diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp index f12d2b0feb..796e8992b8 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp @@ -1,239 +1,240 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPeakImageMapper2D.h" #include "mitkBaseRenderer.h" #include "mitkDataNode.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include class vtkPeakShaderCallback : public vtkCommand { public: static vtkPeakShaderCallback *New() { return new vtkPeakShaderCallback; } mitk::BaseRenderer *renderer; mitk::DataNode *node; void Execute(vtkObject *, unsigned long, void*cbo) override { vtkOpenGLHelper *cellBO = reinterpret_cast(cbo); mitk::Image* image = dynamic_cast(node->GetData()); mitk::Vector3D spacing = image->GetGeometry()->GetSpacing(); float minSpacing = 1; if(spacing[0]GetOpacity(peakOpacity, nullptr); cellBO->Program->SetUniformf("peakOpacity", peakOpacity); cellBO->Program->SetUniformf("clippingPlaneThickness", minSpacing/2); if (this->renderer) { //get information about current position of views mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); //generate according cutting planes based on the view position float planeNormal[3]; planeNormal[0] = planeGeo->GetNormal()[0]; planeNormal[1] = planeGeo->GetNormal()[1]; planeNormal[2] = planeGeo->GetNormal()[2]; float tmp1 = planeGeo->GetOrigin()[0] * planeNormal[0]; float tmp2 = planeGeo->GetOrigin()[1] * planeNormal[1]; float tmp3 = planeGeo->GetOrigin()[2] * planeNormal[2]; float thickness = tmp1 + tmp2 + tmp3; //attention, correct normalvector float* a = new float[4]; for (int i = 0; i < 3; ++i) a[i] = planeNormal[i]; a[3] = thickness; cellBO->Program->SetUniform4f("slicingPlane", a); } } vtkPeakShaderCallback() { this->renderer = 0; } }; mitk::PeakImageMapper2D::PeakImageMapper2D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::PeakImageMapper2D::~PeakImageMapper2D() { } mitk::PeakImage* mitk::PeakImageMapper2D::GetInput() { return dynamic_cast< mitk::PeakImage * > ( GetDataNode()->GetData() ); } void mitk::PeakImageMapper2D::UpdateVtkTransform(mitk::BaseRenderer *) { // don't apply transform since the peak polydata is already in world coordinates. return; } void mitk::PeakImageMapper2D::Update(mitk::BaseRenderer * renderer) { mitk::DataNode* node = this->GetDataNode(); if (node == nullptr) return; bool visible = true; node->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; this->GenerateDataForRenderer( renderer ); } void mitk::PeakImageMapper2D::UpdateShaderParameter(mitk::BaseRenderer *) { // see new vtkPeakShaderCallback } // vtkActors and Mappers are feeded here void mitk::PeakImageMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { mitk::PeakImage* peakImage = this->GetInput(); //the handler of local storage gets feeded in this method with requested data for related renderwindow FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); vtkSmartPointer polyData = peakImage->GetPolyData(); if (polyData == nullptr) return; localStorage->m_Mapper->ScalarVisibilityOn(); localStorage->m_Mapper->SetScalarModeToUsePointFieldData(); localStorage->m_Mapper->SetLookupTable(m_lut); //apply the properties after the slice was set // localStorage->m_PointActor->GetProperty()->SetOpacity(0.999); localStorage->m_Mapper->SelectColorArray("FIBER_COLORS"); localStorage->m_Mapper->SetInputData(polyData); localStorage->m_Mapper->SetVertexShaderCode( "//VTK::System::Dec\n" "attribute vec4 vertexMC;\n" "//VTK::Normal::Dec\n" "uniform mat4 MCDCMatrix;\n" "//VTK::Color::Dec\n" "varying vec4 positionWorld;\n" "varying vec4 colorVertex;\n" "void main(void)\n" "{\n" " colorVertex = scalarColor;\n" " positionWorld = vertexMC;\n" " gl_Position = MCDCMatrix * vertexMC;\n" "}\n" ); localStorage->m_Mapper->SetFragmentShaderCode( "//VTK::System::Dec\n" // always start with this line "//VTK::Output::Dec\n" // always have this line in your FS "uniform vec4 slicingPlane;\n" "uniform float clippingPlaneThickness;\n" "uniform float peakOpacity;\n" "varying vec4 positionWorld;\n" "varying vec4 colorVertex;\n" + "out vec4 out_Color;\n" "void main(void)\n" "{\n" " float r1 = dot(positionWorld.xyz, slicingPlane.xyz) - slicingPlane.w;\n" " if (abs(r1) >= clippingPlaneThickness)\n" " discard;\n" - " gl_FragColor = vec4(colorVertex.xyz,peakOpacity);\n" + " out_Color = vec4(colorVertex.xyz,peakOpacity);\n" "}\n" ); vtkSmartPointer myCallback = vtkSmartPointer::New(); myCallback->renderer = renderer; myCallback->node = this->GetDataNode(); localStorage->m_Mapper->AddObserver(vtkCommand::UpdateShaderEvent,myCallback); localStorage->m_PointActor->SetMapper(localStorage->m_Mapper); localStorage->m_PointActor->GetProperty()->ShadingOn(); float linewidth = 1.0; this->GetDataNode()->GetFloatProperty("shape.linewidth",linewidth); localStorage->m_PointActor->GetProperty()->SetLineWidth(linewidth); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } vtkProp* mitk::PeakImageMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { this->Update(renderer); return m_LocalStorageHandler.GetLocalStorage(renderer)->m_PointActor; } void