diff --git a/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx b/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx
index b6010dd2b6..5f154bc14d 100644
--- a/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx
+++ b/Modules/DiffusionImaging/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx
@@ -1,253 +1,254 @@
/*===================================================================
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.
===================================================================*/
/*=========================================================================
Program: Tensor ToolKit - TTK
Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $
Language: C++
Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
Version: $Revision: 68 $
Copyright (c) INRIA 2010. All rights reserved.
See LICENSE.txt 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 _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_
#define _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_
#endif
#define _USE_MATH_DEFINES
#include "itkElectrostaticRepulsionDiffusionGradientReductionFilter.h"
#include <math.h>
#include <time.h>
#include <itkImageRegionIterator.h>
#include <itkImageRegion.h>
namespace itk
{
template <class TInputScalarType, class TOutputScalarType>
ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
::ElectrostaticRepulsionDiffusionGradientReductionFilter()
{
this->SetNumberOfRequiredInputs( 1 );
}
template <class TInputScalarType, class TOutputScalarType>
double
ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
::Costs()
{
double costs = 2*M_PI;
for (IndicesVector::iterator it = m_UsedGradientIndices.begin(); it!=m_UsedGradientIndices.end(); ++it)
{
for (IndicesVector::iterator it2 = m_UsedGradientIndices.begin(); it2!=m_UsedGradientIndices.end(); ++it2)
if (it != it2)
{
vnl_vector_fixed<double,3> v1 = m_OriginalGradientDirections->at(*it);
vnl_vector_fixed<double,3> v2 = m_OriginalGradientDirections->at(*it2);
v1.normalize(); v2.normalize();
double temp = dot_product(v1,v2);
if (temp>1)
temp = 1;
else if (temp<-1)
temp = -1;
double angle = acos(temp);
if (angle<costs)
costs = angle;
temp = dot_product(-v1,v2);
if (temp>1)
temp = 1;
else if (temp<-1)
temp = -1;
angle = acos(temp);
if (angle<costs)
costs = angle;
}
}
return costs;
}
template <class TInputScalarType, class TOutputScalarType>
void
ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
::GenerateData()
{
unsigned int randSeed = time(NULL);
if(m_InputBValueMap.empty())
{
// if no InputMap is set, do the same for each shell
m_InputBValueMap = m_OriginalBValueMap;
}
if(m_InputBValueMap.find(0) != m_InputBValueMap.end())
{
//delete b0 from input BValueMap
m_InputBValueMap.erase(0);
}
BValueMap manipulatedMap = m_OriginalBValueMap;
int shellCounter = 0;
for(BValueMap::iterator it = m_InputBValueMap.begin(); it != m_InputBValueMap.end(); it++ )
{
srand(randSeed);
// initialize index vectors
m_UsedGradientIndices.clear();
m_UnusedGradientIndices.clear();
if ( it->second.size() <= m_NumGradientDirections[shellCounter] )
{
itkWarningMacro( << "current directions: " << it->second.size() << " wanted directions: " << m_NumGradientDirections[shellCounter]);
m_NumGradientDirections[shellCounter] = it->second.size();
shellCounter++;
continue;
}
MITK_INFO << "Shell number: " << shellCounter;
int c=0;
for (int i=0; i<it->second.size(); i++)
{
if (c<m_NumGradientDirections[shellCounter])
m_UsedGradientIndices.push_back(it->second.at(i));
else
m_UnusedGradientIndices.push_back(it->second.at(i));
c++;
}
double minAngle = Costs();
double newMinAngle = 0;
MITK_INFO << "minimum angle: " << 180*minAngle/M_PI;
int stagnationCount = 0;
int rejectionCount = 0;
int maxRejections = 10000;// m_NumGradientDirections[shellCounter] * 1000;
int iUsed = 0;
- while ( stagnationCount<1000 && rejectionCount<maxRejections )
- {
- // make proposal for new gradient configuration by randomly removing one of the currently used directions and instead adding one of the unused directions
- //int iUsed = rand() % m_UsedGradientIndices.size();
- int iUnUsed = rand() % m_UnusedGradientIndices.size();
- int vUsed = m_UsedGradientIndices.at(iUsed);
- int vUnUsed = m_UnusedGradientIndices.at(iUnUsed);
- m_UsedGradientIndices.at(iUsed) = vUnUsed;
- m_UnusedGradientIndices.at(iUnUsed) = vUsed;
-
- newMinAngle = Costs(); // calculate costs of proposed configuration
- if (newMinAngle > minAngle) // accept or reject proposal
+ if (m_UsedGradientIndices.size()>0)
+ while ( stagnationCount<1000 && rejectionCount<maxRejections )
