diff --git a/Modules/Chart/src/QmitkChartWidget.cpp b/Modules/Chart/src/QmitkChartWidget.cpp index bc6a103532..1474b17696 100644 --- a/Modules/Chart/src/QmitkChartWidget.cpp +++ b/Modules/Chart/src/QmitkChartWidget.cpp @@ -1,497 +1,499 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include "mitkExceptionMacro.h" class QmitkChartWidget::Impl final { public: explicit Impl(QWidget* parent); ~Impl(); Impl(const Impl&) = delete; Impl& operator=(const Impl&) = delete; void AddData1D(const std::vector& data1D, const std::string& label, QmitkChartWidget::ChartType chartType); void AddData2D(const std::map& data2D, const std::string& label, QmitkChartWidget::ChartType chartType); void RemoveData(const std::string& label); void ClearData(); void SetColor(const std::string& label, const std::string& colorName); void SetLineStyle(const std::string& label, LineStyle style); void SetYAxisScale(AxisScale scale); void SetXAxisLabel(const std::string& label); std::string GetXAxisLabel() const; void SetYAxisLabel(const std::string& label); std::string GetYAxisLabel() const; void SetTitle(const std::string &title); std::string GetTitle() const; void SetLegendPosition(LegendPosition position); LegendPosition GetLegendPosition() const; std::string GetLegendPositionAsString() const; void SetShowDataPoints(bool showDataPoints = false); bool GetShowDataPoints() const; void SetChartType(const std::string& label, QmitkChartWidget::ChartType chartType); std::string ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const; void ClearJavaScriptChart(); void InitializeJavaScriptChart(); void CallJavaScriptFuntion(const QString& command); QmitkChartData* GetC3Data() const; std::vector* GetC3xyData() const; private: std::string GetUniqueLabelName(const QList& labelList, const std::string& label) const; QmitkChartxyData* GetDataElementByLabel(const std::vector* c3xyData, const std::string& label) const; QList GetDataLabels(const std::vector* c3xyData) const; QWebChannel* m_WebChannel; QWebEngineView* m_WebEngineView; QmitkChartData * m_C3Data; std::vector * m_C3xyData; std::map m_ChartTypeToName; std::map m_LegendPositionToName; std::map m_LineStyleToName; std::map m_AxisScaleToName; }; QmitkChartWidget::Impl::Impl(QWidget* parent) - : m_WebChannel(new QWebChannel(parent)), - m_WebEngineView(new QWebEngineView(parent)) + : m_WebChannel(new QWebChannel(parent)) + , m_WebEngineView(new QWebEngineView(parent)) { //disable context menu for QWebEngineView m_WebEngineView->setContextMenuPolicy(Qt::NoContextMenu); //Set the webengineview to an initial empty page. The actual chart will be loaded once the data is calculated. m_WebEngineView->setUrl(QUrl(QStringLiteral("qrc:///C3js/empty.html"))); m_WebEngineView->page()->setWebChannel(m_WebChannel); connect(m_WebEngineView, SIGNAL(loadFinished(bool)), parent, SLOT(OnLoadFinished(bool))); auto layout = new QGridLayout(parent); layout->setMargin(0); layout->addWidget(m_WebEngineView); parent->setLayout(layout); m_ChartTypeToName.emplace(ChartType::bar, "bar"); m_ChartTypeToName.emplace(ChartType::line, "line"); m_ChartTypeToName.emplace(ChartType::spline, "spline"); m_ChartTypeToName.emplace(ChartType::pie, "pie"); m_ChartTypeToName.emplace(ChartType::area, "area"); m_ChartTypeToName.emplace(ChartType::area_spline , "area-spline"); m_LegendPositionToName.emplace(LegendPosition::bottom, "bottom"); m_LegendPositionToName.emplace(LegendPosition::right, "right"); m_LegendPositionToName.emplace(LegendPosition::inset, "inset"); m_LineStyleToName.emplace(LineStyle::solid, "solid"); m_LineStyleToName.emplace(LineStyle::dashed, "dashed"); m_AxisScaleToName.emplace(AxisScale::linear, ""); m_AxisScaleToName.emplace(AxisScale::log, "log"); m_C3Data = new QmitkChartData(); m_C3xyData = new std::vector(); } QmitkChartWidget::Impl::~Impl() { delete m_C3Data; + qDeleteAll(m_C3xyData); + delete m_C3xyData; } void QmitkChartWidget::Impl::AddData1D(const std::vector& data1D, const std::string& label, QmitkChartWidget::ChartType type) { std::map transformedData2D; unsigned int count = 0; //transform the 1D data to 2D data for (const auto& ele : data1D) { transformedData2D[count] = ele; count++; } this->AddData2D(transformedData2D, label, type); } void