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 1399a09136..94db678b04 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,526 +1,581 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkImageStatisticsView.h" #include // berry includes #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "mitkImageStatisticsContainerManager.h" #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; QmitkImageStatisticsView::~QmitkImageStatisticsView() { if (nullptr != m_selectedPlanarFigure) { m_selectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); } } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { m_Controls.setupUi(parent); m_Controls.widget_histogram->SetTheme(GetColorTheme()); m_Controls.widget_intensityProfile->SetTheme(GetColorTheme()); m_Controls.groupBox_histogram->setVisible(true); m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.label_currentlyComputingStatistics->setVisible(false); m_Controls.sliderWidget_histogram->setPrefix("Time: "); m_Controls.sliderWidget_histogram->setDecimals(0); m_Controls.sliderWidget_histogram->setVisible(false); m_Controls.sliderWidget_intensityProfile->setPrefix("Time: "); m_Controls.sliderWidget_intensityProfile->setDecimals(0); m_Controls.sliderWidget_intensityProfile->setVisible(false); ResetGUI(); m_Controls.widget_statistics->SetDataStorage(GetDataStorage()); CreateConnections(); } void QmitkImageStatisticsView::CreateConnections() { connect(m_Controls.checkBox_ignoreZero, &QCheckBox::stateChanged, this, &QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged); connect(m_Controls.buttonSelection, &QAbstractButton::clicked, this, &QmitkImageStatisticsView::OnButtonSelectionPressed); } void QmitkImageStatisticsView::CalculateOrGetMultiStatistics() { m_selectedImageNode = nullptr; m_selectedMaskNode = nullptr; if (m_selectedImageNodes.empty()) { // no images selected; reset everything ResetGUI(); } for (auto imageNode : m_selectedImageNodes) { m_selectedImageNode = imageNode; if (m_selectedMaskNodes.empty()) { CalculateOrGetStatistics(); } else { for (auto maskNode : m_selectedMaskNodes) { m_selectedMaskNode = maskNode; CalculateOrGetStatistics(); } } } } void QmitkImageStatisticsView::CalculateOrGetStatistics() { if (nullptr != m_selectedPlanarFigure) { m_selectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); m_selectedPlanarFigure = nullptr; } m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.widget_statistics->setEnabled(m_selectedImageNode.IsNotNull()); if (nullptr != m_selectedImageNode) { auto image = dynamic_cast(m_selectedImageNode->GetData()); mitk::Image *mask = nullptr; mitk::PlanarFigure *maskPlanarFigure = nullptr; if (image->GetDimension() == 4) { m_Controls.sliderWidget_histogram->setVisible(true); unsigned int maxTimestep = image->GetTimeSteps(); m_Controls.sliderWidget_histogram->setMaximum(maxTimestep - 1); } else { m_Controls.sliderWidget_histogram->setVisible(false); } if (nullptr != m_selectedMaskNode) { mask = dynamic_cast(m_selectedMaskNode->GetData()); if (nullptr == mask) { maskPlanarFigure = dynamic_cast(m_selectedMaskNode->GetData()); } } mitk::ImageStatisticsContainer::ConstPointer imageStatistics; if (nullptr != mask) { imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(GetDataStorage(), image, mask); } else if (nullptr != maskPlanarFigure) { m_selectedPlanarFigure = maskPlanarFigure; ITKCommandType::Pointer changeListener = ITKCommandType::New(); changeListener->SetCallbackFunction(this, &QmitkImageStatisticsView::CalculateOrGetMultiStatistics); m_PlanarFigureObserverTag = m_selectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); if (!maskPlanarFigure->IsClosed()) { ComputeAndDisplayIntensityProfile(image, maskPlanarFigure); } imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(GetDataStorage(), image, maskPlanarFigure); } else { imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(GetDataStorage(), image); } bool imageStatisticsOlderThanInputs = false; if (nullptr != imageStatistics && ((nullptr != image && imageStatistics->GetMTime() < image->GetMTime()) || (nullptr != mask && imageStatistics->GetMTime() < mask->GetMTime()) || (nullptr != maskPlanarFigure && imageStatistics->GetMTime() < maskPlanarFigure->GetMTime()))) { imageStatisticsOlderThanInputs = true; } if (nullptr != imageStatistics) { // triggers re-computation when switched between images and the newest one has not 100 bins (default) auto calculatedBins = imageStatistics->GetStatisticsForTimeStep(0).m_Histogram.GetPointer()->Size(); if (calculatedBins != 100) { OnRequestHistogramUpdate(m_Controls.widget_histogram->GetBins()); } } // statistics need to be computed if (!imageStatistics || imageStatisticsOlderThanInputs || m_ForceRecompute) { CalculateStatistics(image, mask, maskPlanarFigure); } // statistics already computed else { /* HISTOGRAM CURRENTLY NOT WORKING - SEE T26269 // Not an open planar figure: show histogram (intensity profile already shown) if (!(maskPlanarFigure && !maskPlanarFigure->IsClosed())) { if (imageStatistics->TimeStepExists(0)) { auto histogram = imageStatistics->GetStatisticsForTimeStep(0).m_Histogram.GetPointer(); std::string imageNodeName = m_selectedImageNode->GetName(); FillHistogramWidget({ histogram }, { imageNodeName }); } } */ } } else { ResetGUI(); } } void QmitkImageStatisticsView::CalculateStatistics(const mitk::Image *image, const mitk::Image *mask, const mitk::PlanarFigure *maskPlanarFigure) { auto runnable = new QmitkImageStatisticsCalculationRunnable(); runnable->Initialize(image, mask, maskPlanarFigure); runnable->setAutoDelete(false); runnable->SetIgnoreZeroValueVoxel(m_IgnoreZeroValueVoxel); m_Runnables.push_back(runnable); connect(runnable, &QmitkImageStatisticsCalculationRunnable::finished, this, &QmitkImageStatisticsView::OnStatisticsCalculationEnds, Qt::QueuedConnection); try { // Compute statistics QThreadPool::globalInstance()->start(runnable); m_Controls.label_currentlyComputingStatistics->setVisible(true); } catch (const mitk::Exception &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.GetDescription()); m_Controls.label_currentlyComputingStatistics->setVisible(false); } catch (const std::runtime_error &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); m_Controls.label_currentlyComputingStatistics->setVisible(false); } catch (const std::exception &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); m_Controls.label_currentlyComputingStatistics->setVisible(false); } } void QmitkImageStatisticsView::ComputeAndDisplayIntensityProfile(mitk::Image *image, mitk::PlanarFigure *maskPlanarFigure) { mitk::Image::Pointer inputImage; if (image->GetDimension() == 4) { m_Controls.sliderWidget_intensityProfile->setVisible(true); unsigned int maxTimestep = image->GetTimeSteps(); m_Controls.sliderWidget_intensityProfile->setMaximum(maxTimestep - 1); // Intensity profile can only be calculated on 3D, so extract if 4D mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); int currentTimestep = static_cast(m_Controls.sliderWidget_intensityProfile->value()); timeSelector->SetInput(image); timeSelector->SetTimeNr(currentTimestep); timeSelector->Update(); inputImage = timeSelector->GetOutput(); } else { m_Controls.sliderWidget_intensityProfile->setVisible(false); inputImage = image; } auto intensityProfile = mitk::ComputeIntensityProfile(inputImage, maskPlanarFigure); // Don't show histogram for intensity profiles m_Controls.groupBox_histogram->setVisible(false); m_Controls.groupBox_intensityProfile->setVisible(true); m_Controls.widget_intensityProfile->Reset(); m_Controls.widget_intensityProfile->SetIntensityProfile(intensityProfile.GetPointer(), "Intensity Profile of " + m_selectedImageNode->GetName()); } void