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 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 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 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( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::UCHAR) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::INT) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::UINT) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::SHORT) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::USHORT) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::LONG) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::ULONG) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::FLOAT) { CompareMultiComponentImage( testInput, validInput); } else if (type.GetComponentType() == itk::ImageIOBase::DOUBLE) { CompareMultiComponentImage( testInput, validInput); } else { mitkThrow() << "Pixel component type not supported!"; } } template 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(testImage), const_cast(testImage)->GetVolumeData(t)); ImageReadAccessor readAccVImage(const_cast(validImage), const_cast(validImage)->GetVolumeData(t)); for( unsigned int p = 0; p < noOfPixels*noOfComponents; ++p ) { TPixel vDataItem = static_cast(const_cast(readAccVImage.GetData()))[p]; TPixel tDataItem = static_cast(const_cast(readAccTImage.GetData()))[p]; - if( tDataItem != vDataItem ) + if( std::abs( static_cast(tDataItem - vDataItem) )>m_Tolerance ) { ++m_CompareDetails->m_PixelsWithDifference; m_CompareDetails->m_MaximumDifference = std::max(m_CompareDetails->m_MaximumDifference, std::abs( static_cast(tDataItem - vDataItem) ) ); double min = std::min(m_CompareDetails->m_MinimumDifference, std::abs( static_cast(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(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 #include "mitkCompareImageDataFilter.h" //VTK #include //Other #include #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(other).GetVolumeData(i); this->SetVolume(volume->GetData(), i); } } else { ImageDataItemPointer volume = const_cast(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 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(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;sSetComplete(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;sGetParent()!=vol) { // copy data of slices in volume size_t offset = ((size_t) s)*size; std::memcpy(static_cast(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;tGetParent()!=ch) { // copy data of volume in channel size_t offset = ((size_t) t)*m_OffsetTable[3]*(ptypeSize); std::memcpy(static_cast(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;sIsComplete())) 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(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(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(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;im_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; im_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.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;iGetDimensions()[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(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_CHAR: //pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_SHORT: //pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_SHORT: //pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_INT: //pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_INT: //pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_LONG: //pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_LONG: //pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_FLOAT: //pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_DOUBLE: //pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), 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(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 & 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("<GetDimension(i) << "leftHandSide->GetDimension("<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(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(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(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(3u, 3u); m_AnotherImage = mitk::ImageGenerator::GenerateRandomImage(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(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 #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include #include #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 ::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 ::Normalize( OdfPixelType odf, typename NumericTraits::AccumulateType b0 ) { switch( m_NormalizationMethod ) { case QBAR_STANDARD: { TOdfPixelType sum = 0; for(int i=0; i0) odf /= sum; return odf; break; } case QBAR_B_ZERO_B_VALUE: { for(int i=0; i vnl_vector itk::AnalyticalDiffusionQballReconstructionImageFilter ::PreNormalize( vnl_vector vec, typename NumericTraits::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=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 ::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 ::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 baselineind; // contains the indicies of // the baseline images std::vector 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::AccumulateType b0 = NumericTraits::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 B(m_NumberOfGradientDirections); if( (b0 != 0) && (b0 >= m_Threshold) ) { for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ ) { B[i] = static_cast(b[gradientind[i]]); } B = PreNormalize(B, b0); if(m_NormalizationMethod == QBAR_SOLID_ANGLE) { vnl_vector 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 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 void AnalyticalDiffusionQballReconstructionImageFilter ::tofile2(vnl_matrix *pA, std::string fname) { vnl_matrix 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 void AnalyticalDiffusionQballReconstructionImageFilter ::Cart2Sph(double x, double y, double z, double *spherical) { double phi, theta, r; r = sqrt(x*x+y*y+z*z); if( r double AnalyticalDiffusionQballReconstructionImageFilter -::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(l,abs(m),-cos(theta)); + double mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(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 ::Legendre0(int l) { if( l%2 != 0 ) { return 0; } else { double prod1 = 1.0; for(int i=1;i void AnalyticalDiffusionQballReconstructionImageFilter ::ComputeReconstructionMatrix() { //for(int i=-6;i<7;i++) // std::cout << boost::math::legendre_p(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 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 *Q = new vnl_matrix(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* B = new vnl_matrix(m_NumberOfGradientDirections,m_NumberCoefficients); vnl_matrix* _L = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); _L->fill(0.0); vnl_matrix* LL = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); LL->fill(0.0); vnl_matrix* P = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); P->fill(0.0); vnl_matrix* Inv = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); P->fill(0.0); vnl_vector* lj = new vnl_vector(m_NumberCoefficients); m_LP = new vnl_vector(m_NumberCoefficients); for(unsigned int i=0; i temp((*_L)*(*_L)); LL->update(*_L); *LL *= *_L; //tofile2(LL,"LL"); for(int i=0; i(B->transpose()); //tofile2(&m_B_t,"m_B_t"); vnl_matrix B_t_B = (*m_B_t) * (*B); //tofile2(&B_t_B,"B_t_B"); vnl_matrix lambdaLL(m_NumberCoefficients,m_NumberCoefficients); lambdaLL.update((*LL)); lambdaLL *= m_Lambda; //tofile2(&lambdaLL,"lLL"); vnl_matrix tmp( B_t_B + lambdaLL); vnl_matrix_inverse *pseudoInverse = new vnl_matrix_inverse( tmp ); (*Inv) = pseudoInverse->pinverse(); //tofile2(Inv,"Inv"); vnl_matrix 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(m_NumberCoefficients,m_NumberOfGradientDirections); for(int i=0; iodfs later int NOdfDirections = NODF; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); m_SphericalHarmonicBasisMatrix = new vnl_matrix(NOdfDirections,m_NumberCoefficients); vnl_matrix* sphericalHarmonicBasisMatrix2 = new vnl_matrix(NOdfDirections,m_NumberCoefficients); for(int i=0; i(NOdfDirections,m_NumberOfGradientDirections); *m_ReconstructionMatrix = (*m_SphericalHarmonicBasisMatrix) * (*m_CoeffReconstructionMatrix); } template< class T, class TG, class TO, int L, int NODF> void AnalyticalDiffusionQballReconstructionImageFilter ::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 ::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 * NRRD * 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[1] * Tuch DS, * "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72. * */ 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 Pointer; typedef SmartPointer 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 *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::AccumulateType b0 ); vnl_vector PreNormalize( vnl_vector vec, typename NumericTraits::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 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)); itkConceptMacro(TensorEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(GradientConvertibleToDoubleCheck, (Concept::Convertible)); itkConceptMacro(DoubleConvertibleToTensorCheck, (Concept::Convertible)); itkConceptMacro(GradientReferenceAdditiveOperatorsCheck, (Concept::AdditiveOperators)); itkConceptMacro(ReferenceOStreamWritableCheck, (Concept::OStreamWritable)); itkConceptMacro(TensorOStreamWritableCheck, (Concept::OStreamWritable)); /** 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* m_B_t; vnl_vector* 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 #include #include #include "itkMrtrixPeakImageConverter.h" #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > MrtrixPeakImageConverter< PixelType >::MrtrixPeakImageConverter(): m_NormalizationMethod(NO_NORM) { } template< class PixelType > void MrtrixPeakImageConverter< PixelType > ::GenerateData() { // output vector field vtkSmartPointer m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); Vector spacing4 = m_InputImage->GetSpacing(); Point origin4 = m_InputImage->GetOrigin(); Matrix direction4 = m_InputImage->GetDirection(); ImageRegion<4> imageRegion4 = m_InputImage->GetLargestPossibleRegion(); Vector spacing3; Point origin3; Matrix 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] 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; iSetSpacing( 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 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 container = vtkSmartPointer::New(); itk::ContinuousIndex center; center[0] = index[0]; center[1] = index[1]; center[2] = index[2]; center[3] = 0; itk::Point 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 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 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; jElementAt(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 directionsPolyData = vtkSmartPointer::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 +#include +#include + +#include "itkShCoefficientImageExporter.h" +#include +#include + +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 spacing4; + Point origin4; + Matrix direction4; direction4.SetIdentity(); + ImageRegion<4> imageRegion4; + + Vector spacing3 = m_InputImage->GetSpacing(); + Point origin3 = m_InputImage->GetOrigin(); + Matrix 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; iSetPixel(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 + +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 Pointer; + typedef SmartPointer 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 #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 ImageType; + typedef itk::VectorImage ImageType; itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New(); typedef itk::ImageFileReader 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 spacing; - spacing[0] = img->GetSpacing()[0]; - spacing[1] = img->GetSpacing()[1]; - spacing[2] = img->GetSpacing()[2]; - itk::Point origin; - origin[0] = img->GetOrigin()[0]; - origin[1] = img->GetOrigin()[1]; - origin[2] = img->GetOrigin()[2]; - itk::Matrix 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,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 ot (vecImg, vecImg->GetLargestPossibleRegion() ); ot = ot.Begin(); - while (!ot.IsAtEnd()) - { - itk::DiffusionTensor3D tensor; - ImageType::IndexType idx; - idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2]; + itk::ImageRegionIterator 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; teGetPixel(idx)); - } + VarPixType vec = it.Get(); + FixPixType fixVec(vec.GetDataPointer()); + + itk::DiffusionTensor3D 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 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 ImageType; + itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New(); + typedef itk::ImageFileReader 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 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; teGetPixel(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 ImageType; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); typedef itk::ImageFileReader FileReaderType; FileReaderType::Pointer reader = FileReaderType::New(); reader->SetImageIO(io); reader->SetFileName(this->m_FileName); reader->Update(); ImageType::Pointer img = reader->GetOutput(); typedef itk::Image,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 ot (vecImg, vecImg->GetLargestPossibleRegion() ); ot = ot.Begin(); itk::ImageRegionIterator 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 imgMetaKeys = imgMetaDictionary.GetKeys(); std::vector::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 (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 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 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 ImageType; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); typedef itk::ImageFileReader 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 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; teGetPixel(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 NrrdTensorImageReader ::ConvertMatrixTypeToFixedArrayType(const itk::DiffusionTensor3D::Superclass::MatrixType & matrix) { /* | 0 1 2 | * | X 3 4 | * | X X 5 | */ itk::DiffusionTensor3D 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 +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +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::Pointer dwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData()); + + { + MITK_INFO << "Tensor reconstruction " << argv[2]; + mitk::TensorImage::Pointer tensorImage = dynamic_cast(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::IOUtil::LoadDataNode(argv[3])->GetData()); + typedef itk::DiffusionQballReconstructionImageFilter 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::IOUtil::LoadDataNode(argv[4])->GetData()); + typedef itk::AnalyticalDiffusionQballReconstructionImageFilter 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::IOUtil::LoadDataNode(argv[5])->GetData()); + typedef itk::AnalyticalDiffusionQballReconstructionImageFilter 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::IOUtil::LoadDataNode(argv[6])->GetData()); + typedef itk::AnalyticalDiffusionQballReconstructionImageFilter 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::IOUtil::LoadDataNode(argv[7])->GetData()); + typedef itk::AnalyticalDiffusionQballReconstructionImageFilter 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 #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include 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 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::Pointer duplicator = itk::ImageDuplicator::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 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; iGetVectorLength()); 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; gGetVectorLength(); 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; zGetAbortGenerateData()) + { + m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; + return; + } + std::vector< SliceType::Pointer > compartmentSlices; // extract slice from channel g for (unsigned int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMap.IsNotNull()) fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D)); } if (m_AddGibbsRinging) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::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; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().