diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp index 936217f330..9035c9faa8 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp @@ -1,236 +1,242 @@ /*============================================================================ 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 "QmitkDataSelectionWidget.h" #include "../mitkPluginActivator.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static mitk::NodePredicateBase::Pointer CreatePredicate(QmitkDataSelectionWidget::Predicate predicate) { auto imageType = mitk::TNodePredicateDataType::New(); auto labelSetImageType = mitk::TNodePredicateDataType::New(); auto surfaceType = mitk::TNodePredicateDataType::New(); auto contourModelType = mitk::TNodePredicateDataType::New(); auto contourModelSetType = mitk::TNodePredicateDataType::New(); auto nonLabelSetImageType = mitk::NodePredicateAnd::New(imageType, mitk::NodePredicateNot::New(labelSetImageType)); auto nonHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateOr::New( mitk::NodePredicateProperty::New("helper object"), mitk::NodePredicateProperty::New("hidden object"))); auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); auto isSegmentation = mitk::NodePredicateProperty::New("segmentation", mitk::BoolProperty::New(true)); auto isBinaryOrSegmentation = mitk::NodePredicateOr::New(isBinary, isSegmentation); mitk::NodePredicateBase::Pointer returnValue; switch(predicate) { case QmitkDataSelectionWidget::ImagePredicate: returnValue = mitk::NodePredicateAnd::New( mitk::NodePredicateNot::New(isBinaryOrSegmentation), nonLabelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SegmentationPredicate: returnValue = mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), labelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SurfacePredicate: returnValue = surfaceType.GetPointer(); break; case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: returnValue = imageType.GetPointer(); break; case QmitkDataSelectionWidget::ContourModelPredicate: returnValue = mitk::NodePredicateOr::New( contourModelSetType, contourModelSetType).GetPointer(); break; case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: returnValue = mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), labelSetImageType).GetPointer(); returnValue = mitk::NodePredicateOr::New(returnValue, surfaceType).GetPointer(); break; default: assert(false && "Unknown predefined predicate!"); return nullptr; } return mitk::NodePredicateAnd::New(returnValue, nonHelperObject).GetPointer(); } QmitkDataSelectionWidget::QmitkDataSelectionWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.helpLabel->hide(); } QmitkDataSelectionWidget::~QmitkDataSelectionWidget() { } unsigned int QmitkDataSelectionWidget::AddDataSelection(QmitkDataSelectionWidget::Predicate predicate) { QString hint = "Select node"; switch (predicate) { case QmitkDataSelectionWidget::ImagePredicate: hint = "Select an image"; break; case QmitkDataSelectionWidget::SegmentationPredicate: hint = "Select a segmentation"; break; case QmitkDataSelectionWidget::SurfacePredicate: hint = "Select a surface"; break; case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: hint = "Select an image or segmentation"; break; case QmitkDataSelectionWidget::ContourModelPredicate: hint = "Select a contour model"; break; case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: hint = "Select a segmentation or surface"; break; } return this->AddDataSelection("", hint, hint, "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(mitk::NodePredicateBase* predicate) { return this->AddDataSelection("", "Select a node", "Select a node", "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, QmitkDataSelectionWidget::Predicate predicate) { return this->AddDataSelection(labelText, info, popupHint, popupTitel, CreatePredicate(predicate)); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate) { int row = m_Controls.gridLayout->rowCount(); if (!labelText.isEmpty()) { QLabel* label = new QLabel(labelText, m_Controls.dataSelectionWidget); label->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); m_Controls.gridLayout->addWidget(label, row, 0); } QmitkSingleNodeSelectionWidget* nodeSelection = new QmitkSingleNodeSelectionWidget(m_Controls.dataSelectionWidget); nodeSelection->SetSelectionIsOptional(false); nodeSelection->SetInvalidInfo(info); nodeSelection->SetPopUpTitel(popupTitel); nodeSelection->SetPopUpHint(popupHint); nodeSelection->SetDataStorage(this->GetDataStorage()); nodeSelection->SetNodePredicate(predicate); nodeSelection->SetAutoSelectNewNodes(true); nodeSelection->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); nodeSelection->setMinimumSize(0, 40); connect(nodeSelection, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkDataSelectionWidget::OnSelectionChanged); m_Controls.gridLayout->addWidget(nodeSelection, row, 1); m_NodeSelectionWidgets.push_back(nodeSelection); return