mitk::PeakImageMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { Superclass::SetDefaultProperties(node, renderer, overwrite); //add other parameters to propertylist node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite); node->AddProperty( "shape.linewidth", mitk::FloatProperty::New(1.0), renderer, overwrite); } mitk::PeakImageMapper2D::FBXLocalStorage::FBXLocalStorage() { m_PointActor = vtkSmartPointer::New(); m_Mapper = vtkSmartPointer::New(); } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp index 366e1d3577..3a4b97baa2 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,1295 +1,1295 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkImageStatisticsView.h" // Qt includes #include #include #include // berry includes #include // mitk includes #include #include #include #include #include #include #include // itk includes #include "itksys/SystemTools.hxx" #include "itkImageRegionConstIteratorWithIndex.h" #include //blueberry includes #include #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; const int QmitkImageStatisticsView::STAT_TABLE_BASE_HEIGHT = 180; QmitkImageStatisticsView::QmitkImageStatisticsView(QObject* /*parent*/, const char* /*name*/) : m_Controls( nullptr ), m_SelectedImage( nullptr ), m_SelectedImageMask( nullptr ), m_SelectedPlanarFigure( nullptr ), m_ImageObserverTag( -1 ), m_ImageMaskObserverTag( -1 ), m_PlanarFigureObserverTag( -1 ), m_TimeObserverTag( -1 ), m_CurrentStatisticsValid( false ), m_StatisticsUpdatePending( false ), m_DataNodeSelectionChanged ( false ), m_Visible(false) { this->m_CalculationThread = new QmitkImageStatisticsCalculationThread; } QmitkImageStatisticsView::~QmitkImageStatisticsView() { if ( m_SelectedImage != nullptr ) m_SelectedImage->RemoveObserver( m_ImageObserverTag ); if ( m_SelectedImageMask != nullptr ) m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); if ( m_SelectedPlanarFigure != nullptr ) m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); while(this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } delete this->m_CalculationThread; } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { if (m_Controls == nullptr) { m_Controls = new Ui::QmitkImageStatisticsViewControls; m_Controls->setupUi(parent); CreateConnections(); m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_Controls->m_BinSizeFrame->setEnabled(false); #if QT_VERSION < QT_VERSION_CHECK(5, 10, 0) m_Controls->m_StatisticsWidgetStack->setVisible(false); m_Controls->label_HistogramIsInvisibleWarning->setEnabled(true); m_Controls->label_HistogramIsInvisibleWarning->setVisible(true); m_Controls->label_HistogramIsInvisibleWarning->setText("Histogram is not visible because Qt 5.10 is required. You can use the button Copy to Clipboard below to retrieve values."); m_Controls->groupBox_plot->setVisible(false); #else m_Controls->label_HistogramIsInvisibleWarning->setVisible(false); #endif } } void QmitkImageStatisticsView::OnPageSuccessfullyLoaded() { berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, ""); if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss") { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::darkstyle); } else { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::lightstyle); } } void QmitkImageStatisticsView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(this->m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardHistogramButtonClicked()) ); connect( (QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardStatisticsButtonClicked()) ); connect( (QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()),(QObject*) this, SLOT(OnIgnoreZerosCheckboxClicked()) ); connect( (QObject*) this->m_CalculationThread, SIGNAL(finished()),this, SLOT( OnThreadedStatisticsCalculationEnds()),Qt::QueuedConnection); connect( (QObject*) this, SIGNAL(StatisticsUpdate()),this, SLOT( RequestStatisticsUpdate()), Qt::QueuedConnection); connect( (QObject*) this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int,int)),this, SLOT( JumpToCoordinates(int,int)) ); connect((QObject*)(this->m_Controls->m_barRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnBarRadioButtonSelected())); connect((QObject*)(this->m_Controls->m_lineRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnLineRadioButtonSelected())); connect( (QObject*) (this->m_Controls->m_HistogramNBinsSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramNBinsCheckBoxValueChanged())); connect((QObject*)(this->m_Controls->m_UseDefaultNBinsCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnDefaultNBinsSpinBoxChanged())); connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnShowSubchartBoxChanged())); connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); } } void QmitkImageStatisticsView::OnDefaultNBinsSpinBoxChanged() { if (this->m_Controls->m_UseDefaultNBinsCheckBox->isChecked()) { m_Controls->m_HistogramNBinsSpinbox->setValue(100); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); } m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultNBinsCheckBox->isChecked()); this->UpdateStatistics(); } void