{
- MITK_INFO << "minimum angle: " << 180*newMinAngle/M_PI;
-
- if ( (newMinAngle-minAngle)<0.01 )
- stagnationCount++;
+ // make proposal for new gradient configuration by randomly removing one of the currently used directions and instead adding one of the unused directions
+ //int iUsed = rand() % m_UsedGradientIndices.size();
+ int iUnUsed = rand() % m_UnusedGradientIndices.size();
+ int vUsed = m_UsedGradientIndices.at(iUsed);
+ int vUnUsed = m_UnusedGradientIndices.at(iUnUsed);
+ m_UsedGradientIndices.at(iUsed) = vUnUsed;
+ m_UnusedGradientIndices.at(iUnUsed) = vUsed;
+
+ newMinAngle = Costs(); // calculate costs of proposed configuration
+ if (newMinAngle > minAngle) // accept or reject proposal
+ {
+ MITK_INFO << "minimum angle: " << 180*newMinAngle/M_PI;
+
+ if ( (newMinAngle-minAngle)<0.01 )
+ stagnationCount++;
+ else
+ stagnationCount = 0;
+
+ minAngle = newMinAngle;
+ rejectionCount = 0;
+ }
else
- stagnationCount = 0;
-
- minAngle = newMinAngle;
- rejectionCount = 0;
+ {
+ rejectionCount++;
+ m_UsedGradientIndices.at(iUsed) = vUsed;
+ m_UnusedGradientIndices.at(iUnUsed) = vUnUsed;
+ }
+ iUsed++;
+ iUsed = iUsed % m_UsedGradientIndices.size();
}
- else
- {
- rejectionCount++;
- m_UsedGradientIndices.at(iUsed) = vUsed;
- m_UnusedGradientIndices.at(iUnUsed) = vUnUsed;
- }
- iUsed++;
- iUsed = iUsed % m_UsedGradientIndices.size();
- }
manipulatedMap[it->first] = m_UsedGradientIndices;
shellCounter++;
}
int vecLength = 0 ;
for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++)
vecLength += it->second.size();
// initialize output image
typename OutputImageType::Pointer outImage = OutputImageType::New();
outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing
outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin
outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction
outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
outImage->SetVectorLength( vecLength ); // Set the vector length
outImage->Allocate();
itk::ImageRegionIterator< OutputImageType > newIt(outImage, outImage->GetLargestPossibleRegion());
newIt.GoToBegin();
typename InputImageType::Pointer inImage = const_cast<InputImageType*>(this->GetInput(0));
itk::ImageRegionIterator< InputImageType > oldIt(inImage, inImage->GetLargestPossibleRegion());
oldIt.GoToBegin();
// initial new value of voxel
OutputPixelType newVec;
newVec.SetSize( vecLength );
newVec.AllocateElements( vecLength );
// generate new pixel values
while(!newIt.IsAtEnd())
{
// init new vector with zeros
newVec.Fill(0.0);
InputPixelType oldVec = oldIt.Get();
int index = 0;
for(BValueMap::iterator it=manipulatedMap.begin(); it!=manipulatedMap.end(); it++)
for(int j=0; j<it->second.size(); j++)
{
newVec[index] = oldVec[it->second.at(j)];
index++;
}
newIt.Set(newVec);
++newIt;
++oldIt;
}
// set new gradient directions
m_GradientDirections = GradientDirectionContainerType::New();
int index = 0;
for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++)
for(int j = 0; j < it->second.size(); j++)
{
m_GradientDirections->InsertElement(index, m_OriginalGradientDirections->at(it->second.at(j)));
index++;
}
this->SetNumberOfRequiredOutputs (1);
this->SetNthOutput (0, outImage);
MITK_INFO << "...done";
}
} // end of namespace
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp
index 1f2e3b2634..17d080956d 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp
@@ -1,520 +1,521 @@
/*===================================================================
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 MBILOG_ENABLE_DEBUG
#include "QmitkPreprocessingView.h"
#include "mitkDiffusionImagingConfigure.h"
// qt includes
#include <QMessageBox>
// itk includes
#include "itkTimeProbe.h"
#include "itkB0ImageExtractionImageFilter.h"
#include "itkB0ImageExtractionToSeparateImageFilter.h"
#include "itkBrainMaskExtractionImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkVectorContainer.h"
#include <itkElectrostaticRepulsionDiffusionGradientReductionFilter.h>
// mitk includes
#include "QmitkDataStorageComboBox.h"
#include "QmitkStdMultiWidget.h"
#include "mitkProgressBar.h"
#include "mitkStatusBar.h"
#include "mitkNodePredicateDataType.h"
#include "mitkProperties.h"
#include "mitkVtkResliceInterpolationProperty.h"
#include "mitkLookupTable.h"
#include "mitkLookupTableProperty.h"
#include "mitkTransferFunction.h"
#include "mitkTransferFunctionProperty.h"
#include "mitkDataNodeObject.h"
#include "mitkOdfNormalizationMethodProperty.h"
#include "mitkOdfScaleByProperty.h"
#include <mitkPointSet.h>