QmitkChartWidget::Impl::AddData2D(const std::map& data2D, const std::string& label, QmitkChartWidget::ChartType type) { QMap data2DConverted; for (const auto& aValue : data2D) { data2DConverted.insert(aValue.first, aValue.second); } const std::string chartTypeName(m_ChartTypeToName.at(type)); auto definedLabels = GetDataLabels(GetC3xyData()); auto uniqueLabel = GetUniqueLabelName(definedLabels, label); GetC3xyData()->push_back(new QmitkChartxyData(data2DConverted, QVariant(QString::fromStdString(uniqueLabel)), QVariant(QString::fromStdString(chartTypeName)))); } -void QmitkChartWidget::Impl::RemoveData(const std::string& label) { - std::vector::iterator iter_temp = GetC3xyData()->end(); +void QmitkChartWidget::Impl::RemoveData(const std::string& label) +{ for (std::vector::iterator iter = GetC3xyData()->begin(); iter != GetC3xyData()->end(); ++iter) { const auto &temp = *iter; if (temp->GetLabel().toString().toStdString() == label) { - iter_temp = iter; - break; + delete temp; + GetC3xyData()->erase(iter); + return; } } - if (iter_temp == GetC3xyData()->end()) { - throw std::invalid_argument("Cannot Remove Data because the label does not exist."); - } - else - { - GetC3xyData()->erase(iter_temp); - } + + throw std::invalid_argument("Cannot Remove Data because the label does not exist."); } void QmitkChartWidget::Impl::ClearData() { - for (auto& xyData : *m_C3xyData) { + for (auto& xyData : *m_C3xyData) + { m_WebChannel->deregisterObject(xyData); + delete xyData; + xyData = nullptr; } GetC3xyData()->clear(); } void QmitkChartWidget::Impl::SetColor(const std::string& label, const std::string& colorName) { auto element = GetDataElementByLabel(GetC3xyData(), label); if (element) { element->SetColor(QVariant(QString::fromStdString(colorName))); } } void QmitkChartWidget::Impl::SetLineStyle(const std::string& label, LineStyle style) { auto element = GetDataElementByLabel(GetC3xyData(), label); //only has effect with chart type line if (element && element->GetChartType()==QVariant(QString::fromStdString(ConvertChartTypeToString(ChartType::line)))) { const std::string lineStyleName(m_LineStyleToName.at(style)); element->SetLineStyle(QVariant(QString::fromStdString(lineStyleName))); } } void QmitkChartWidget::Impl::SetYAxisScale(AxisScale scale) { const std::string axisScaleName(m_AxisScaleToName.at(scale)); GetC3Data()->SetYAxisScale(QString::fromStdString(axisScaleName)); } QmitkChartxyData* QmitkChartWidget::Impl::GetDataElementByLabel(const std::vector* c3xyData, const std::string& label) const { for (auto element = c3xyData->begin(); element != c3xyData->end(); ++element) { if ((*element)->GetLabel().toString().toStdString() == label) { return *element; } } MITK_WARN << "label " << label << " not found in QmitkChartWidget"; return nullptr; } QList QmitkChartWidget::Impl::GetDataLabels(const std::vector* c3xyData) const { QList dataLabels; for (auto element = c3xyData->begin(); element != c3xyData->end(); ++element) { dataLabels.push_back((*element)->GetLabel()); } return dataLabels; } void QmitkChartWidget::Impl::SetXAxisLabel(const std::string& label) { GetC3Data()->SetXAxisLabel(QString::fromStdString(label)); } std::string QmitkChartWidget::Impl::GetXAxisLabel() const { return GetC3Data()->GetXAxisLabel().toString().toStdString(); } void QmitkChartWidget::Impl::SetYAxisLabel(const std::string& label) { GetC3Data()->SetYAxisLabel(QString::fromStdString(label)); } std::string QmitkChartWidget::Impl::GetYAxisLabel() const { return GetC3Data()->GetYAxisLabel().toString().toStdString(); } void QmitkChartWidget::Impl::SetTitle(const std::string& title) { GetC3Data()->SetTitle(QString::fromStdString(title)); } std::string QmitkChartWidget::Impl::GetTitle() const { return GetC3Data()->GetTitle().toString().toStdString(); } void QmitkChartWidget::Impl::SetLegendPosition(QmitkChartWidget::LegendPosition legendPosition) { const std::string legendPositionName(m_LegendPositionToName.at(legendPosition)); GetC3Data()->SetLegendPosition(QString::fromStdString(legendPositionName)); } QmitkChartWidget::LegendPosition QmitkChartWidget::Impl::GetLegendPosition() const { for (const auto& aLegendPosition : m_LegendPositionToName) { if (aLegendPosition.second == GetLegendPositionAsString()) { return aLegendPosition.first; } } mitkThrow() << "can't find legend position!"; } std::string QmitkChartWidget::Impl::GetLegendPositionAsString() const { return GetC3Data()->GetLegendPosition().toString().toStdString(); } void QmitkChartWidget::Impl::SetShowDataPoints(bool showDataPoints) { if (showDataPoints == true) { GetC3Data()->SetDataPointSize(3); } else { GetC3Data()->SetDataPointSize(0); } } bool QmitkChartWidget::Impl::GetShowDataPoints() const{ int value = GetC3Data()->GetDataPointSize().toInt(); if (value > 0) { return true; } else { return false; } } void QmitkChartWidget::Impl::SetChartType(const std::string& label, QmitkChartWidget::ChartType chartType) { auto element = GetDataElementByLabel(GetC3xyData(), label); if (element) { const std::string chartTypeName(m_ChartTypeToName.at(chartType)); element->SetChartType(QVariant(QString::fromStdString(chartTypeName))); } } std::string QmitkChartWidget::Impl::ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const { return m_ChartTypeToName.at(chartType); } QmitkChartData* QmitkChartWidget::Impl::GetC3Data() const { return m_C3Data; } std::vector* QmitkChartWidget::Impl::GetC3xyData() const { return m_C3xyData; } void QmitkChartWidget::Impl::CallJavaScriptFuntion(const QString& command) { m_WebEngineView->page()->runJavaScript(command); } void QmitkChartWidget::Impl::ClearJavaScriptChart() { m_WebEngineView->setUrl(QUrl(QStringLiteral("qrc:///C3js/empty.html"))); } void QmitkChartWidget::Impl::InitializeJavaScriptChart() { m_WebChannel->registerObject(QStringLiteral("chartData"), m_C3Data); unsigned count = 0; for (auto& xyData : *m_C3xyData) { QString variableName = "xyData" + QString::number(count); m_WebChannel->registerObject(variableName, xyData); count++; } m_WebEngineView->load(QUrl(QStringLiteral("qrc:///C3js/QmitkChartWidget.html"))); } std::string QmitkChartWidget::Impl::GetUniqueLabelName(const QList& labelList, const std::string& label) const { QString currentLabel = QString::fromStdString(label); int counter = 0; while (labelList.contains(currentLabel)) { currentLabel = QString::fromStdString(label + std::to_string(counter)); counter++; } return currentLabel.toStdString(); } QmitkChartWidget::QmitkChartWidget(QWidget* parent) : QWidget(parent), m_Impl(new Impl(this)) { } QmitkChartWidget::~QmitkChartWidget() { delete m_Impl; } void QmitkChartWidget::AddData2D(const std::map& data2D, const std::string& label, ChartType type) { m_Impl->AddData2D(data2D, label, type); } void QmitkChartWidget::SetColor(const std::string& label, const std::string& colorName) { m_Impl->SetColor(label, colorName); } void QmitkChartWidget::SetLineStyle(const std::string& label, LineStyle style) { m_Impl->SetLineStyle(label, style); } void QmitkChartWidget::SetYAxisScale(AxisScale scale) { m_Impl->SetYAxisScale(scale); } void QmitkChartWidget::AddData1D(const std::vector& data1D, const std::string& label, ChartType type) { m_Impl->AddData1D(data1D, label, type); } void QmitkChartWidget::RemoveData(const std::string& label) { m_Impl->RemoveData(label); } void QmitkChartWidget::SetXAxisLabel(const std::string & label) { m_Impl->SetXAxisLabel(label); } std::string QmitkChartWidget::GetXAxisLabel() const { return m_Impl->GetXAxisLabel(); } void QmitkChartWidget::SetYAxisLabel(const std::string & label) { m_Impl->SetYAxisLabel(label); } std::string QmitkChartWidget::GetYAxisLabel() const { return m_Impl->GetYAxisLabel(); } void QmitkChartWidget::SetTitle(const std::string & title) { m_Impl->SetTitle(title); } std::string QmitkChartWidget::GetTitle() const { return m_Impl->GetTitle(); } void QmitkChartWidget::SetShowDataPoints(bool showDataPoints) { - m_Impl->SetShowDataPoints(showDataPoints); + m_Impl->SetShowDataPoints(showDataPoints); } + bool QmitkChartWidget::GetShowDataPoints() const { return m_Impl->GetShowDataPoints(); } void QmitkChartWidget::SetChartType(const std::string& label, ChartType type) { m_Impl->SetChartType(label, type); } void QmitkChartWidget::SetLegendPosition(LegendPosition position) { m_Impl->SetLegendPosition(position); } QmitkChartWidget::LegendPosition