QmitkImageStatisticsView::OnShowSubchartBoxChanged() { bool showSubchart = this->m_Controls->m_ShowSubchartCheckBox->isChecked(); this->m_Controls->m_JSHistogram->Reload(showSubchart); } void QmitkImageStatisticsView::OnBarRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::bar); } void QmitkImageStatisticsView::OnLineRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::line); } void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& ) { } void QmitkImageStatisticsView::OnTimeChanged(const itk::EventObject& e) { if (this->m_SelectedDataNodes.isEmpty() || this->m_SelectedImage == nullptr) return; const mitk::SliceNavigationController::GeometryTimeEvent* timeEvent = dynamic_cast(&e); assert(timeEvent != nullptr); int timestep = timeEvent->GetPos(); if (this->m_SelectedImage->GetTimeSteps() > 1) { for (int x = 0; x < this->m_Controls->m_StatisticsTable->columnCount(); x++) { for (int y = 0; y < this->m_Controls->m_StatisticsTable->rowCount(); y++) { QTableWidgetItem* item = this->m_Controls->m_StatisticsTable->item(y, x); if (item == nullptr) break; if (x == timestep) { item->setBackgroundColor(Qt::yellow); } else { if (y % 2 == 0) item->setBackground(this->m_Controls->m_StatisticsTable->palette().base()); else item->setBackground(this->m_Controls->m_StatisticsTable->palette().alternateBase()); } } } this->m_Controls->m_StatisticsTable->viewport()->update(); } if ((this->m_SelectedImage->GetTimeSteps() == 1 && timestep == 0) || this->m_SelectedImage->GetTimeSteps() > 1) { // display histogram for selected timestep this->m_Controls->m_JSHistogram->Clear(); QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer histogram = (QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep); if (histogram.IsNotNull()) { bool closedFigure = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag(); if (closedFigure) { auto imageNameLabel = m_Controls->m_SelectedFeatureImageLabel->text().toStdString(); this->m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram), imageNameLabel); if (this->m_Controls->m_lineRadioButton->isChecked()) { this->m_Controls->m_JSHistogram->SetChartType(imageNameLabel, QmitkChartWidget::ChartType::line); } else { this->m_Controls->m_JSHistogram->SetChartType(imageNameLabel, QmitkChartWidget::ChartType::bar); } this->m_Controls->m_JSHistogram->SetXAxisLabel("Grey value"); this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); this->m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); } } } } void QmitkImageStatisticsView::JumpToCoordinates(int row ,int col) { if(m_SelectedDataNodes.isEmpty()) { MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation." ; return; } mitk::Point3D world; if (row==5 && !m_WorldMinList.empty()) world = m_WorldMinList[col]; else if (row==4 && !m_WorldMaxList.empty()) world = m_WorldMaxList[col]; else return; mitk::IRenderWindowPart* part = this->GetRenderWindowPart(); if (part) { part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SelectSliceByPoint(world); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), col); part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetGeometryTime(timeEvent); } } void QmitkImageStatisticsView::OnIgnoreZerosCheckboxClicked() { emit StatisticsUpdate(); } void QmitkImageStatisticsView::OnClipboardHistogramButtonClicked() { if (!m_CurrentStatisticsValid) { QApplication::clipboard()->clear(); } if (m_SelectedPlanarFigure == nullptr) { const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); typedef mitk::ImageStatisticsCalculator::HistogramType HistogramType; const HistogramType *histogram = this->m_CalculationThread->GetTimeStepHistogram(t).GetPointer(); QString clipboard("Measurement \t Frequency\n"); for (HistogramType::ConstIterator it = histogram->Begin(); it != histogram->End(); ++it) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(it.GetMeasurementVector()[0], 0, 'f', 2) .arg(it.GetFrequency()); } QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard); } //If a (non-closed) PlanarFigure is selected, display a line profile widget else if (m_SelectedPlanarFigure != nullptr) { QString clipboard("Pixel \t Intensity\n"); - for (auto i = 0; i < m_IntensityProfileList.size(); i++) + for (unsigned int i = 0; i < m_IntensityProfileList.size(); i++) { clipboard = clipboard.append("%L1 \t %L2\n").arg(QString::number(i)).arg(QString::number(m_IntensityProfileList.at(i))); } QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } } void QmitkImageStatisticsView::OnClipboardStatisticsButtonClicked() { QLocale tempLocal; QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates)); if ( m_CurrentStatisticsValid && !