#include <QTableWidgetItem>
#include <QTableWidget>
const std::string QmitkPreprocessingView::VIEW_ID =
"org.mitk.views.preprocessing";
#define DI_INFO MITK_INFO("DiffusionImaging")
typedef float TTensorPixelType;
QmitkPreprocessingView::QmitkPreprocessingView()
: QmitkFunctionality(),
m_Controls(NULL),
m_MultiWidget(NULL),
m_DiffusionImage(NULL)
{
}
QmitkPreprocessingView::QmitkPreprocessingView(const QmitkPreprocessingView& other)
{
Q_UNUSED(other)
throw std::runtime_error("Copy constructor not implemented");
}
QmitkPreprocessingView::~QmitkPreprocessingView()
{
}
void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent)
{
if (!m_Controls)
{
// create GUI widgets
m_Controls = new Ui::QmitkPreprocessingViewControls;
m_Controls->setupUi(parent);
this->CreateConnections();
m_Controls->m_MeasurementFrameTable->horizontalHeader()->setResizeMode(QHeaderView::Stretch);
m_Controls->m_MeasurementFrameTable->verticalHeader()->setResizeMode(QHeaderView::Stretch);
}
}
void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
{
m_MultiWidget = &stdMultiWidget;
}
void QmitkPreprocessingView::StdMultiWidgetNotAvailable()
{
m_MultiWidget = NULL;
}
void QmitkPreprocessingView::CreateConnections()
{
if ( m_Controls )
{
+ m_Controls->m_ReductionFrame->setLayout(new QGridLayout);
connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) );
connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) );
connect( (QObject*)(m_Controls->m_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) );
connect( (QObject*)(m_Controls->m_ModifyMeasurementFrame), SIGNAL(clicked()), this, SLOT(DoApplyMesurementFrame()) );
connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) );
connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) );
connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) );
}
}
void QmitkPreprocessingView::OnSelectionChanged( std::vector<mitk::DataNode*> nodes )
{
bool foundDwiVolume = false;
m_DiffusionImage = NULL;
m_SelectedDiffusionNodes.clear();
// iterate selection
for( std::vector<mitk::DataNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it )
{
mitk::DataNode::Pointer node = *it;
if( node.IsNotNull() && dynamic_cast<mitk::DiffusionImage<short>*>(node->GetData()) )
{
foundDwiVolume = true;
m_DiffusionImage = dynamic_cast<mitk::DiffusionImage<DiffusionPixelType>*>(node->GetData());
m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str());
m_SelectedDiffusionNodes.push_back(node);
}
}
m_Controls->m_ButtonBrainMask->setEnabled(foundDwiVolume);
m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume);
m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume);
m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume);
m_Controls->m_ModifyMeasurementFrame->setEnabled(foundDwiVolume);
m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume);
m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume);
m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume);
m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume);
foreach(QCheckBox * box, m_ReduceGradientCheckboxes)
{
m_Controls->m_ReductionFrame->layout()->removeWidget(box);
delete box;
}
foreach(QSpinBox * box, m_ReduceGradientSpinboxes)
{
m_Controls->m_ReductionFrame->layout()->removeWidget(box);
delete box;
}
m_ReduceGradientCheckboxes.clear();
m_ReduceGradientSpinboxes.clear();
if (foundDwiVolume)
{
vnl_matrix_fixed< double, 3, 3 > mf = m_DiffusionImage->GetMeasurementFrame();
for (int r=0; r<3; r++)
for (int c=0; c<3; c++)
{
QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c);
delete item;
item = new QTableWidgetItem();
item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter);
item->setText(QString::number(mf.get(r,c)));
m_Controls->m_MeasurementFrameTable->setItem(r,c,item);
}
typedef mitk::DiffusionImage<short*>::BValueMap BValueMap;
typedef mitk::DiffusionImage<short*>::BValueMap::iterator BValueMapIterator;
BValueMap bValMap = m_DiffusionImage->GetB_ValueMap();
BValueMapIterator it = bValMap.begin();
m_Controls->m_BvalueTable->clear();
m_Controls->m_BvalueTable->setRowCount(bValMap.size() );
QStringList headerList;
headerList << "b-Value" << "Number of gradients";
m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList);
QCheckBox* checkBox;
QSpinBox* spinBox;
int i = 0 ;
for(;it != bValMap.end(); it++)
{
m_Controls->m_BvalueTable->setItem(i,0,new QTableWidgetItem(QString::number(it->first)));
m_Controls->m_BvalueTable->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size())));
// Reduce Gradients GUI adaption
if(it->first != 0 && bValMap.size() > 1){
