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 4d19624dbb..b70465da37 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,1295 +1,1295 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkImageStatisticsView.h" // Qt includes #include #include #include // berry includes #include // mitk includes #include #include #include #include #include #include #include #include // itk includes #include "itksys/SystemTools.hxx" #include "itkImageRegionConstIteratorWithIndex.h" #include //blueberry includes #include #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; const int QmitkImageStatisticsView::STAT_TABLE_BASE_HEIGHT = 180; QmitkImageStatisticsView::QmitkImageStatisticsView(QObject* /*parent*/, const char* /*name*/) -: m_Controls( nullptr ), - m_SelectedImage( nullptr ), - m_SelectedImageMask( nullptr ), - m_SelectedPlanarFigure( nullptr ), - m_ImageObserverTag( -1 ), - m_ImageMaskObserverTag( -1 ), - m_PlanarFigureObserverTag( -1 ), - m_TimeObserverTag( -1 ), - m_CurrentStatisticsValid( false ), - m_StatisticsUpdatePending( false ), - m_DataNodeSelectionChanged ( false ), + : m_Controls(nullptr), + m_SelectedImage(nullptr), + m_SelectedImageMask(nullptr), + m_SelectedPlanarFigure(nullptr), + m_ImageObserverTag(-1), + m_ImageMaskObserverTag(-1), + m_PlanarFigureObserverTag(-1), + m_TimeObserverTag(-1), + m_CurrentStatisticsValid(false), + m_StatisticsUpdatePending(false), + m_DataNodeSelectionChanged(false), m_Visible(false) { this->m_CalculationThread = new QmitkImageStatisticsCalculationJob; } 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 + if (m_SelectedImage != nullptr) + m_SelectedImage->RemoveObserver(m_ImageObserverTag); + if (m_SelectedImageMask != nullptr) + m_SelectedImageMask->RemoveObserver(m_ImageMaskObserverTag); + if (m_SelectedPlanarFigure != nullptr) + m_SelectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); + + while (this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } delete this->m_CalculationThread; } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { if (m_Controls == nullptr) { m_Controls = new Ui::QmitkImageStatisticsViewControls; m_Controls->setupUi(parent); CreateConnections(); m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_Controls->m_BinSizeFrame->setEnabled(false); - #if QT_VERSION < QT_VERSION_CHECK(5, 10, 0) - m_Controls->m_StatisticsWidgetStack->setVisible(false); - m_Controls->label_HistogramIsInvisibleWarning->setEnabled(true); - m_Controls->label_HistogramIsInvisibleWarning->setVisible(true); - m_Controls->label_HistogramIsInvisibleWarning->setText("Histogram is not visible because Qt 5.10 is required. You can use the button Copy to Clipboard below to retrieve values."); - m_Controls->groupBox_plot->setVisible(false); - #else - m_Controls->label_HistogramIsInvisibleWarning->setVisible(false); - #endif +#if QT_VERSION < QT_VERSION_CHECK(5, 10, 0) + m_Controls->m_StatisticsWidgetStack->setVisible(false); + m_Controls->label_HistogramIsInvisibleWarning->setEnabled(true); + m_Controls->label_HistogramIsInvisibleWarning->setVisible(true); + m_Controls->label_HistogramIsInvisibleWarning->setText("Histogram is not visible because Qt 5.10 is required. You can use the button Copy to Clipboard below to retrieve values."); + m_Controls->groupBox_plot->setVisible(false); +#else + m_Controls->label_HistogramIsInvisibleWarning->setVisible(false); +#endif } } void QmitkImageStatisticsView::OnPageSuccessfullyLoaded() { berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, ""); if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss") { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::darkstyle); } else { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::lightstyle); } } void QmitkImageStatisticsView::CreateConnections() { - if ( m_Controls ) + 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_ButtonCopyHistogramToClipboard), SIGNAL(clicked()), (QObject*)this, SLOT(OnClipboardHistogramButtonClicked())); + connect((QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()), (QObject*)this, SLOT(OnClipboardStatisticsButtonClicked())); + connect((QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()), (QObject*)this, SLOT(OnIgnoreZerosCheckboxClicked())); + connect((QObject*)this->m_CalculationThread, SIGNAL(finished()), this, SLOT(OnThreadedStatisticsCalculationEnds()), Qt::QueuedConnection); + connect((QObject*)this, SIGNAL(StatisticsUpdate()), this, SLOT(RequestStatisticsUpdate()), Qt::QueuedConnection); + connect((QObject*)this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int, int)), this, SLOT(JumpToCoordinates(int, int))); connect((QObject*)(this->m_Controls->m_barRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnBarRadioButtonSelected())); connect((QObject*)(this->m_Controls->m_lineRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnLineRadioButtonSelected())); - connect( (QObject*) (this->m_Controls->m_HistogramNBinsSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramNBinsCheckBoxValueChanged())); - connect((QObject*)(this->m_Controls->m_UseDefaultNBinsCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnDefaultNBinsSpinBoxChanged())); - connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnShowSubchartBoxChanged())); - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); + connect((QObject*)(this->m_Controls->m_HistogramNBinsSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramNBinsCheckBoxValueChanged())); + connect((QObject*)(this->m_Controls->m_UseDefaultNBinsCheckBox), SIGNAL(clicked()), (QObject*)this, SLOT(OnDefaultNBinsSpinBoxChanged())); + connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*)this, SLOT(OnShowSubchartBoxChanged())); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnPageSuccessfullyLoaded())); } } void QmitkImageStatisticsView::OnDefaultNBinsSpinBoxChanged() { if (this->m_Controls->m_UseDefaultNBinsCheckBox->isChecked()) { m_Controls->m_HistogramNBinsSpinbox->setValue(100); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); } m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultNBinsCheckBox->isChecked()); this->UpdateStatistics(); } void QmitkImageStatisticsView::OnShowSubchartBoxChanged() { bool showSubchart = this->m_Controls->m_ShowSubchartCheckBox->isChecked(); this->m_Controls->m_JSHistogram->Reload(showSubchart); } void QmitkImageStatisticsView::OnBarRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::bar); } void QmitkImageStatisticsView::OnLineRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::line); } -void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& ) +void QmitkImageStatisticsView::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); + 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) + this->m_SelectedImage->GetTimeSteps() > 1) { // display histogram for selected timestep //bug in Qt thats leads to crash in debug builds. Fixed in Qt 5.10 - #if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) - m_Controls->m_JSHistogram->Clear(); - #endif +#if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) + m_Controls->m_JSHistogram->Clear(); +#endif QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer histogram = - (QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep); + (QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep); if (histogram.IsNotNull()) { bool statisticsUpdateSuccessful = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag(); if (statisticsUpdateSuccessful) { 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) +void QmitkImageStatisticsView::JumpToCoordinates(int row, int col) { - if(m_SelectedDataNodes.isEmpty()) + if (m_SelectedDataNodes.isEmpty()) { - MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation." ; + MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation."; return; } mitk::Point3D world; - if (row==5 && !m_WorldMinList.empty()) + if (row == 5 && !m_WorldMinList.empty()) world = m_WorldMinList[col]; - else if (row==4 && !m_WorldMaxList.empty()) + else if (row == 4 && !m_WorldMaxList.empty()) world = m_WorldMaxList[col]; else return; mitk::IRenderWindowPart* part = this->GetRenderWindowPart(); if (part) { part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SelectSliceByPoint(world); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), col); part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetGeometryTime(timeEvent); } } void QmitkImageStatisticsView::OnIgnoreZerosCheckboxClicked() { emit StatisticsUpdate(); } void QmitkImageStatisticsView::OnClipboardHistogramButtonClicked() { if (!m_CurrentStatisticsValid) { QApplication::clipboard()->clear(); } if (m_SelectedPlanarFigure == nullptr) { const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); typedef mitk::ImageStatisticsCalculator::HistogramType HistogramType; const HistogramType *histogram = this->m_CalculationThread->GetTimeStepHistogram(t).GetPointer(); QString clipboard("Measurement \t Frequency\n"); for (HistogramType::ConstIterator it = histogram->Begin(); it != histogram->End(); ++it) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(it.GetMeasurementVector()[0], 0, 'f', 2) .arg(it.GetFrequency()); } QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard); } //If a (non-closed) PlanarFigure is selected, display a line profile widget else if (m_SelectedPlanarFigure != nullptr) { QString clipboard("Pixel \t Intensity\n"); for (unsigned int i = 0; i < m_IntensityProfileList.size(); i++) { clipboard = clipboard.append("%L1 \t %L2\n").arg(QString::number(i)).arg(QString::number(m_IntensityProfileList.at(i))); } QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } } void QmitkImageStatisticsView::OnClipboardStatisticsButtonClicked() { QLocale tempLocal; QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates)); - if ( m_CurrentStatisticsValid && !