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 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(hours)); + out.append(":"); + out.append(boost::lexical_cast(minutes)); + out.append(":"); + out.append(boost::lexical_cast(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 #include #include #include #include #include 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 Pointer; typedef SmartPointer 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 NoiseModelType; typedef itk::Image< double, 2 > SliceType; typedef typename itk::KspaceImageFilter< double >::OutputImageType ComplexSliceType; typedef itk::Image ItkDoubleImgType; typedef itk::Matrix 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::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::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 #include #include #include #define _USE_MATH_DEFINES #include 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; iSize(); i++) { typename itk::ImageDuplicator< DirectionImageType >::Pointer duplicator = itk::ImageDuplicator< DirectionImageType >::New(); duplicator->SetInputImage( m_ImageSet->GetElement(i) ); duplicator->Update(); set1->InsertElement(i, dynamic_cast(duplicator->GetOutput())); } for (int i=0; iSize(); i++) { typename itk::ImageDuplicator< DirectionImageType >::Pointer duplicator = itk::ImageDuplicator< DirectionImageType >::New(); duplicator->SetInputImage( m_ReferenceImageSet->GetElement(i) ); duplicator->Update(); set2->InsertElement(i, dynamic_cast(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::max(); m_VarAngularError = 0.0; m_AngularErrorVector.clear(); m_MeanLengthError = 0.0; m_MedianLengthError = 0; m_MaxLengthError = 0.0; m_MinLengthError = itk::NumericTraits::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; iSetOrigin( 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; iSetOrigin( 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 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 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 refDir; if (i testDir; if (j1.0) 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 small error) - for (int i=0; ierror && 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; ierror) { error = diffM_copy[i][b]; a = i; } } else if (b>=numTestDirs) // missing test direction (find next closest) { for (int i=0; ierror) { 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; im_MaxAngularError ) m_MaxAngularError = m_AngularErrorVector.at(i); if ( m_AngularErrorVector.at(i)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; im_MaxLengthError ) m_MaxLengthError = m_LengthErrorVector.at(i); if ( m_LengthErrorVector.at(i)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 // MITK #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include // MISC -#include -#include -#include #include 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_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); vector< mitk::PlanarEllipse::Pointer > bundle = m_Fiducials.at(i); vector< unsigned int > fliplist; if (i container = vtkSmartPointer::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 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 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(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; kGetControlPoint(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(figure->GetGeometry2D()); mitk::PlaneGeometry* planeGeo = dynamic_cast(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 fiberPolyData = vtkSmartPointer::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 #include #include #include "itkStreamlineTrackingFilter.h" #include #include #include #define _USE_MATH_DEFINES #include 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]::New(); - for (int i=0; iGetNumberOfThreads(); i++) + for (unsigned int i=0; iGetNumberOfThreads(); 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; iGetNumberOfIndexedInputs(); 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 TensorType; typename TensorType::EigenValuesArrayType eigenvalues; typename TensorType::EigenVectorsMatrixType eigenvectors; + + for (int x=0; xGetPixel(index); - - vnl_vector_fixed 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; iGetPixel(index); + vnl_vector_fixed 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& pos, vnl_vector_fixed& 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& pos, typename InputImageType::IndexType &index, vnl_vector_fixed< float, 8 >& interpWeights) +::IsValidPosition(itk::ContinuousIndex& 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 (FAGetPixel(index) float StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> -::FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids) +::FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids, int imageIdx) { float tractLength = 0; typedef itk::DiffusionTensor3D 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 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 dir = m_PdImage->GetPixel(index); + + vnl_vector_fixed dir = m_PdImage.at(imageIdx)->GetPixel(index); dir *= dirSign; // reverse direction vnl_vector_fixed dirOld = dir; if (dir.magnitude()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 newDir = m_PdImage.at(img)->GetPixel(index); // get principal direction + if (newDir.magnitude()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 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 (rGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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; imgGetPixel(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() 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 void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId) { FiberPolyDataType poly = m_PolyDataContainer->GetElement(threadId); vtkSmartPointer points = vtkSmartPointer::New(); vtkSmartPointer Cells = vtkSmartPointer::New(); typedef itk::DiffusionTensor3D 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 worldPos; - while( !it.IsAtEnd() ) + for (int img=0; img worldPos; + while( !sit.IsAtEnd() ) { - vtkSmartPointer line = vtkSmartPointer::New(); - std::vector< vtkIdType > pointIDs; - typename InputImageType::IndexType index = it.GetIndex(); - itk::ContinuousIndex start; - unsigned int counter = 0; - - if (m_SeedsPerVoxel>1) + if (sit.Value()==0 || fit.Value() line = vtkSmartPointer::New(); + std::vector< vtkIdType > pointIDs; + typename InputImageType::IndexType index = sit.GetIndex(); + itk::ContinuousIndex 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 (tractLengthGetPointIds()->InsertNextId(pointIDs.at(i)); + //MITK_INFO << "Tract length " << tractLength; - Cells->InsertNextCell(line); + if (tractLengthGetPointIds()->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 vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = poly1->GetLines(); vtkSmartPointer vNewPoints = poly1->GetPoints(); vtkSmartPointer vLines = poly2->GetLines(); vLines->InitTraversal(); for( int i=0; iGetNumberOfCells(); i++ ) { vtkIdType numPoints(0); vtkIdType* points(NULL); vLines->GetNextCell ( numPoints, points ); vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(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; iGetNumberOfThreads(); i++) + for (unsigned int i=1; iGetNumberOfThreads(); 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 #include #include #include #include #include #include #include #include namespace itk{ /** * \brief Performes deterministic streamline tracking on the input tensor image. */ template< class TTensorPixelType, class TPDPixelType=double> class StreamlineTrackingFilter : public ImageToImageFilter< Image< DiffusionTensor3D, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > { public: typedef StreamlineTrackingFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< Image< DiffusionTensor3D, 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 ItkUcharImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image< vnl_vector_fixed, 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& pos, vnl_vector_fixed& dir, typename InputImageType::IndexType& index); - float FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids); - bool IsValidPosition(itk::ContinuousIndex& pos, typename InputImageType::IndexType& index, vnl_vector_fixed< float, 8 >& interpWeights); + float FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids, int imageIdx); + bool IsValidPosition(itk::ContinuousIndex& 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 m_Points; vtkSmartPointer 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include +#include +#include +#include +#include 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; iGetVectorLength()); 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; gGetVectorLength(); 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; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( 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; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().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; iAddArtifact(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; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().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 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; iSetSpacing( 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; iSetSpacing( 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::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_TissueMask); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::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::Pointer resampler = itk::ResampleImageFilter::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]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(m_MaxRotation) + "°\n"; + m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_MaxTranslation) + "mm\n"; + } + else + { + m_StatusText += "Adding linear motion artifacts:\n"; + m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_MaxRotation) + "°\n"; + m_StatusText += "Maximum translation: " + boost::lexical_cast(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(m_FiberModels.size()) + " fiber compartments\n"; MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments"; - vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); - boost::progress_display disp(numFibers); - for( int i=0; iGetNumGradients()); + + 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::Pointer duplicator = itk::ImageDuplicator::New(); + duplicator->SetInputImage(m_TissueMask); + duplicator->Update(); + tempTissueMask = duplicator->GetOutput(); + + // second upsampling needed for motion artifacts + ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; + itk::Vector 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 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::Pointer upsampler = itk::ResampleImageFilter::New(); + upsampler->SetInput(m_TissueMask); + upsampler->SetOutputParametersFromImage(m_TissueMask); + upsampler->SetSize(upsampledImageRegion.GetSize()); + upsampler->SetOutputSpacing(upsampledSpacing); + upsampler->SetOutputOrigin(upsampledOrigin); + itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator + = itk::NearestNeighborInterpolateImageFunction::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; gGetNumGradients(); 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; iGetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); - if (numPoints<2) - continue; + if (numPoints<2) + continue; - for( int j=0; jGetPoint(j); - itk::Point vertex = GetItkPoint(temp); - itk::Vector v = GetItkVector(temp); + for( int j=0; jGetAbortGenerateData()) + { + m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; + return; + } - itk::Vector dir(3); - if (jGetPoint(j+1))-v; - else - dir = v-GetItkVector(points->GetPoint(j-1)); + double* temp = points->GetPoint(j); + itk::Point vertex = GetItkPoint(temp); + itk::Vector v = GetItkVector(temp); - itk::Index<3> idx; - itk::ContinuousIndex contIndex; - m_TissueMask->TransformPhysicalPointToIndex(vertex, idx); - m_TissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); + itk::Vector dir(3); + if (jGetPoint(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 idx; + itk::ContinuousIndex 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; kSetFiberDirection(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; kSetFiberDirection(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; kSetFiberDirection(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 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 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; iGetPixel(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; iGetPixel(index); + // if (dynamic_cast< mitk::AstroStickModel* >(m_NonFiberModels.at(i))) + // { + // mitk::AstroStickModel* model = dynamic_cast< mitk::AstroStickModel* >(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 maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion()); + tempTissueMask->FillBuffer(0); - // adjust non-fiber and intra-axonal signal - for (unsigned int i=1; iGetPixel(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; iGetPixel(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 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::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::max(); ImageRegionIterator 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; iAddNoise(temp); accu += temp; } signal = accu/m_NumberOfRepetitions; } for (unsigned int i=0; i0) 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]SetNthOutput(0, outImage); + + m_StatusText += "\n\n"; + m_StatusText += "Finished simulation\n"; + m_StatusText += "Simulation time: "+GetTime(); } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed 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(hours)); + out.append(":"); + out.append(boost::lexical_cast(minutes)); + out.append(":"); + out.append(boost::lexical_cast(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 #include #include -#include // ITK #include #include #include #include #include +#include #include +#include 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 ItkDoubleImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; - typedef std::vector< mitk::KspaceArtifact* > KspaceArtifactList; typedef std::vector< mitk::DiffusionSignalModel* > DiffusionModelList; typedef itk::Matrix MatrixType; typedef mitk::DiffusionNoiseModel NoiseModelType; typedef itk::Image< double, 2 > SliceType; typedef itk::VnlForwardFFTImageFilter::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 GetItkPoint(double point[3]); itk::Vector GetItkVector(double point[3]); vnl_vector_fixed GetVnlVector(double point[3]); vnl_vector_fixed 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 m_Spacing; ///< output image spacing itk::Vector m_UpsampledSpacing; itk::Point m_Origin; ///< output image origin + itk::Point 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 #include #include // ITK #include #include // misc #define _USE_MATH_DEFINES #include #include 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 TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > itk::Point TractsToVectorImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point 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 spacing; itk::Point origin; itk::Matrix 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]GetDeepCopy(); // resample fiber bundle for sufficient voxel coverage - m_FiberBundle->ResampleFibers(minSpacing/10); + m_FiberBundle->ResampleFibers(minSpacing/3); // iterate over all fibers vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); vtkSmartPointer 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; iGetNextCell ( numPoints, points ); if (numPoints<2) continue; itk::Index<3> index; index.Fill(0); itk::ContinuousIndex contIndex; vnl_vector_fixed dir, wDir; itk::Point worldPos; vnl_vector v; for( int j=0; jGetPoint(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 m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); itk::ImageRegionIterator dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion()); itk::ImageRegionIterator 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; iSize(); 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; iSetSpacing( 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 container = vtkSmartPointer::New(); itk::ContinuousIndex center; center[0] = index[0]; center[1] = index[1]; center[2] = index[2]; itk::Point 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 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 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 directionsPolyData = vtkSmartPointer::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; i0.0001) { counter = 0; oldMean = currentMean; workingMean = oldMean; workingMean.normalize(); currentMean.fill(0.0); for (int i=0; i=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; i0) for (int i=0; i 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; i0.0001) { counter = 0; oldMean = currentMean; workingMean = oldMean; workingMean.normalize(); currentMean.fill(0.0); for (int i=0; i=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 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; i0) for (int i=0; i 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 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 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; iSize(); i++) container->ElementAt(i) /= max; if (container->Size()Size()) return MeanShiftClustering(container); else return container; } template< class PixelType > vnl_vector_fixed TractsToVectorImageFilter< PixelType >::ClusterStep(DirectionContainerType::Pointer dirCont, vnl_vector_fixed currentMean) { vnl_vector_fixed newMean; newMean.fill(0); for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it) { vnl_vector_fixed 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 #include #include #include "mitkImagePixelReadAccessor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include 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::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 mitk::FiberBundleX::GeneratePolyDataByIds(std::vector 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 newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); // if FA array available, initialize fa double array // if color orient array is available init color array vtkSmartPointer faValueArray; vtkSmartPointer 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::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::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 fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); 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 vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(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 vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // iterate over current fibers - int numFibers = GetNumFibers(); - boost::progress_display disp(numFibers); - for( int i=0; iGetCell(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; i2GetFiberPolyData()->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 point_start = GetItkPoint(points->GetPoint(0)); - itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); - itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); - itk::Point 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 point_start = GetItkPoint(points->GetPoint(0)); + itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); + itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); + itk::Point 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 container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(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 mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point 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 fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer 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 colorsT = vtkSmartPointer::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; fiGetNextCell(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 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 (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); 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 (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); if (ColorArray==NULL) return; for(long i=0; iGetNumberOfTuples(); 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 void mitk::FiberBundleX::SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer FAimage) { - MITK_DEBUG << "SetFAMap"; - vtkSmartPointer faValues = vtkSmartPointer::New(); - faValues->SetName(COLORCODING_FA_BASED); - faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); - faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); - - mitk::ImagePixelReadAccessor readFAimage (FAimage, FAimage->GetVolumeData(0)); - - vtkPoints* pointSet = m_FiberPolyData->GetPoints(); - for(long i=0; iGetNumberOfPoints(); ++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 faValues = vtkSmartPointer::New(); + faValues->SetName(COLORCODING_FA_BASED); + faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); + faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); + + mitk::ImagePixelReadAccessor readFAimage (FAimage, FAimage->GetVolumeData(0)); + + vtkPoints* pointSet = m_FiberPolyData->GetPoints(); + for(long i=0; iGetNumberOfPoints(); ++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 idFiberFilter = vtkSmartPointer::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 polyData = m_FiberPolyData; if (anyPoint) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Extracting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cellOriginal = m_FiberPolyData->GetCell(i); int numPointsOriginal = cellOriginal->GetNumberOfPoints(); vtkPoints* pointsOriginal = cellOriginal->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1 && numPointsOriginal) { if (anyPoint) { for (int j=0; jGetPoint(j); itk::Point 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; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } break; } } } else { double* start = pointsOriginal->GetPoint(0); itk::Point 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 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; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::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]GetSpacing()[1] && mask->GetSpacing()[0]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 polyData =fibCopy->GetFiberPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Cutting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1) { int newNumPoints = 0; for (int j=0; jGetPoint(j); itk::Point 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::New(); } } if (newNumPoints>0) vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::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 tmp = ExtractFiberIdSubset(pf); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(mitk::PlanarFigure* pf) { MITK_DEBUG << "Extracting fibers!"; // vector which is returned, contains all extracted FiberIds std::vector FibersInROI; if (pf==NULL) return FibersInROI; /* Handle type of planarfigure */ // if incoming pf is a pfc mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast(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 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 AND_Assamblage(childResults.size()); //std::vector AND_Assamblage; fill(AND_Assamblage.begin(), AND_Assamblage.end(), -1); //AND_Assamblage.reserve(childResults.size()); //max size AND can reach anyway std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector 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 OR_Assamblage = this->ExtractFiberIdSubset(pfcomp->getChildAt(0)); std::vector::iterator it; MITK_DEBUG << OR_Assamblage.size(); for (int i=1; igetNumberOfChildren(); ++i) { it = OR_Assamblage.end(); std::vector 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 childResults; childResults.reserve(this->GetNumFibers()); vtkSmartPointer idSet = m_FiberIdDataSet->GetCellData()->GetArray(FIBER_ID_ARRAY); MITK_DEBUG << "m_NumOfFib: " << this->GetNumFibers() << " cellIdNum: " << idSet->GetNumberOfTuples(); for(long i=0; iGetNumFibers(); 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 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::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector 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 (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 PointsOnPlane; // contains all pointIds which are crossing the cutting plane std::vector PointsInROI; // based on PointsOnPlane, all ROI relevant point IDs are stored here /* Define cutting plane by ROI (PlanarFigure) */ vtkSmartPointer plane = vtkSmartPointer::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 clipper = vtkSmartPointer::New(); clipper->SetInputData(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); clipper->Update(); vtkSmartPointer 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 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; iGetTuple(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; iGetPoint(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 polygonVtk = vtkSmartPointer::New(); //get the control points from pf and insert them to vtkPolygon unsigned int nrCtrlPnts = pf->GetNumberOfControlPoints(); for (int i=0; iGetPoints()->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(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); for (int i=0; iGetPoint(PointsOnPlane[i])[0], clipperout->GetPoint(PointsOnPlane[i])[1], clipperout->GetPoint(PointsOnPlane[i])[2]}; int isInPolygon = polygonVtk->PointInPolygon(checkIn, polygonVtk->GetPoints()->GetNumberOfPoints() , static_cast(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 ; iGetCell(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; jGetCellData()->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::iterator it; it = unique (FibersInROI.begin(), FibersInROI.end()); FibersInROI.resize( it - FibersInROI.begin() ); } return FibersInROI; } void mitk::FiberBundleX::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::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::NonpositiveMin(); float max = itk::NumericTraits::max(); float b[] = {max, min, max, min, max, min}; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); if (p1[0]b[1]) b[1]=p1[0]; if (p1[1]b[3]) b[3]=p1[1]; if (p1[2]b[5]) b[5]=p1[2]; // calculate statistics if (jGetPoint(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 (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) 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 mitk::FiberBundleX::GetAvailableColorCodings() { std::vector availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->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 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 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 vtkNewPoints = vtkSmartPointer::New(); + vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); + + for (int i=0; iGetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vtkSmartPointer container = vtkSmartPointer::New(); + for (int j=0; jGetPoint(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::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(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::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(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::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(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::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(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 && rInsertNextCell(container); container = vtkSmartPointer::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::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 || lengthInMMm_MaxFiberLength) // can't remove all fibers { MITK_WARN << "Process aborted. No fibers would be left!"; return false; } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::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 vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::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 vtkSmoothPoints = vtkSmartPointer::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 vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines vtkIdType pointHelperCnt = 0; MITK_INFO << "Smoothing fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer newPoints = vtkSmartPointer::New(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); float length = m_FiberLengths.at(i); int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::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 spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::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 smoothLine = vtkSmartPointer::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::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 newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); int numberOfLines = m_NumFibers; MITK_INFO << "Resampling fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); double* point = points->GetPoint(0); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); float dtau = 0; int cur_p = 1; itk::Vector dR; float normdR = 0; for (;;) { while (dtau <= pointDistance && cur_p < numPoints) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector 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 v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector 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; iGetCell(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; jGetPoint(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 #include "FiberTrackingExports.h" #include //includes storing fiberdata -#include //may be replaced by class precompile argument -#include // may be replaced by class -#include // my be replaced by class +#include +#include +#include #include +#include //#include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class FiberTracking_EXPORT FiberBundleX : public BaseData { public: typedef itk::Image 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) // custom constructor // colorcoding related methods void SetColorCoding(const char*); void SetFAMap(mitk::Image::Pointer); template 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 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 ExtractFiberIdSubset(PlanarFigure* pf); FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint); FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); vtkSmartPointer GeneratePolyDataByIds( std::vector ); // TODO: make protected void GenerateFiberIds(); // TODO: make protected // get/set data void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer 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 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 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 m_FiberPolyData; // contains fiber ids vtkSmartPointer 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 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 #include 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* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); for (int i=0; iget(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 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; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { for (int j=0; j #include 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 sticks; switch (order) { case 1: m_NumSticks = 12; sticks = itk::PointShell<12, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 2: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 3: m_NumSticks = 92; sticks = itk::PointShell<92, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 4: m_NumSticks = 162; sticks = itk::PointShell<162, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 5: m_NumSticks = 252; sticks = itk::PointShell<252, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; default: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; } for (int i=0; i #include 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; im_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 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 #include +#include + +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 #include 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(var); } + double GetNoiseVariance(){ return m_Distribution.n(); } - itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; +protected: + boost::random::mt19937 m_Randgen; + boost::random::chi_squared_distribution 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 #include +#include + +using namespace mitk; template< class ScalarType > -DotModel< ScalarType >::DotModel() +ChisquareNoiseModel< ScalarType >::ChisquareNoiseModel() { - + this->m_NoiseVariance = 0; + m_Distribution = std::chi_squared_distribution(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 #include +#include 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 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 #include #include #include +#include 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 #include #include #include 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 GradientType; typedef std::vector 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; im_GradientList.size(); i++) if (m_GradientList.at(i).GetNorm()<0.0001) result.push_back(i); return result; } int GetFirstBaselineIndex() { for( unsigned int i=0; im_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 #include 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 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 -#include -#include - -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 #include 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 #include 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; im_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 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 #include 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 axis = itk::CrossProduct(m_KernelDirection, this->m_FiberDirection).GetVnlVector(); axis.normalize(); + vnl_quaternion rotation(axis, acos(m_KernelDirection*this->m_FiberDirection)); + rotation.normalize(); + vnl_matrix_fixed matrix = rotation.rotation_matrix_transpose(); + + vnl_matrix_fixed 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 axis = itk::CrossProduct(m_KernelDirection, this->m_FiberDirection).GetVnlVector(); axis.normalize(); vnl_quaternion rotation(axis, acos(m_KernelDirection*this->m_FiberDirection)); rotation.normalize(); vnl_matrix_fixed matrix = rotation.rotation_matrix_transpose(); vnl_matrix_fixed 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; im_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 #include 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 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 -#include -#include -#include -#include -#include -#include -#include - -/**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 fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false ); - mitk::BaseData::Pointer baseData = fibInfile.at(0); - fib1 = dynamic_cast(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(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 +#include +#include +#include +#include +#include +#include +#include + +/**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::IOUtil::LoadDataNode(argv[1])->GetData()); + mitk::FiberBundleX::Pointer testFibs = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); + + // test planar figure based extraction + mitk::PlanarFigure::Pointer pf1 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); + mitk::PlanarFigure::Pointer pf2 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); + mitk::PlanarFigure::Pointer pf3 = dynamic_cast(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(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::IOUtil::LoadDataNode(argv[11])->GetData()); + MITK_TEST_CONDITION_REQUIRED(notExtractedFibs->Equals(testFibs),"check bundle subtraction") + + testFibs = dynamic_cast(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::IOUtil::LoadDataNode(argv[6])->GetData()); + typedef itk::Image< unsigned char, 3 > itkUCharImageType; + itkUCharImageType::Pointer itkRoiImage = itkUCharImageType::New(); + mitk::CastToItkImage(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::IOUtil::LoadDataNode(argv[7])->GetData()); + MITK_TEST_CONDITION_REQUIRED(inside->Equals(testFibs),"check inside mask extraction") + + testFibs = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); + MITK_TEST_CONDITION_REQUIRED(outside->Equals(testFibs),"check outside mask extraction") + + testFibs = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); + MITK_TEST_CONDITION_REQUIRED(passing->Equals(testFibs),"check passing mask extraction") + + testFibs = dynamic_cast(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 +#include +#include +#include +#include +#include +#include + +/**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::IOUtil::LoadDataNode(argv[1])->GetData()); + mitk::PlanarEllipse::Pointer pf2 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); + mitk::PlanarEllipse::Pointer pf3 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); + mitk::FiberBundleX::Pointer uniform = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); + mitk::FiberBundleX::Pointer gaussian = dynamic_cast(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 +#include +#include +#include +#include + +/**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::IOUtil::LoadDataNode(argv[1])->GetData()); + mitk::FiberBundleX::Pointer transformedFibs = dynamic_cast(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 +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +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 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::IOUtil::LoadDataNode(fibFile)->GetData()); + + // load reference directions + ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); + for (int i=0; i(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::Pointer fOdfFilter = itk::TractsToVectorImageFilter::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::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE)->GetData()); + mitk::Image::Pointer gtNumTestDirImage = dynamic_cast(mitk::IOUtil::LoadDataNode(LDFP_NUM_DIRECTIONS)->GetData()); + mitk::FiberBundleX::Pointer gtTestDirections = dynamic_cast(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::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; iSize(); i++) + { + MITK_INFO << "Checking direction image " << i; + itk::TractsToVectorImageFilter::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::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 +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +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 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(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 infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false ); + mitk::FiberBundleX::Pointer fib2 = dynamic_cast(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 +#include +#include +#include +#include +#include +#include +#include +#include +#include + +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 infile = mitk::BaseDataIO::LoadBaseDataFromFile( dtiFileName, s1, s2, false ); + + MITK_INFO << "Loading tensor image ..."; + typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; + mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); + ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); + mitk::CastToItkImage(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(mitkSeedImage, mask); + filter->SetSeedImage(mask); + } + + if (mitkMaskImage.IsNotNull()) + { + ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); + mitk::CastToItkImage(mitkMaskImage, mask); + filter->SetMaskImage(mask); + } + + filter->Update(); + + vtkSmartPointer 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(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 +#include +#include +#include +#include +#include +#include "ctkCommandLineParser.h" +#include +#include +#include +#include +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +template +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 parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + string inFile = us::any_cast(parsedArgs["input"]); + string outFile = us::any_cast(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::Pointer filter = itk::ShCoefficientImageExporter::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 parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + int shOrder = -1; + if (parsedArgs.count("shOrder")) + shOrder = us::any_cast(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 #include #include #include #include #include #include #include //#include "ctkCommandLineParser.h" #include "ctkCommandLineParser.h" #include #include #include #include "boost/property_tree/ptree.hpp" #include "boost/property_tree/xml_parser.hpp" #include "boost/foreach.hpp" #include #include #include #include #include using namespace mitk; struct ImageParameters { itk::ImageRegion<3> imageRegion; itk::Vector imageSpacing; itk::Point imageOrigin; itk::Matrix 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 ricianNoiseModel; mitk::DiffusionSignalModel::GradientListType gradientDirections; itk::TractsToDWIImageFilter< short >::DiffusionModelList fiberModelList, nonFiberModelList; - itk::TractsToDWIImageFilter< short >::KspaceArtifactList artifactList; std::string signalModelString, artifactModelString; itk::Image::Pointer frequencyMap; itk::Image::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 * m_StickModel1, mitk::StickModel * m_StickModel2, mitk::TensorModel * m_ZeppelinModel1, mitk::TensorModel * m_ZeppelinModel2, mitk::TensorModel * m_TensorModel1, mitk::TensorModel * m_TensorModel2, // extra axonal compartment models mitk::BallModel * m_BallModel1, mitk::BallModel * m_BallModel2, mitk::AstroStickModel * m_AstrosticksModel1, mitk::AstroStickModel * m_AstrosticksModel2, mitk::DotModel * m_DotModel1, mitk::DotModel * 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("tEcho"); m_ImageGenParameters.tLine = v1.second.get("tLine"); m_ImageGenParameters.doSimulateEddyCurrents = v1.second.get("artifacts.addeddy"); m_ImageGenParameters.eddyStrength = 0; if (m_ImageGenParameters.doSimulateEddyCurrents) { m_ImageGenParameters.eddyStrength = v1.second.get("artifacts.eddyStrength"); } // signal relaxation m_ImageGenParameters.doSimulateRelaxation = v1.second.get("doSimulateRelaxation"); if (m_ImageGenParameters.doSimulateRelaxation) // N/2 ghosts if (v1.second.get("artifacts.addghost")) { m_ImageGenParameters.kspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset"); } else { m_ImageGenParameters.kspaceLineOffset = 0; } if (v1.second.get("artifacts.addspikes")) { m_ImageGenParameters.spikes = v1.second.get("artifacts.spikesnum"); m_ImageGenParameters.spikeAmplitude = v1.second.get("artifacts.spikesscale"); } // add distortions if (v1.second.get("artifacts.distortions") && m_fImage) { itk::Image::Pointer itkImg = itk::Image::New(); mitk::CastToItkImage< itk::Image >(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("artifacts.addnoise")) m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(v1.second.get("artifacts.noisevariance")); else m_ImageGenParameters.ricianNoiseModel.SetNoiseVariance(0); // gibbs ringing m_ImageGenParameters.upsampling = 1; if (v1.second.get("artifacts.addringing")) m_ImageGenParameters.upsampling = v1.second.get("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::New(); mitk::CastToItkImage >(m_maskImage.GetPointer(), m_ImageGenParameters.tissueMaskImage); } // signal models m_ImageGenParameters.comp3Weight = 1; m_ImageGenParameters.comp4Weight = 0; if (v1.second.get("compartment4.index") > 0) { m_ImageGenParameters.comp4Weight = v1.second.get("compartment4.weight"); m_ImageGenParameters.comp3Weight -= m_ImageGenParameters.comp4Weight; } // compartment 1 switch(v1.second.get("compartment1.index")){ case 0: m_StickModel1->SetGradientList(m_ImageGenParameters.gradientDirections); m_StickModel1->SetBvalue(m_ImageGenParameters.b_value); m_StickModel1->SetDiffusivity(v1.second.get("compartment1.stick.d")); m_StickModel1->SetT2(v1.second.get("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("compartment1.zeppelin.d1")); m_ZeppelinModel1->SetDiffusivity2(v1.second.get("compartment1.zeppelin.d2")); m_ZeppelinModel1->SetDiffusivity3(v1.second.get("compartment1.zeppelin.d2")); m_ZeppelinModel1->SetT2(v1.second.get("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("compartment1.tensor.d1")); m_TensorModel1->SetDiffusivity2(v1.second.get("compartment1.tensor.d2")); m_TensorModel1->SetDiffusivity3(v1.second.get("compartment1.tensor.d3")); m_TensorModel1->SetT2(v1.second.get("compartment1.tensor.t2")); m_ImageGenParameters.fiberModelList.push_back(m_TensorModel1); break; } // compartment 2 switch(v1.second.get("compartment2.index")){ case 0: m_StickModel2->SetGradientList(m_ImageGenParameters.gradientDirections); m_StickModel2->SetBvalue(m_ImageGenParameters.b_value); m_StickModel2->SetDiffusivity(v1.second.get("compartment2.stick.d")); m_StickModel2->SetT2(v1.second.get("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("compartment2.zeppelin.d1")); m_ZeppelinModel2->SetDiffusivity2(v1.second.get("compartment2.zeppelin.d2")); m_ZeppelinModel2->SetDiffusivity3(v1.second.get("compartment2.zeppelin.d2")); m_ZeppelinModel2->SetT2(v1.second.get("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("compartment2.tensor.d1")); m_TensorModel2->SetDiffusivity2(v1.second.get("compartment2.tensor.d2")); m_TensorModel2->SetDiffusivity3(v1.second.get("compartment2.tensor.d3")); m_TensorModel2->SetT2(v1.second.get("compartment2.tensor.t2")); m_ImageGenParameters.fiberModelList.push_back(m_TensorModel2); break; } // compartment 3 switch(v1.second.get("compartment3.index")){ case 0: m_BallModel1->SetGradientList(m_ImageGenParameters.gradientDirections); m_BallModel1->SetBvalue(m_ImageGenParameters.b_value); m_BallModel1->SetDiffusivity(v1.second.get("compartment3.ball.d")); m_BallModel1->SetT2(v1.second.get("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("compartment3.astrosticks.d")); m_AstrosticksModel1->SetT2(v1.second.get("compartment3.astrosticks.t2")); m_AstrosticksModel1->SetRandomizeSticks(v1.second.get("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("compartment3.dot.t2")); m_DotModel1->SetWeight(m_ImageGenParameters.comp3Weight); m_ImageGenParameters.nonFiberModelList.push_back(m_DotModel1); break; } // compartment 4 switch(v1.second.get("compartment4.index")){ case 0: m_BallModel2->SetGradientList(m_ImageGenParameters.gradientDirections); m_BallModel2->SetBvalue(m_ImageGenParameters.b_value); m_BallModel2->SetDiffusivity(v1.second.get("compartment4.ball.d")); m_BallModel2->SetT2(v1.second.get("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("compartment4.astrosticks.d")); m_AstrosticksModel2->SetT2(v1.second.get("compartment4.astrosticks.t2")); m_AstrosticksModel2->SetRandomizeSticks(v1.second.get("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("compartment4.dot.t2")); m_DotModel2->SetWeight(m_ImageGenParameters.comp4Weight); m_ImageGenParameters.nonFiberModelList.push_back(m_DotModel2); break; } m_ImageGenParameters.signalScale = v1.second.get("signalScale"); m_ImageGenParameters.repetitions = v1.second.get("repetitions"); m_ImageGenParameters.tInhom = v1.second.get("tInhom"); m_ImageGenParameters.doDisablePartialVolume = v1.second.get("doDisablePartialVolume"); m_ImageGenParameters.interpolationShrink = v1.second.get("interpolationShrink"); m_ImageGenParameters.axonRadius = v1.second.get("axonRadius"); } /* m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); m_Controls->m_RealTimeFibers->setChecked(v1.second.get("realtime")); m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("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("sampling")); m_Controls->m_TensionBox->setValue(v2.second.get("tension")); m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); m_Controls->m_BiasBox->setValue(v2.second.get("bias")); } if( v2.first == "rotation" ) { m_Controls->m_XrotBox->setValue(v2.second.get("x")); m_Controls->m_YrotBox->setValue(v2.second.get("y")); m_Controls->m_ZrotBox->setValue(v2.second.get("z")); } if( v2.first == "translation" ) { m_Controls->m_XtransBox->setValue(v2.second.get("x")); m_Controls->m_YtransBox->setValue(v2.second.get("y")); m_Controls->m_ZtransBox->setValue(v2.second.get("z")); } if( v2.first == "scale" ) { m_Controls->m_XscaleBox->setValue(v2.second.get("x")); m_Controls->m_YscaleBox->setValue(v2.second.get("y")); m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); } } } if( v1.first == "image" ) { m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); m_Controls->m_BvalueBox->setValue(v1.second.get("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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); string fbName = us::any_cast(parsedArgs["fiberbundle"]); string paramName = us::any_cast(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 infile = BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); MITK_INFO << "Loading " << fbName; std::vector infile2 = BaseDataIO::LoadBaseDataFromFile( fbName, s1, s2, false ); mitk::BaseData::Pointer baseData2 = infile2.at(0); DiffusionImage::Pointer dwi; FiberBundleX::Pointer fbi; if ( dynamic_cast*>(baseData.GetPointer()) ) dwi = dynamic_cast*>(baseData.GetPointer()); else MITK_ERROR << "LOADING DWI FAILD: " << inName; if ( dynamic_cast(baseData2.GetPointer()) ) fbi = dynamic_cast(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::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); m_ImageGenParameters.numGradients = 0; for (int i=0; iSize(); i++) { DiffusionSignalModel::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 m_StickModel1; mitk::StickModel m_StickModel2; mitk::TensorModel m_ZeppelinModel1; mitk::TensorModel m_ZeppelinModel2; mitk::TensorModel m_TensorModel1; mitk::TensorModel m_TensorModel2; // extra axonal compartment models mitk::BallModel m_BallModel1; mitk::BallModel m_BallModel2; mitk::AstroStickModel m_AstrosticksModel1; mitk::AstroStickModel m_AstrosticksModel2; mitk::DotModel m_DotModel1; mitk::DotModel 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::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( tractsToDwiFilter->GetOutput() ); image->SetB_Value(dwi->GetB_Value()); image->SetDirections(dwi->GetDirections()); image->InitializeFromVectorImage(); MITK_INFO << "Writing " << outName; NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::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 #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include +#include template -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 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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); string paramFileName = us::any_cast(parsedArgs["parameters"]); string outFileName = us::any_cast(parsedArgs["outFile"]); + bool noFlip = false; + if (parsedArgs.count("noFlip")) + noFlip = us::any_cast(parsedArgs["noFlip"]); + try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); // instantiate gibbs tracker typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; typedef itk::GibbsTrackingFilter GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector 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(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(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, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(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(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(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 MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage(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 #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include +#include #define _USE_MATH_DEFINES #include -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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); + ctkCommandLineParser::StringContainerType maskImages; + if (parsedArgs.count("mask")) + maskImages = us::any_cast(parsedArgs["mask"]); string fibFile = us::any_cast(parsedArgs["input"]); - string maskImage(""); - if (parsedArgs.count("mask")) - maskImage = us::any_cast(parsedArgs["mask"]); - float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); typedef itk::Image 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::IOUtil::LoadDataNode(fibFile)->GetData()); // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (int i=0; i(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::IOUtil::LoadDataNode(maskImage)->GetData()); - mitk::CastToItkImage(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::Pointer fOdfFilter = itk::TractsToVectorImageFilter::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; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(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(mitk::IOUtil::LoadDataNode(maskImages.at(i))->GetData()); + mitk::CastToItkImage(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(evaluationFilter->GetMeanAngularError())); + sens.append(","); + + sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); + sens.append(","); + + sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); + sens.append(","); + + sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); + sens.append(","); + + sens.append(boost::lexical_cast(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(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(evaluationFilter->GetMedianAngularError())); - sens.append(";\n"); + sens.append("FULL"); + sens.append(","); - sens.append("Maximum:"); - sens.append(","); - sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); - sens.append(";\n"); + sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); + sens.append(","); - sens.append("Minimum:"); - sens.append(","); - sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); - sens.append(";\n"); + sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); + sens.append(","); - sens.append("STDEV:"); - sens.append(","); - sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); - sens.append(";\n"); + sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); + sens.append(","); - file << sens; + sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); + sens.append(","); + sens.append(boost::lexical_cast(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 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(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 #include #include #include #include #include #include #include #include #include -#include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include mitk::Image::Pointer LoadData(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector 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(baseData.GetPointer()); } template -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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["image"]); string outRoot = us::any_cast(parsedArgs["outroot"]); // optional arguments string maskImageName(""); if (parsedArgs.count("mask")) maskImageName = us::any_cast(parsedArgs["mask"]); int normalization = 1; if (parsedArgs.count("normalization")) normalization = us::any_cast(parsedArgs["normalization"]); int numPeaks = 2; if (parsedArgs.count("numpeaks")) numPeaks = us::any_cast(parsedArgs["numpeaks"]); float peakThres = 0.4; if (parsedArgs.count("peakthres")) peakThres = us::any_cast(parsedArgs["peakthres"]); float absPeakThres = 0.06; if (parsedArgs.count("abspeakthres")) absPeakThres = us::any_cast(parsedArgs["abspeakthres"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(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 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(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(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 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; iSize(); 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(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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(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 #include #include "ctkCommandLineParser.h" #include #include 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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(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(parsedArgs["b0Threshold"]); int shOrder = 4; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); float lambda = 0.006; if (parsedArgs.count("lambda")) lambda = us::any_cast(parsedArgs["lambda"]); int normalization = 0; if (parsedArgs.count("csa") && us::any_cast(parsedArgs["csa"])) normalization = 6; bool outCoeffs = false; if (parsedArgs.count("outputCoeffs")) outCoeffs = us::any_cast(parsedArgs["outputCoeffs"]); + bool mrTrix = false; + if (parsedArgs.count("mrtrix")) + mrTrix = us::any_cast(parsedArgs["mrtrix"]); + try { RegisterDiffusionCoreObjectFactory(); MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(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 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 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 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 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 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 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 #include #include #include #include #include #include #include #include #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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; - string dtiFileName = us::any_cast(parsedArgs["input"]); + ctkCommandLineParser::StringContainerType inputImages = us::any_cast(parsedArgs["input"]); + string dtiFileName; string outFileName = us::any_cast(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(parsedArgs["minCurv"]); if (parsedArgs.count("minFA")) minFA = us::any_cast(parsedArgs["minFA"]); if (parsedArgs.count("stepSize")) stepSize = us::any_cast(parsedArgs["stepSize"]); if (parsedArgs.count("tendf")) tendf = us::any_cast(parsedArgs["tendf"]); if (parsedArgs.count("tendg")) tendg = us::any_cast(parsedArgs["tendg"]); if (parsedArgs.count("minLength")) minLength = us::any_cast(parsedArgs["minLength"]); if (parsedArgs.count("numSeeds")) numSeeds = us::any_cast(parsedArgs["numSeeds"]); if (parsedArgs.count("interpolate")) interpolate = us::any_cast(parsedArgs["interpolate"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); - // load input image - const std::string s1="", s2=""; - std::vector 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, 3 > ItkTensorImage; - mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); - ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); - mitk::CastToItkImage(mitkTensorImage, itk_dti); + dtiFileName = inputImages.at(0); + for (int i=0; i(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData()); + ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); + mitk::CastToItkImage(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(parsedArgs["seed"])); MITK_INFO << "Loading mask image ..."; mitk::Image::Pointer mitkMaskImage = NULL; if (parsedArgs.count("mask")) mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(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(mitkSeedImage, mask); filter->SetSeedImage(mask); } if (mitkMaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkMaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer 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 #include #include #include #include "ctkCommandLineParser.h" #include 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 parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(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(parsedArgs["b0Threshold"]); try { RegisterDiffusionCoreObjectFactory(); MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(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). Available sections: - \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. Example: \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. Fiber Options: \li Real Time Fibers: 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 Advanced Options: Show/hide advanced options \li #Fibers: Specifies the number of fibers that will be generated for the selected bundle. \li Fiber Sampling: Adjusts the distenace of the fiber sampling points (in mm). A higher sampling rate is needed if high curvatures are modeled. \li Tension, Continuity, Bias: Parameters controlling the shape of the splines interpolation the fiducials. See Wikipedia for details. Fiducial Options: \li Use Constant Fiducial Radius: 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 Align with grid: Click to shift all fiducial center points to the next voxel center. Operations: \li Rotation: Define the rotation of the selected fiber bundle around each axis (in degree). \li Translation: Define the translation of the selected fiber bundle along each axis (in mm). \li Scaling: Define a scaling factor for the selected fiber bundle in each dimension. \li Transform Selection: Apply specified rotation, translation and scaling to the selected Bundle/Fiducial \li Copy Bundles: Add copies of the selected fiber bundles to the datamanager. \li Join Bundles: Add new bundle to the datamanager that contains all fibers from the selected bundles. \li Include Fiducials: 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. Basic Image Settings: \li Image Dimensions: Specifies actual image size (number of voxels in each dimension). \li Image Spacing: Specifies voxel size in mm. Beware that changing the voxel size also changes the signal strength, e.g. increasing the resolution from 2x2x2 mm to 1x1x1 mm decreases the signal obtained for each voxel by a factor 8. \li Gradient Directions: Number of gradients directions distributed equally over the half sphere. 10% baseline images are automatically added. \li b-Value: 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. Advanced Image Settings (activate checkbox "Advanced Options"): \li Repetitions: Specifies the number of averages used for the acquisition to reduce noise. \li Signal Scale: Additional scaling factor for the signal in each voxel. The default value of 125 results in a maximum signal amplitude of 1000 for 2x2x2 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 Echo Time TE: Time between the 90° excitation pulse and the first spin echo. Increasing this time results in a stronger T2-relaxation effect (Wikipedia). \li Line Readout Time: Time to read one line in k-space. Increasing this time results in a stronger T2* 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 Tinhom Relaxation: Time constant specifying the signal decay due to magnetic field inhomogeneities (also called T2'). Together with the tissue specific relaxation time constant T2 this defines the T2* decay constant: T2*=(T2 T2')/(T2+T2') \li Fiber Radius (in µm): 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 Interpolation Shrink: 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 Simulate Signal Relaxation: If checked, the relaxation induced signal decay is simulated, other wise the parameters TE, Line Readout Time, Tinhom, and T2 are ignored. \li Disable Partial Volume Effects: 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 Output Volume Fractions: Output a double image for each compartment. The voxel values correspond to the volume fraction of the respective compartment. Compartment Settings: 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 Stick: The “stick” model describes diffusion in an idealized cylinder with zero radius. Parameter: Diffusivity d \li Zeppelin: Cylindrically symmetric diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity d⊥ \li Tensor: Full diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity constants d⊥1 and d⊥2 \li Ball: Isotropic compartment. Parameter: Diffusivity d \li Astrosticks: 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 d. \li Dot: Isotropically restricted compartment. No parameter. For a detailed description of the single models, please refer to Panagiotaki et al. "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 T2 signal relaxation constant (in ms). Noise and Artifacts: \li Rician Noise: Add Rician noise with the specified variance to the signal. -\li Rician Spikes: Add signal spikes to the k-space signal resulting in stripe artifacts across the corresponding image slice. +\li Spikes: Add signal spikes to the k-space signal resulting in stripe artifacts across the corresponding image slice. +\li Aliasing: 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 N/2 Ghosts: 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 Distortions: 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 Motion Artifacts: 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 Eddy Currents: EXPERIMENTAL! This feature is currently being tested and might not yet behave as expected! -\li Gibbs Ringing: 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 Gibbs Ringing: 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 @@ qball.png tensor.png dwi.png dwiimport.png quantification.png reconodf.png recontensor.png texIntONIcon.png texIntOFFIcon.png vizControls.png Refresh_48.png QBallData24.png glyphsoff_C.png glyphsoff_S.png glyphsoff_T.png glyphson_C.png glyphson_S.png glyphson_T.png FiberBundle.png FiberBundleX.png connectomics/ConnectomicsNetwork.png rectangle.png circle.png polygon.png color24.gif color48.gif color64.gif crosshair.png paint2.png IVIM_48.png reset.png MapperEfx2D.png 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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 // 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 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 seriesUIDs(0); std::vector > 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 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 & 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 b_vals; double maxb = 0; for(unsigned int i=0; ibValue; if(maxb 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 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 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 <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 #include // Qmitk #include "QmitkFiberExtractionView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" // ITK #include #include #include #include #include #include #include #include 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(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(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(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(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(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(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(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(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(m_SelectedFB.front()->GetData()); geometry = fib->GetGeometry(); } else if (m_SelectedImage) geometry = m_SelectedImage->GetGeometry(); else return; itk::Vector 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 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; iInitializeByItk(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(node.GetPointer()->GetData()) && !dynamic_cast(node.GetPointer()->GetData())) { m_PlanarFigure = dynamic_cast(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 ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(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; cSetOutputDirection( 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 GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { // typedef typename itk::BSplineInterpolateImageFunction // InterpolatorType; typedef typename itk::LinearInterpolateImageFunction 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 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 itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator 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 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 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("mandatory"); m_Controls->m_PfLabel->setText("needed for extraction"); for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { m_Controls->m_FibLabel->setText(node->GetName().c_str()); m_SelectedFB.push_back(node); } else if (dynamic_cast(node->GetData())) { m_Controls->m_PfLabel->setText(node->GetName().c_str()); m_SelectedPF.push_back(node); } else if (dynamic_cast(node->GetData())) { m_SelectedImage = dynamic_cast(node->GetData()); bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_MaskImageNode = node; m_Controls->m_PfLabel->setText(node->GetName().c_str()); } } else if (dynamic_cast(node->GetData())) { m_Controls->m_PfLabel->setText(node->GetName().c_str()); m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } } + + if (m_SelectedFB.empty()) + { + int maxLayer = 0; + itk::VectorContainer::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll(); + for (unsigned int i=0; iSize(); i++) + if (dynamic_cast(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::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll(); +// for (unsigned int i=0; iSize(); i++) +// if (dynamic_cast(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(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { - figureInteractor = dynamic_cast(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(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(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(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 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.at(i)->GetData()); mitk::PlanarFigure::Pointer roi = dynamic_cast (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( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCAnd->SetGeometry2D(currentGeometry2D); PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( 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( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCOr->SetGeometry2D(currentGeometry2D); PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( 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( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCNot->SetGeometry2D(currentGeometry2D); PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( 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; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(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; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(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; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(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(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; iAddBundle(dynamic_cast(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(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; iSubtractBundle(dynamic_cast(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(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(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 #include "ui_QmitkFiberExtractionViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \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 nodes ); Ui::QmitkFiberExtractionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; /** Connection from VTK to ITK */ template 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 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 m_SelectedFB; ///< selected fiber bundle nodes std::vector m_SelectedPF; ///< selected planar figure nodes std::vector 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 // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include -#include #include #include #include #include #include #include "usModuleRegistry.h" +#include +#include +#include #define _USE_MATH_DEFINES #include +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::Pointer mitkImage = mitk::DiffusionImage::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; kInitializeByItk(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::Pointer diffImg = dynamic_cast*>(m_ImageGenParametersBackup.parentNode->GetData()); + mitkImage = mitk::DiffusionImage::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::Pointer writer = NrrdDiffusionImageWriter::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 = "
"+statusText+"
