);
+ void OnfChanged(int value);
+ void OngChanged(int value);
+ void OnStepsizeChanged(int value);
private:
- mitk::Image::Pointer m_MaskImage; ///< abort tracking if leaving mask
- mitk::Image::Pointer m_SeedRoi; ///< binary image defining seed voxels for tracking process
- mitk::TensorImage::Pointer m_TensorImage; ///< input image
- mitk::DataNode::Pointer m_TensorImageNode; ///< input image datanode
-
+ mitk::Image::Pointer m_MaskImage; ///< abort tracking if leaving mask
+ mitk::Image::Pointer m_SeedRoi; ///< binary image defining seed voxels for tracking process
+ std::vector< mitk::DataNode::Pointer > m_TensorImageNodes; ///< input images
+ std::vector< mitk::TensorImage::Pointer > m_TensorImages; ///< input image datanode
};
#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui
index c2fc05f0cf..2a0bb579b7 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui
@@ -1,383 +1,412 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkStreamlineTrackingViewControls</class>
<widget class="QWidget" name="QmitkStreamlineTrackingViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
- <width>368</width>
- <height>477</height>
+ <width>382</width>
+ <height>538</height>
</rect>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="windowTitle">
<string>QmitkTemplate</string>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<property name="topMargin">
<number>3</number>
</property>
<property name="bottomMargin">
<number>3</number>
</property>
<property name="spacing">
<number>0</number>
</property>
<item row="8" column="0">
<spacer name="spacer1">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeType">
<enum>QSizePolicy::Expanding</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>220</height>
</size>
</property>
</spacer>
</item>
<item row="1" column="0">
<widget class="QCommandLinkButton" name="commandLinkButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="text">
<string>Start Tractography</string>
</property>
</widget>
</item>
<item row="5" column="0">
<widget class="QGroupBox" name="groupBox_2">
<property name="title">
<string>Parameters</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="3" column="0">
<widget class="QLabel" name="m_fLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>f: 1</string>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="m_gLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>g: 0</string>
</property>
</widget>
</item>
<item row="8" column="0">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeType">
<enum>QSizePolicy::Fixed</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>200</width>
<height>0</height>
</size>
</property>
</spacer>
</item>
<item row="5" column="0">
<widget class="QLabel" name="m_StepsizeLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>Step Size: auto</string>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QSlider" name="m_fSlider">
<property name="toolTip">
<string>Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="value">
<number>100</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="5" column="1">
<widget class="QSlider" name="m_StepsizeSlider">
<property name="toolTip">
<string>Stepsize in mm (auto = 0.1*minimal spacing)</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="value">
<number>0</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="m_FaThresholdLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>FA Threshold: 0.2</string>
</property>
</widget>
</item>
<item row="4" column="1">
<widget class="QSlider" name="m_gSlider">
<property name="toolTip">
<string>Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="value">
<number>0</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="7" column="0">
<widget class="QLabel" name="m_SeedsPerVoxelLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>Seeds per Voxel: 1</string>
</property>
</widget>
</item>
<item row="7" column="1">
<widget class="QSlider" name="m_SeedsPerVoxelSlider">
<property name="toolTip">
<string>Number of tracts started in each voxel of the seed ROI.</string>
</property>
<property name="minimum">
<number>1</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="9" column="0">
<widget class="QCheckBox" name="m_InterpolationBox">
<property name="toolTip">
<string>Default is nearest neighbor interpolation.</string>
</property>
<property name="text">
<string>Enable trilinear interpolation</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QSlider" name="m_AngularThresholdSlider">
<property name="toolTip">
<string>Minimally allowed curcature radius (in mm, interpolated auto = 0.5 minimal spacing, noninterpolated auto = 0.1 minimal spacing)</string>
</property>
<property name="minimum">
<number>-1</number>
</property>
<property name="maximum">
<number>50</number>
</property>
<property name="value">
<number>-1</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLabel" name="m_MinTractLengthLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>Min. Tract Length: 40mm</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QSlider" name="m_FaThresholdSlider">
<property name="toolTip">
<string>Fractional Anisotropy Threshold</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>100</number>
</property>
<property name="value">
<number>20</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="6" column="1">
<widget class="QSlider" name="m_MinTractLengthSlider">
<property name="toolTip">
<string>Minimum tract length in mm.</string>
</property>
<property name="minimum">
<number>0</number>
</property>
<property name="maximum">
<number>500</number>
</property>
<property name="value">
<number>40</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLabel" name="m_AngularThresholdLabel">
<property name="toolTip">
<string/>
</property>
<property name="text">
<string>Min. Curvature Radius: auto</string>
</property>
</widget>
</item>
<item row="10" column="0">
<widget class="QCheckBox" name="m_ResampleFibersBox">
<property name="toolTip">
<string>Resample fibers to 0.5*voxel size (recommended for small step sizes to avoid memory issues).</string>
</property>
<property name="text">
<string>Resample fibers</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="0" column="0">
<widget class="QGroupBox" name="m_InputData">
<property name="title">
<string>Please Select Input Data</string>
</property>
<layout class="QGridLayout" name="gridLayout">
+ <item row="2" column="1">
+ <widget class="QLabel" name="m_MaskImageLabel">
+ <property name="text">
+ <string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
+ </property>
+ <property name="wordWrap">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="1">
+ <widget class="QmitkDataStorageComboBox" name="m_FaImageBox">
+ <item>
+ <property name="text">
+ <string>-</string>
+ </property>
+ </item>
+ </widget>
+ </item>
<item row="1" column="1">
<widget class="QLabel" name="m_RoiImageLabel">
<property name="text">
<string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_6">
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_7">
<property name="toolTip">
- <string>Binary seed ROI. If not specified, the whole image area is seeded.</string>
+ <string>Only track insida mask area.</string>
</property>
<property name="text">
- <string>Seed ROI:</string>
+ <string>Mask Image:</string>
</property>
</widget>
</item>
- <item row="0" column="0">
- <widget class="QLabel" name="label_2">
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_6">
<property name="toolTip">
- <string>Input DTI</string>
+ <string>Binary seed ROI. If not specified, the whole image area is seeded.</string>
</property>
<property name="text">
- <string>Tensor Image:</string>
+ <string>Seed ROI:</string>
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QLabel" name="m_MaskImageLabel">
+ <item row="0" column="1">
+ <widget class="QLabel" name="m_TensorImageLabel">
<property name="text">
- <string><html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html></string>
+ <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_7">
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_2">
<property name="toolTip">
- <string>Only track insida mask area.</string>
+ <string>Input DTI</string>
</property>
<property name="text">
- <string>Mask Image:</string>
+ <string>Tensor Image:</string>
</property>
</widget>
</item>
- <item row="0" column="1">
- <widget class="QLabel" name="m_TensorImageLabel">
+ <item row="4" column="0">
+ <widget class="QCheckBox" name="m_UseFaImage">
+ <property name="toolTip">
+ <string>Check to use selected FA image instead of internally calculated one. Recommended for multi-tensor tractography.</string>
+ </property>
<property name="text">
- <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
+ <string>FA image</string>
</property>
- <property name="wordWrap">
- <bool>true</bool>
+ <property name="checked">
+ <bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
+ <customwidgets>
+ <customwidget>
+ <class>QmitkDataStorageComboBox</class>
+ <extends>QComboBox</extends>
+ <header location="global">QmitkDataStorageComboBox.h</header>
+ </customwidget>
+ </customwidgets>
<resources/>
<connections/>
</ui>