( m_SelectedPlanarFigure != nullptr)) - { + if (m_CurrentStatisticsValid && !(m_SelectedPlanarFigure != nullptr)) + { const auto &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) + if (this->m_Controls->m_CheckBox4dCompleteTable->checkState() == Qt::CheckState::Unchecked) { - startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> - GetPos(); - endT = startT+1; + startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> + GetPos(); + endT = startT + 1; } else { - startT = 0; - endT = statistics.size(); + startT = 0; + endT = statistics->GetNumberOfTimeSteps(); } QVector< QVector > statisticsTable; QStringList headline{ "Timestep", "Mean", "Median", "StdDev", "RMS", "Max", "Min", "NumberOfVoxels", "Skewness", "Kurtosis", "Uniformity", "Entropy", "MPP", "UPP", "V [mm³]" }; - for(int i=0;i row; - row.append(headline.at(i)); - statisticsTable.append(row); + QVector 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;zGetStatisticsForTimeStep(t).m_Mean) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Median) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Std) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_RMS) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Max) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Min) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_N) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Skewness) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Kurtosis) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Uniformity) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_Entropy) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_MPP) + << QString::number(statistics->GetStatisticsForTimeStep(t).m_UPP) + << QString::number(m_Controls->m_StatisticsTable->item(7, 0)->data(Qt::DisplayRole).toDouble()); + + for (int z = 0; z < value.size(); z++) + { + statisticsTable[z].append(value.at(z)); + } } // Create output string QString clipboard; - for(int i=0;isetText(clipboard, QClipboard::Clipboard); } else { QApplication::clipboard()->clear(); } QLocale::setDefault(tempLocal); } -void QmitkImageStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*part*/, - const QList &nodes ) +void QmitkImageStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, + const QList &nodes) { if (this->m_Visible) { - this->SelectionChanged( nodes ); + this->SelectionChanged(nodes); } else { this->m_DataNodeSelectionChanged = true; } } void QmitkImageStatisticsView::SelectionChanged(const QList &selectedNodes) { //Clear Histogram if data node is deselected //bug in Qt thats leads to crash in debug builds. Fixed in Qt 5.10 - #if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) +#if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) m_Controls->m_JSHistogram->Clear(); - #endif +#endif - if( this->m_StatisticsUpdatePending ) + if (this->m_StatisticsUpdatePending) { this->m_DataNodeSelectionChanged = true; return; // not ready for new data now! } if (selectedNodes.size() == this->m_SelectedDataNodes.size()) { int i = 0; for (; i < selectedNodes.size(); ++i) { if (selectedNodes.at(i) != this->m_SelectedDataNodes.at(i)) { break; } } // node selection did not change if (i == selectedNodes.size()) return; } //reset the feature image and image mask field m_Controls->m_SelectedFeatureImageLabel->setText("None"); m_Controls->m_SelectedMaskLabel->setText("None"); this->ReinitData(); if (selectedNodes.isEmpty()) { DisableHistogramGUIElements(); } else { EnableHistogramGUIElements(); ResetHistogramGUIElementsToDefault(); } - if(selectedNodes.size() == 1 || selectedNodes.size() == 2) + if (selectedNodes.size() == 1 || selectedNodes.size() == 2) { bool isBinary = false; - selectedNodes.value(0)->GetBoolProperty("binary",isBinary); + selectedNodes.value(0)->GetBoolProperty("binary", isBinary); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); isBinary |= isLabelSet->CheckNode(selectedNodes.value(0)); - if(isBinary) + if (isBinary) { EnableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); } - for (int i= 0; i< selectedNodes.size(); ++i) + 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->setText(""); this->m_Controls->m_ErrorMessageLabel->hide(); emit