"; + 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::Pointer isMitkImage = mitk::TNodePredicateDataType::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::Pointer dwi = dynamic_cast*>(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::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); m_ImageGenParameters.numGradients = 0; for (int i=0; iSize(); i++) { DiffusionSignalModel::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(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(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* rician = new mitk::RicianNoiseModel(); + 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* chiSquare = new mitk::ChiSquareNoiseModel(); + 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* rician = new mitk::RicianNoiseModel(); + 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* rician = new mitk::RicianNoiseModel(); + rician->SetNoiseVariance(noiseVariance); + m_ImageGenParameters.noiseModelShort = rician; + break; + } + case 1: + { + mitk::ChiSquareNoiseModel* chiSquare = new mitk::ChiSquareNoiseModel(); + chiSquare->SetDOF(noiseVariance/2); + m_ImageGenParameters.noiseModelShort = chiSquare; + break; + } + default: + { + mitk::RicianNoiseModel* rician = new mitk::RicianNoiseModel(); + 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(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("realtime")); m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("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("sampling")); m_Controls->m_TensionBox->setValue(v2.second.get("tension")); m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); m_Controls->m_BiasBox->setValue(v2.second.get("bias")); } if( v2.first == "rotation" ) { m_Controls->m_XrotBox->setValue(v2.second.get("x")); m_Controls->m_YrotBox->setValue(v2.second.get("y")); m_Controls->m_ZrotBox->setValue(v2.second.get("z")); } if( v2.first == "translation" ) { m_Controls->m_XtransBox->setValue(v2.second.get("x")); m_Controls->m_YtransBox->setValue(v2.second.get("y")); m_Controls->m_ZtransBox->setValue(v2.second.get("z")); } if( v2.first == "scale" ) { m_Controls->m_XscaleBox->setValue(v2.second.get("x")); m_Controls->m_YscaleBox->setValue(v2.second.get("y")); m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); } } } if( v1.first == "image" ) { m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); m_Controls->m_BvalueBox->setValue(v1.second.get("basic.bvalue")); m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); m_Controls->m_RepetitionsBox->setValue(v1.second.get("repetitions")); m_Controls->m_SignalScaleBox->setValue(v1.second.get("signalScale")); m_Controls->m_TEbox->setValue(v1.second.get("tEcho")); m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get("tLine")); m_Controls->m_T2starBox->setValue(v1.second.get("tInhom")); m_Controls->m_FiberRadius->setValue(v1.second.get("axonRadius")); m_Controls->m_InterpolationShrink->setValue(v1.second.get("interpolationShrink")); m_Controls->m_RelaxationBox->setChecked(v1.second.get("doSimulateRelaxation")); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get("doDisablePartialVolume")); m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); m_Controls->m_AddNoise->setChecked(v1.second.get("artifacts.addnoise")); + m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get("artifacts.noisedistribution")); m_Controls->m_NoiseLevel->setValue(v1.second.get("artifacts.noisevariance")); m_Controls->m_AddGhosts->setChecked(v1.second.get("artifacts.addghost")); m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.kspaceLineOffset")); m_Controls->m_AddAliasing->setChecked(v1.second.get("artifacts.addaliasing")); m_Controls->m_WrapBox->setValue(v1.second.get("artifacts.aliasingfactor")); m_Controls->m_AddDistortions->setChecked(v1.second.get("artifacts.distortions")); - m_Controls->m_AddSpikes->setChecked(v1.second.get("artifacts.addspikes")); m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.spikesnum")); m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.spikesscale")); m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.eddyStrength")); m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); + m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.doAddMotion")); + m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.randomMotion")); + m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.translation0")); + m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.translation1")); + m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.translation2")); + m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.rotation0")); + m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.rotation1")); + m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.rotation2")); m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get("compartment1.index")); m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get("compartment2.index")); m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get("compartment3.index")); m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get("compartment4.index")); - m_Controls->m_StickWidget1->SetD(v1.second.get("compartment1.stick.d")); m_Controls->m_StickWidget1->SetT2(v1.second.get("compartment1.stick.t2")); m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get("compartment1.zeppelin.d1")); m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get("compartment1.zeppelin.d2")); m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_Controls->m_TensorWidget1->SetD1(v1.second.get("compartment1.tensor.d1")); m_Controls->m_TensorWidget1->SetD2(v1.second.get("compartment1.tensor.d2")); m_Controls->m_TensorWidget1->SetD3(v1.second.get("compartment1.tensor.d3")); m_Controls->m_TensorWidget1->SetT2(v1.second.get("compartment1.tensor.t2")); m_Controls->m_StickWidget2->SetD(v1.second.get("compartment2.stick.d")); m_Controls->m_StickWidget2->SetT2(v1.second.get("compartment2.stick.t2")); m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get("compartment2.zeppelin.d1")); m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get("compartment2.zeppelin.d2")); m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_Controls->m_TensorWidget2->SetD1(v1.second.get("compartment2.tensor.d1")); m_Controls->m_TensorWidget2->SetD2(v1.second.get("compartment2.tensor.d2")); m_Controls->m_TensorWidget2->SetD3(v1.second.get("compartment2.tensor.d3")); m_Controls->m_TensorWidget2->SetT2(v1.second.get("compartment2.tensor.t2")); m_Controls->m_BallWidget1->SetD(v1.second.get("compartment3.ball.d")); m_Controls->m_BallWidget1->SetT2(v1.second.get("compartment3.ball.t2")); m_Controls->m_AstrosticksWidget1->SetD(v1.second.get("compartment3.astrosticks.d")); m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get("compartment3.astrosticks.t2")); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); m_Controls->m_DotWidget1->SetT2(v1.second.get("compartment3.dot.t2")); m_Controls->m_BallWidget2->SetD(v1.second.get("compartment4.ball.d")); m_Controls->m_BallWidget2->SetT2(v1.second.get("compartment4.ball.t2")); m_Controls->m_AstrosticksWidget2->SetD(v1.second.get("compartment4.astrosticks.d")); m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get("compartment4.astrosticks.t2")); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); m_Controls->m_DotWidget2->SetT2(v1.second.get("compartment4.dot.t2")); m_Controls->m_Comp4FractionBox->setValue(v1.second.get("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.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(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(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(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; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(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(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(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.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(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(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(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::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 theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i 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 nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(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(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 liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*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; iGetDerivations(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(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(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::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; iSetData( 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.at(i)->GetData())) - continue; - - m_SelectedDWI = m_SelectedImages.at(i); - UpdateImageParameters(); - - mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedImages.at(i)->GetData()); - - mitk::RicianNoiseModel 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::Pointer image = mitk::DiffusionImage::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( 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*>(imageNode->GetData())) return; - } - for (int i=0; i(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::Pointer image = mitk::DiffusionImage::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::Pointer diffImg = dynamic_cast*>(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; kInitializeByItk(volumeFractions.at(k).GetPointer()); - image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); +void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) +{ + mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(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; iGetDerivations(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(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*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(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(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.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::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(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*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(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(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::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*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("mandatory"); 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& 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("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; - bool isBinary = false; - node->GetPropertyValue("binary", isBinary); - if (isBinary) + mitk::Image::Pointer image = dynamic_cast(node->GetData()); + bool isbinary = false; + node->GetPropertyValue("binary", isbinary); + if (isbinary) { - m_TissueMask = dynamic_cast(node->GetData()); + mitk::CastToItkImage(image, m_ImageGenParameters.maskImage); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(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(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(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(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(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(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(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(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( 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::Pointer isPf = mitk::TNodePredicateDataType::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 #include #include #include "ui_QmitkFiberfoxViewControls.h" #include #include #include #include #include #include #include #include #include +#include #include #include #include #include #include +#include +#include +#include +#include /*! \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 ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > 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&); 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 imageSpacing; itk::Point imageOrigin; itk::Matrix 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 translation; + itk::Vector rotation; bool doSimulateRelaxation; bool doSimulateEddyCurrents; bool doDisablePartialVolume; + bool doAddMotion; + bool randomMotion; - mitk::RicianNoiseModel ricianNoiseModel; + mitk::DiffusionNoiseModel* noiseModel; + mitk::DiffusionNoiseModel* noiseModelShort; mitk::DiffusionSignalModel::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 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 m_StickModel1; mitk::StickModel m_StickModel2; mitk::TensorModel m_ZeppelinModel1; mitk::TensorModel m_ZeppelinModel2; mitk::TensorModel m_TensorModel1; mitk::TensorModel m_TensorModel2; // extra axonal compartment models mitk::BallModel m_BallModel1; mitk::BallModel m_BallModel2; mitk::AstroStickModel m_AstrosticksModel1; mitk::AstroStickModel m_AstrosticksModel2; mitk::DotModel m_DotModel1; mitk::DotModel 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 @@ QmitkFiberfoxViewControls 0 0 435 - 1792 + 2274 Form - - + + - Save Parameters + Load Parameters + + + + :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico - + 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); 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. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid + + + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico + Operations false Join Bundles + + + :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico + QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles + + + :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico + false Transform Selection + + + :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico + If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers + + + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico + QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation - + Data + + + + + + + + + + + + + Tissue Mask: + + + false + + + + + + + <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> + + + true + + + Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true - - + + - Tissue Mask: + Save path: false - - - - <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> + + + + QFrame::NoFrame - - true + + QFrame::Raised + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + - + + + + + + + ... + + + + - - + + - Image Settings + Noise and other Artifacts - - - + + + + + Qt::Horizontal + + + + + + + Add Noise + + + false + + + + + + + Add ringing artifacts occuring at strong edges in the image. + + + Add Gibbs Ringing + + + false + + + + + + + true + QFrame::NoFrame QFrame::Raised - + + + 6 + 0 0 0 0 - - 6 - - - + + - <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> + - - Simulate Signal Relaxation + + - - true + + - - - - - Repetitions: + Shrink FOV (%): + + + false - - + + - T2* relaxation time (in milliseconds). + Shrink FOV by this percentage. + + + 1 + + + 0.000000000000000 - 100.000000000000000 + 90.000000000000000 0.100000000000000 - 1.000000000000000 + 25.000000000000000 - - + + + + + + + Qt::Horizontal + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + - Fiber Radius: + Num. Spikes: - - + + - Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. - - - 0 - - - 1000 + The number of randomly occurring signal spikes. - 0 + 1 - + - TE in milliseconds - - - 1 - - - 10000 + Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. - 1 + 0.100000000000000 - 100 + 0.100000000000000 - - + + - Interpolation Shrink: + Scale: - - - - - - - - - - - - - Line Readout Time: - - - false + + + + + + + !!!EXPERIMENTAL!!! + + + Add Eddy Current Effects + + + false + + + + + + + Add Spikes + + + false + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Variance: - - + + - + Variance of selected noise distribution. - - + + 4 - - + + 0.000000000000000 - - <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> + + 100000.000000000000000 - - false + + 0.001000000000000 + + + 50.000000000000000 - - - - Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. - + + - Disable Partial Volume Effects - - - false + Distribution: - - + + - Output one image per compartment containing the corresponding volume fractions per voxel. - - - Output Volume Fractions - - - false + Noise distribution + + + Rician + + + + + Chi-squared + + - - + + + + + + + Add N/2 Ghosts + + + false + + + + + + + true + + + QFrame::NoFrame + + + QFrame::Raised + + + + 6 + + + 0 + + + 0 + + + 0 + + + 0 + + + - <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> + Frequency Map: false - + - Number of signal averages. Increase to reduce noise. - - - 1 - - - 100 - - - 1 - - - 1 + Select image specifying the frequency inhomogeneities (in Hz). - - + + + + + + + Qt::Horizontal + + + + + + + Qt::Horizontal + + + + + + + Qt::Horizontal + + + + + + + true + + + QFrame::NoFrame + + + QFrame::Raised + + + + QFormLayout::AllNonFixedFieldsGrow + + + 6 + + + 0 + + + 6 + + + 0 + + + 0 + + + - Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). - - - 1 + Toggle between random movement and linear movement. - - 10000 - - - 1 + + Randomize motion - - 50 + + true - - - - TE in milliseconds - - - 1 - - - 10000 - - - 1 - - - 100 - - - - - - - <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> - - - 0 - - - 10000 - - - 0 + + + + Rotation + + + 0 + + + 9 + + + 0 + + + 0 + + + + + + + + + + + + + + Degree: + + + false + + + + + + + + + + + + + + + + x + + + false + + + + + + + + + + + + + + + + Axis: + + + false + + + + + + + Maximum rotation around x-axis. + + + 1 + + + 360.