diff --git a/Modules/C3js/resource/Chart.js b/Modules/C3js/resource/Chart.js index 1fa45df13e..30babd9167 100644 --- a/Modules/C3js/resource/Chart.js +++ b/Modules/C3js/resource/Chart.js @@ -1,213 +1,218 @@ //Based on C3.js (http://c3js.org). See Website for examples! document.body.style.backgroundColor = 'rgb(240, 240, 240)'; var minHeight = 255; var chart; GenerateChart('bar', false, false) var chartData; var xValues=[]; var yValues=[]; var xs = {}; //Is executed when js is loaded first. //Extracts relevant information from chartData in variables window.onload = function() { new QWebChannel(qt.webChannelTransport, function(channel) { chartData = channel.objects.chartData; var count = 0; for(var propertyName in channel.objects) { if (propertyName != 'chartData'){ var xDataTemp = channel.objects[propertyName].m_XData var yDataTemp = channel.objects[propertyName].m_YData var dataLabelsTemp; //add label to x array xDataTemp.unshift('x'+count.toString()) if (count < chartData.m_dataLabels.length){ dataLabelsTemp = chartData.m_dataLabels[count] } else { dataLabelsTemp = "data" + count.toString() } xs[dataLabelsTemp] = 'x'+count.toString() xDataTemp.push(null); //append null value, to make sure the last tick on x-axis is displayed correctly yDataTemp.unshift(dataLabelsTemp) yDataTemp.push(null); //append null value, to make sure the last tick on y-axis is displayed correctly xValues[count] = xDataTemp yValues[count] = yDataTemp count++; } } setupChart(chartData) }); } //This is necessary to resize the chart, after the size of the parent changed window.onresize = function () { var size = window.innerHeight-(window.innerHeight/100*10); //subtract 5% of height to hide vertical scrool bar if (size < minHeight) { size = minHeight; } chart.resize({ height: size, }); } function ReloadChart(showSubchart) { chartData.m_ShowSubchart = showSubchart; setupChart(chartData); } function setupChart(chartData) { window.onresize(); GenerateChart(chartData.m_DiagramTypeName, chartData.m_ShowSubchart, chartData.m_UsePercentageInPieChart, chartData.m_xAxisLabel, chartData.m_yAxisLabel) chart.unload(); //unload data before loading new data //for multiple xy line chart, see http://c3js.org/samples/simple_xy_multiple.html var columns = []; for (var i in xValues){ columns.push(xValues[i]) } for (var i in yValues){ columns.push(yValues[i]) } chart.load({ xs: xs, columns: columns }); } //Transformation between different chart types //takes the name of the chart type as a parameter //called by QmitkC3jsWidget function transformView(TransformTo) { chart.transform(TransformTo); }; function changeTheme(color) { if (color == 'dark') { link = document.getElementsByTagName("link")[0]; link.href = "Chart_dark.css"; } else { link = document.getElementsByTagName("link")[0]; link.href = "Chart.css"; } }; //Here, the chart magic takes place. C3js is called //chartType: either bar, line or pie //showSubchart: see http://c3js.org/samples/options_subchart.html //usePercentageInPieChart: percentage labels (only for pie chart) function GenerateChart(chartType, showSubchart, usePercentageInPieChart, xAxisLabel, yAxisLabel) { //adaption for bar ratio indepenend of amount of data points //otherwise, bars could be covered. var barRatio; try { barRatio = 0.8*Math.exp(-0.015*xValues[0].length); } catch (err){ barRatio=0.42 } var formatCharacter; if (usePercentageInPieChart==true){ formatCharacter = '%' } else{ formatCharacter = 's' } chart = c3.generate({ data: { xs: {}, //use first "column" as x axis values columns: [], //initialize empty. Data will be loaded in function setupChart(chartData) type: chartType, selection: { enabled: false, multiple: false, } }, legend: { position: 'bottom' }, grid: { y: { lines: [{value:0}] //Draws a horizontal line at y=0 } }, bar: { width: { ratio: barRatio } }, pie:{ label: { format: function (value, ratio, id) { if (usePercentageInPieChart==true){ return d3.format('%') (ratio); } else{ return value; } } } }, zoom: { enabled: true, }, subchart: { show: showSubchart //Shows a subchart that shows the region the primary chart is zoomed in to by overlay. }, axis: { x: { tick: { multiline: false, fit: false, //to make more x labels appear on zoom centered: true, format: d3.format(".1f"), }, - label : xAxisLabel, + label: { + text: xAxisLabel, + position: 'outer-center' + } }, y: { tick: { format: d3.format(formatCharacter) }, - label: yAxisLabel + label: { + text: yAxisLabel, + position: 'outer-middle' + } } }, tooltip: { format: { - title: function (x) { return d3.format(".2f")(x)} , - value: function (x) { return d3.format(".2f")(x)} , + title: function (x) { return xAxisLabel + ': ' + d3.format(".2f")(x)} }, }, //Style data points in linegraph point: { r: 0.2, focus: { expand: { r: 4 } } }, }); } 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 a913e0a0a0..79cba555d3 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,1308 +1,1314 @@ /*=================================================================== 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" // itk includes #include "itksys/SystemTools.hxx" #include #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( NULL ), m_TimeStepperAdapter( NULL ), m_SelectedImage( NULL ), m_SelectedImageMask( NULL ), m_SelectedPlanarFigure( NULL ), 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 != NULL ) m_SelectedImage->RemoveObserver( m_ImageObserverTag ); if ( m_SelectedImageMask != NULL ) m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); if ( m_SelectedPlanarFigure != NULL ) 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 == NULL) { 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->setVisible(false); + m_Controls->m_BinSizeFrame->setEnabled(false); } } 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())); } } void QmitkImageStatisticsView::OnDefaultBinSizeBoxChanged() { - m_Controls->m_BinSizeFrame->setVisible(!m_Controls->m_UseDefaultBinSizeBox->isChecked()); + m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultBinSizeBox->isChecked()); -if (m_CalculationThread != NULL){ - m_Controls->m_HistogramBinSizeSpinbox->setValue(m_CalculationThread->GetHistogramBinSize()); - m_CalculationThread->SetUseDefaultNBins(m_Controls->m_UseDefaultBinSizeBox->isChecked()); -} -this->UpdateStatistics(); + if (m_CalculationThread != NULL) { + m_Controls->m_HistogramBinSizeSpinbox->setValue(m_CalculationThread->GetHistogramBinSize()); + m_CalculationThread->SetUseDefaultNBins(m_Controls->m_UseDefaultBinSizeBox->isChecked()); + } + this->UpdateStatistics(); } void QmitkImageStatisticsView::OnShowSubchartBoxChanged() { QString showSubchart = "false"; if (this->m_Controls->m_ShowSubchartCheckBox->isChecked()) showSubchart = "true"; this->m_Controls->m_JSHistogram->SendCommand( "ReloadChart(" + showSubchart + ")"); } void QmitkImageStatisticsView::OnBarRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::bar); this->m_Controls->m_JSHistogram->TransformView("bar"); } void QmitkImageStatisticsView::OnLineRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::line); this->m_Controls->m_JSHistogram->TransformView("line"); } void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& ) { } void QmitkImageStatisticsView::OnTimeChanged(const itk::EventObject& e) { if (this->m_SelectedDataNodes.isEmpty() || this->m_SelectedImage == NULL) return; const mitk::SliceNavigationController::GeometryTimeEvent* timeEvent = dynamic_cast(&e); assert(timeEvent != NULL); unsigned 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 == NULL) 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->ClearDiagram(); QmitkImageStatisticsCalculationThread::HistogramType::Pointer histogram = this->m_CalculationThread->GetTimeStepHistogram(timestep); if (histogram.IsNotNull()) { bool closedFigure = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag(); if ( closedFigure ) { this->m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram) ); if (this->m_Controls->m_lineRadioButton->isChecked()) { this->m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::line); } else { this->m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::bar); } - this->m_Controls->m_JSHistogram->SetDataLabels({"Histogram"}); + this->m_Controls->m_JSHistogram->SetDataLabels({ m_Controls->m_SelectedFeatureImageLabel->text() }); + this->m_Controls->m_JSHistogram->SetXAxisLabel("Grey value"); + this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); this->m_Controls->m_JSHistogram->ShowDiagram(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==4 && !m_WorldMinList.empty()) world = m_WorldMinList[col]; else if (row==3 && !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 != NULL)) { 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 != NULL)) { //================================================================================ /*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 != NULL)) { 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 &selectedNodes ) { if (this->m_Visible) { this->SelectionChanged( selectedNodes ); } else { this->m_DataNodeSelectionChanged = true; } } void QmitkImageStatisticsView::SelectionChanged(const QList &selectedNodes) { //Clear Histogram if data node is deselected m_Controls->m_JSHistogram->ClearDiagram(); 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_InfoLabel->setText(QString("")); m_Controls->groupBox->setEnabled(false); m_Controls->groupBox_3->setEnabled(false); } else { m_Controls->groupBox->setEnabled(true); m_Controls->groupBox_3->setEnabled(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_InfoLabel->setText(QString("")); } 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 != NULL) { this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag); this->m_SelectedImage = NULL; } if(this->m_SelectedImageMask != NULL) { this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag); this->m_SelectedImageMask = NULL; } if(this->m_SelectedPlanarFigure != NULL) { this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag); this->m_SelectedPlanarFigure = NULL; } 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 == NULL ) { 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 == NULL && 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 == NULL) { 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 == NULL) { 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 != NULL && m_SelectedImage == NULL) { mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode); for (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 == NULL) { 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 != NULL && 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_InfoLabel->setText(QString("")); 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 != NULL) { 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(")")); } //// 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; } } 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 = NULL; } } void QmitkImageStatisticsView::RequestStatisticsUpdate() { if ( !m_StatisticsUpdatePending ) { if(this->m_DataNodeSelectionChanged) { std::cout << "ICH WERDE AUFGERUFEN" << std::endl; 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->ClearDiagram(); //Disconnect OnLineRadioButtonSelected() to prevent reloading chart when radiobutton is checked programmatically disconnect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), 0, 0); 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(QString("")); - 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; } - 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(); - m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram)); - m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::bar); - this->m_Controls->m_JSHistogram->SetDataLabels({ "Histogram" }); - m_Controls->m_JSHistogram->ShowDiagram(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); - this->FillStatisticsTableView( this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage()); + 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(); + m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram)); + m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::bar); + this->m_Controls->m_JSHistogram->SetDataLabels({ m_Controls->m_SelectedFeatureImageLabel->text() }); + this->m_Controls->m_JSHistogram->SetXAxisLabel("Grey value"); + this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); + m_Controls->m_JSHistogram->ShowDiagram(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_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_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; // If a (non-closed) PlanarFigure is selected, display a line profile widget - if ( m_SelectedPlanarFigure != NULL ) + if (m_SelectedPlanarFigure != NULL) { // 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 == NULL) + if (m_SelectedPlanarFigure->IsClosed() && m_SelectedImageMask == NULL) { outOfBounds = true; std::stringstream message; message << "Planar figure is on a rotated image plane or outside the image bounds."; m_Controls->m_InfoLabel->setText(message.str().c_str()); } // check whether PlanarFigure is initialized const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); - if ( !(planarFigurePlaneGeometry == NULL || outOfBounds)) + if (!(planarFigurePlaneGeometry == NULL || 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::Pointer intensityProfile = mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); - - auto intensityProfileList = ConvertIntensityProfileToList(intensityProfile); - m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::line); - m_Controls->m_JSHistogram->AddData1D(intensityProfileList); - m_Controls->m_JSHistogram->SetDataLabels({"Intensity profile"}); - m_Controls->m_JSHistogram->ShowDiagram(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); - - //Reconnect OnLineRadioButtonSelected() + 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::Pointer intensityProfile = mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); + + auto intensityProfileList = ConvertIntensityProfileToList(intensityProfile); + m_Controls->m_JSHistogram->SetDiagramType(QmitkC3jsWidget::DiagramType::line); + m_Controls->m_JSHistogram->AddData1D(intensityProfileList); + m_Controls->m_JSHistogram->SetDataLabels({ "Intensity profile" }); + m_Controls->m_JSHistogram->SetXAxisLabel("Distance"); + m_Controls->m_JSHistogram->SetYAxisLabel("Intensity"); + m_Controls->m_JSHistogram->ShowDiagram(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); + + //Reconnect OnLineRadioButtonSelected() connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected())); - - this->FillLinearProfileStatisticsTableView( intensityProfile, this->m_CalculationThread->GetStatisticsImage().GetPointer() ); + + this->FillLinearProfileStatisticsTableView(intensityProfile, this->m_CalculationThread->GetStatisticsImage().GetPointer()); std::stringstream message; message << "Only linegraph available for an intensity profile!"; m_Controls->m_InfoLabel->setText(message.str().c_str()); m_CurrentStatisticsValid = true; } else { // Clear statistics, histogram, and GUI this->InvalidateStatisticsTableView(); - m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); + m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; m_Controls->m_ErrorMessageLabel->hide(); - m_Controls->m_SelectedMaskLabel->setText( "None" ); + 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(QString("")); return; // Sebastian Wirkert: would suggest to remove this return, since it is an artifact of previous // code architecture. However, removing it will cause m_StatisticsUpdatePending to be set to false // in case of invalid statistics which it previously was not. } } } 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), 