static_cast(m_NodeSelectionWidgets.size() - 1); } mitk::DataStorage::Pointer QmitkDataSelectionWidget::GetDataStorage() const { ctkServiceReference ref = mitk::PluginActivator::getContext()->getServiceReference(); assert(ref == true); mitk::IDataStorageService* service = mitk::PluginActivator::getContext()->getService(ref); assert(service); return service->GetDefaultDataStorage()->GetDataStorage(); } mitk::DataNode::Pointer QmitkDataSelectionWidget::GetSelection(unsigned int index) { assert(index < m_NodeSelectionWidgets.size()); return m_NodeSelectionWidgets[index]->GetSelectedNode(); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, Predicate predicate) { this->SetPredicate(index, CreatePredicate(predicate)); } -void QmitkDataSelectionWidget::SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate) +void QmitkDataSelectionWidget::SetPredicate(unsigned int index, const mitk::NodePredicateBase* predicate) { assert(index < m_NodeSelectionWidgets.size()); m_NodeSelectionWidgets[index]->SetNodePredicate(predicate); } +const mitk::NodePredicateBase *QmitkDataSelectionWidget::GetPredicate(unsigned int index) const +{ + assert(index < m_NodeSelectionWidgets.size()); + return m_NodeSelectionWidgets[index]->GetNodePredicate(); +} + void QmitkDataSelectionWidget::SetHelpText(const QString& text) { if (!text.isEmpty()) { m_Controls.helpLabel->setText(text); if (!m_Controls.helpLabel->isVisible()) m_Controls.helpLabel->show(); } else { m_Controls.helpLabel->hide(); } } void QmitkDataSelectionWidget::OnSelectionChanged(QList selection) { std::vector::iterator it = std::find(m_NodeSelectionWidgets.begin(), m_NodeSelectionWidgets.end(), sender()); assert(it != m_NodeSelectionWidgets.end()); const mitk::DataNode* result = nullptr; if (!selection.empty()) { result = selection.front(); } emit SelectionChanged(std::distance(m_NodeSelectionWidgets.begin(), it), result); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h index f702654857..2586454d2d 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h @@ -1,68 +1,69 @@ /*============================================================================ 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 QmitkDataSelectionWidget_h #define QmitkDataSelectionWidget_h #include #include #include #include namespace mitk { class NodePredicateBase; } class QmitkSingleNodeSelectionWidget; class QmitkDataSelectionWidget : public QWidget { Q_OBJECT public: enum Predicate { ImagePredicate, SegmentationPredicate, SurfacePredicate, ImageAndSegmentationPredicate, ContourModelPredicate, SegmentationOrSurfacePredicate }; explicit QmitkDataSelectionWidget(QWidget* parent = nullptr); ~QmitkDataSelectionWidget() override; unsigned int AddDataSelection(Predicate predicate); unsigned int AddDataSelection(mitk::NodePredicateBase* predicate = nullptr); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, Predicate predicate); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate = nullptr); mitk::DataStorage::Pointer GetDataStorage() const; mitk::DataNode::Pointer GetSelection(unsigned int index); void SetPredicate(unsigned int index, Predicate predicate); - void SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate); + void SetPredicate(unsigned int index, const mitk::NodePredicateBase* predicate); + const mitk::NodePredicateBase *GetPredicate(unsigned int index) const; void SetHelpText(const QString& text); signals: void SelectionChanged(unsigned int index, const mitk::DataNode* selection); private slots: void OnSelectionChanged(QList selection); private: Ui::QmitkDataSelectionWidgetControls m_Controls; std::vector m_NodeSelectionWidgets; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp index 0ee6636348..86a5468a8c 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp @@ -1,356 +1,382 @@ /*============================================================================ 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 "QmitkImageMaskingWidget.h" #include "mitkImage.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include #include #include #include #include #include #include +#include +#include +#include +#include #include #include namespace { bool IsSurface(const mitk::DataNode* dataNode) { if (nullptr != dataNode) { if (nullptr != dynamic_cast(dataNode->GetData())) return true; } return false; } } static const char* const HelpText = "Select an image and a segmentation or surface"; QmitkImageMaskingWidget::QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImagePredicate); m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SegmentationOrSurfacePredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); + // T28795: Disable 2-d reference images since they do not work yet (segmentations are at least 3-d images with a single