StatisticsUpdate(); } else { this->m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::DisableHistogramGUIElements() { m_Controls->m_InfoLabel->setText(""); m_Controls->groupBox_histogram->setEnabled(false); m_Controls->groupBox_statistics->setEnabled(false); } void QmitkImageStatisticsView::ResetHistogramGUIElementsToDefault() { m_Controls->m_barRadioButton->setChecked(true); m_Controls->m_HistogramNBinsSpinbox->setValue(100); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); m_Controls->m_UseDefaultNBinsCheckBox->setChecked(true); m_Controls->m_ShowSubchartCheckBox->setChecked(true); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_HistogramNBinsSpinbox->setEnabled(true); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); } void QmitkImageStatisticsView::EnableHistogramGUIElements() { m_Controls->groupBox_histogram->setEnabled(true); m_Controls->groupBox_plot->setEnabled(true); m_Controls->groupBox_statistics->setEnabled(true); } void QmitkImageStatisticsView::ReinitData() { - while( this->m_CalculationThread->isRunning()) // wait until thread has finished + while (this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } - if(this->m_SelectedImage != nullptr) + if (this->m_SelectedImage != nullptr) { - this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag); + this->m_SelectedImage->RemoveObserver(this->m_ImageObserverTag); this->m_SelectedImage = nullptr; } - if(this->m_SelectedImageMask != nullptr) + if (this->m_SelectedImageMask != nullptr) { - this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag); + this->m_SelectedImageMask->RemoveObserver(this->m_ImageMaskObserverTag); this->m_SelectedImageMask = nullptr; } - if(this->m_SelectedPlanarFigure != nullptr) + if (this->m_SelectedPlanarFigure != nullptr) { - this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag); + 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->setText(""); m_Controls->m_ErrorMessageLabel->hide(); this->InvalidateStatisticsTableView(); - m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); + m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); } void QmitkImageStatisticsView::OnThreadedStatisticsCalculationEnds() { m_Controls->m_ErrorMessageLabel->setText(""); m_Controls->m_ErrorMessageLabel->hide(); this->WriteStatisticsToGUI(); } void QmitkImageStatisticsView::UpdateStatistics() { mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart(); - if ( renderPart == nullptr ) + if (renderPart == nullptr) { - this->m_StatisticsUpdatePending = false; + 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 ); + changeListener->SetCallbackFunction(this, &QmitkImageStatisticsView::SelectedDataModified); mitk::DataNode::Pointer planarFigureNode; - for( int i= 0 ; i < this->m_SelectedDataNodes.size(); ++i) + 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)) ) + 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) + 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 ) + else if (!isMask) { - if(this->m_SelectedImage == nullptr) + 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) + if (this->m_SelectedPlanarFigure == nullptr) { this->m_SelectedPlanarFigure = planarFig; - this->m_PlanarFigureObserverTag = - this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); + this->m_PlanarFigureObserverTag = + this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = this->m_SelectedPlanarFigure->GetNameOfClass(); maskDimension = 2; planarFigureNode = m_SelectedDataNodes.at(i); } } else { m_Controls->m_ErrorMessageLabel->setText("Invalid data node type!"); m_Controls->m_ErrorMessageLabel->show(); } } - if(maskName == "") + if (maskName == "") { maskName = "None"; maskType = ""; maskDimension = 0; } - if(featureImageName == "") + 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++) + for (unsigned int i = 0; i < parentSet->Size(); i++) { mitk::DataNode::Pointer node = parentSet->ElementAt(i); - if( imagePredicate->CheckNode(node) ) + if (imagePredicate->CheckNode(node)) { bool isMask = false; node->GetPropertyValue("binary", isMask); isMask |= isLabelSet->CheckNode(node); - if( !isMask ) + if (!isMask) { - if(this->m_SelectedImage == nullptr) + 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()) + 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 ) + if (m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1) { - m_Controls->m_ErrorMessageLabel->setText( "Multi-component images not supported." ); + m_Controls->m_ErrorMessageLabel->setText("Multi-component images not supported."); m_Controls->m_ErrorMessageLabel->show(); this->InvalidateStatisticsTableView(); - m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); + m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; this->m_StatisticsUpdatePending = false; this->DisableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); return; } std::stringstream maskLabel; maskLabel << maskName; - if ( maskDimension > 0 ) + if (maskDimension > 0) { maskLabel << " [" << maskDimension << "D " << maskType << "]"; } - m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() ); + 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) + if (m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3) - 1) { - 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(")")); + QString(" (t=") + + QString::number(maskTimeStep) + + QString(")")); } // check if the segmentation mask is empty if (m_SelectedImageMask != nullptr) { auto maskStatistics = m_SelectedImageMask->GetStatistics(); mitk::ScalarType maskMaxValue = maskStatistics->GetScalarValueMax(0); if (m_SelectedImageMask->GetDimension() == 4) { for (unsigned int curTimestep = 1; curTimestep < m_SelectedImageMask->GetTimeSteps(); curTimestep++) { maskMaxValue = std::max(maskStatistics->GetScalarValueMax(curTimestep), maskMaxValue); } } bool segmentationIsEmpty = maskMaxValue == 0; if (segmentationIsEmpty) { - m_Controls->m_ErrorMessageLabel->setText( "Empty segmentation mask selected..." ); + m_Controls->m_ErrorMessageLabel->setText("Empty segmentation mask selected..."); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; 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 ); + this->m_CalculationThread->SetIgnoreZeroValueVoxel(m_Controls->m_IgnoreZerosCheckbox->isChecked()); + this->m_CalculationThread->Initialize(m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure); + this->m_CalculationThread->SetTimeStep(timeStep); m_Controls->m_ErrorMessageLabel->setText("Calculating statistics..."); m_Controls->m_ErrorMessageLabel->show(); try { // Compute statistics this->m_CalculationThread->start(); } - catch ( const mitk::Exception& e) + catch (const mitk::Exception& e) { m_Controls->m_ErrorMessageLabel->setText("" + QString(e.GetDescription()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } - catch ( const std::runtime_error &e ) + catch (const std::runtime_error &e) { // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } - catch ( const std::exception &e ) + catch (const std::exception &e) { MITK_ERROR << "Caught exception: " << e.what(); // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } } else { this->m_StatisticsUpdatePending = false; } } void QmitkImageStatisticsView::SelectedDataModified() { - if( !m_StatisticsUpdatePending ) + if (!m_StatisticsUpdatePending) { emit StatisticsUpdate(); } } void QmitkImageStatisticsView::NodeRemoved(const mitk::DataNode *node) { - while(this->m_CalculationThread->isRunning()) // wait until thread has finished + 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 (!m_StatisticsUpdatePending) { - if(this->m_DataNodeSelectionChanged) + if (this->m_DataNodeSelectionChanged) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->m_StatisticsUpdatePending = true; this->UpdateStatistics(); } } if (this->GetRenderWindowPart()) this->GetRenderWindowPart()->RequestUpdate(); } void QmitkImageStatisticsView::OnHistogramNBinsCheckBoxValueChanged() { - if (static_cast(m_Controls->m_HistogramNBinsSpinbox->value()) != m_HistogramNBins) - { - m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); - this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); - this->UpdateStatistics(); - } + if (static_cast(m_Controls->m_HistogramNBinsSpinbox->value()) != m_HistogramNBins) + { + m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); + this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); + this->UpdateStatistics(); + } } void QmitkImageStatisticsView::WriteStatisticsToGUI() { //bug in Qt thats leads to crash in debug builds. Fixed in Qt 5.10 - #if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) +#if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) m_Controls->m_JSHistogram->Clear(); - #endif +#endif m_IntensityProfileList.clear(); //Disconnect OnLineRadioButtonSelected() to prevent reloading chart when radiobutton is checked programmatically disconnect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), 0, 0); - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnPageSuccessfullyLoaded())); m_Controls->m_InfoLabel->setText(""); if (m_DataNodeSelectionChanged) { this->m_StatisticsUpdatePending = false; this->RequestStatisticsUpdate(); return; // stop visualization of results and calculate statistics of new selection } if (this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) { if (this->m_CalculationThread->GetStatisticsChangedFlag()) { // Do not show any error messages m_Controls->m_ErrorMessageLabel->hide(); m_CurrentStatisticsValid = true; } if (m_SelectedImage != nullptr) { //all statistics are now computed also on planar figures (lines, paths...)