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum rotation around z-axis. + + + 1 + + + 360.000000000000000 + + + 1.000000000000000 + + + 15.000000000000000 + + + + + + + + + + + + + + + + y + + + false + + + + + + + + + + + + + + + + z + + + false + + + + + + + Maximum rotation around y-axis. + + + 1 + + + 360.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + - - - - Signal Scale: + + + + Translation + + + 0 + + + 0 + + + 0 + + + + + + + + + + + + + + Distance: + + + false + + + + + + + + + + + + + + + + x + + + false + + + + + + + + + + + + + + + + y + + + false + + + + + + + + + + + + + + + + Axis: + + + false + + + + + + + + + + + + + + + + z + + + false + + + + + + + Maximum translation along x-axis. + + + 1 + + + 1000.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum translation along y-axis. + + + 1 + + + 1000.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum translation along z-axis. + + + 1 + + + 1000.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + - - - - color: rgb(255, 0, 0); - + + - Using geometry of selected image! + Add Motion Artifacts + + + false - - - - color: rgb(255, 0, 0); + + + + Add Distortions + + + false + + + + - Using gradients of selected DWI! + Add Aliasing + + + false - - + + + + true + QFrame::NoFrame QFrame::Raised - + + + 6 + 0 0 0 0 - - - - 3 - - - 0.100000000000000 - - - 50.000000000000000 + + + + - - 0.100000000000000 + + - - 2.000000000000000 + + - - - - - Image Spacing: - - - - - - - 3 - - - 0.100000000000000 - - - 50.000000000000000 - - - 0.100000000000000 + K-Space Line Offset: - - 2.000000000000000 + + false - - + + + + A larger offset increases the inensity of the ghost image. + 3 - - 0.100000000000000 - - 50.000000000000000 + 1.000000000000000 - 0.100000000000000 + 0.010000000000000 - 2.000000000000000 - - - - - - - Image Dimensions: + 0.250000000000000 - - + + + + + + + true + + + QFrame::NoFrame + + + QFrame::Raised + + + + QFormLayout::AllNonFixedFieldsGrow + + + 6 + + + 0 + + + 0 + + + 0 + + + 0 + + + - Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + - - 1 + + - - 1000 + + - - 1 + + Magnitude: - - 11 + + false - - + + - Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). - - 1 + + 5 - 1000 + 1000.000000000000000 - 1 + 0.001000000000000 - 11 + 0.005000000000000 - - - - Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. - - - 1 - - - 1000 - - - 1 + + + + color: rgb(255, 0, 0); - - 3 + + Experimental! - + + + Qt::Horizontal + + + + + + + Qt::Horizontal + + + + + + + + + + Image Settings + + + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - + 6 + + + + <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> + + + Simulate Signal Relaxation + + + true + + + - + - Gradient Directions: + Repetitions: - - + + - Number of gradient directions distributed over the half sphere. + T2* relaxation time (in milliseconds). + + + 100.000000000000000 + + + 0.100000000000000 + + + 1.000000000000000 + + + + + + + Fiber Radius: + + + + + + + Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. + + + 0 + + + 1000 + + + 0 + + + + + + + TE in milliseconds 1 10000 1 - 30 + 100 - - + + + + Interpolation Shrink: + + + + + - b-Value: + Line Readout Time: false - - + + - b-value in mm/s² - - - 0 - - - 10000 + - - 100 + + - - 1000 + + - - - - - - - - - Advanced Options - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - Noise and other Artifacts - - - - - - Add Distortions - - - false - - - - - - - Add Rician Noise - - - false - - - - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - - Variance: + <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> + + + false - - + + - Variance of Rician noise model. - - - 4 - - - 0.000000000000000 - - - 100000.000000000000000 + Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. - - 0.001000000000000 + + Disable Partial Volume Effects - - 50.000000000000000 + + false - - - - - - - Add ringing artifacts occuring at strong edges in the image. - - - Add Gibbs Ringing - - - false - - - - - - - true - - - QFrame::NoFrame - - - QFrame::Raised - - - - 6 - - - 0 - - - 0 - - - 0 - - - 0 - - - + + + + Output one image per compartment containing the corresponding volume fractions per voxel. + + + Output Volume Fractions + + + false + + + + + - K-Space Line Offset: + <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> false - + - A larger offset increases the inensity of the ghost image. + Number of signal averages. Increase to reduce noise. - - 3 + + 1 - 1.000000000000000 + 100 - 0.010000000000000 + 1 - 0.250000000000000 + 1 - - - - - - - !!!EXPERIMENTAL!!! - - - Add Eddy Current Effects - - - false - - - - - - - true - - - QFrame::NoFrame - - - QFrame::Raised - - - - 6 - - - 0 - - - 0 - - - 0 - - - 0 - - - + + - + Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). - - + + 1 - - + + 10000 - - Frequency Map: + + 1 - - false + + 50 - - + + - Select image specifying the frequency inhomogeneities (in Hz). + TE in milliseconds - - - - - - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Num. Spikes: + + 1 - - - - - - The number of randomly occurring signal spikes. + + 10000 - + 1 + + 100 + - - + + - Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. + <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> - - 0.100000000000000 + + 0 + + + 10000 - 0.100000000000000 + 0 - + - Scale: + Signal Scale: - - - Add Spikes + + + color: rgb(255, 0, 0); - - false + + Using geometry of selected image! - - - Add N/2 Ghosts + + + color: rgb(255, 0, 0); - - false + + Using gradients of selected DWI! - - - - true - + + QFrame::NoFrame QFrame::Raised - - - QFormLayout::AllNonFixedFieldsGrow - - - 6 - + 0 0 0 0 - - - - + + + + 3 + + + 0.100000000000000 + + + 50.000000000000000 + + + 0.100000000000000 + + + 2.000000000000000 + + + + + + + Image Spacing: + + + + + + + 3 + + + 0.100000000000000 + + + 50.000000000000000 + + + 0.100000000000000 + + + 2.000000000000000 + + + + + + + 3 + + + 0.100000000000000 + + + 50.000000000000000 - - + + 0.100000000000000 - - + + 2.000000000000000 + + + + - Magnitude: + Image Dimensions: - - false + + + + + + Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + + + 1 + + + 1000 + + + 1 + + + 11 - - + + - Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). + Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. - - 5 + + 1 - 1000.000000000000000 + 1000 - 0.001000000000000 + 1 - 0.005000000000000 + 11 - - - - color: rgb(255, 0, 0); + + + + Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. - - Experimental! + + 1 + + + 1000 + + + 1 + + + 3 - - - - Add Aliasing - - - false - - - - - - - true - + + QFrame::NoFrame QFrame::Raised - - - 6 - + 0 0 0 0 + + 6 + - + + + Gradient Directions: + + + + + + + Number of gradient directions distributed over the half sphere. + + + 1 + + + 10000 + + + 1 + + + 30 + + + + + - Undersampling: + b-Value: false - - + + - Shrink FOV by this factor. - - - 3 + b-value in mm/s² - 1.000000000000000 + 0 - 10.000000000000000 + 10000 - 0.100000000000000 + 100 - 1.300000000000000 + 1000 + + + + Advanced Options + + + - - + + + + true + + + Start DWI generation from selected fiber bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. + + + Start Simulation + + + + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico + + + + + - Inter-axonal Compartment + Intra-axonal Compartment - - - - - - - + - + Select signal model for intra-axonal compartment. - - - -- - - Stick Model Zeppelin Model Tensor Model + + + - + + + + - + + + + true + + + Stop current simulation. + + + Abort Simulation + + + + :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico + + + + Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Weighting factor between the two extra-axonal compartments. 1.000000000000000 0.100000000000000 0.300000000000000 Compartment Fraction: - - - - true - - - Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. + + + + Qt::Vertical - - Generate Image + + + 20 + 40 + - + - - + + - Intra-axonal Compartment + Inter-axonal Compartment - + + + + + + + - + Select signal model for intra-axonal compartment. + + + -- + + Stick Model Zeppelin Model Tensor Model - - - - - - - + + + + + + 8 + + + + true + + + - + - Load Parameters + Save Parameters + + + + :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox + m_AddAliasing + m_WrapBox m_AddDistortions m_FrequencyMapBox + m_AddMotion + m_RandomMotion + m_MaxRotationBoxX + m_MaxRotationBoxY + m_MaxRotationBoxZ + m_MaxTranslationBoxX + m_MaxTranslationBoxY + m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget 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 #include // Blueberry #include #include // Qmitk #include "QmitkOdfMaximaExtractionView.h" // MITK #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include // Qt #include 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("mandatory"); 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("optional"); } } template 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(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.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; iSize(); 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(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; iSize(); 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(m_TensorImageNodes.at(0)->GetData()); ItkTensorImage::Pointer itkImage = ItkTensorImage::New(); CastToItkImage(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(m_BinaryImageNodes.at(0)->GetData()); CastToItkImage(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]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 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(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(m_BinaryImageNodes.at(0)->GetData()); CastToItkImage(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; iSize(); 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]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(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(m_BinaryImageNodes.at(0)->GetData()); CastToItkImage(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; iSize(); 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]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 nodes ) { m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->m_DwiFibLabel->setText("mandatory"); m_Controls->m_MaskLabel->setText("optional"); m_BinaryImageNodes.clear(); m_ImageNodes.clear(); m_TensorImageNodes.clear(); // iterate all selected objects, adjust warning visibility for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_TensorImageNodes.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { bool isBinary = false; node->GetPropertyValue("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 #include #include // Qmitk #include "QmitkStreamlineTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include #include +#include +#include +#include +#include +#include // VTK #include #include #include #include #include #include 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::Pointer isImagePredicate = mitk::TNodePredicateDataType::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 nodes ) { - m_TensorImageNode = NULL; - m_TensorImage = NULL; + m_TensorImageNodes.clear(); + m_TensorImages.clear(); m_SeedRoi = NULL; m_MaskImage = NULL; m_Controls->m_TensorImageLabel->setText("mandatory"); m_Controls->m_RoiImageLabel->setText("optional"); m_Controls->m_MaskImageLabel->setText("optional"); for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) ) { - m_TensorImageNode = node; - m_TensorImage = dynamic_cast(node->GetData()); - m_Controls->m_TensorImageLabel->setText(node->GetName().c_str()); + m_TensorImageNodes.push_back(node); + m_TensorImages.push_back(dynamic_cast(node->GetData())); } else { bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary && m_SeedRoi.IsNull()) { m_SeedRoi = dynamic_cast(node->GetData()); m_Controls->m_RoiImageLabel->setText(node->GetName().c_str()); } else if (isBinary) { m_MaskImage = dynamic_cast(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, 3> TensorImageType; typedef mitk::ImageToItk CastType; typedef mitk::ImageToItk 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::Pointer floatCast = mitk::ImageToItk::New(); + floatCast->SetInput(dynamic_cast(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(m_SeedRoi, mask); filter->SetSeedImage(mask); } if (m_MaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(m_MaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer 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 #include "ui_QmitkStreamlineTrackingViewControls.h" #include #include #include #include #include /*! \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 nodes ); - Ui::QmitkStreamlineTrackingViewControls* m_Controls; - QmitkStdMultiWidget* m_MultiWidget; + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector 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 @@ QmitkStreamlineTrackingViewControls 0 0 - 368 - 477 + 382 + 538 0 0 QmitkTemplate 3 3 0 Qt::Vertical QSizePolicy::Expanding 20 220 false Start Tractography Parameters f: 1 g: 0 Qt::Horizontal QSizePolicy::Fixed 200 0 Step Size: auto Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0). 0 100 100 Qt::Horizontal Stepsize in mm (auto = 0.1*minimal spacing) 0 100 0 Qt::Horizontal FA Threshold: 0.2 Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking) 0 100 0 Qt::Horizontal Seeds per Voxel: 1 Number of tracts started in each voxel of the seed ROI. 1 100 Qt::Horizontal Default is nearest neighbor interpolation. Enable trilinear interpolation false Minimally allowed curcature radius (in mm, interpolated auto = 0.5 minimal spacing, noninterpolated auto = 0.1 minimal spacing) -1 50 -1 Qt::Horizontal Min. Tract Length: 40mm Fractional Anisotropy Threshold 0 100 20 Qt::Horizontal Minimum tract length in mm. 0 500 40 Qt::Horizontal Min. Curvature Radius: auto Resample fibers to 0.5*voxel size (recommended for small step sizes to avoid memory issues). Resample fibers false Please Select Input Data + + + + <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> + + + true + + + + + + + + - + + + + <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true - - + + - Binary seed ROI. If not specified, the whole image area is seeded. + Only track insida mask area. - Seed ROI: + Mask Image: - - + + - Input DTI + Binary seed ROI. If not specified, the whole image area is seeded. - Tensor Image: + Seed ROI: - - + + - <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> + <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true - - + + - Only track insida mask area. + Input DTI - Mask Image: + Tensor Image: - - + + + + Check to use selected FA image instead of internally calculated one. Recommended for multi-tensor tractography. + - <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> + FA image - - true + + false + + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+ +