( m_SelectedPlanarFigure != nullptr)) { const std::vector &statistics = this->m_CalculationThread->GetStatisticsData(); // Set time borders for for loop ;) unsigned int startT, endT; if(this->m_Controls->m_CheckBox4dCompleteTable->checkState()==Qt::CheckState::Unchecked) { startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> GetPos(); endT = startT+1; } else { startT = 0; endT = statistics.size(); } QVector< QVector > statisticsTable; QStringList headline{ "Timestep", "Mean", "Median", "StdDev", "RMS", "Max", "Min", "NumberOfVoxels", "Skewness", "Kurtosis", "Uniformity", "Entropy", "MPP", "UPP", "V [mm³]" }; for(int i=0;i row; row.append(headline.at(i)); statisticsTable.append(row); } // Fill Table for(unsigned int t=startT;tGetMean()) << QString::number(statistics[t]->GetMedian()) << QString::number(statistics[t]->GetStd()) << QString::number(statistics[t]->GetRMS()) << QString::number(statistics[t]->GetMax()) << QString::number(statistics[t]->GetMin()) << QString::number(statistics[t]->GetN()) << QString::number(statistics[t]->GetSkewness()) << QString::number(statistics[t]->GetKurtosis()) << QString::number(statistics[t]->GetUniformity()) << QString::number(statistics[t]->GetEntropy()) << QString::number(statistics[t]->GetMPP()) << QString::number(statistics[t]->GetUPP()) << QString::number(m_Controls->m_StatisticsTable->item(7, 0)->data(Qt::DisplayRole).toDouble()); for(int z=0;zsetText(clipboard, QClipboard::Clipboard); } else { QApplication::clipboard()->clear(); } QLocale::setDefault(tempLocal); } void QmitkImageStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*part*/, const QList &nodes ) { if (this->m_Visible) { this->SelectionChanged( nodes ); } else { this->m_DataNodeSelectionChanged = true; } } void QmitkImageStatisticsView::SelectionChanged(const QList &selectedNodes) { //Clear Histogram if data node is deselected m_Controls->m_JSHistogram->Clear(); if( this->m_StatisticsUpdatePending ) { this->m_DataNodeSelectionChanged = true; return; // not ready for new data now! } if (selectedNodes.size() == this->m_SelectedDataNodes.size()) { int i = 0; for (; i < selectedNodes.size(); ++i) { if (selectedNodes.at(i) != this->m_SelectedDataNodes.at(i)) { break; } } // node selection did not change if (i == selectedNodes.size()) return; } //reset the feature image and image mask field m_Controls->m_SelectedFeatureImageLabel->setText("None"); m_Controls->m_SelectedMaskLabel->setText("None"); this->ReinitData(); if (selectedNodes.isEmpty()) { DisableHistogramGUIElements(); } else { EnableHistogramGUIElements(); ResetHistogramGUIElementsToDefault(); } if(selectedNodes.size() == 1 || selectedNodes.size() == 2) { bool isBinary = false; selectedNodes.value(0)->GetBoolProperty("binary",isBinary); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); isBinary |= isLabelSet->CheckNode(selectedNodes.value(0)); if(isBinary) { EnableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); } for (int i= 0; i< selectedNodes.size(); ++i) { this->m_SelectedDataNodes.push_back(selectedNodes.at(i)); } this->m_DataNodeSelectionChanged = false; this->m_Controls->m_ErrorMessageLabel->setText( "" ); this->m_Controls->m_ErrorMessageLabel->hide(); emit StatisticsUpdate(); } else { this->m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::DisableHistogramGUIElements() { m_Controls->m_InfoLabel->setText(""); m_Controls->groupBox_histogram->setEnabled(false); m_Controls->groupBox_statistics->setEnabled(false); } void QmitkImageStatisticsView::ResetHistogramGUIElementsToDefault() { m_Controls->m_barRadioButton->setChecked(true); m_Controls->m_HistogramNBinsSpinbox->setValue(100); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); m_Controls->m_UseDefaultNBinsCheckBox->setChecked(true); m_Controls->m_ShowSubchartCheckBox->setChecked(true); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_HistogramNBinsSpinbox->setEnabled(true); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); } void QmitkImageStatisticsView::EnableHistogramGUIElements() { m_Controls->groupBox_histogram->setEnabled(true); m_Controls->groupBox_plot->setEnabled(true); m_Controls->groupBox_statistics->setEnabled(true); } void QmitkImageStatisticsView::ReinitData() { while( this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } if(this->m_SelectedImage != nullptr) { this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag); this->m_SelectedImage = nullptr; } if(this->m_SelectedImageMask != nullptr) { this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag); this->m_SelectedImageMask = nullptr; } if(this->m_SelectedPlanarFigure != nullptr) { this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag); this->m_SelectedPlanarFigure = nullptr; } this->m_SelectedDataNodes.clear(); this->m_StatisticsUpdatePending = false; m_Controls->m_ErrorMessageLabel->setText( "" ); m_Controls->m_ErrorMessageLabel->hide(); this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); } void QmitkImageStatisticsView::OnThreadedStatisticsCalculationEnds() { m_Controls->m_ErrorMessageLabel->setText(""); m_Controls->m_ErrorMessageLabel->hide(); this->WriteStatisticsToGUI(); } void QmitkImageStatisticsView::UpdateStatistics() { mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart(); if ( renderPart == nullptr ) { this->m_StatisticsUpdatePending = false; return; } m_WorldMinList.clear(); m_WorldMaxList.clear(); // classify selected nodes mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateOr::Pointer imagePredicate = mitk::NodePredicateOr::New(isImage, isLabelSet); std::string