! // If a (non-closed) PlanarFigure is selected, display a line profile widget if (m_SelectedPlanarFigure != nullptr && !m_SelectedPlanarFigure->IsClosed()) { // check whether PlanarFigure is initialized const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); if (planarFigurePlaneGeometry != nullptr) { 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()->Clone(); } mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); m_IntensityProfileList = ConvertIntensityProfileToVector(intensityProfile); auto lineDataLabel = "Intensity profile " + m_Controls->m_SelectedMaskLabel->text().toStdString(); m_Controls->m_JSHistogram->SetChartType(lineDataLabel, QmitkChartWidget::ChartType::line); m_Controls->m_JSHistogram->AddData1D(m_IntensityProfileList, lineDataLabel); m_Controls->m_JSHistogram->SetXAxisLabel("Distance"); m_Controls->m_JSHistogram->SetYAxisLabel("Intensity"); m_Controls->m_JSHistogram->Show(m_Controls->m_ShowSubchartCheckBox->isChecked()); m_Controls->m_lineRadioButton->setChecked(true); m_Controls->m_lineRadioButton->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(false); m_Controls->m_HistogramNBinsSpinbox->setEnabled(false); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(false); //Reconnect OnLineRadioButtonSelected() - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected())); - auto statisticsVector = this->m_CalculationThread->GetStatisticsData(); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnLineRadioButtonSelected())); + auto statisticsContainer = this->m_CalculationThread->GetStatisticsData(); //only one entry (current timestep) - this->FillLinearProfileStatisticsTableView(statisticsVector.front().GetPointer(), this->m_CalculationThread->GetStatisticsImage()); + this->FillLinearProfileStatisticsTableView(statisticsContainer, this->m_CalculationThread->GetStatisticsImage()); QString message("Only linegraph available for an intensity profile!"); if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) { message += "Only current timestep displayed!"; } message += ""; m_Controls->m_InfoLabel->setText(message); m_CurrentStatisticsValid = true; } else { // Clear statistics, histogram, and GUI this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_SelectedMaskLabel->setText("None"); this->m_StatisticsUpdatePending = false; m_Controls->m_InfoLabel->setText(""); return; } } else { m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); auto histogram = this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer(); auto imageLabelName = m_Controls->m_SelectedFeatureImageLabel->text().toStdString(); m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram), imageLabelName); m_Controls->m_JSHistogram->SetChartType(imageLabelName, QmitkChartWidget::ChartType::bar); this->m_Controls->m_JSHistogram->SetXAxisLabel("Gray value"); this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(true); m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); this->FillStatisticsTableView(this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage()); - for (const auto& aStatistic: this->m_CalculationThread->GetStatisticsData()) { - auto statisticsNode = mitk::DataNode::New(); - statisticsNode->SetName(m_Controls->m_SelectedFeatureImageLabel->text().toStdString()); - statisticsNode->SetData(aStatistic->Clone()); - statisticsNode->SetProperty("helper object", mitk::BoolProperty::New(true)); - this->GetDataStorage()->Add(statisticsNode); - } + auto aStatistic = this->m_CalculationThread->GetStatisticsData(); + auto statisticsNode = mitk::DataNode::New(); + statisticsNode->SetName(m_Controls->m_SelectedFeatureImageLabel->text().toStdString()); + statisticsNode->SetData(aStatistic->Clone()); + statisticsNode->SetProperty("helper object", mitk::BoolProperty::New(true)); + this->GetDataStorage()->Add(statisticsNode); + } 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 ) + mitk::StatisticsContainer::ConstPointer 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) + 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))); + new QTableWidgetItem(QString::number(t))); - if (statistics.at(t)->GetMaxIndex().size()==3) + if (statistics->GetStatisticsForTimeStep(t).m_MaxIndex.