diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake index 525cd9521b..91f43c4ac5 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake @@ -1,102 +1,111 @@ SET(SRC_CPP_FILES QmitkODFDetailsWidget.cpp QmitkODFRenderWidget.cpp QmitkPartialVolumeAnalysisWidget.cpp QmitkIVIMWidget.cpp + QmitkTbssRoiAnalysisWidget.cpp ) SET(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkQBallReconstructionView.cpp QmitkPreprocessingView.cpp QmitkDiffusionDicomImportView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkDiffusionImagingPublicPerspective.cpp QmitkControlVisualizationPropertiesView.cpp QmitkODFDetailsView.cpp QmitkGibbsTrackingView.cpp QmitkStochasticFiberTrackingView.cpp QmitkFiberProcessingView.cpp QmitkFiberBundleDeveloperView.cpp QmitkPartialVolumeAnalysisView.cpp QmitkIVIMView.cpp QmitkScreenshotMaker.cpp + QmitkTractbasedSpatialStatisticsView.cpp + QmitkTbssTableModel.cpp + QmitkTbssMetaTableModel.cpp ) SET(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkPreprocessingViewControls.ui src/internal/QmitkDiffusionDicomImportViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkControlVisualizationPropertiesViewControls.ui src/internal/QmitkODFDetailsViewControls.ui src/internal/QmitkGibbsTrackingViewControls.ui src/internal/QmitkStochasticFiberTrackingViewControls.ui src/internal/QmitkFiberProcessingViewControls.ui src/internal/QmitkFiberBundleDeveloperViewControls.ui src/internal/QmitkPartialVolumeAnalysisViewControls.ui src/internal/QmitkIVIMViewControls.ui src/internal/QmitkScreenshotMakerControls.ui + src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui ) SET(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkQBallReconstructionView.h src/internal/QmitkPreprocessingView.h src/internal/QmitkDiffusionDicomImportView.h src/internal/QmitkDiffusionImagingPublicPerspective.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkControlVisualizationPropertiesView.h src/internal/QmitkODFDetailsView.h src/QmitkODFRenderWidget.h src/QmitkODFDetailsWidget.h src/internal/QmitkGibbsTrackingView.h src/internal/QmitkStochasticFiberTrackingView.h src/internal/QmitkFiberProcessingView.h src/internal/QmitkFiberBundleDeveloperView.h src/internal/QmitkPartialVolumeAnalysisView.h src/QmitkPartialVolumeAnalysisWidget.h src/internal/QmitkIVIMView.h src/internal/QmitkScreenshotMaker.h + src/internal/QmitkTractbasedSpatialStatisticsView.h + src/QmitkTbssRoiAnalysisWidget.h ) SET(CACHED_RESOURCE_FILES # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench plugin.xml resources/preprocessing.png resources/dwiimport.png resources/quantification.png resources/reconodf.png resources/recontensor.png resources/vizControls.png resources/OdfDetails.png resources/GibbsTracking.png resources/FiberBundleOperations.png resources/PartialVolumeAnalysis_24.png resources/IVIM_48.png resources/screenshot_maker.png resources/stochFB.png + resources/tbss.png ) SET(QRC_FILES # uncomment the following line if you want to use Qt resources resources/QmitkDiffusionImaging.qrc + #resources/QmitkTractbasedSpatialStatisticsView.qrc ) SET(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/plugin.xml b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/plugin.xml index cc0063c353..466160f756 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/plugin.xml +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/plugin.xml @@ -1,110 +1,117 @@ + + + + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/resources/tbss.png b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/resources/tbss.png new file mode 100755 index 0000000000..15950524ae Binary files /dev/null and b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/resources/tbss.png differ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.cpp new file mode 100644 index 0000000000..ba87ece4fd --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.cpp @@ -0,0 +1,256 @@ +/*========================================================================= +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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. + +=========================================================================*/ + +#include "QmitkTbssRoiAnalysisWidget.h" + + +#include +#include +#include + +#include +#include +#include +#include +#include + + +#include +#include + + +QmitkTbssRoiAnalysisWidget::QmitkTbssRoiAnalysisWidget( QWidget * parent ) + : QmitkPlotWidget(parent) +{ + m_PlotPicker = new QwtPlotPicker(m_Plot->canvas()); + m_PlotPicker->setSelectionFlags(QwtPicker::PointSelection | QwtPicker::ClickSelection | QwtPicker::DragSelection); + m_PlotPicker->setTrackerMode(QwtPicker::ActiveOnly); +} + +std::vector< std::vector > QmitkTbssRoiAnalysisWidget::CalculateGroupProfiles(std::string preprocessed) +{ + MITK_INFO << "make profiles!"; + std::vector< std::vector > profiles; + + //No results were preprocessed, so they must be calculated now. + if(preprocessed == "") + { + // Iterate through the 4th dim (corresponding to subjects) + // and create a profile for every subject + int size = m_Projections->GetVectorLength(); + for(int s=0; s profile; + RoiType::iterator it; + it = m_Roi.begin(); + while(it != m_Roi.end()) + { + itk::Index<3> ix = *it; + profile.push_back(m_Projections->GetPixel(ix).GetElement(s)); + it++; + } + int pSize = profile.size(); + profiles.push_back(profile); + } + } + else{ // Use preprocessed results + std::ifstream file(preprocessed.c_str()); + if(file.is_open()) + { + std::string line; + while(getline(file,line)) + { + std::vector tokens; + Tokenize(line, tokens); + std::vector::iterator it; + it = tokens.begin(); + std::vector< double > profile; + while(it != tokens.end()) + { + std::string s = *it; + profile.push_back (atof( s.c_str() ) ); + ++it; + } + profiles.push_back(profile); + } + } + } + // Calculate the averages + + // Here a check could be build in to check whether all profiles have + // the same length, but this should normally be the case if the input + // data were corrected with the TBSS Module. + + std::vector< std::vector > groupProfiles; + + std::vector< std::pair >::iterator it; + it = m_Groups.begin(); + + int c = 0; //the current profile number + + int nprof = profiles.size(); + + while(it != m_Groups.end() && profiles.size() > 0) + { + std::pair p = *it; + int size = p.second; + + //initialize a vector of the right length with zeroes + std::vector averageProfile; + for(int i=0; iClear(); + + + + m_Vals.clear(); + + std::vector v1; + + + std::vector > groupProfiles = CalculateGroupProfiles(preprocessed); + + + std::vector xAxis; + for(int i=0; iSetPlotTitle( title.c_str() ); + QPen pen( Qt::SolidLine ); + pen.setWidth(2); + + + + std::vector< std::pair >::iterator it; + it = m_Groups.begin(); + + int c = 0; //the current profile number + + QColor colors[4] = {Qt::green, Qt::blue, Qt::yellow, Qt::red}; + + while(it != m_Groups.end() && groupProfiles.size() > 0) + { + + std::pair< std::string, int > group = *it; + + pen.setColor(colors[c]); + int curveId = this->InsertCurve( group.first.c_str() ); + this->SetCurveData( curveId, xAxis, groupProfiles.at(c) ); + + + this->SetCurvePen( curveId, pen ); + + c++; + it++; + + } + + + QwtLegend *legend = new QwtLegend; + this->SetLegend(legend, QwtPlot::RightLegend, 0.5); + + + std::cout << m_Measure << std::endl; + this->m_Plot->setAxisTitle(0, m_Measure.c_str()); + this->m_Plot->setAxisTitle(3, "Position"); + + this->Replot(); + +} + +void QmitkTbssRoiAnalysisWidget::Boxplots() +{ + this->Clear(); +} + +void QmitkTbssRoiAnalysisWidget::drawBar(int x) +{ + + m_Plot->detachItems(QwtPlotItem::Rtti_PlotMarker, true); + + + QwtPlotMarker *mX = new QwtPlotMarker(); + //mX->setLabel(QString::fromLatin1("selected point")); + mX->setLabelAlignment(Qt::AlignLeft | Qt::AlignBottom); + mX->setLabelOrientation(Qt::Vertical); + mX->setLineStyle(QwtPlotMarker::VLine); + mX->setLinePen(QPen(Qt::black, 0, Qt::SolidLine)); + mX->setXValue(x); + mX->attach(m_Plot); + + + this->Replot(); + +} + +QmitkTbssRoiAnalysisWidget::~QmitkTbssRoiAnalysisWidget() +{ + delete m_PlotPicker; + +} + + + + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h new file mode 100644 index 0000000000..c68f4aaa50 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/QmitkTbssRoiAnalysisWidget.h @@ -0,0 +1,148 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-15 18:09:46 +0200 (Fr, 15 Mai 2009) $ +Version: $Revision: 1.12 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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 QmitkTbssRoiAnalysisWidget_H_ +#define QmitkTbssRoiAnalysisWidget_H_ + +#include "QmitkPlotWidget.h" + +#include + +//#include "QmitkHistogram.h" +#include "QmitkExtExports.h" +#include "mitkImage.h" +#include "mitkPlanarFigure.h" +#include "itkVectorImage.h" + + +//#include + +//#include +#include +#include +#include +#include +#include + +typedef itk::VectorImage VectorImageType; + +typedef std::vector< itk::Index<3> > RoiType; + +/** + * \brief Widget for displaying boxplots + * framework + */ +class DIFFUSIONIMAGING_EXPORT QmitkTbssRoiAnalysisWidget : public QmitkPlotWidget +{ + +Q_OBJECT + +public: + + + QmitkTbssRoiAnalysisWidget( QWidget * parent); + virtual ~QmitkTbssRoiAnalysisWidget(); + + void SetGroups(std::vector< std::pair > groups) + { + m_Groups = groups; + } + + void DrawProfiles(std::string preprocessed); + + void Boxplots(); + + void SetProjections(VectorImageType::Pointer projections) + { + m_Projections = projections; + } + + void SetRoi(RoiType roi) + { + m_Roi = roi; + } + + void SetStructure(std::string structure) + { + m_Structure = structure; + } + + void SetMeasure(std::string measure) + { + m_Measure = measure; + } + + QwtPlot* GetPlot() + { + return m_Plot; + } + + QwtPlotPicker* m_PlotPicker; + + + + void drawBar(int x); + + std::vector > GetVals() + { + return m_Vals; + } + + +protected: + + std::vector< std::vector > m_Vals; + + + + + std::vector< std::vector > CalculateGroupProfiles(std::string preprocessed); + + + + void Tokenize(const std::string& str, + std::vector& tokens, + const std::string& delimiters = " ") + { + // Skip delimiters at beginning. + std::string::size_type lastPos = str.find_first_not_of(delimiters, 0); + // Find first "non-delimiter". + std::string::size_type pos = str.find_first_of(delimiters, lastPos); + + while (std::string::npos != pos || std::string::npos != lastPos) + { + // Found a token, add it to the vector. + tokens.push_back(str.substr(lastPos, pos - lastPos)); + // Skip delimiters. Note the "not_of" + lastPos = str.find_first_not_of(delimiters, pos); + // Find next "non-delimiter" + pos = str.find_first_of(delimiters, lastPos); + } + } + + std::vector< std::pair > m_Groups; + + VectorImageType::Pointer m_Projections; + RoiType m_Roi; + std::string m_Structure; + std::string m_Measure; + + + +}; + +#endif diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.cpp new file mode 100644 index 0000000000..dafdc3f1f9 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.cpp @@ -0,0 +1,150 @@ + + +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 18127 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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. + +=========================================================================*/ + + + +#include "QmitkTbssMetaTableModel.h" + +QmitkTbssMetaTableModel::QmitkTbssMetaTableModel(QObject *parent) + : QAbstractTableModel(parent) +{ +} + +QmitkTbssMetaTableModel::QmitkTbssMetaTableModel(QList< QPair > pairs, QObject *parent) + : QAbstractTableModel(parent) +{ + listOfPairs=pairs; +} + +int QmitkTbssMetaTableModel::rowCount(const QModelIndex &parent) const +{ + Q_UNUSED(parent); + return listOfPairs.size(); +} + +int QmitkTbssMetaTableModel::columnCount(const QModelIndex &parent) const +{ + Q_UNUSED(parent); + return 2; +} + +QVariant QmitkTbssMetaTableModel::data(const QModelIndex &index, int role) const +{ + if (!index.isValid()) + return QVariant(); + + if (index.row() >= listOfPairs.size() || index.row() < 0) + return QVariant(); + + if (role == Qt::DisplayRole) { + QPair pair = listOfPairs.at(index.row()); + + if (index.column() == 0) + return pair.first; + else if (index.column() == 1) + return pair.second; + } + return QVariant(); +} + +QVariant QmitkTbssMetaTableModel::headerData(int section, Qt::Orientation orientation, int role) const +{ + if (role != Qt::DisplayRole) + return QVariant(); + + if (orientation == Qt::Horizontal) { + switch (section) { + case 0: + return tr("Image"); + + case 1: + return tr("Filename"); + + default: + return QVariant(); + } + } + return QVariant(); +} + +bool QmitkTbssMetaTableModel::insertRows(int position, int rows, const QModelIndex &index) +{ + Q_UNUSED(index); + beginInsertRows(QModelIndex(), position, position+rows-1); + + for (int row=0; row < rows; row++) { + QPair pair("Image ", "Filename"); + listOfPairs.insert(position, pair); + } + + endInsertRows(); + return true; +} + +bool QmitkTbssMetaTableModel::removeRows(int position, int rows, const QModelIndex &index) +{ + Q_UNUSED(index); + beginRemoveRows(QModelIndex(), position, position+rows-1); + + for (int row=0; row < rows; ++row) { + listOfPairs.removeAt(position); + } + + endRemoveRows(); + return true; +} + +bool QmitkTbssMetaTableModel::setData(const QModelIndex &index, const QVariant &value, int role) +{ + if (index.isValid() && role == Qt::EditRole) { + int row = index.row(); + + QPair p = listOfPairs.value(row); + + if (index.column() == 0) + p.first = value.toString(); + else if (index.column() == 1) + p.second = value.toString(); + else + return false; + + listOfPairs.replace(row, p); + emit(dataChanged(index, index)); + + return true; + } + + return false; +} + +Qt::ItemFlags QmitkTbssMetaTableModel::flags(const QModelIndex &index) const +{ + if (!index.isValid()) + return Qt::ItemIsEnabled; + + return QAbstractTableModel::flags(index) | Qt::ItemIsEditable; +} + +QList< QPair > QmitkTbssMetaTableModel::getList() +{ + return listOfPairs; +} + + + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.h new file mode 100644 index 0000000000..112b33bc45 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssMetaTableModel.h @@ -0,0 +1,55 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 18127 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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 QmitkTbssMetaTableModel_h +#define QmitkTbssMetaTableModel_h + + +#include + +#include +#include +#include +#include + + +class QmitkTbssMetaTableModel : public QAbstractTableModel +{ + + //Q_OBJECT + +public: + QmitkTbssMetaTableModel(QObject *parent=0); + QmitkTbssMetaTableModel(QList< QPair > listofPairs, QObject *parent=0); + + int rowCount(const QModelIndex &parent) const; + int columnCount(const QModelIndex &parent) const; + QVariant data(const QModelIndex &index, int role) const; + QVariant headerData(int section, Qt::Orientation orientation, int role) const; + Qt::ItemFlags flags(const QModelIndex &index) const; + bool setData(const QModelIndex &index, const QVariant &value, int role=Qt::EditRole); + bool insertRows(int position, int rows, const QModelIndex &index=QModelIndex()); + bool removeRows(int position, int rows, const QModelIndex &index=QModelIndex()); + QList< QPair > getList(); + +private: + QList< QPair > listOfPairs; +}; + +#endif diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.cpp new file mode 100644 index 0000000000..6319490fff --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.cpp @@ -0,0 +1,150 @@ + + +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 18127 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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. + +=========================================================================*/ + + + +#include "QmitkTbssTableModel.h" + +QmitkTbssTableModel::QmitkTbssTableModel(QObject *parent) + : QAbstractTableModel(parent) +{ +} + +QmitkTbssTableModel::QmitkTbssTableModel(QList< QPair > pairs, QObject *parent) + : QAbstractTableModel(parent) +{ + listOfPairs=pairs; +} + +int QmitkTbssTableModel::rowCount(const QModelIndex &parent) const +{ + Q_UNUSED(parent); + return listOfPairs.size(); +} + +int QmitkTbssTableModel::columnCount(const QModelIndex &parent) const +{ + Q_UNUSED(parent); + return 2; +} + +QVariant QmitkTbssTableModel::data(const QModelIndex &index, int role) const +{ + if (!index.isValid()) + return QVariant(); + + if (index.row() >= listOfPairs.size() || index.row() < 0) + return QVariant(); + + if (role == Qt::DisplayRole) { + QPair pair = listOfPairs.at(index.row()); + + if (index.column() == 0) + return pair.first; + else if (index.column() == 1) + return pair.second; + } + return QVariant(); +} + +QVariant QmitkTbssTableModel::headerData(int section, Qt::Orientation orientation, int role) const +{ + if (role != Qt::DisplayRole) + return QVariant(); + + if (orientation == Qt::Horizontal) { + switch (section) { + case 0: + return tr("Group"); + + case 1: + return tr("Size"); + + default: + return QVariant(); + } + } + return QVariant(); +} + +bool QmitkTbssTableModel::insertRows(int position, int rows, const QModelIndex &index) +{ + Q_UNUSED(index); + beginInsertRows(QModelIndex(), position, position+rows-1); + + for (int row=0; row < rows; row++) { + QPair pair(" ", 0); + listOfPairs.insert(position, pair); + } + + endInsertRows(); + return true; +} + +bool QmitkTbssTableModel::removeRows(int