checkBox = new QCheckBox(QString::number(it->first) + " with " + QString::number(it->second.size()) + " directions");
checkBox->setEnabled(true);
checkBox->setChecked(true);
checkBox->setCheckable(true);
m_ReduceGradientCheckboxes.push_back(checkBox);
m_Controls->m_ReductionFrame->layout()->addWidget(checkBox);
spinBox = new QSpinBox();
spinBox->setValue(std::ceil((float)it->second.size()/2));
spinBox->setMaximum(it->second.size());
spinBox->setMinimum(0);
m_ReduceGradientSpinboxes.push_back(spinBox);
m_Controls->m_ReductionFrame->layout()->addWidget(spinBox);
}
i++;
}
}
else
{
for (int r=0; r<3; r++)
for (int c=0; c<3; c++)
{
QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c);
delete item;
item = new QTableWidgetItem();
m_Controls->m_MeasurementFrameTable->setItem(r,c,item);
}
m_Controls->m_BvalueTable->clear();
m_Controls->m_BvalueTable->setRowCount(1);
QStringList headerList;
headerList << "b-Value" << "Number of gradients";
m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList);
m_Controls->m_BvalueTable->setItem(0,0,new QTableWidgetItem("-"));
m_Controls->m_BvalueTable->setItem(0,1,new QTableWidgetItem("-"));
m_Controls->m_DiffusionImageLabel->setText("-");
}
}
void QmitkPreprocessingView::Activated()
{
QmitkFunctionality::Activated();
}
void QmitkPreprocessingView::Deactivated()
{
QmitkFunctionality::Deactivated();
}
void QmitkPreprocessingView::DoHalfSphereGradientDirections()
{
GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections();
for (int j=0; j<gradientContainer->Size(); j++)
if (gradientContainer->at(j)[0]<0)
gradientContainer->at(j) = -gradientContainer->at(j);
m_DiffusionImage->SetDirections(gradientContainer);
}
void QmitkPreprocessingView::DoApplyMesurementFrame()
{
if (m_DiffusionImage.IsNull())
return;
vnl_matrix_fixed< double, 3, 3 > mf;
for (int r=0; r<3; r++)
for (int c=0; c<3; c++)
{
QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c);
if (!item)
return;
mf[r][c] = item->text().toDouble();
}
m_DiffusionImage->SetMeasurementFrame(mf);
}
void QmitkPreprocessingView::DoShowGradientDirections()
{
if (m_DiffusionImage.IsNull())
return;
GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections();
mitk::PointSet::Pointer pointset = mitk::PointSet::New();
for (int j=0; j<gradientContainer->Size(); j++)
{
mitk::Point3D p;
vnl_vector_fixed< double, 3 > v = gradientContainer->at(j);
if (v.magnitude()>mitk::eps)
{
p[0] = v[0]*100;
p[1] = v[1]*100;
p[2] = v[2]*100;
pointset->InsertPoint(j, p);
}
}
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(pointset);
QString name = m_SelectedDiffusionNodes.front()->GetName().c_str();
name += "_GradientDirections";
node->SetName(name.toStdString().c_str());
node->SetProperty("pointsize", mitk::FloatProperty::New(2.5));
node->SetProperty("color", mitk::ColorProperty::New(1,0,0));
GetDefaultDataStorage()->Add(node);
}
void QmitkPreprocessingView::DoReduceGradientDirections()
{
if (m_DiffusionImage.IsNull())
return;
typedef mitk::DiffusionImage<DiffusionPixelType> DiffusionImageType;
typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
typedef DiffusionImageType::BValueMap BValueMap;
// GetShellSelection from GUI
BValueMap shellSlectionMap;
BValueMap originalShellMap = m_DiffusionImage->GetB_ValueMap();
std::vector<int> newNumGradientDirections;
int shellCounter = 0;
foreach(QCheckBox * box , m_ReduceGradientCheckboxes)
{
if(box->isChecked())
{
double BValue = (box->text().split(' ')).at(0).toDouble();
shellSlectionMap[BValue] = originalShellMap[BValue];
newNumGradientDirections.push_back(m_ReduceGradientSpinboxes.at(shellCounter)->value());
}
shellCounter++;
}
GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections();
FilterType::Pointer filter = FilterType::New();
filter->SetInput(m_DiffusionImage->GetVectorImage());
filter->SetOriginalGradientDirections(gradientContainer);
filter->SetNumGradientDirections(newNumGradientDirections);
filter->SetOriginalBValueMap(originalShellMap);
filter->SetShellSelectionBValueMap(shellSlectionMap);
filter->Update();
DiffusionImageType::Pointer image = DiffusionImageType::New();
image->SetVectorImage( filter->GetOutput() );
image->SetB_Value(m_DiffusionImage->GetB_Value());
image->SetDirections(filter->GetGradientDirections());
image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame());
image->InitializeFromVectorImage();
mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
imageNode->SetData( image );
QString name = m_SelectedDiffusionNodes.front()->GetName().c_str();
foreach(QSpinBox* box, m_ReduceGradientSpinboxes)