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]; + index[0] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[0]; + index[1] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[1]; + index[2] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[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]; + index[0] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[0]; + index[1] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[1]; + index[2] = statistics->GetStatisticsForTimeStep(t).m_MaxIndex[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, min); this->m_WorldMinList.push_back(min); } - auto statisticsVector = AssembleStatisticsIntoVector(statistics.at(t).GetPointer(), image); + auto statisticsVector = AssembleStatisticsIntoVector(statistics, 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(); + GetPos(); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), - t); + 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::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())); + auto statistic = statistics->GetStatisticsForTimeStep(0); + result.push_back(GetFormattedString(statistic.m_Mean, decimals)); + result.push_back(GetFormattedString(statistic.m_Median, decimals)); + result.push_back(GetFormattedString(statistic.m_Std, decimals)); + result.push_back(GetFormattedString(statistic.m_RMS, decimals)); + result.push_back(GetFormattedString(statistic.m_Max, decimals) + " " + GetFormattedIndex(statistic.m_MaxIndex)); + result.push_back(GetFormattedString(statistic.m_Min, decimals) + " " + GetFormattedIndex(statistic.m_MinIndex)); //to prevent large negative values of empty image statistics - if (statistics->GetN() != std::numeric_limits::min()) { - result.push_back(GetFormattedString(statistics->GetN(), 0)); + if (statistic.m_N != std::numeric_limits::min()) { + result.push_back(GetFormattedString(statistic.m_N, 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()); + double volume = spacing[0] * spacing[1] * spacing[2] * static_cast(statistic.m_N); 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)); + result.push_back(GetFormattedString(statistic.m_Skewness, decimalsHigherOrderStatistics)); + result.push_back(GetFormattedString(statistic.m_Kurtosis, decimalsHigherOrderStatistics)); + result.push_back(GetFormattedString(statistic.m_Uniformity, decimalsHigherOrderStatistics)); + result.push_back(GetFormattedString(statistic.m_Entropy, decimalsHigherOrderStatistics)); + result.push_back(GetFormattedString(statistic.m_MPP, decimals)); + result.push_back(GetFormattedString(statistic.m_UPP, decimalsHigherOrderStatistics)); return result; } void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView(mitk::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++) + 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->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 ) + 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->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(); + 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); + 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 ) + if (m_TimeObserverTag != 0) { mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()-> - RemoveObserver( m_TimeObserverTag ); + RemoveObserver(m_TimeObserverTag); } m_TimeObserverTag = 0; } } void QmitkImageStatisticsView::SetFocus() { } std::map QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; auto endIt = histogram->End(); auto it = histogram->Begin(); // 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::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; } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h index a1e305ddd9..314c626bca 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h @@ -1,191 +1,191 @@ /*=================================================================== 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. ===================================================================*/ #ifndef QmitkImageStatisticsView_H__INCLUDED #define QmitkImageStatisticsView_H__INCLUDED #include "ui_QmitkImageStatisticsViewControls.h" // Qmitk includes #include #include #include #include // mitk includes #include #include #include #include /*! \brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics of an image and a Planar Figure. The statistics calculation is realized in a separate thread to keep the gui accessible during calculation. \ingroup Plugins/org.mitk.gui.qt.measurementtoolbox */ class QmitkImageStatisticsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart, public berry::IPartListener { Q_OBJECT private: /*! \ Convenient typedefs */ typedef QList SelectedDataNodeVectorType; typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType; std::map ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const; std::vector ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const; std::vector