position, int rows, const QModelIndex &index) +{ + Q_UNUSED(index); + beginRemoveRows(QModelIndex(), position, position+rows-1); + + for (int row=0; row < rows; ++row) { + listOfPairs.removeAt(position); + } + + endRemoveRows(); + return true; +} + +bool QmitkTbssTableModel::setData(const QModelIndex &index, const QVariant &value, int role) +{ + if (index.isValid() && role == Qt::EditRole) { + int row = index.row(); + + QPair p = listOfPairs.value(row); + + if (index.column() == 0) + p.first = value.toString(); + else if (index.column() == 1) + p.second = value.toInt(); + else + return false; + + listOfPairs.replace(row, p); + emit(dataChanged(index, index)); + + return true; + } + + return false; +} + +Qt::ItemFlags QmitkTbssTableModel::flags(const QModelIndex &index) const +{ + if (!index.isValid()) + return Qt::ItemIsEnabled; + + return QAbstractTableModel::flags(index) | Qt::ItemIsEditable; +} + +QList< QPair > QmitkTbssTableModel::getList() +{ + return listOfPairs; +} + + + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.h new file mode 100644 index 0000000000..3f900fd02b --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssTableModel.h @@ -0,0 +1,53 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 18127 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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 QmitkTbssTableModel_h +#define QmitkTbssTableModel_h + + +#include + +#include +#include +#include + +class QmitkTbssTableModel : public QAbstractTableModel +{ + + //Q_OBJECT + +public: + QmitkTbssTableModel(QObject *parent=0); + QmitkTbssTableModel(QList< QPair > listofPairs, QObject *parent=0); + + int rowCount(const QModelIndex &parent) const; + int columnCount(const QModelIndex &parent) const; + QVariant data(const QModelIndex &index, int role) const; + QVariant headerData(int section, Qt::Orientation orientation, int role) const; + Qt::ItemFlags flags(const QModelIndex &index) const; + bool setData(const QModelIndex &index, const QVariant &value, int role=Qt::EditRole); + bool insertRows(int position, int rows, const QModelIndex &index=QModelIndex()); + bool removeRows(int position, int rows, const QModelIndex &index=QModelIndex()); + QList< QPair > getList(); + +private: + QList< QPair > listOfPairs; +}; + +#endif diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp new file mode 100644 index 0000000000..0a5be3ac4a --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp @@ -0,0 +1,1601 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ +Version: $Revision: 21975 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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. + +=========================================================================*/ + +// Blueberry +#include "berryIWorkbenchWindow.h" +#include "berryIWorkbenchPage.h" +#include "berryISelectionService.h" +#include "berryConstants.h" +#include "berryPlatformUI.h" + +// Qmitk +#include "QmitkTractbasedSpatialStatisticsView.h" +#include "QmitkStdMultiWidget.h" + +#include "mitkDataNodeObject.h" +#include + +// Qt +#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 + + +#include "mitkPartialVolumeAnalysisClusteringCalculator.h" +#include "mitkPartialVolumeAnalysisHistogramCalculator.h" + +#include +#include "vtkFloatArray.h" +#include "vtkLinearTransform.h" +#include "vtkPoints.h" +#include "mitkSurface.h" +#include +#include "vtkArrowSource.h" +#include "vtkUnstructuredGrid.h" +#include "vtkPointData.h" + +#include +#include +#include + +#include + +#include "mitkITKImageImport.h" +// #include "mitkImageMapperGL2D.h" +#include "mitkVolumeDataVtkMapper3D.h" +#include "mitkImageAccessByItk.h" + + +#define SEARCHSIGMA 10 /* length in linear voxel dimens + { + // create new ones + m_PointSetNode = mitk::PointSet::New();ions */ +#define MAXSEARCHLENGTH (3*SEARCHSIGMA) + +const std::string QmitkTractbasedSpatialStatisticsView::VIEW_ID = "org.mitk.views.tractbasedspatialstatistics"; + +using namespace berry; + + +struct TbssSelListener : ISelectionListener +{ + + berryObjectMacro(TbssSelListener) + + TbssSelListener(QmitkTractbasedSpatialStatisticsView* view) + { + m_View = view; + } + + + void DoSelectionChanged(ISelection::ConstPointer selection) + { + // save current selection in member variable + m_View->m_CurrentSelection = selection.Cast(); + + // do something with the selected items + if(m_View->m_CurrentSelection) + { + bool foundTbssRoi = false; + bool foundTbss = false; + bool found3dImage = false; + bool found4dImage = false; + + mitk::TbssRoiImage* roiImage; + mitk::TbssImage* image; + + + // iterate selection + for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); + i != m_View->m_CurrentSelection->End(); ++i) + { + + // extract datatree node + if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) + { + mitk::DataNode::Pointer node = nodeObj->GetDataNode(); + + // only look at interesting types + + if(QString("TbssRoiImage").compare(node->GetData()->GetNameOfClass())==0) + { + foundTbssRoi = true; + roiImage = static_cast(node->GetData()); + } + else if (QString("TbssImage").compare(node->GetData()->GetNameOfClass())==0) + { + foundTbss = true; + image = static_cast(node->GetData()); + } + else if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::Image* img = static_cast(node->GetData()); + if(img->GetDimension() == 3) + { + found3dImage = true; + } + else if(img->GetDimension() == 4) + { + found4dImage = true; + } + } + + + } + + } + + + m_View->m_Controls->m_CreateRoi->setEnabled(found3dImage); + m_View->m_Controls->m_ImportFsl->setEnabled(found4dImage); + if(found3dImage) + { + m_View->InitPointsets(); + } + + } + } + + + void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) + { + // check, if selection comes from datamanager + if (part) + { + QString partname(part->GetPartName().c_str()); + if(partname.compare("Datamanager")==0) + { + // apply selection + DoSelectionChanged(selection); + } + } + } + + QmitkTractbasedSpatialStatisticsView* m_View; +}; + + +QmitkTractbasedSpatialStatisticsView::QmitkTractbasedSpatialStatisticsView() +: QmitkFunctionality() +, m_Controls( 0 ) +, m_MultiWidget( NULL ) +{ + +} + +QmitkTractbasedSpatialStatisticsView::~QmitkTractbasedSpatialStatisticsView() +{ +} + +void QmitkTractbasedSpatialStatisticsView::OnSelectionChanged(std::vector nodes) +{ + //datamanager selection changed + if (!this->IsActivated()) + return; + + + // Get DataManagerSelection + if (!this->GetDataManagerSelection().empty()) + { + mitk::DataNode::Pointer sourceImageNode = this->GetDataManagerSelection().front(); + mitk::Image::Pointer sourceImage = dynamic_cast(sourceImageNode->GetData()); + + if (!sourceImage) + { + m_Controls->m_TbssImageLabel->setText( + QString( sourceImageNode->GetName().c_str() ) + " is no image" + ); + + return; + } + + // set Text + m_Controls->m_TbssImageLabel->setText( + QString( sourceImageNode->GetName().c_str() ) + " (" + + QString::number(sourceImage->GetDimension()) + "D)" + ); + + + } + else + { + m_Controls->m_TbssImageLabel->setText("Please select an image"); + } + +} + +void QmitkTractbasedSpatialStatisticsView::InitPointsets() +{ + // Check if PointSetStart exsits, if not create it. + m_P1 = this->GetDefaultDataStorage()->GetNamedNode("PointSetNode"); + + if (m_PointSetNode) + { + //m_PointSetNode = dynamic_cast(m_P1->GetData()); + return; + } + + if ((!m_P1) || (!m_PointSetNode)) + { + // create new ones + m_PointSetNode = mitk::PointSet::New(); + m_P1 = mitk::DataNode::New(); + m_P1->SetData( m_PointSetNode ); + m_P1->SetProperty( "name", mitk::StringProperty::New( "PointSet" ) ); + m_P1->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) ); + m_P1->SetProperty( "helper object", mitk::BoolProperty::New(false) ); // CHANGE if wanted + m_P1->SetProperty( "pointsize", mitk::FloatProperty::New( 0.1 ) ); + m_P1->SetColor( 1.0, 0.0, 0.0 ); + this->GetDefaultDataStorage()->Add(m_P1); + m_Controls->m_PointWidget->SetPointSetNode(m_P1); + m_Controls->m_PointWidget->SetMultiWidget(GetActiveStdMultiWidget()); + } +} + +void QmitkTractbasedSpatialStatisticsView::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::QmitkTractbasedSpatialStatisticsViewControls; + m_Controls->setupUi( parent ); + this->CreateConnections(); + } + + m_SelListener = berry::ISelectionListener::Pointer(new TbssSelListener(this)); + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); + berry::ISelection::ConstPointer sel( + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); + m_CurrentSelection = sel.Cast(); + m_SelListener.Cast()->DoSelectionChanged(sel); + + m_IsInitialized = false; + + + + // Table for the FSL TBSS import + m_GroupModel = new