QmitkImageStatisticsView::FillHistogramWidget(const std::vector &histogram, const std::vector &dataLabels) { m_Controls.groupBox_histogram->setVisible(true); m_Controls.widget_histogram->SetTheme(GetColorTheme()); m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->SetHistogram(histogram.front(), dataLabels.front()); connect(m_Controls.widget_histogram, &QmitkHistogramVisualizationWidget::RequestHistogramUpdate, this, &QmitkImageStatisticsView::OnRequestHistogramUpdate); } QmitkChartWidget::ColorTheme QmitkImageStatisticsView::GetColorTheme() const { ctkPluginContext *context = berry::WorkbenchPlugin::GetDefault()->GetPluginContext(); ctkServiceReference styleManagerRef = context->getServiceReference(); if (styleManagerRef) { auto styleManager = context->getService(styleManagerRef); if (styleManager->GetStyle().name == "Dark") { return QmitkChartWidget::ColorTheme::darkstyle; } else { return QmitkChartWidget::ColorTheme::lightstyle; } } return QmitkChartWidget::ColorTheme::darkstyle; } void QmitkImageStatisticsView::ResetGUI() { m_Controls.widget_statistics->Reset(); m_Controls.widget_statistics->setEnabled(false); m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->setEnabled(false); } void QmitkImageStatisticsView::ResetGUIDefault() { m_Controls.widget_histogram->ResetDefault(); m_Controls.checkBox_ignoreZero->setChecked(false); m_IgnoreZeroValueVoxel = false; } void QmitkImageStatisticsView::OnStatisticsCalculationEnds() { mitk::StatusBar::GetInstance()->Clear(); auto runnable = m_Runnables[0]; m_Runnables.erase(m_Runnables.begin()); auto image = runnable->GetStatisticsImage(); // get mask mitk::BaseData::ConstPointer mask = nullptr; if (runnable->GetMaskImage()) { mask = runnable->GetMaskImage(); } else if (runnable->GetPlanarFigure()) { mask = runnable->GetPlanarFigure(); } // get current statistics auto currentImageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(GetDataStorage(), image, mask); if (runnable->GetStatisticsUpdateSuccessFlag()) // case: calculation was successful { auto statistic = runnable->GetStatisticsData(); auto imageRule = mitk::StatisticsToImageRelationRule::New(); imageRule->Connect(statistic, image); SetupRelationRules(statistic, mask); // checks for existing statistic, and add it to data manager HandleExistingStatistics(image, mask, statistic); /* HISTOGRAM CURRENTLY NOT WORKING - SEE T26269 if (!m_selectedPlanarFigure || m_selectedPlanarFigure->IsClosed()) { FillHistogramWidget({ m_CalculationJob->GetTimeStepHistogram() }, { m_selectedImageNode->GetName() }); } */ } else // case: calculation was not successful { // handle histogram const HistogramType* emptyHistogram = HistogramType::New(); // HISTOGRAM CURRENTLY NOT WORKING - SEE T26269 //FillHistogramWidget({ emptyHistogram }, { m_selectedImageNode->GetName() }); // handle statistics mitk::ImageStatisticsContainer::Pointer statistic = mitk::ImageStatisticsContainer::New(); statistic->SetTimeGeometry(const_cast(image->GetTimeGeometry())); /* HISTOGRAM CURRENTLY NOT WORKING - SEE T26269 // add empty histogram to statistics for all time steps for (unsigned int i = 0; i < image->GetTimeSteps(); ++i) { auto statisticObject = mitk::ImageStatisticsContainer::ImageStatisticsObject(); statisticObject.m_Histogram = emptyHistogram; statistic->SetStatisticsForTimeStep(i, statisticObject); } */ SetupRelationRules(statistic, mask); HandleExistingStatistics(image, mask, statistic); mitk::StatusBar::GetInstance()->DisplayErrorText(runnable->GetLastErrorMessage().c_str()); m_Controls.widget_histogram->setEnabled(false); } m_Controls.label_currentlyComputingStatistics->setVisible(false); } void QmitkImageStatisticsView::OnRequestHistogramUpdate(unsigned int nBins) { } void QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged(int state) { m_ForceRecompute = true; m_IgnoreZeroValueVoxel = (state == Qt::Unchecked) ? false : true; CalculateOrGetMultiStatistics(); m_ForceRecompute = false; } void QmitkImageStatisticsView::OnButtonSelectionPressed() { m_SelectionDialog = new QmitkNodeSelectionDialog(); m_SelectionDialog->SetDataStorage(GetDataStorage()); + m_SelectionDialog->SetSelectionCheckFunction(CheckForSameGeometry()); // set predicates auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); auto isImageOrMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isMaskOrPlanarFigurePredicate, isImagePredicate); m_SelectionDialog->SetNodePredicate(isImageOrMaskOrPlanarFigurePredicate); m_SelectionDialog->SetSelectionMode(QAbstractItemView::MultiSelection); connect(m_SelectionDialog, &QmitkNodeSelectionDialog::accepted, this, &QmitkImageStatisticsView::OnDialogSelectionChanged); m_SelectionDialog->show(); } void QmitkImageStatisticsView::OnDialogSelectionChanged() { m_selectedImageNodes.resize(0); m_selectedMaskNodes.resize(0); QmitkNodeSelectionDialog::NodeList selectedNodeList = m_SelectionDialog->GetSelectedNodes(); auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); for (const auto& node : selectedNodeList) { if (isImagePredicate->CheckNode(node)) { m_selectedImageNodes.push_back(node.GetPointer()); } else { m_selectedMaskNodes.push_back(node.GetPointer()); } } if (!m_selectedImageNodes.empty()) { m_Controls.widget_statistics->SetImageNodes(m_selectedImageNodes); } if (!m_selectedMaskNodes.empty()) { m_Controls.widget_statistics->SetMaskNodes(m_selectedMaskNodes); } CalculateOrGetMultiStatistics(); } std::string QmitkImageStatisticsView::GenerateStatisticsNodeName() { auto statisticsNodeName = m_selectedImageNode->GetName(); if (m_selectedMaskNode) { statisticsNodeName += "_" + m_selectedMaskNode->GetName(); } statisticsNodeName += "_statistics"; return statisticsNodeName; } void QmitkImageStatisticsView::HandleExistingStatistics(mitk::Image::ConstPointer image, mitk::BaseData::ConstPointer mask, mitk::ImageStatisticsContainer::Pointer statistic) { auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(GetDataStorage(), image, mask); // if statistics base data already exist: add to existing node if (imageStatistics) { auto node = GetNodeForStatisticsContainer(imageStatistics); node->SetData(statistic); } // statistics base data does not exist: add new node else { auto statisticsNodeName = GenerateStatisticsNodeName(); // ## ADD IMAGE AND MASK? auto statisticsNode = mitk::CreateImageStatisticsNode(statistic, statisticsNodeName); GetDataStorage()->Add(statisticsNode); } } void QmitkImageStatisticsView::SetupRelationRules(mitk::ImageStatisticsContainer::Pointer statistic, mitk::BaseData::ConstPointer mask) { if (nullptr != mask) { auto maskRule = mitk::StatisticsToMaskRelationRule::New(); maskRule->Connect(statistic, mask); } } mitk::DataNode::Pointer QmitkImageStatisticsView::GetNodeForStatisticsContainer( mitk::ImageStatisticsContainer::ConstPointer container) { if (!container) { mitkThrow() << "Given container is null!"; } auto allDataNodes = GetDataStorage()->GetAll()->CastToSTLConstContainer(); for (auto node : allDataNodes) { auto nodeData = node->GetData(); if (nodeData && nodeData->GetUID() == container->GetUID()) { return node; } } mitkThrow() << "No DataNode is found which holds the given statistics container!"; } +QmitkNodeSelectionDialog::SelectionCheckFunctionType QmitkImageStatisticsView::CheckForSameGeometry() const +{ + auto lambda = [this](const QmitkNodeSelectionDialog::NodeList& nodes) + { + if (nodes.empty()) + { + return std::string(); + } + + auto leftNode = nodes[0]; + for (int i = 1; i < nodes.size(); ++i) + { + auto rightNode = nodes[i]; + + bool sameGeometry = CheckForSameGeometry(leftNode, rightNode); + if (!sameGeometry) + { + std::stringstream ss; + ss << "

Invalid selection: All selected nodes must have the same geometry.