{
name += "_";
name += QString::number(box->value());
}
imageNode->SetName(name.toStdString().c_str());
GetDefaultDataStorage()->Add(imageNode);
}
void QmitkPreprocessingView::ExtractB0()
{
typedef mitk::DiffusionImage<DiffusionPixelType> DiffusionImageType;
typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType;
int nrFiles = m_SelectedDiffusionNodes.size();
if (!nrFiles) return;
// call the extraction withou averaging if the check-box is checked
if( this->m_Controls->m_CheckExtractAll->isChecked() )
{
DoExtractBOWithoutAveraging();
return;
}
mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
DiffusionImageType* vols =
static_cast<DiffusionImageType*>(
(*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
// Extract image using found index
typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vols->GetVectorImage());
filter->SetDirections(vols->GetDirections());
filter->Update();
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( filter->GetOutput() );
mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( mitkImage );
node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0"));
GetDefaultDataStorage()->Add(node);
++itemiter;
}
}
void QmitkPreprocessingView::DoExtractBOWithoutAveraging()
{
// typedefs
typedef mitk::DiffusionImage<DiffusionPixelType> DiffusionImageType;
typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType;
typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType;
// check number of selected objects, return if empty
int nrFiles = m_SelectedDiffusionNodes.size();
if (!nrFiles)
return;
mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() );
while ( itemiter != itemiterend ) // for all items
{
DiffusionImageType* vols =
static_cast<DiffusionImageType*>(
(*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
// Extract image using found index
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vols->GetVectorImage());
filter->SetDirections(vols->GetDirections());
filter->Update();
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( filter->GetOutput() );
mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( mitkImage );
node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0_ALL"));
GetDefaultDataStorage()->Add(node);
++itemiter;
}
}
void QmitkPreprocessingView::AverageGradients()
{
int nrFiles = m_SelectedDiffusionNodes.size();
if (!nrFiles) return;
mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
mitk::DiffusionImage<DiffusionPixelType>* vols =
static_cast<mitk::DiffusionImage<DiffusionPixelType>*>(
(*itemiter)->GetData());
vols->AverageRedundantGradients(m_Controls->m_Blur->value());
++itemiter;
}
}
void QmitkPreprocessingView::BrainMask()
{
int nrFiles = m_SelectedDiffusionNodes.size();
if (!nrFiles) return;
mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() );
while ( itemiter != itemiterend ) // for all items
{
mitk::DiffusionImage<DiffusionPixelType>* vols =
static_cast<mitk::DiffusionImage<DiffusionPixelType>*>(
(*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
// Extract image using found index
typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vols->GetVectorImage());
filter->SetDirections(vols->GetDirections());
typedef itk::CastImageFilter<itk::Image<short,3>, itk::Image<unsigned short,3> > CastFilterType;
CastFilterType::Pointer castfilter = CastFilterType::New();
castfilter->SetInput(filter->GetOutput());
typedef itk::BrainMaskExtractionImageFilter<unsigned char> MaskFilterType;
MaskFilterType::Pointer maskfilter = MaskFilterType::New();
maskfilter->SetInput(castfilter->GetOutput());
maskfilter->Update();
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( maskfilter->GetOutput() );
mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( mitkImage );
node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask"));
GetDefaultDataStorage()->Add(node);
++itemiter;
}
}
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui
index 0a0a71dcc0..e38818d6bf 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui
@@ -1,535 +1,549 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkPreprocessingViewControls</class>
<widget class="QWidget" name="QmitkPreprocessingViewControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>389</width>
<height>989</height>
</rect>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="acceptDrops">
<bool>false</bool>
</property>
<property name="windowTitle">
<string>QmitkPreprocessingViewControls</string>
</property>
<property name="autoFillBackground">
<bool>true</bool>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<widget class="QGroupBox" name="groupBox_6">