maskName; std::string maskType; std::string featureImageName; unsigned int maskDimension = 0; // reset data from last run ITKCommandType::Pointer changeListener = ITKCommandType::New(); changeListener->SetCallbackFunction( this, &QmitkImageStatisticsView::SelectedDataModified ); mitk::DataNode::Pointer planarFigureNode; for( int i= 0 ; i < this->m_SelectedDataNodes.size(); ++i) { mitk::PlanarFigure::Pointer planarFig = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); if( imagePredicate->CheckNode(this->m_SelectedDataNodes.at(i)) ) { bool isMask = false; this->m_SelectedDataNodes.at(i)->GetPropertyValue("binary", isMask); isMask |= isLabelSet->CheckNode(this->m_SelectedDataNodes.at(i)); if( this->m_SelectedImageMask == nullptr && isMask) { this->m_SelectedImageMask = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageMaskObserverTag = this->m_SelectedImageMask->AddObserver(itk::ModifiedEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = m_SelectedImageMask->GetNameOfClass(); maskDimension = 3; } else if( !isMask ) { if(this->m_SelectedImage == nullptr) { this->m_SelectedImage = static_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } featureImageName = this->m_SelectedDataNodes.at(i)->GetName(); } } else if (planarFig.IsNotNull()) { if(this->m_SelectedPlanarFigure == nullptr) { this->m_SelectedPlanarFigure = planarFig; this->m_PlanarFigureObserverTag = this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = this->m_SelectedPlanarFigure->GetNameOfClass(); maskDimension = 2; planarFigureNode = m_SelectedDataNodes.at(i); } } else { m_Controls->m_ErrorMessageLabel->setText("Invalid data node type!"); m_Controls->m_ErrorMessageLabel->show(); } } if(maskName == "") { maskName = "None"; maskType = ""; maskDimension = 0; } if(featureImageName == "") { featureImageName = "None"; } if (m_SelectedPlanarFigure != nullptr && m_SelectedImage == nullptr) { mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode); for (unsigned int i=0; iSize(); i++) { mitk::DataNode::Pointer node = parentSet->ElementAt(i); if( imagePredicate->CheckNode(node) ) { bool isMask = false; node->GetPropertyValue("binary", isMask); isMask |= isLabelSet->CheckNode(node); if( !isMask ) { if(this->m_SelectedImage == nullptr) { this->m_SelectedImage = static_cast(node->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } } } } } unsigned int timeStep = renderPart->GetTimeNavigationController()->GetTime()->GetPos(); if ( m_SelectedImage != nullptr && m_SelectedImage->IsInitialized()) { // Check if a the selected image is a multi-channel image. If yes, statistics // cannot be calculated currently. if ( m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 ) { m_Controls->m_ErrorMessageLabel->setText( "Multi-component images not supported." ); m_Controls->m_ErrorMessageLabel->show(); this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_CurrentStatisticsValid = false; this->m_StatisticsUpdatePending = false; this->DisableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); return; } std::stringstream maskLabel; maskLabel << maskName; if ( maskDimension > 0 ) { maskLabel << " [" << maskDimension << "D " << maskType << "]"; } m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() ); m_Controls->m_SelectedFeatureImageLabel->setText(featureImageName.c_str()); // check time step validity if(m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3)-1) { timeStep = m_SelectedImage->GetDimension(3)-1; } // Add the used mask time step to the mask label so the user knows which mask time step was used // if the image time step is bigger than the total number of mask time steps (see // ImageStatisticsCalculator::ExtractImageAndMask) if (m_SelectedImageMask != nullptr) { unsigned int maskTimeStep = timeStep; if (maskTimeStep >= m_SelectedImageMask->GetTimeSteps()) { maskTimeStep = m_SelectedImageMask->GetTimeSteps() - 1; } m_Controls->m_SelectedMaskLabel->setText(m_Controls->m_SelectedMaskLabel->text() + QString(" (t=") + QString::number(maskTimeStep) + QString(")")); } // check if the segmentation mask is empty if (m_SelectedImageMask != NULL) { typedef itk::Image ItkImageType; typedef itk::ImageRegionConstIteratorWithIndex< ItkImageType > IteratorType; ItkImageType::Pointer itkImage; mitk::CastToItkImage( m_SelectedImageMask, itkImage ); bool empty = true; IteratorType it( itkImage, itkImage->GetLargestPossibleRegion() ); while ( !it.IsAtEnd() ) { ItkImageType::ValueType val = it.Get(); if ( val != 0 ) { empty = false; break; } ++it; } if ( empty ) { m_Controls->m_ErrorMessageLabel->setText( "Empty segmentation mask selected..." ); m_Controls->m_ErrorMessageLabel->show(); return; } } //// initialize thread and trigger it this->m_CalculationThread->SetIgnoreZeroValueVoxel( m_Controls->m_IgnoreZerosCheckbox->isChecked() ); this->m_CalculationThread->Initialize( m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure ); this->m_CalculationThread->SetTimeStep( timeStep ); m_Controls->m_ErrorMessageLabel->setText("Calculating statistics..."); m_Controls->m_ErrorMessageLabel->show(); try { // Compute statistics this->m_CalculationThread->start(); } catch ( const mitk::Exception& e) { m_Controls->m_ErrorMessageLabel->setText("" + QString(e.GetDescription()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } catch ( const std::runtime_error &e ) { // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } catch ( const std::exception &e ) { MITK_ERROR << "Caught exception: " << e.what(); // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } } else { this->m_StatisticsUpdatePending = false; } } void QmitkImageStatisticsView::SelectedDataModified() { if( !m_StatisticsUpdatePending ) { emit StatisticsUpdate(); } } void QmitkImageStatisticsView::NodeRemoved(const mitk::DataNode *node) { while(this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } if (node->GetData() == m_SelectedImage) { m_SelectedImage = nullptr; } } void QmitkImageStatisticsView::RequestStatisticsUpdate() { if ( !m_StatisticsUpdatePending ) { if(this->m_DataNodeSelectionChanged) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->m_StatisticsUpdatePending = true; this->UpdateStatistics(); } } if (this->GetRenderWindowPart()) this->GetRenderWindowPart()->RequestUpdate(); } void QmitkImageStatisticsView::OnHistogramNBinsCheckBoxValueChanged() { if (static_cast(m_Controls->m_HistogramNBinsSpinbox->value()) != m_HistogramNBins) { m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); this->UpdateStatistics(); } } void QmitkImageStatisticsView::WriteStatisticsToGUI() { m_Controls->m_JSHistogram->Clear(); m_IntensityProfileList.clear(); //Disconnect OnLineRadioButtonSelected() to prevent reloading chart when radiobutton is checked programmatically disconnect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), 0, 0); connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); m_Controls->m_InfoLabel->setText(""); if (m_DataNodeSelectionChanged) { this->m_StatisticsUpdatePending = false; this->RequestStatisticsUpdate(); return; // stop visualization of results and calculate statistics of new selection } if (this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) { if (this->m_CalculationThread->GetStatisticsChangedFlag()) { // Do not show any error messages m_Controls->m_ErrorMessageLabel->hide(); m_CurrentStatisticsValid = true; } if (m_SelectedImage != nullptr) { //all statistics are now computed also on planar figures (lines, paths...)! // If a (non-closed) PlanarFigure is selected, display a line profile widget if (m_SelectedPlanarFigure != nullptr) { // Check if the (closed) planar figure is out of bounds and so no image mask could be calculated--> Intensity Profile can not be calculated bool outOfBounds = false; if (m_SelectedPlanarFigure->IsClosed() && m_SelectedImageMask == nullptr) { outOfBounds = true; const QString message("Planar figure is on a rotated image plane or outside the image bounds."); m_Controls->m_InfoLabel->setText(message); } // check whether PlanarFigure is initialized const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); if (!(planarFigurePlaneGeometry == nullptr || outOfBounds)) { unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); mitk::Image::Pointer image; if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(this->m_CalculationThread->GetStatisticsImage()); timeSelector->SetTimeNr(timeStep); timeSelector->Update(); image = timeSelector->GetOutput(); } else { image = this->m_CalculationThread->GetStatisticsImage(); } mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); m_IntensityProfileList = ConvertIntensityProfileToVector(intensityProfile); auto lineDataLabel = "Intensity profile " + m_Controls->m_SelectedMaskLabel->text().toStdString(); m_Controls->m_JSHistogram->SetChartType(lineDataLabel, QmitkChartWidget::ChartType::line); m_Controls->m_JSHistogram->AddData1D(m_IntensityProfileList, lineDataLabel); m_Controls->m_JSHistogram->SetXAxisLabel("Distance"); m_Controls->m_JSHistogram->SetYAxisLabel("Intensity"); m_Controls->m_JSHistogram->Show(m_Controls->m_ShowSubchartCheckBox->isChecked()); m_Controls->m_lineRadioButton->setChecked(true); m_Controls->m_lineRadioButton->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(false); m_Controls->m_HistogramNBinsSpinbox->setEnabled(false); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(false); //Reconnect OnLineRadioButtonSelected() connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected())); auto statisticsVector = this->m_CalculationThread->GetStatisticsData(); //only one entry (current timestep) this->FillLinearProfileStatisticsTableView(statisticsVector.front().GetPointer(), this->m_CalculationThread->GetStatisticsImage()); QString message("Only linegraph available for an intensity profile!"); if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) { message += "Only current timestep displayed!"; } message += ""; m_Controls->m_InfoLabel->setText(message); m_CurrentStatisticsValid = true; } else { // Clear statistics, histogram, and GUI this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_SelectedMaskLabel->setText("None"); this->m_StatisticsUpdatePending = false; if (!outOfBounds) m_Controls->m_InfoLabel->setText(""); return; } } else { m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); auto histogram = this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer(); auto imageLabelName = m_Controls->m_SelectedFeatureImageLabel->text().toStdString(); m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram), imageLabelName); m_Controls->m_JSHistogram->SetChartType(imageLabelName, QmitkChartWidget::ChartType::bar); this->m_Controls->m_JSHistogram->SetXAxisLabel("Gray value"); this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(true); m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); this->FillStatisticsTableView(this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage()); } m_CurrentStatisticsValid = true; } } else { m_Controls->m_SelectedMaskLabel->setText("None"); m_Controls->m_ErrorMessageLabel->setText(m_CalculationThread->GetLastErrorMessage().c_str()); m_Controls->m_ErrorMessageLabel->show(); // Clear statistics and histogram this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; } berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); this->m_StatisticsUpdatePending = false; } void QmitkImageStatisticsView::FillStatisticsTableView( const std::vector &statistics, const mitk::Image *image ) { this->m_Controls->m_StatisticsTable->setColumnCount(image->GetTimeSteps()); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(image->GetTimeSteps() > 1); // Set Checkbox for complete copy of statistic table if(image->GetTimeSteps()>1) { this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(true); } else { this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(false); this->m_Controls->m_CheckBox4dCompleteTable->setChecked(false); } for (unsigned int t = 0; t < image->GetTimeSteps(); t++) { this->m_Controls->m_StatisticsTable->setHorizontalHeaderItem(t, new QTableWidgetItem(QString::number(t))); if (statistics.at(t)->GetMaxIndex().size()==3) { mitk::Point3D index, max, min; index[0] = statistics.at(t)->GetMaxIndex()[0]; index[1] = statistics.at(t)->GetMaxIndex()[1]; index[2] = statistics.at(t)->GetMaxIndex()[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, max); this->m_WorldMaxList.push_back(max); index[0] = statistics.at(t)->GetMinIndex()[0]; index[1] = statistics.at(t)->GetMinIndex()[1]; index[2] = statistics.at(t)->GetMinIndex()[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, min); this->m_WorldMinList.push_back(min); } auto statisticsVector = AssembleStatisticsIntoVector(statistics.at(t).GetPointer(), image); unsigned int count = 0; for (const auto& entry : statisticsVector) { auto item = new QTableWidgetItem(entry); this->m_Controls->m_StatisticsTable->setItem(count, t, item); count++; } } this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); int height = STAT_TABLE_BASE_HEIGHT; if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); this->m_Controls->m_StatisticsTable->setMinimumHeight(height); // make sure the current timestep's column is highlighted (and the correct histogram is displayed) unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> GetPos(); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), t); this->OnTimeChanged(timeEvent); t = std::min(image->GetTimeSteps() - 1, t); // See bug 18340 /*QString hotspotMean; hotspotMean.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMean(), 0, 'f', decimals)); hotspotMean += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 7, t, new QTableWidgetItem( hotspotMean ) ); QString hotspotMax; hotspotMax.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMax(), 0, 'f', decimals)); hotspotMax += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 8, t, new QTableWidgetItem( hotspotMax ) ); QString hotspotMin; hotspotMin.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMin(), 0, 'f', decimals)); hotspotMin += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 9, t, new QTableWidgetItem( hotspotMin ) );*/ } std::vector QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined) const { std::vector result; unsigned int decimals = 2; //statistics of higher order should have 5 decimal places because they used to be very small unsigned int decimalsHigherOrderStatistics = 5; if (image->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE || image->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT) { decimals = 5; } result.push_back(GetFormattedString(statistics->GetMean(), decimals)); result.push_back(GetFormattedString(statistics->GetMedian(), decimals)); result.push_back(GetFormattedString(statistics->GetStd(), decimals)); result.push_back(GetFormattedString(statistics->GetRMS(), decimals)); result.push_back(GetFormattedString(statistics->GetMax(), decimals) + " " + GetFormattedIndex(statistics->GetMaxIndex())); result.push_back(GetFormattedString(statistics->GetMin(), decimals) + " " + GetFormattedIndex(statistics->GetMinIndex())); //to prevent large negative values of empty image statistics if (statistics->GetN() != std::numeric_limits::min()) { result.push_back(GetFormattedString(statistics->GetN(), 