AssembleStatisticsIntoVector(mitk::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined=false) const; QString GetFormattedIndex(const vnl_vector& vector) const; QString GetFormattedString(double value, unsigned int decimals) const; public: /*! \brief default constructor */ QmitkImageStatisticsView(QObject *parent = nullptr, const char *name = nullptr); /*! \brief default destructor */ virtual ~QmitkImageStatisticsView(); /*! \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ virtual void CreateQtPartControl(QWidget *parent) override; /*! \brief method for creating the connections of main and control widget */ virtual void CreateConnections(); /*! \brief Is called from the selection mechanism once the data manager selection has changed*/ void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &selectedNodes) override; static const std::string VIEW_ID; static const int STAT_TABLE_BASE_HEIGHT; public slots: /** \brief Called when the statistics update is finished, sets the results to GUI.*/ void OnThreadedStatisticsCalculationEnds(); /** \brief Update bin size for histogram resolution. */ void OnHistogramNBinsCheckBoxValueChanged(); protected slots: /** \brief Saves the histogram to the clipboard */ void OnClipboardHistogramButtonClicked(); /** \brief Saves the statistics to the clipboard */ void OnClipboardStatisticsButtonClicked(); /** \brief Indicates if zeros should be excluded from statistics calculation */ void OnIgnoreZerosCheckboxClicked(); /** \brief Checks if update is possible and calls StatisticsUpdate() possible */ void RequestStatisticsUpdate(); /** \brief Jump to coordinates stored in the double clicked cell */ void JumpToCoordinates(int row, int col); /** \brief Toogle GUI elements if histogram default bin size checkbox value changed. */ void OnDefaultNBinsSpinBoxChanged(); void OnShowSubchartBoxChanged(); void OnBarRadioButtonSelected(); void OnLineRadioButtonSelected(); void OnPageSuccessfullyLoaded(); signals: /** \brief Method to set the data to the member and start the threaded statistics update */ void StatisticsUpdate(); protected: /** \brief Writes the calculated statistics to the GUI */ - void FillStatisticsTableView(const std::vector &statistics, + void FillStatisticsTableView(mitk::StatisticsContainer::ConstPointer statistics, const mitk::Image *image); void FillLinearProfileStatisticsTableView(mitk::StatisticsContainer::ConstPointer statistics, const mitk::Image *image); /** \brief Removes statistics from the GUI */ void InvalidateStatisticsTableView(); /** \brief Recalculate statistics for currently selected image and mask and * update the GUI. */ void UpdateStatistics(); virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; virtual void SetFocus() override; /** \brief Method called when itkModifiedEvent is called by selected data. */ void SelectedDataModified(); /** \brief Method called when the data manager selection changes */ void SelectionChanged(const QList &selectedNodes); void DisableHistogramGUIElements(); void ResetHistogramGUIElementsToDefault(); void EnableHistogramGUIElements(); /** \brief Method called to remove old selection when a new selection is present */ void ReinitData(); /** \brief writes the statistics to the gui*/ void WriteStatisticsToGUI(); void NodeRemoved(const mitk::DataNode *node) override; /** \brief Is called right before the view closes (before the destructor) */ virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer&) override; /** \brief Is called from the image navigator once the time step has changed */ void OnTimeChanged(const itk::EventObject&); /** \brief Required for berry::IPartListener */ virtual Events::Types GetPartEventTypes() const override { return Events::CLOSED; } // member variables Ui::QmitkImageStatisticsViewControls *m_Controls; // if you have a planar figure selected, the statistics values will be saved in this one. std::vector m_PlanarFigureStatistics; QmitkImageStatisticsCalculationJob* m_CalculationThread; // Image and mask data mitk::Image* m_SelectedImage; mitk::Image* m_SelectedImageMask; mitk::PlanarFigure* m_SelectedPlanarFigure; // observer tags long m_ImageObserverTag; long m_ImageMaskObserverTag; long m_PlanarFigureObserverTag; long m_TimeObserverTag; SelectedDataNodeVectorType m_SelectedDataNodes; bool m_CurrentStatisticsValid; bool m_StatisticsUpdatePending; bool m_DataNodeSelectionChanged; bool m_Visible; unsigned int m_HistogramNBins; std::vector m_WorldMinList; std::vector m_WorldMaxList; std::vector m_IntensityProfileList; berry::IPreferences::Pointer m_StylePref; }; #endif // QmitkImageStatisticsView_H__INCLUDED