QmitkTbssTableModel(); + m_Controls->m_GroupInfo->setModel(m_GroupModel); + + +} + +void QmitkTractbasedSpatialStatisticsView::Activated() +{ + QmitkFunctionality::Activated(); + + berry::ISelection::ConstPointer sel( + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); + m_CurrentSelection = sel.Cast(); + m_SelListener.Cast()->DoSelectionChanged(sel); +} + +void QmitkTractbasedSpatialStatisticsView::Deactivated() +{ + QmitkFunctionality::Deactivated(); +} + +void QmitkTractbasedSpatialStatisticsView::CreateConnections() +{ + if ( m_Controls ) + { + connect( (QObject*)(m_Controls->m_CreateRoi), SIGNAL(clicked()), this, SLOT(CreateRoi()) ); + connect( (QObject*)(m_Controls->m_ImportFsl), SIGNAL(clicked()), this, SLOT(TbssImport()) ); + connect( (QObject*)(m_Controls->m_AddGroup), SIGNAL(clicked()), this, SLOT(AddGroup()) ); + connect( (QObject*)(m_Controls->m_RemoveGroup), SIGNAL(clicked()), this, SLOT(RemoveGroup()) ); + connect( (QObject*)(m_Controls->m_Clipboard), SIGNAL(clicked()), this, SLOT(CopyToClipboard()) ); + connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(selected(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) ); + connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(moved(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) ); + } +} + +void QmitkTractbasedSpatialStatisticsView::CopyToClipboard() +{ + std::vector > vals = m_Controls->m_RoiPlotWidget->GetVals(); + QString clipboardText; + for (std::vector >::iterator it = vals.begin(); it + != vals.end(); ++it) + { + for (std::vector::iterator it2 = (*it).begin(); it2 != + (*it).end(); ++it2) + { + clipboardText.append(QString("%1 \t").arg(*it2)); + + double d = *it2; + std::cout << d <setText(clipboardText, QClipboard::Clipboard); + +} + +void QmitkTractbasedSpatialStatisticsView::RemoveGroup() +{ + + QTableView *temp = static_cast(m_Controls->m_GroupInfo); + // QSortFilterProxyModel *proxy = static_cast(temp->model()); + QItemSelectionModel *selectionModel = temp->selectionModel(); + + QModelIndexList indices = selectionModel->selectedRows(); + + QModelIndex index; + + foreach(index, indices) + { + int row = index.row(); + m_GroupModel->removeRows(row, 1, QModelIndex()); + } + +} + +std::string QmitkTractbasedSpatialStatisticsView::ReadFile(std::string whatfile) +{ + std::string s = "Select a" + whatfile; + QFileDialog* w = new QFileDialog(this->m_Controls->m_ImportFsl, QString(s.c_str()) ); + w->setFileMode(QFileDialog::ExistingFiles); + w->setDirectory("/home"); + + if(whatfile == "gradient image") + { + w->setNameFilter("Tbss gradient images (*.tgi)"); + } + + // RETRIEVE SELECTION + if ( w->exec() != QDialog::Accepted ) + { + return ""; + MITK_INFO << "Failed to load"; + } + + QStringList filenames = w->selectedFiles(); + if (filenames.size() > 0) + { + std::string retval = filenames.at(0).toStdString(); + return retval; + } + return ""; +} + +void QmitkTractbasedSpatialStatisticsView::AddGroup() +{ + QString group("Group"); + int number = 0; + QPair pair(group, number); + QList< QPair >list = m_GroupModel->getList(); + + + if(!list.contains(pair)) + { + m_GroupModel->insertRows(0, 1, QModelIndex()); + + QModelIndex index = m_GroupModel->index(0, 0, QModelIndex()); + m_GroupModel->setData(index, group, Qt::EditRole); + index = m_GroupModel->index(0, 1, QModelIndex()); + m_GroupModel->setData(index, number, Qt::EditRole); + + } + else + { + //QMessageBox::information(this, "Duplicate name"); + } + + +} + + +void QmitkTractbasedSpatialStatisticsView::TbssImport() +{ + + // Read groups from the interface + mitk::TbssImporter::Pointer importer = mitk::TbssImporter::New(); + + QList< QPair >list = m_GroupModel->getList(); + + if(list.size() == 0) + { + QMessageBox msgBox; + msgBox.setText("No study group information has been set yet."); + msgBox.exec(); + return; + } + + + std::vector < std::pair > groups; + for(int i=0; i pair = list.at(i); + std::string s = pair.first.toStdString(); + int n = pair.second; + + std::pair p; + p.first = s; + p.second = n; + groups.push_back(p); + } + + importer->SetGroupInfo(groups); + + std::string minfo = m_Controls->m_MeasurementInfo->text().toStdString(); + importer->SetMeasurementInfo(minfo); + + + std::string name = ""; + for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); + i != m_CurrentSelection->End(); ++i) + { + // extract datatree node + if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) + { + mitk::DataNode::Pointer node = nodeObj->GetDataNode(); + + if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::Image* img = static_cast(node->GetData()); + if(img->GetDimension() == 4) + { + //importer->SetImportVolume(img); + name = node->GetName(); + } + } + } + } + + mitk::TbssImage::Pointer tbssImage; + + tbssImage = importer->Import(); + name += "_tbss"; + AddTbssToDataStorage(tbssImage, name); + + +} + + +void QmitkTractbasedSpatialStatisticsView::AddTbssToDataStorage(mitk::Image* image, std::string name) +{ + mitk::LevelWindow levelwindow; + levelwindow.SetAuto( image ); + mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); + levWinProp->SetLevelWindow( levelwindow ); + + mitk::DataNode::Pointer result = mitk::DataNode::New(); + result->SetProperty( "name", mitk::StringProperty::New(name) ); + result->SetData( image ); + result->SetProperty( "levelwindow", levWinProp ); + + + // add new image to data storage and set as active to ease further processing + GetDefaultDataStorage()->Add( result ); + + // show the results + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +} + +void QmitkTractbasedSpatialStatisticsView::Clicked(const QwtDoublePoint& pos) +{ + if(m_Roi.size() > 0 && m_CurrentGeometry != NULL) + { + int index = (int)pos.x(); + index = std::max(0, index); + index = std::min(index, (int)m_Roi.size()); + itk::Index<3> ix = m_Roi.at(index); + + mitk::Vector3D i; + i[0] = ix[0]; + i[1] = ix[1]; + i[2] = ix[2]; + + mitk::Vector3D w; + + m_CurrentGeometry->IndexToWorld(i, w); + + mitk::Point3D origin = m_CurrentGeometry->GetOrigin(); + + mitk::Point3D p; + p[0] = w[0] + origin[0]; + p[1] = w[1] + origin[1]; + p[2] = w[2] + origin[2]; + + + + + m_MultiWidget->MoveCrossToPosition(p); + + m_Controls->m_RoiPlotWidget->drawBar(index); + + } + +} + +void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) +{ + m_MultiWidget = &stdMultiWidget; +} + + +void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetNotAvailable() +{ + m_MultiWidget = NULL; +} + +void QmitkTractbasedSpatialStatisticsView::AdjustPlotMeasure(const QString & text) +{ + berry::ISelection::ConstPointer sel( + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); + m_CurrentSelection = sel.Cast(); + m_SelListener.Cast()->DoSelectionChanged(sel); +} + +void QmitkTractbasedSpatialStatisticsView::Clustering() +{ +/* + + + // Create a mask using the distance map + typedef itk::ImageFileReader< VectorImageType > DirectionReader; + DirectionReader::Pointer directionReader = DirectionReader::New(); + directionReader->SetFileName(m_TbssWorkspaceManager.GetInputDir().toStdString() + "/tbss/" + m_TbssWorkspaceManager.GetGradient().toStdString()); + directionReader->Update(); + VectorImageType::Pointer directions = directionReader->GetOutput(); + + FloatReaderType::Pointer distMapReader = FloatReaderType::New(); + distMapReader->SetFileName(m_TbssWorkspaceManager.GetInputDir().toStdString() + "/stats/" + m_TbssWorkspaceManager.GetDistanceMap().toStdString()); + distMapReader->Update(); + FloatImageType::Pointer distanceMap = distMapReader->GetOutput(); + + + std::string line; + std::string path = "/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/rois/cc.txt"; + std::ifstream file(path.c_str()); + std::vector< itk::Index< 3 > > roi; + + if(file.is_open()) + { + + while(getline(file,line)) + { + + std::vector tokens; + Tokenize(line, tokens); + + itk::Index<3> ix; + ix[0] = atoi(tokens[0].c_str()); + ix[1] = atoi(tokens[1].c_str()); + ix[2] = atoi(tokens[2].c_str()); + roi.push_back(ix); + } + } + + if(roi.size() == 0) + { + return; + } + + + + // Some code from the projection algorithm of tbss to create a mask + + + std::vector< std::vector< itk::Index< 3 > > > rois; + + for(int j=0; j > indices; + + FloatImageType::SizeType size = distanceMap->GetLargestPossibleRegion().GetSize(); + + bool roiDone = false; + + while(!roiDone && j ix = roi[j]; + int x=ix[0]; + int y=ix[1]; + int z=ix[2]; + VectorImageType::PixelType dir = directions->GetPixel(ix); + + indices.push_back(ix); + + + for(int iters=0;iters<2;iters++) + { + float distance=0; + + for(int d=1;d=size[0] && dy<=size[1] && dz<=size[2]) + { + d=MAXSEARCHLENGTH; + } + else if(distanceMap->GetPixel(ix)>=distance) + { + distance = distanceMap->GetPixel(ix); + indices.push_back(ix); + } + else{ + d=MAXSEARCHLENGTH; + } + + } + + } + j++; + } + + + // Create a mask from indices + UCharImageType::Pointer maskItk = UCharImageType::New(); + maskItk->SetRegions(distanceMap->GetRequestedRegion()); + maskItk->SetDirection(distanceMap->GetDirection()); + maskItk->SetSpacing(distanceMap->GetSpacing()); + maskItk->SetOrigin(distanceMap->GetOrigin()); + maskItk->Allocate(); + + + + + + + + // For every point on the roi create a mask and feed it to the partial voluming algorithm + + + //maskItk->FillBuffer(0); + + + + // Create a bounding box from current ROI + int xMin = numeric_limits::max(); + int yMin = numeric_limits::max(); + int zMin = numeric_limits::max(); + int xMax = numeric_limits::min(); + int yMax = numeric_limits::min(); + int zMax = numeriUCharImageType::Pointer newMask = UCharImageType::New();c_limits::min(); + + + for(int i=0; i ix = indices[i]; + + if(ix[0] < xMin) + xMin=ix[0]; + + if(ix[1] < yMin) + yMin=ix[1]; + + if(ix[2] < zMin) + zMin=ix[2]; + + if(ix[0] > xMax) + xMax=ix[0]; + + if(ix[1] > yMax) + yMax=ix[1]; + + if(ix[2] > zMax) + zMax=ix[2]; + } + + FloatImageType::PointType origin = distanceMap->GetOrigin(); + CharImageType::PointType originMask; + originMask[0] = origin[0] + xMin; + originMask[1] = origin[1] + -yMin; + originMask[2] = origin[2] + zMin; + + CharImageType::RegionType region; + CharImageType::RegionType::SizeType s; + s[0] = xMax-xMin + 1; + s[1] = yMax-yMin + 1; + s[2] = zMax-zMin + 1; + region.SetSize(s); + + + UCharImageType::Pointer newMask = UCharImageType::New(); + newMask->SetSpacing( distanceMap->GetSpacing() ); // Set the image spacing + newMask->SetOrigin( originMask ); // Set the image origin + newMask->SetDirection( distanceMap->GetDirection() ); // Set the image direction + newMask->SetRegions( region ); + newMask->Allocate(); + newMask->FillBuffer(0); + + + + for(int i=0; i ix = indices[i]; + + itk::Point< double, 3 > point; + itk::Index< 3 > index; + + distanceMap->TransformIndexToPhysicalPoint (ix, point); + + + + newMask->TransformPhysicalPointToIndex(point, index); + + + + newMask->SetPixel(index, 1); + } + + + +*/ + + + + + + + + UCharImageType::Pointer newMask = UCharImageType::New(); + UCharReaderType::Pointer cReader = UCharReaderType::New(); + cReader->SetFileName("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/ClusteringFornix/fornix_central_maxFA_path_Dilated_by_3.nrrd"); + cReader->Update(); + newMask = cReader->GetOutput(); + + + // mitk::DataNode::Pointer maskNode = readNode("itk image/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/clusterMasks/area2.nii"); + // mitk::Image::Pointer mask = dynamic_cast(maskNode->GetData()); + mitk::Image::Pointer mask; + mitk::CastToMitkImage(newMask, mask); + + typedef mitk::PartialVolumeAnalysisHistogramCalculator HistorgramCalculator; + typedef mitk::PartialVolumeAnalysisClusteringCalculator ClusteringType; + typedef HistorgramCalculator::HistogramType HistogramType; + + HistorgramCalculator::Pointer histogramCalculator = HistorgramCalculator::New(); + + + + + + // Make list of subjects + + std::vector paths; + paths.push_back("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/FA/SORTEDBYCONDITION/FA/subset"); + // paths.push_back("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/FA/SORTEDBYCONDITION/AXD/"); + + for(int j=0; j values; + + for(int i=0; i(node->GetData()); + + + histogramCalculator->SetImage(image); + histogramCalculator->SetImageMask( mask ); + histogramCalculator->SetMaskingModeToImage(); + histogramCalculator->SetNumberOfBins(25); + histogramCalculator->SetUpsamplingFactor(5); + histogramCalculator->SetGaussianSigma(0.0); + histogramCalculator->SetForceUpdate(true); + + bool statisticsChanged = histogramCalculator->ComputeStatistics( ); + + + ClusteringType::ParamsType *cparams = 0; + ClusteringType::ClusterResultType *cresult = 0; + ClusteringType::HistType *chist = 0; + ClusteringType::HelperStructPerformClusteringRetval *currentPerformClusteringResults; + + try{ + + + mitk::Image* tmpImg = histogramCalculator->GetInternalImage(); + mitk::Image::ConstPointer imgToCluster = tmpImg; + + if(imgToCluster.IsNotNull()) + { + + // perform clustering + const HistogramType *histogram = histogramCalculator->GetHistogram( ); + ClusteringType::Pointer clusterer = ClusteringType::New(); + clusterer->SetStepsNumIntegration(200); + clusterer->SetMaxIt(1000); + + mitk::Image::Pointer pFiberImg; + + currentPerformClusteringResults = + clusterer->PerformClustering(imgToCluster, histogram, 2); + + pFiberImg = currentPerformClusteringResults->clusteredImage; + cparams = currentPerformClusteringResults->params; + cresult = currentPerformClusteringResults->result; + chist = currentPerformClusteringResults->hist; + + + // m_Controls->m_HistogramWidget->SetParameters( + // cparams, cresult, chist ); + + + + std::vector *xVals = chist->GetXVals(); + + std::vector *fiberVals = new std::vector(cresult->GetFiberVals()); + + + + double fiberFA = 0.0; + double weights = 0.0; + + // std::cout << "x, y, fiber, nonFiber, mixed, combi" << std::endl; + for(int k=0; ksize(); ++k) + { + + fiberFA += xVals->at(k) * fiberVals->at(k); + weights += fiberVals->at(k); + + + } + + fiberFA = fiberFA / weights; + std::cout << "FA: " << fiberFA << std::endl; + values.push_back(fiberFA); + + } + + + } + + catch ( const std::runtime_error &e ) + { + std::cout << "noooooooooooooooooooooooooooooooo!"; + } + + //MITK_INFO << "number of voxels: " << indices.size(); + } + + std::vector::iterator it = values.begin(); + while(it!=values.end()) + { + std::cout << *it << std::endl; + ++it; + } + + } +} + + +void QmitkTractbasedSpatialStatisticsView::CreateRoi() +{ + + // It is important to load the MeanFASkeletonMask image in MITK to make sure that point selection and + // pathfinding is done on the same image + //string filename = m_TbssWorkspaceManager.GetInputDir().toStdString() + "/stats/" + m_TbssWorkspaceManager.GetMeanFASkeletonMask().toStdString(); + + // Implement a way to obtain skeleton and skeletonFA without sml workspace + + double threshold = QInputDialog::getDouble(m_Controls->m_CreateRoi, tr("Set an FA threshold"), + tr("Threshold:"), QLineEdit::Normal, + 0.2); + + + mitk::Image::Pointer image; + + for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); + i != m_CurrentSelection->End(); ++i) + { + // extract datatree node + if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) + { + mitk::DataNode::Pointer node = nodeObj->GetDataNode(); + + if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::Image* img = static_cast(node->GetData()); + if(img->GetDimension() == 3) + { + image = img; + } + } + } + } + + + + if(image.IsNull()) + { + return; + } + + mitk::TractAnalyzer analyzer; + analyzer.SetInputImage(image); + analyzer.SetThreshold(threshold); + + + + int n = 0; + if(m_PointSetNode.IsNotNull()) + { + n = m_PointSetNode->GetSize(); + if(n==0) + { + QMessageBox msgBox; + msgBox.setText("No points have been set yet."); + msgBox.exec(); + } + } + else{ + QMessageBox msgBox; + msgBox.setText("No points have been set yet."); + msgBox.exec(); + } + + std::string pathDescription = ""; + std::vector< itk::Index<3> > totalPath; + + if(n>0) + { + for(int i=0; iGetPoint(i); + mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1); + + + itk::Index<3> StartPoint; + itk::Index<3> EndPoint; + image->GetGeometry()->WorldToIndex(p,StartPoint); + image->GetGeometry()->WorldToIndex(p2,EndPoint); + MITK_INFO << "create roi"; + + + analyzer.BuildGraph(StartPoint, EndPoint); + std::vector< itk::Index<3> > path = analyzer.GetPath(); + + + for(std::vector< itk::Index<3> >::iterator it = path.begin(); + it != path.end(); it++) + { + itk::Index<3> ix = *it; + + if (!