<property name="title">
<string>Data</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
<string>Diffusion Image:</string>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QLabel" name="m_DiffusionImageLabel">
<property name="text">
<string>-</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupBox_5">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="title">
<string>Info</string>
</property>
<layout class="QGridLayout" name="gridLayout_3">
<item row="0" column="0">
<widget class="QTableWidget" name="m_BvalueTable">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="verticalScrollBarPolicy">
<enum>Qt::ScrollBarAsNeeded</enum>
</property>
<property name="horizontalScrollBarPolicy">
<enum>Qt::ScrollBarAlwaysOff</enum>
</property>
<attribute name="horizontalHeaderCascadingSectionResizes">
<bool>true</bool>
</attribute>
<attribute name="horizontalHeaderDefaultSectionSize">
<number>100</number>
</attribute>
<attribute name="horizontalHeaderStretchLastSection">
<bool>true</bool>
</attribute>
<attribute name="verticalHeaderVisible">
<bool>false</bool>
</attribute>
<attribute name="verticalHeaderCascadingSectionResizes">
<bool>true</bool>
</attribute>
<column>
<property name="text">
<string>b-Value</string>
</property>
</column>
<column>
<property name="text">
<string>Number of gradients</string>
</property>
</column>
</widget>
</item>
<item row="1" column="0">
<widget class="QCommandLinkButton" name="m_ShowGradientsButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Generate pointset displaying the gradient vectors.</string>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Show gradients</string>
</property>
</widget>
</item>
<item row="0" column="1">
<spacer name="horizontalSpacer_2">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="m_ReduceSizeLayout">
<property name="title">
<string>Reduce size</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_4">
<item>
<widget class="QLabel" name="label_2">
<property name="minimumSize">
<size>
<width>0</width>
<height>70</height>
</size>
</property>
<property name="text">
<string>Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them anyway by taking into account all directions within a certain radius.</string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QFrame" name="frame">
<property name="frameShape">
<enum>QFrame::NoFrame</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Raised</enum>
</property>
<layout class="QFormLayout" name="formLayout_2">
<property name="margin">
<number>0</number>
</property>
<item row="0" column="1">
<widget class="QDoubleSpinBox" name="m_Blur">
<property name="toolTip">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="statusTip">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="whatsThis">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="decimals">
<number>6</number>
</property>
<property name="maximum">
<double>2.000000000000000</double>
</property>
<property name="singleStep">
<double>0.000100000000000</double>
</property>
<property name="value">
<double>0.001000000000000</double>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="label">
<property name="toolTip">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="statusTip">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="whatsThis">
<string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
</property>
<property name="text">
<string>Merge radius</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QCommandLinkButton" name="m_ButtonAverageGradients">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Average redundant gradients</string>
</property>
</widget>
</item>
<item>
<widget class="QCommandLinkButton" name="m_MirrorGradientToHalfSphereButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Mirror all gradients around one axis.</string>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Mirror gradients to half sphere</string>
</property>
</widget>
</item>
<item>
<widget class="Line" name="line">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
</widget>
</item>
+ <item>
+ <widget class="QFrame" name="m_ReductionFrame">
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="frameShadow">
+ <enum>QFrame::Raised</enum>
+ </property>
+ <layout class="QGridLayout" name="gridLayout_4">
+ <property name="margin">
+ <number>9</number>
+ </property>
+ <property name="spacing">
+ <number>9</number>
+ </property>
+ <item row="0" column="0">
+ <widget class="QLabel" name="label_4">
+ <property name="text">