QmitkChartWidget::GetLegendPosition() const { return m_Impl->GetLegendPosition(); } void QmitkChartWidget::Show(bool showSubChart) { if (m_Impl->GetC3xyData()->empty()) { mitkThrow() << "no data available for display in chart"; } this->m_Impl->GetC3Data()->SetAppearance(showSubChart, m_Impl->GetC3xyData()->front()->GetChartType()== QVariant("pie")); m_Impl->InitializeJavaScriptChart(); } void QmitkChartWidget::Clear() { m_Impl->ClearData(); m_Impl->ClearJavaScriptChart(); } void QmitkChartWidget::OnLoadFinished(bool isLoadSuccessfull) { if(isLoadSuccessfull) { emit PageSuccessfullyLoaded(); } } void QmitkChartWidget::SetChartTypeForAllDataAndReload(ChartType type) { auto allData = this->m_Impl->GetC3xyData(); for (auto iterator = allData->begin(); iterator != allData->end(); ++iterator) { SetChartType((*iterator)->GetLabel().toString().toStdString(), type); } auto chartTypeName = m_Impl->ConvertChartTypeToString(type); const QString command = QString::fromStdString("transformView('" + chartTypeName + "')"); m_Impl->CallJavaScriptFuntion(command); } void QmitkChartWidget::SetTheme(ChartStyle themeEnabled) { QString command; if (themeEnabled == ChartStyle::darkstyle) { command = QString("changeTheme('dark')"); } else { command = QString("changeTheme('default')"); } m_Impl->CallJavaScriptFuntion(command); } void QmitkChartWidget::Reload(bool showSubChart) { QString subChartString; if (showSubChart) { subChartString = "true"; } else { subChartString = "false"; } const QString command = QString("ReloadChart(" + subChartString + ")"); m_Impl->CallJavaScriptFuntion(command); } 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 24191f8d00..6f72495f8f 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,1373 +1,1375 @@ /*=================================================================== 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 "mitkNodePredicateDataType.h" #include "mitkNodePredicateOr.h" #include "mitkPlanarFigureInteractor.h" #include "mitkImageTimeSelector.h" #include #include // itk includes #include "itksys/SystemTools.hxx" #include #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_TimeStepperAdapter( 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); } } 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::defaultstyle); } } 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_HistogramBinSizeSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramBinSizeBoxValueChanged())); connect((QObject*)(this->m_Controls->m_UseDefaultBinSizeBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnDefaultBinSizeBoxChanged())); 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::OnDefaultBinSizeBoxChanged() { m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultBinSizeBox->isChecked()); if (m_CalculationThread != nullptr){ m_Controls->m_HistogramBinSizeSpinbox->setValue(m_CalculationThread->GetHistogramBinSize()); m_CalculationThread->SetUseDefaultNBins(m_Controls->m_UseDefaultBinSizeBox->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 && !( 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 ) { if( m_Controls->m_HistogramBinSizeSpinbox->value() == 1.0) { clipboard = clipboard.append( "%L1 \t %L2\n" ) .arg( it.GetMeasurementVector()[0], 0, 'f', 0 ) .arg( it.GetFrequency() ); } else { 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_CurrentStatisticsValid && (m_SelectedPlanarFigure != nullptr )) { /*auto intensity = m_Controls->m_JSHistogram->GetFrequency(); auto pixel = m_Controls->m_JSHistogram->GetMeasurement(); QString clipboard( "Pixel \t Intensity\n" ); auto j = pixel.begin(); for (auto i = intensity.begin(); i < intensity.end(); i++) { assert(j != pixel.end()); clipboard = clipboard.append( "%L1 \t %L2\n" ) .arg( (*j).toString()) .arg( (*i).toString()); j++; } QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard ); */ } else { QApplication::clipboard()->clear(); } } 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; // Create Headline headline << " " << "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()) { m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); m_Controls->m_UseDefaultBinSizeBox->setEnabled(true); m_Controls->m_InfoLabel->setText(""); m_Controls->groupBox->setEnabled(false); m_Controls->groupBox_3->setEnabled(false); } else { m_Controls->groupBox->setEnabled(true); m_Controls->groupBox_3->setEnabled(true); m_Controls->m_barRadioButton->setChecked(true); } 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) { m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); m_Controls->m_UseDefaultBinSizeBox->setEnabled(true); 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::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() { std::stringstream message; message << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); 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 { std::stringstream message; message << "" << "Invalid data node type!" << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); 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 ) { std::stringstream message; message << "Multi-component images not supported."; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_CurrentStatisticsValid = false; this->m_StatisticsUpdatePending = false; m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); m_Controls->m_UseDefaultBinSizeBox->setEnabled(true); 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 ) { std::stringstream message; message << "Empty segmentation mask selected..."; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); 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 ); std::stringstream message; message << "Calculating statistics..."; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); try { // Compute statistics // this->m_CalculationThread->SetUseDefaultBinSize(m_Controls->m_UseDefaultBinSizeBox->isChecked()); this->m_CalculationThread->start(); } catch ( const mitk::Exception& e) { std::stringstream message; message << "" << e.GetDescription() << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } catch ( const std::runtime_error &e ) { // In case of exception, print error message on GUI std::stringstream message; message << "" << e.what() << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); 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 std::stringstream message; message << "Error! Unequal Dimensions of Image and Segmentation. No recompute possible "; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } AdaptBinSizeCheckboxStepsize(m_SelectedImage); } 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::OnHistogramBinSizeBoxValueChanged() { if (m_Controls->m_HistogramBinSizeSpinbox->value() != m_HistogramBinSize) { m_HistogramBinSize = m_Controls->m_HistogramBinSizeSpinbox->value(); this->m_CalculationThread->SetHistogramBinSize(m_Controls->m_HistogramBinSizeSpinbox->value()); this->UpdateStatistics(); } } + void QmitkImageStatisticsView::WriteStatisticsToGUI() { m_Controls->m_JSHistogram->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_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); m_Controls->m_InfoLabel->setText(""); - if(m_DataNodeSelectionChanged) + 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->GetStatisticsUpdateSuccessFlag()) { - if ( this->m_CalculationThread->GetStatisticsChangedFlag() ) + 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 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(); + // check whether PlanarFigure is initialized + const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); - if ( !(planarFigurePlaneGeometry == nullptr || outOfBounds)) - { - unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); + if (!(planarFigurePlaneGeometry == nullptr || outOfBounds)) + { + unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); - mitk::Image::Pointer image; + 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(); + 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(); - } + image = timeSelector->GetOutput(); + } + else + { + image = this->m_CalculationThread->GetStatisticsImage(); + } - mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); - - auto 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(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_HistogramBinSizeSpinbox->setEnabled(false); - m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(false); + mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); + + auto 