(ix==EndPoint)) + { + totalPath.push_back(ix); + std::stringstream ss; + ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n"; + pathDescription += ss.str(); + } + else + { + // Only when dealing with the last segment the last point should be added. This one will not occur + // as the first point of the next roi segment. + if(i == (n-2)) + { + totalPath.push_back(EndPoint); + std::stringstream ss; + ss << EndPoint[0] << " " << EndPoint[1] << " " << EndPoint[2] << "\n"; + pathDescription += ss.str(); + } + + } + } + + + + } + + m_Controls->m_PathTextEdit->setPlainText(QString(pathDescription.c_str())); + + + FloatImageType::Pointer itkImg = FloatImageType::New(); + mitk::CastToItkImage(image, itkImg); + + CharImageType::Pointer roiImg = CharImageType::New(); + roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize()); + roiImg->SetOrigin(itkImg->GetOrigin()); + roiImg->SetSpacing(itkImg->GetSpacing()); + roiImg->SetDirection(itkImg->GetDirection()); + roiImg->Allocate(); + roiImg->FillBuffer(0); + + + std::vector< itk::Index<3> > roi; + + std::vector< itk::Index<3> >::iterator it; + for(it = totalPath.begin(); + it != totalPath.end(); + it++) + { + itk::Index<3> ix = *it; + roiImg->SetPixel(ix, 1); + roi.push_back(ix); + } + + + mitk::TbssRoiImage::Pointer tbssRoi = mitk::TbssRoiImage::New(); + //mitk::CastToTbssImage(m_CurrentRoi.GetPointer(), tbssRoi); + tbssRoi->SetRoi(roi); + tbssRoi->SetImage(roiImg); + tbssRoi->SetStructure(m_Controls->m_Structure->text().toStdString()); + tbssRoi->InitializeFromImage(); + + + // mitk::Image::Pointer tbssRoi = mitk::Image::New(); + //mitk::CastToTbssImage(m_CurrentRoi.GetPointer(), tbssRoi); + // mitk::CastToMitkImage(roiImg, tbssRoi); + + AddTbssToDataStorage(tbssRoi, m_Controls->m_RoiName->text().toStdString()); + + } + +} + + + + + +void QmitkTractbasedSpatialStatisticsView::Plot(mitk::TbssImage* image, mitk::TbssRoiImage* roiImage) +{ + if(m_Controls->m_TabWidget->currentWidget() == m_Controls->m_MeasureTAB) + { + + std::vector< itk::Index<3> > roi = roiImage->GetRoi(); + m_Roi = roi; + m_CurrentGeometry = image->GetGeometry(); + + + std::string resultfile = ""; + + /* + if(image->GetPreprocessedFA()) + { + resultFile = image->GetPreprocessedFAFile(); + } + */ + std::string structure = roiImage->GetStructure(); + + + + //m_View->m_CurrentGeometry = image->GetGeometry(); + + m_Controls->m_RoiPlotWidget->SetGroups(image->GetGroupInfo()); + + + // Check for preprocessed results to save time + + //if(resultfile == "") + // { + // Need to calculate the results using the 4D volume + // Can save the time this takes if there are results available already + + //std::string type = m_Controls->m_MeasureType->itemText(m_Controls->m_MeasureType->currentIndex()).toStdString(); + m_Controls->m_RoiPlotWidget->SetProjections(image->GetImage()); + + + // } + + m_Controls->m_RoiPlotWidget->SetRoi(roi); + m_Controls->m_RoiPlotWidget->SetStructure(structure); + m_Controls->m_RoiPlotWidget->SetMeasure( image->GetMeasurementInfo() ); + m_Controls->m_RoiPlotWidget->DrawProfiles(resultfile); + } +} + + + + +void QmitkTractbasedSpatialStatisticsView::Masking() +{ + //QString filename = m_Controls->m_WorkingDirectory->text(); + QString filename = "E:/Experiments/tbss"; + QString faFiles = filename + "/AxD"; + QString maskFiles = filename + "/bin_masks"; + + + QDirIterator faDirIt(faFiles, QDir::Files | QDir::NoSymLinks, QDirIterator::Subdirectories); + QDirIterator maskDirIt(maskFiles, QDir::Files | QDir::NoSymLinks, QDirIterator::Subdirectories); + + std::vector faFilenames; + std::vector maskFilenames; + std::vector outputFilenames; + + while(faDirIt.hasNext() && maskDirIt.hasNext()) + { + faDirIt.next(); + maskDirIt.next(); + if((faDirIt.fileInfo().completeSuffix() == "nii" + || faDirIt.fileInfo().completeSuffix() == "mhd" + || faDirIt.fileInfo().completeSuffix() == "nii.gz") + && (maskDirIt.fileInfo().completeSuffix() == "nii" + || maskDirIt.fileInfo().completeSuffix() == "mhd" + || maskDirIt.fileInfo().completeSuffix() == "nii.gz")) + { + faFilenames.push_back(faDirIt.filePath().toStdString()); + outputFilenames.push_back(faDirIt.fileName().toStdString()); + maskFilenames.push_back(maskDirIt.filePath().toStdString()); + } + } + + std::vector::iterator faIt = faFilenames.begin(); + std::vector::iterator maskIt = maskFilenames.begin(); + std::vector::iterator outputIt = outputFilenames.begin(); + + // Now multiply all FA images with their corresponding masks + + QString outputDir = filename; + while(faIt != faFilenames.end() && maskIt != maskFilenames.end() && outputIt != outputFilenames.end()) + { + std::cout << "Mask " << *faIt << " with " << *maskIt << std::endl; + + typedef itk::MultiplyImageFilter MultiplicationFilterType; + + FloatReaderType::Pointer floatReader = FloatReaderType::New(); + CharReaderType::Pointer charReader = CharReaderType::New(); + + floatReader->SetFileName(*faIt); + //floatReader->Update(); + //FloatImageType::Pointer faImage = floatReader->GetOutput(); + + charReader->SetFileName(*maskIt); + //charReader->Update(); + // CharImageType::Pointer maskImage = charReader->GetOutput(); + + MultiplicationFilterType::Pointer multiplicationFilter = MultiplicationFilterType::New(); + multiplicationFilter->SetInput1(floatReader->GetOutput()); + multiplicationFilter->SetInput2(charReader->GetOutput()); + multiplicationFilter->Update(); + + //FloatImageType::Pointer maskedImage = FloatImageType::New(); + //maskedImage = MultiplicationFilter->GetOutput(); + + FloatWriterType::Pointer floatWriter = FloatWriterType::New(); + std::string s = faFiles.toStdString().append("/"+*outputIt); + floatWriter->SetFileName(s.c_str()); + floatWriter->SetInput(multiplicationFilter->GetOutput()); + floatWriter->Update(); + + ++faIt; + ++maskIt; + ++outputIt; + } +} +/* +void QmitkTractbasedSpatialStatisticsView::Project() +{ + + typedef itk::SkeletonizationFilter SkeletonizationFilter; + SkeletonizationFilter::Pointer skeletonizer = SkeletonizationFilter::New(); + + if (m_CurrentSelection) + { + mitk::DataStorage::SetOfObjects::Pointer set = + mitk::DataStorage::SetOfObjects::New(); + + + mitk::Image::Pointer vol4d; + mitk::TbssImage::Pointer tbssImg; + bool containsSkeleton = false; + bool containsSkeletonMask = false; + bool containsDistanceMap = false; + bool containsGradient = false; + + + for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); + i != m_CurrentSelection->End(); + ++i) + { + if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) + { + mitk::DataNode::Pointer node = nodeObj->GetDataNode(); + + if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::Image* img = static_cast(node->GetData()); + if(img->GetDimension() == 4) + { + // 4d volume + vol4d = img; + } + } + else if(QString("TbssImage").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::TbssImage::Pointer tempTbss = static_cast(node->GetData()); + if(tempTbss->GetIsMeta()) + { + containsDistanceMap = tempTbss->GetContainsDistanceMap(); + containsSkeleton = tempTbss->GetContainsDistanceMap(); + containsSkeletonMask = tempTbss->GetContainsSkeletonMask(); + containsGradient = tempTbss->GetContainsGradient(); + + + if(containsDistanceMap && containsSkeleton && containsSkeletonMask && containsGradient) + { + tbssImg = tempTbss; + } + } + } + } + } + + if(vol4d.IsNotNull() && tbssImg.IsNotNull()) + { + typedef itk::ProjectionFilter ProjectionFilterType; + ProjectionFilterType::Pointer projector = ProjectionFilterType::New(); + + VectorImageType::Pointer vecImg = ConvertToVectorImage(vol4d); + + + + } + } + + + +} +*/ + + +VectorImageType::Pointer QmitkTractbasedSpatialStatisticsView::ConvertToVectorImage(mitk::Image::Pointer mitkImage) +{ + VectorImageType::Pointer vecImg = VectorImageType::New(); + + mitk::Geometry3D* geo = mitkImage->GetGeometry(); + mitk::Vector3D spacing = geo->GetSpacing(); + mitk::Point3D origin = geo->GetOrigin(); + + VectorImageType::SpacingType vecSpacing; + vecSpacing[0] = spacing[0]; + vecSpacing[1] = spacing[1]; + vecSpacing[2] = spacing[2]; + + VectorImageType::PointType vecOrigin; + vecOrigin[0] = origin[0]; + vecOrigin[1] = origin[1]; + vecOrigin[2] = origin[2]; + + VectorImageType::SizeType size; + size[0] = mitkImage->GetDimension(0); + size[1] = mitkImage->GetDimension(1); + size[2] = mitkImage->GetDimension(2); + + + vecImg->SetSpacing(vecSpacing); + vecImg->SetOrigin(vecOrigin); + vecImg->SetRegions(size); + vecImg->SetVectorLength(mitkImage->GetDimension(3)); + vecImg->Allocate(); + + + for(int x=0; x pixel = vecImg->GetPixel(ix); + + for (int t=0; tGetPixelValueByIndex(ix, t); + pixel.SetElement(t, f); + } + vecImg->SetPixel(ix, pixel); + } + } + } + + return vecImg; + +} +/* +void QmitkTractbasedSpatialStatisticsView::Skeletonize() +{ + + typedef itk::SkeletonizationFilter SkeletonizationFilter; + SkeletonizationFilter::Pointer skeletonizer = SkeletonizationFilter::New(); + + if (m_CurrentSelection) + { + mitk::DataStorage::SetOfObjects::Pointer set = + mitk::DataStorage::SetOfObjects::New(); + + + for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); + i != m_CurrentSelection->End(); + ++i) + { + + if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) + { + mitk::DataNode::Pointer node = nodeObj->GetDataNode(); + if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) + { + mitk::Image* img = static_cast(node->GetData()); + if(img->GetDimension() == 3) + { + FloatImageType::Pointer itkImg = FloatImageType::New(); + mitk::CastToItkImage(img, itkImg); + skeletonizer->SetInput(itkImg); + skeletonizer->Update(); + + + // Retrieve skeletonize image and put it in the datamanager + FloatImageType::Pointer skeletonizedImg = skeletonizer->GetOutput(); + mitk::Image::Pointer mitkSkeleton = mitk::Image::New(); + mitk::CastToMitkImage(skeletonizedImg, mitkSkeleton); + AddTbssToDataStorage(mitkSkeleton, "Skeletonized"); + + double threshold = -1.0; + while(threshold == -1.0) + { + // threshold = QInputDialog::getDouble(m_Controls->m_Skeletonize, tr("Specify the FA threshold"), + // tr("Threshold:"), QLineEdit::Normal, + // 0.2); + + if(threshold < 0.0 || threshold > 1.0) + { + QMessageBox msgBox; + msgBox.setText("Please choose a value between 0 and 1"); + msgBox.exec(); + threshold = -1.0; + } + } + + typedef itk::BinaryThresholdImageFilter ThresholdFilterType; + CharImageType::Pointer thresholded = CharImageType::New(); + ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New(); + thresholder->SetInput(skeletonizedImg); + thresholder->SetLowerThreshold(threshold); + thresholder->SetUpperThreshold(std::numeric_limits::max()); + thresholder->SetOutsideValue(0); + thresholder->SetInsideValue(1); + thresholder->Update(); + + + CharImageType::Pointer thresholdedImg = thresholder->GetOutput(); + mitk::Image::Pointer mitkThresholded = mitk::Image::New(); + mitk::CastToMitkImage(thresholdedImg, mitkThresholded); + AddTbssToDataStorage(mitkThresholded, "Skeleton mask"); + + + typedef itk::DistanceMapFilter DistanceMapFilterType; + DistanceMapFilterType::Pointer distanceMapper = DistanceMapFilterType::New(); + distanceMapper->SetInput(thresholdedImg); + distanceMapper->Update(); + + FloatImageType::Pointer distanceMap = distanceMapper->GetOutput(); + mitk::Image::Pointer mitkDistMap = mitk::Image::New(); + mitk::CastToMitkImage(distanceMap, mitkDistMap); + AddTbssToDataStorage(mitkDistMap, "Distance map"); + + DirectionImageType::Pointer dirImage = skeletonizer->GetDirectionImage(); + + mitk::TbssGradientImage::Pointer tbssGradImg = mitk::TbssGradientImage::New(); + tbssGradImg->SetImage(dirImage); + tbssGradImg->InitializeFromVectorImage(); + AddTbssToDataStorage(tbssGradImg, "Gradient image"); + + } + } + } + } + } + + + +} + +/* +void QmitkTractbasedSpatialStatisticsView::InitializeGridByVectorImage() +{ + // Read vector image from file + typedef itk::ImageFileReader< FloatVectorImageType > VectorReaderType; + VectorReaderType::Pointer vectorReader = VectorReaderType::New(); + vectorReader->SetFileName("E:\\tbss\\testing\\Gradient.mhd"); + vectorReader->Update(); + FloatVectorImageType::Pointer directions = vectorReader->GetOutput(); + + + // Read roi from file. + CharReaderType::Pointer roiReader = CharReaderType::New(); + roiReader->SetFileName("E:\\tbss\\testing\\debugging skeletonization\\segment2.mhd"); + roiReader->Update(); + CharImageType::Pointer roi = roiReader->GetOutput(); + + DoInitializeGridByVectorImage(directions, roi, std::string("directions")); + + +} + + + + +void QmitkTractbasedSpatialStatisticsView::DoInitializeGridByVectorImage(FloatVectorImageType::Pointer vectorpic, CharImageType::Pointer roi, std::string name) +{ + //vtkStructuredGrid* grid = vtkStructuredGrid::New(); + itk::Matrix itkdirection = vectorpic->GetDirection(); + itk::Matrix itkinversedirection = itk::Matrix(itkdirection.GetInverse()); + std::vector GridPoints; + vtkPoints *points = vtkPoints::New(); + mitk::Geometry3D::Pointer geom = mitk::Geometry3D::New(); + vtkLinearTransform *vtktransform; + vtkLinearTransform *inverse; + mitk::Image::Pointer geomget = mitk::Image::New(); + geomget->InitializeByItk(vectorpic.GetPointer()); + geom = geomget->GetGeometry(); + vtktransform = geom->GetVtkTransform(); + inverse = vtktransform->GetLinearInverse(); + vtkFloatArray * directions = vtkFloatArray::New(); + directions->SetName("Vectors"); + directions->SetNumberOfComponents(3); + + // Iterator for the vector image + itk::ImageRegionIterator it_input(vectorpic, vectorpic->GetLargestPossibleRegion()); + FloatVectorType nullvector; + nullvector.Fill(0); + double lengthsum = 0; + int id = 0; + + // Iterator for the roi + itk::ImageRegionIterator roiIt(roi, roi->GetLargestPossibleRegion()); + roiIt.GoToBegin(); + + for(it_input.GoToBegin(); !( it_input.IsAtEnd() || roiIt.IsAtEnd() ); ++it_input) + { + //VectorType val = it_input.Value(); + if(it_input.Value() != nullvector && roiIt.Get() != 0) + { + //itk::Point point; + mitk::Point3D mitkpoint, mitkworldpoint; + mitk::Point3D mitkendpoint, mitkworldendpoint; + mitk::Vector3D mitkvector, mitktransvector; + itk::Point direction = it_input.Value().GetDataPointer(); + //itk::Index<3> in_input = it_input.GetIndex(); + //itk::ContinuousIndex cindirection; + FloatVectorType transvec = it_input.Value(); + mitkvector[0] = transvec[0]; + mitkvector[1] = transvec[1]; + mitkvector[2] = transvec[2]; + //mitkvector[2] = 0.0; + + + mitkpoint[0] = it_input.GetIndex()[0]; + mitkpoint[1] = it_input.GetIndex()[1]; + mitkpoint[2] = it_input.GetIndex()[2]; + + mitkendpoint[0] = mitkpoint[0] + mitkvector[0]; + mitkendpoint[1] = mitkpoint[1] + mitkvector[1]; + mitkendpoint[2] = mitkpoint[2] + mitkvector[2]; + + //mitkpoint.setXYZ((ScalarType)point[0],(ScalarType)point[1],(ScalarType)point[2]); + geom->IndexToWorld(mitkpoint, mitkworldpoint); + geom->IndexToWorld(mitkendpoint, mitkworldendpoint); + mitktransvector[0] = mitkworldendpoint[0] - mitkworldpoint[0]; + mitktransvector[1] = mitkworldendpoint[1] - mitkworldpoint[1]; + mitktransvector[2] = mitkworldendpoint[2] - mitkworldpoint[2]; + + lengthsum += mitktransvector.GetNorm(); + + directions->InsertTuple3(id,mitktransvector[0],mitktransvector[1],mitktransvector[2]); + + points->InsertPoint(id,mitkworldpoint[0],mitkworldpoint[1],mitkworldpoint[2]); + id++; + //for (unsigned short loop = 0; (loop < 20) && (!it_input.IsAtEnd()); loop++) + //{ + // ++it_input; + //} + if(it_input.IsAtEnd()) + { + break; + } + } + ++roiIt; + } + double meanlength = lengthsum / id; + vtkGlyph3D* glyph = vtkGlyph3D::New(); + vtkUnstructuredGrid* ugrid = vtkUnstructuredGrid::New(); + ugrid->SetPoints(points); + ugrid->GetPointData()->SetVectors(directions); + glyph->SetInput(ugrid); + glyph->SetScaleModeToScaleByVector(); + glyph->SetScaleFactor(0.5); + glyph->SetColorModeToColorByScalar(); + //glyph->ClampingOn(); + vtkArrowSource* arrow = vtkArrowSource::New(); + if(meanlength > 5) {arrow->SetTipLength(0);arrow->SetTipRadius(0);} + + arrow->SetShaftRadius(0.03/meanlength); + //arrow->SetTipRadius(0.05/meanlength); + + glyph->SetSource(arrow->GetOutput()); + glyph->Update(); + + mitk::Surface::Pointer glyph_surface = mitk::Surface::New(); + + glyph_surface->SetVtkPolyData(glyph->GetOutput()); + glyph_surface->UpdateOutputInformation(); + + mitk::DataNode::Pointer gridNode = mitk::DataNode::New(); + gridNode->SetProperty( "name", mitk::StringProperty::New(name.c_str()) ); + //m_GridNode->SetProperty( "color" , m_GridColor); + gridNode->SetProperty( "visible", mitk::BoolProperty::New(true) ); + gridNode->SetProperty( "segmentation", mitk::BoolProperty::New(true) ); + gridNode->SetProperty( "ID-Tag", mitk::StringProperty::New("grid") ); + gridNode->SetProperty( "shader", mitk::StringProperty::New("mitkShaderLightning") ); + gridNode->SetData( glyph_surface ); + GetDefaultDataStorage()->Add(gridNode); + + +} + +*/ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h new file mode 100644 index 0000000000..c2eb8883e4 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h @@ -0,0 +1,252 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ +Version: $Revision: 21975 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html 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 QmitkTractbasedSpatialStatisticsView_h +#define QmitkTractbasedSpatialStatisticsView_h + + +#include +#include +#include + + +#include + +#include "ui_QmitkTractbasedSpatialStatisticsViewControls.h" +#include + +#include +#include + +#include +#include +#include + +#include + +#include +#include + +#include "QmitkTbssTableModel.h" +#include "QmitkTbssMetaTableModel.h" + + + + +typedef short DiffusionPixelType; +typedef itk::Image CharImageType; +typedef itk::Image UCharImageType; +typedef itk::Image Float4DImageType; +typedef itk::Image FloatImageType; +typedef itk::Vector IntVectorType; +typedef itk::VectorImage DirectionImageType; +typedef itk::VectorImage VectorImageType; + + +typedef itk::ImageFileReader< CharImageType > CharReaderType; +typedef itk::ImageFileReader< UCharImageType > UCharReaderType; +typedef itk::ImageFileWriter< CharImageType > CharWriterType; +typedef itk::ImageFileReader< FloatImageType > FloatReaderType; +typedef itk::ImageFileWriter< FloatImageType > FloatWriterType; +typedef itk::ImageFileReader< Float4DImageType > Float4DReaderType; +typedef itk::ImageFileWriter< Float4DImageType > Float4DWriterType; + + +struct TbssSelListener; + + + +/*! + \brief