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::AssembleStatisticsIntoVectorForPlanarFigure(mitk::IntensityProfile::Pointer intensityProfile, mitk::Image::ConstPointer image) { 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; } mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats = mitk::ImageStatisticsCalculator::StatisticsContainer::New(); mitk::ComputeIntensityProfileStatistics(intensityProfile, stats); result.push_back(GetFormattedString(stats->GetMean(), decimals)); result.push_back(GetFormattedString(stats->GetMedian(), decimals)); result.push_back(GetFormattedString(stats->GetStd(), decimals)); result.push_back(GetFormattedString(stats->GetRMS(), decimals)); result.push_back(GetFormattedString(stats->GetMax(), decimals)); result.push_back(GetFormattedString(stats->GetMin(), decimals)); result.push_back(GetFormattedString(stats->GetN(), 0)); result.push_back(QString("NA")); //Volume can't be computed on a line result.push_back(GetFormattedString(stats->GetSkewness(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(stats->GetKurtosis(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(stats->GetUniformity(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(stats->GetEntropy(), decimalsHigherOrderStatistics)); result.push_back(GetFormattedString(stats->GetMPP(), decimals)); result.push_back(GetFormattedString(stats->GetUPP(), decimalsHigherOrderStatistics)); return result; } std::vector QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer statistics, mitk::Image::ConstPointer image) 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())); result.push_back(GetFormattedString(statistics->GetN(), 0)); const mitk::BaseGeometry *geometry = image->GetGeometry(); if (geometry != NULL) { 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"); } 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::IntensityProfile::Pointer intensityProfile, mitk::Image::ConstPointer image ) { this->m_Controls->m_StatisticsTable->setColumnCount(1); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); m_PlanarFigureStatistics = this->AssembleStatisticsIntoVectorForPlanarFigure( intensityProfile, image); for (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 ( unsigned 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(NULL, 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 != NULL ) { mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()-> RemoveObserver( m_TimeObserverTag ); } m_TimeObserverTag = NULL; } } void QmitkImageStatisticsView::SetFocus() { } QMap QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram::Pointer histogram) const { QMap histogramMap; auto startIt = histogram->End(); auto endIt = histogram->End(); auto it = histogram->Begin(); unsigned int i = 0; bool firstValue = false; // removes frequencies of 0, which are outside the first and last bin //for (; it != endIt; ++it) //{ // if (it.GetFrequency() > 0.0) // { // endIt = it; // if (!firstValue) // { // firstValue = true; // startIt = it; // } // } //} //++endIt; // generating Lists of measurement and frequencies for (; it != endIt; ++it, ++i) { QVariant frequency = QVariant::fromValue(it.GetFrequency()); QVariant measurement = it.GetMeasurementVector()[0]; histogramMap.insert(measurement, frequency); } return histogramMap; } QList QmitkImageStatisticsView::ConvertIntensityProfileToList(mitk::IntensityProfile::Pointer intensityProfile) const { QList intensityProfileList; auto end = intensityProfile->End(); for (auto it = intensityProfile->Begin(); it != end; ++it) { intensityProfileList.append(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 { QString formattedIndex("("); for (const auto& entry : vector) { formattedIndex += QString::number(entry); formattedIndex += ","; } formattedIndex.chop(1); formattedIndex += ")"; return formattedIndex; } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui index 2d4b3edae3..8e790d1380 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui @@ -1,643 +1,643 @@ QmitkImageStatisticsViewControls true 0 0 548 800 Form 0 0 Qt::LeftToRight Feature Image: 0 0 None 0 0 Mask: 0 0 None -1 0 0 color: rgb(255, 0, 0); Error Message Qt::AutoText Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Ignore zero-valued voxels false Statistics 9 9 9 100 180 16777215 16777215 Qt::ScrollBarAsNeeded Qt::ScrollBarAsNeeded true QAbstractItemView::NoEditTriggers true true Qt::DotLine false 14 1 false false 80 true 80 false true true false 25 25 false false Mean Median StdDev RMS Max Min N V (mm³) Skewness Kurtosis Uniformity Entropy MPP UPP 0 0 0 0 0 0 Copy to Clipboard Qt::Horizontal QSizePolicy::Fixed 20 20 false copy complete table Qt::Horizontal 40 20 false 400 450 Histogram false 0 0 0 0 16777215 16777215 Plot 0 0 Barchart true 0 0 0 0 Linegraph Qt::Horizontal 40 20 - + - Use default bin size + Show Subchart true - + - Show Subchart + Use default bin size true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 60 0 100 16777215 Bin size: Press enter to recalculate statistics with new bin size. true 5 0.000010000000000 1000000.000000000000000 100.000000000000000 0 0 0 0 0 0 0 0 0 0 Copy to Clipboard Qt::Horizontal 413 17 Qt::Vertical 20 40 QmitkC3jsWidget QWidget
QmitkC3jsWidget.h