"; + return ss.str(); + } + } + + return std::string(); + }; + + return lambda; +} + +bool QmitkImageStatisticsView::CheckForSameGeometry(const mitk::DataNode* node1, const mitk::DataNode* node2) const +{ + bool isSameGeometry(true); + + mitk::Image* image1 = dynamic_cast(node1->GetData()); + mitk::Image* image2 = dynamic_cast(node2->GetData()); + if (image1 && image2) + { + mitk::BaseGeometry* geo1 = image1->GetGeometry(); + mitk::BaseGeometry* geo2 = image2->GetGeometry(); + + isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetOrigin(), geo2->GetOrigin()); + isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(0), geo2->GetExtent(0)); + isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(1), geo2->GetExtent(1)); + isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(2), geo2->GetExtent(2)); + isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetSpacing(), geo2->GetSpacing()); + isSameGeometry = isSameGeometry && mitk::MatrixEqualElementWise(geo1->GetIndexToWorldTransform()->GetMatrix(), geo2->GetIndexToWorldTransform()->GetMatrix()); + + return isSameGeometry; + } + else + { + return false; + } +} 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 96a1a33ffb..c2080e168f 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h @@ -1,106 +1,109 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QMITKIMAGESTATISTICSVIEW_H #define QMITKIMAGESTATISTICSVIEW_H #include "ui_QmitkImageStatisticsViewControls.h" #include #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 { Q_OBJECT public: static const std::string VIEW_ID; /*! \brief default destructor */ ~QmitkImageStatisticsView() override; /*! \brief Creates the widget containing the application controls, like sliders, buttons etc.*/ void CreateQtPartControl(QWidget *parent) override; protected: using HistogramType = mitk::ImageStatisticsContainer::HistogramType; void SetFocus() override { }; virtual void CreateConnections(); void CalculateOrGetMultiStatistics(); void CalculateOrGetStatistics(); void CalculateStatistics(const mitk::Image* image, const mitk::Image* mask = nullptr, const mitk::PlanarFigure* maskPlanarFigure = nullptr); void ComputeAndDisplayIntensityProfile(mitk::Image * image, mitk::PlanarFigure* maskPlanarFigure); void FillHistogramWidget(const std::vector &histogram, const std::vector &dataLabels); QmitkChartWidget::ColorTheme GetColorTheme() const; void ResetGUI(); void ResetGUIDefault(); void OnStatisticsCalculationEnds(); void OnRequestHistogramUpdate(unsigned int nBins); void OnCheckBoxIgnoreZeroStateChanged(int state); void OnButtonSelectionPressed(); void OnDialogSelectionChanged(); // member variable Ui::QmitkImageStatisticsViewControls m_Controls; private: std::string GenerateStatisticsNodeName(); void HandleExistingStatistics(mitk::Image::ConstPointer image, mitk::BaseData::ConstPointer mask, mitk::ImageStatisticsContainer::Pointer); void SetupRelationRules(mitk::ImageStatisticsContainer::Pointer, mitk::BaseData::ConstPointer mask); mitk::DataNode::Pointer GetNodeForStatisticsContainer(mitk::ImageStatisticsContainer::ConstPointer container); + QmitkNodeSelectionDialog::SelectionCheckFunctionType CheckForSameGeometry() const; + bool CheckForSameGeometry(const mitk::DataNode* node1, const mitk::DataNode* node2) const; + typedef itk::SimpleMemberCommand ITKCommandType; mitk::DataNode::ConstPointer m_selectedImageNode = nullptr; mitk::DataNode::ConstPointer m_selectedMaskNode = nullptr; mitk::PlanarFigure::Pointer m_selectedPlanarFigure = nullptr; QmitkNodeSelectionDialog* m_SelectionDialog = nullptr; long m_PlanarFigureObserverTag; bool m_ForceRecompute = false; bool m_IgnoreZeroValueVoxel = false; std::vector m_selectedMaskNodes; std::vector m_selectedImageNodes; std::vector m_StatisticsForSelection; std::vector m_Runnables; }; #endif // QMITKIMAGESTATISTICSVIEW_H