0)); const mitk::BaseGeometry *geometry = image->GetGeometry(); if (geometry != NULL && !noVolumeDefined) { const mitk::Vector3D &spacing = image->GetGeometry()->GetSpacing(); double volume = spacing[0] * spacing[1] * spacing[2] * static_cast(statistics->GetN()); result.push_back(GetFormattedString(volume, decimals)); } else { result.push_back("NA"); } } else { result.push_back("NA"); result.push_back("NA"); } result.push_back(GetFormattedString(statistics->GetSkewness(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(statistics->GetKurtosis(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(statistics->GetUniformity(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(statistics->GetEntropy(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(statistics->GetMPP(), decimals)); result.push_back(GetFormattedString(statistics->GetUPP(), decimalsHigherOrderStatistics)); return result; } void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, const mitk::Image *image) { this->m_Controls->m_StatisticsTable->setColumnCount(1); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); m_PlanarFigureStatistics = this->AssembleStatisticsIntoVector(statistics, image, true); for (unsigned int i = 0; i< m_PlanarFigureStatistics.size(); i++) { this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem(m_PlanarFigureStatistics[i] )); } this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); int height = STAT_TABLE_BASE_HEIGHT; if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); this->m_Controls->m_StatisticsTable->setMinimumHeight(height); } void QmitkImageStatisticsView::InvalidateStatisticsTableView() { this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); this->m_Controls->m_StatisticsTable->setColumnCount(1); for ( int i = 0; i < this->m_Controls->m_StatisticsTable->rowCount(); ++i ) { { this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem( "NA" ) ); } } this->m_Controls->m_StatisticsTable->setMinimumHeight(STAT_TABLE_BASE_HEIGHT); } void QmitkImageStatisticsView::Activated() { } void QmitkImageStatisticsView::Deactivated() { } void QmitkImageStatisticsView::Visible() { m_Visible = true; mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { itk::ReceptorMemberCommand::Pointer cmdTimeEvent = itk::ReceptorMemberCommand::New(); cmdTimeEvent->SetCallbackFunction(this, &QmitkImageStatisticsView::OnTimeChanged); // It is sufficient to add the observer to the axial render window since the GeometryTimeEvent // is always triggered by all views. m_TimeObserverTag = renderWindow->GetQmitkRenderWindow("axial")-> GetSliceNavigationController()-> AddObserver(mitk::SliceNavigationController::GeometryTimeEvent(nullptr, 0), cmdTimeEvent); } if (m_DataNodeSelectionChanged) { if (this->IsCurrentSelectionValid()) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->SelectionChanged(this->GetDataManagerSelection()); } m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::Hidden() { m_Visible = false; // The slice navigation controller observer is removed here instead of in the destructor. // If it was called in the destructor, the application would freeze because the view's // destructor gets called after the render windows have been destructed. if ( m_TimeObserverTag != 0 ) { mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()-> RemoveObserver( m_TimeObserverTag ); } m_TimeObserverTag = 0; } } void QmitkImageStatisticsView::SetFocus() { } std::map QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; - auto endIt = histogram->End(); - auto it = histogram->Begin(); + auto endIt = histogram->End(); + auto it = histogram->Begin(); - // generating Lists of measurement and frequencies + // generating Lists of measurement and frequencies for (; it != endIt; ++it) - { + { double frequency = it.GetFrequency(); double measurement = it.GetMeasurementVector()[0]; histogramMap.emplace(measurement, frequency); - } + } - return histogramMap; + return histogramMap; } std::vector QmitkImageStatisticsView::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const { std::vector intensityProfileList; auto end = intensityProfile->End(); - for (auto it = intensityProfile->Begin(); it != end; ++it) - { + for (auto it = intensityProfile->Begin(); it != end; ++it) + { intensityProfileList.push_back(it.GetMeasurementVector()[0]); - } - return intensityProfileList; + } + return intensityProfileList; } QString QmitkImageStatisticsView::GetFormattedString(double value, unsigned int decimals) const { typedef mitk::ImageStatisticsCalculator::StatisticsContainer::RealType RealType; RealType maxVal = std::numeric_limits::max(); if (value == maxVal) { return QString("NA"); } else { return QString("%1").arg(value, 0, 'f', decimals); } } QString QmitkImageStatisticsView::GetFormattedIndex(const vnl_vector& vector) const { if (vector.empty()) { return QString(); } QString formattedIndex("("); for (const auto& entry : vector) { formattedIndex += QString::number(entry); formattedIndex += ","; } formattedIndex.chop(1); formattedIndex += ")"; return formattedIndex; }