+ <string>Specify desired number of gradients per shell.</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <widget class="QLabel" name="label_6">
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
<item>
<widget class="QCommandLinkButton" name="m_ReduceGradientsButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere.</string>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Reduce number of gradients</string>
</property>
</widget>
</item>
- <item>
- <widget class="QFrame" name="m_ReductionFrame">
- <property name="frameShape">
- <enum>QFrame::NoFrame</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <property name="margin">
- <number>0</number>
- </property>
- <property name="spacing">
- <number>0</number>
- </property>
- </layout>
- </widget>
- </item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupBox_2">
<property name="title">
<string>Non diffusion weighted image</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_3">
<item>
<widget class="QLabel" name="label_3">
<property name="minimumSize">
<size>
<width>0</width>
<height>30</height>
</size>
</property>
<property name="text">
<string>Average and extract all images that were acquired without diffusion weighting.</string>
</property>
<property name="wordWrap">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QCommandLinkButton" name="m_ButtonExtractB0">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Extract B0</string>
</property>
</widget>
</item>
<item>
<widget class="QCheckBox" name="m_CheckExtractAll">
<property name="toolTip">
<string>Create a 3D+t data set containing all b0 images as timesteps</string>
</property>
<property name="text">
<string>Extract all B0 without averaging</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupBox_3">
<property name="title">
<string>Brain mask</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_5">
<item>
<widget class="QCommandLinkButton" name="m_ButtonBrainMask">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Estimate binary brain mask</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="QGroupBox" name="groupBox_4">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="title">
<string>Measurment frame</string>
</property>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="1">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="0" column="0">
<widget class="QTableWidget" name="m_MeasurementFrameTable">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>10</width>
<height>10</height>
</size>
</property>
<property name="cursor" stdset="0">
<cursorShape>IBeamCursor</cursorShape>
</property>
<property name="autoFillBackground">
<bool>true</bool>
</property>
<property name="verticalScrollBarPolicy">
<enum>Qt::ScrollBarAlwaysOff</enum>
</property>
<property name="horizontalScrollBarPolicy">
<enum>Qt::ScrollBarAlwaysOff</enum>
</property>
<property name="showGrid">
<bool>true</bool>
</property>
<property name="cornerButtonEnabled">
<bool>false</bool>
</property>
<attribute name="horizontalHeaderVisible">
<bool>false</bool>
</attribute>
<attribute name="horizontalHeaderCascadingSectionResizes">
<bool>true</bool>
</attribute>
<attribute name="horizontalHeaderHighlightSections">
<bool>true</bool>
</attribute>
<attribute name="verticalHeaderVisible">
<bool>false</bool>
</attribute>
<attribute name="verticalHeaderCascadingSectionResizes">
<bool>true</bool>
</attribute>
<attribute name="verticalHeaderHighlightSections">
<bool>true</bool>
</attribute>
<row>
<property name="text">
<string>New Row</string>
</property>
</row>
<row>
<property name="text">
<string>New Row</string>
</property>
</row>
<row>
<property name="text">
<string>New Row</string>
</property>
</row>
<column>
<property name="text">
<string>New Column</string>
</property>
</column>
<column>
<property name="text">
<string>New Column</string>
</property>
</column>
<column>
<property name="text">
<string>New Column</string>
</property>
</column>
</widget>
</item>
<item row="1" column="0">
<widget class="QCommandLinkButton" name="m_ModifyMeasurementFrame">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string/>
</property>
<property name="statusTip">
<string/>
</property>
<property name="whatsThis">
<string notr="true"/>
</property>
<property name="text">
<string>Apply new mesurement frame</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<spacer name="verticalSpacer">
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>20</width>
<height>40</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
<resources/>
<connections/>
</ui>