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(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_HistogramBinSizeSpinbox->setEnabled(false); + m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(false); m_Controls->m_UseDefaultBinSizeBox->setEnabled(false); - //Reconnect OnLineRadioButtonSelected() - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected())); + //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; + 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; + m_Controls->m_lineRadioButton->setEnabled(true); + m_Controls->m_barRadioButton->setEnabled(true); + m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); + m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); + if (!outOfBounds) + m_Controls->m_InfoLabel->setText(""); + return; + } } 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; - m_Controls->m_lineRadioButton->setEnabled(true); - m_Controls->m_barRadioButton->setEnabled(true); - m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); - m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); - if (!outOfBounds) - m_Controls->m_InfoLabel->setText(""); - return; - } - } - else { m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_Controls->m_HistogramBinSizeSpinbox->setValue(this->m_CalculationThread->GetHistogramBinSize()); 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->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_UseDefaultBinSizeBox->setEnabled(true); m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); auto currentTime = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); this->AdaptBinSizeCheckBoxMinMax((this->m_CalculationThread->GetStatisticsData()).at(currentTime).GetPointer(), this->m_CalculationThread->GetStatisticsImage()->GetPixelType().GetComponentType()); 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() { } void QmitkImageStatisticsView::AdaptBinSizeCheckboxStepsize(mitk::Image::ConstPointer image) { auto componentType = image->GetPixelType().GetComponentType(); if (componentType == itk::ImageIOBase::DOUBLE || componentType == itk::ImageIOBase::FLOAT) { m_Controls->m_HistogramBinSizeSpinbox->setDecimals(2); m_Controls->m_HistogramBinSizeSpinbox->setSingleStep(.01); } else { m_Controls->m_HistogramBinSizeSpinbox->setDecimals(0); m_Controls->m_HistogramBinSizeSpinbox->setSingleStep(1); } } void QmitkImageStatisticsView::AdaptBinSizeCheckBoxMinMax(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, int componentType) { auto minValue = statistics->GetMin(); auto maxValue = statistics->GetMax(); //10 bins are minimum as defined in ImageStatisticsCalculator::GetStatistics const unsigned int minHistogramBins = 10; //10000 bins are just a maximum arbitrary number to keep computation time reasonable const unsigned int maxHistogramBins = 10000; double minHistogramBinSize = static_cast((maxValue - minValue) / maxHistogramBins); double maxHistogramBinSize = static_cast((maxValue - minValue) / minHistogramBins); if (componentType == itk::ImageIOBase::DOUBLE || componentType == itk::ImageIOBase::FLOAT) { //smallest value for double/float images const double minHistogramBinSizeValid = 0.01; m_Controls->m_HistogramBinSizeSpinbox->setMinimum(std::max(minHistogramBinSize, minHistogramBinSizeValid)); m_Controls->m_HistogramBinSizeSpinbox->setMaximum(maxHistogramBinSize); } else { //smallest valid value for int/short images const double minHistogramBinSizeValid = 1; m_Controls->m_HistogramBinSizeSpinbox->setMinimum(std::max(static_cast(minHistogramBinSize), static_cast(minHistogramBinSizeValid))); m_Controls->m_HistogramBinSizeSpinbox->setMaximum(static_cast(maxHistogramBinSize)); } } std::map QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; auto endIt = histogram->End(); auto it = histogram->Begin(); // 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; } std::vector QmitkImageStatisticsView::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const { std::vector intensityProfileList; auto end = intensityProfile->End(); for (auto it = intensityProfile->Begin(); it != end; ++it) { intensityProfileList.push_back(it.GetMeasurementVector()[0]); } 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; }