QmitkTractbasedSpatialStatisticsView + + \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. + + \sa QmitkFunctionalitymitkTbssWorkspaceManager + \ingroup Functionalities +*/ +class QmitkTractbasedSpatialStatisticsView : public QmitkFunctionality +{ + + + friend struct TbssSelListener; + + + + // this is needed for all Qt objesetupUicts 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; + + QmitkTractbasedSpatialStatisticsView(); + virtual ~QmitkTractbasedSpatialStatisticsView(); + + virtual void CreateQtPartControl(QWidget *parent); + + /// \brief Creation of the connections of main and control widget + virtual void CreateConnections(); + + virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); + virtual void StdMultiWidgetNotAvailable(); + + /// \brief Called when the functionality is activated + virtual void Activated(); + + virtual void Deactivated(); + + + protected slots: + + + //void OutputValues(); + + + + // void InitializeGridByVectorImage(); + + void Masking(); + + + + void CreateRoi(); + + + void Clustering(); + + void AdjustPlotMeasure(const QString & text); + + void Clicked(const QwtDoublePoint& pos); + + void TbssImport(); + + + void AddGroup(); + void RemoveGroup(); + + void CopyToClipboard(); + + + + protected: + + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector nodes ); + + void Plot(mitk::TbssImage*, mitk::TbssRoiImage*); + + void InitPointsets(); + + void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); + + berry::ISelectionListener::Pointer m_SelListener; + berry::IStructuredSelection::ConstPointer m_CurrentSelection; + + bool m_IsInitialized; + + mitk::PointSet::Pointer m_PointSetNode; + mitk::DataNode::Pointer m_P1; + + Ui::QmitkTractbasedSpatialStatisticsViewControls* m_Controls; + + QmitkStdMultiWidget* m_MultiWidget; + + + std::vector SortPoints(CharImageType::Pointer roi, CharImageType::IndexType currentPoint); + + bool PointVisited(std::vector points, CharImageType::IndexType point); + + // Modifies the current point by reference and returns true if no more points need to be visited + CharImageType::IndexType FindNextPoint(std::vector pointsVisited, + CharImageType::IndexType currentPoint, CharImageType::Pointer roi, bool &ready); + + + + + //void DoInitializeGridByVectorImage(FloatVectorImageType::Pointer vectorpic, CharImageType::Pointer roi ,std::string name); + + + + // Tokenizer needed for the roi files + void Tokenize(const std::string& str, + std::vector& tokens, + const std::string& delimiters = " ") + { + // Skip delimiters at beginning. + std::string::size_type lastPos = str.find_first_not_of(delimiters, 0); + // Find first "non-delimiter". + std::string::size_type pos = str.find_first_of(delimiters, lastPos); + + while (std::string::npos != pos || std::string::npos != lastPos) + { + // Found a token, add it to the vector. + tokens.push_back(str.substr(lastPos, pos - lastPos)); + // Skip delimiters. Note the "not_of" + lastPos = str.find_first_not_of(delimiters, pos); + // Find next "non-delimiter" + pos = str.find_first_of(delimiters, lastPos); + } + } + + mitk::DataNode::Pointer readNode(std::string f) + { + mitk::DataNode::Pointer node; + mitk::DataNodeFactory::Pointer nodeReader = mitk::DataNodeFactory::New(); + try + { + nodeReader->SetFileName(f); + nodeReader->Update(); + node = nodeReader->GetOutput(); + } + catch(...) { + MITK_ERROR << "Could not read file"; + return NULL; + } + + return node; + } + + /*template < typename TPixel, unsigned int VImageDimension > + void ToITK4D( itk::Image* inputImage, Float4DImageType::Pointer& outputImage );*/ + + + std::string ReadFile(std::string whatfile); + + + std::vector< itk::Index<3> > m_Roi; + + std::string m_CurrentStructure; + + mitk::Geometry3D* m_CurrentGeometry; + + QmitkTbssTableModel* m_GroupModel; + + + + void AddTbssToDataStorage(mitk::Image* image, std::string name); + + mitk::TbssImage::Pointer m_CurrentTbssMetaImage; + + VectorImageType::Pointer ConvertToVectorImage(mitk::Image::Pointer mitkImg); + +}; + + + +#endif // _QMITKTRACTBASEDSPATIALSTATISTICSVIEW_H_INCLUDED + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui new file mode 100644 index 0000000000..0ac2df05ff --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui @@ -0,0 +1,402 @@ + + + QmitkTractbasedSpatialStatisticsViewControls + + + + 0 + 0 + 431 + 811 + + + + + 0 + 0 + + + + QmitkTemplate + + + + + + FSL import + + + false + + + false + + + + + + Here subject data and tbss meta data can be imported from FSL into the MITK TBSS module + + + 0 + + + + Subject data + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + + + Group information + + + QAbstractItemView::SelectRows + + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + + + Add group entry. After that give the group a name and the correct number + + + Add + + + + + + + Remove selected entries + + + Remove + + + + + + + false + + + Import a 4D image containing group data after group information has been set + + + Import subject data + + + + + + + + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + + + Diffusion measure + + + + + + + Measurement in the to be imported 4D image + + + Fractional Anisotropy + + + + + + + + + + + Meta data + + + + + + true + + + Meta data + + + QAbstractItemView::SelectRows + + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + + + Select the function of the tbss image + + + + Add skeleton mask + + + + + Add mean FA Skeleton + + + + + Add gradient image + + + + + Add tubular structure + + + + + Add distance map + + + + + + + + Remove meta data entries + + + Remove + + + + + + + Create a tbss meta image with the images in the table. + + + Create TBSS meta file + + + + + + + + + + + + + + + + + Tract-specific analysis + + + + + + true + + + To create a roi first load a tbss meta image into the datamanager + + + 1 + + + + ROIs + + + + QFormLayout::AllNonFixedFieldsGrow + + + + + current selection + + + mean FA skeleton: + + + + + + + Points on Roi + + + + + + + + 100 + 100 + + + + + 0 + 100 + + + + Use this widget to create points on the ROI by shift-leftclick on the right positions on the skeleton. Then click Create Roi. The Roi that will be created will pass through the points in the order of occurence in this list + + + + + + + false + + + No suitable tbss meta image selected yet. The meta image needs to contain a mean FA skeleton and a skeleton mask + + + Create ROI + + + + + + + + 0 + 0 + + + + Points on the ROI + + + + + + + Name + + + + + + + Give a name to the region of interest + + + roiname + + + + + + + Structure info + + + + + + + On what anatomical structure lies the ROI? + + + Structure + + + + + + + + Measuring + + + + + + To plot, load a tbss image with subject information and a region of interest corresponding to the study and select them both + + + + + + + Copy to clipboard + + + + + + + + + + + + + + + + QmitkPointListWidget + QWidget +
QmitkPointListWidget.h
+ + + QmitkTbssRoiAnalysisWidget + QWidget +
QmitkTbssRoiAnalysisWidget.h
+ 1 + + + + + diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp index 5ff89f0889..988aa100a2 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp @@ -1,52 +1,54 @@ #include "mitkPluginActivator.h" #include #include "src/internal/QmitkDiffusionImagingPublicPerspective.h" #include "src/internal/QmitkQBallReconstructionView.h" #include "src/internal/QmitkPreprocessingView.h" #include "src/internal/QmitkDiffusionDicomImportView.h" #include "src/internal/QmitkDiffusionQuantificationView.h" #include "src/internal/QmitkTensorReconstructionView.h" #include "src/internal/QmitkControlVisualizationPropertiesView.h" #include "src/internal/QmitkODFDetailsView.h" #include "src/internal/QmitkGibbsTrackingView.h" #include "src/internal/QmitkStochasticFiberTrackingView.h" #include "src/internal/QmitkFiberProcessingView.h" #include "src/internal/QmitkFiberBundleDeveloperView.h" #include "src/internal/QmitkPartialVolumeAnalysisView.h" #include "src/internal/QmitkIVIMView.h" #include "src/internal/QmitkScreenshotMaker.h" +#include "src/internal/QmitkTractbasedSpatialStatisticsView.h" namespace mitk { void PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingPublicPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStochasticFiberTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberBundleDeveloperView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPartialVolumeAnalysisView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkScreenshotMaker, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkTractbasedSpatialStatisticsView, context) } void PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) } } Q_EXPORT_PLUGIN2(org_mitk_gui_qt_diffusionimaging, mitk::PluginActivator)