slice) + m_Controls.dataSelectionWidget->SetPredicate(0, mitk::NodePredicateAnd::New( + mitk::NodePredicateNot::New(mitk::NodePredicateDimension::New(2)), + m_Controls.dataSelectionWidget->GetPredicate(0))); + this->EnableButtons(false); connect(m_Controls.btnMaskImage, SIGNAL(clicked()), this, SLOT(OnMaskImagePressed())); connect(m_Controls.rbnCustom, SIGNAL(toggled(bool)), this, SLOT(OnCustomValueButtonToggled(bool))); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged(0, m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkImageMaskingWidget::~QmitkImageMaskingWidget() { } -void QmitkImageMaskingWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) +void QmitkImageMaskingWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode *selection) { - QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; - mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); - mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); + auto *dataSelectionWidget = m_Controls.dataSelectionWidget; + auto node0 = dataSelectionWidget->GetSelection(0); + + if (index == 0) + { + dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SegmentationOrSurfacePredicate); + + if (node0.IsNotNull()) + { + dataSelectionWidget->SetPredicate(1, mitk::NodePredicateAnd::New( + mitk::NodePredicateGeometry::New(node0->GetData()->GetGeometry()), + dataSelectionWidget->GetPredicate(1))); + } + } - if (node0.IsNull() || node1.IsNull() ) + auto node1 = dataSelectionWidget->GetSelection(1); + + if (node0.IsNull() || node1.IsNull()) { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } else { this->SelectionControl(index, selection); } } void QmitkImageMaskingWidget::SelectionControl(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); //if Image-Masking is enabled, check if image-dimension of reference and binary image is identical if( !IsSurface(dataSelectionWidget->GetSelection(1)) ) { if( dataSelectionWidget->GetSelection(0) == dataSelectionWidget->GetSelection(1) ) { dataSelectionWidget->SetHelpText("Select two different images above"); this->EnableButtons(false); return; } else if( node.IsNotNull() && selection ) { mitk::Image::Pointer referenceImage = dynamic_cast ( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Image::Pointer maskImage = dynamic_cast ( dataSelectionWidget->GetSelection(1)->GetData() ); - if( maskImage.IsNull() || referenceImage->GetLargestPossibleRegion().GetSize() != maskImage->GetLargestPossibleRegion().GetSize() ) + if (maskImage.IsNull()) { dataSelectionWidget->SetHelpText("Different image sizes cannot be masked"); this->EnableButtons(false); return; } } else { dataSelectionWidget->SetHelpText(HelpText); return; } } dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } void QmitkImageMaskingWidget::EnableButtons(bool enable) { m_Controls.grpBackgroundValue->setEnabled(enable); m_Controls.btnMaskImage->setEnabled(enable); } template void GetRange(const itk::Image*, double& bottom, double& top) { bottom = std::numeric_limits::lowest(); top = std::numeric_limits::max(); } void QmitkImageMaskingWidget::OnCustomValueButtonToggled(bool checked) { m_Controls.txtCustom->setEnabled(checked); } void QmitkImageMaskingWidget::OnMaskImagePressed() { //Disable Buttons during calculation and initialize Progressbar this->EnableButtons(false); mitk::ProgressBar::GetInstance()->AddStepsToDo(4); mitk::ProgressBar::GetInstance()->Progress(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; //create result image, get mask node and reference image mitk::Image::Pointer resultImage(nullptr); mitk::DataNode::Pointer maskingNode = dataSelectionWidget->GetSelection(1); mitk::Image::Pointer referenceImage = static_cast(dataSelectionWidget->GetSelection(0)->GetData()); if(referenceImage.IsNull() || maskingNode.IsNull() ) { MITK_ERROR << "Selection does not contain an image"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain an image", QMessageBox::Ok ); m_Controls.btnMaskImage->setEnabled(true); return; } //Do Image-Masking if (!IsSurface(maskingNode)) { mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer maskImage = dynamic_cast ( maskingNode->GetData() ); if(maskImage.IsNull() ) { MITK_ERROR << "Selection does not contain a segmentation"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a segmentation", QMessageBox::Ok ); this->EnableButtons(); return; } - if( referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) - { - resultImage = this->MaskImage( referenceImage, maskImage ); - } + resultImage = this->MaskImage(referenceImage, maskImage); } //Do Surface-Masking else { mitk::ProgressBar::GetInstance()->Progress(); //1. convert surface to image mitk::Surface::Pointer surface = dynamic_cast ( maskingNode->GetData() ); //TODO Get 3D Surface of current time step if(surface.IsNull()) { MITK_ERROR << "Selection does not contain a surface"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer maskImage = this->ConvertSurfaceToImage( referenceImage, surface ); //2. mask reference image with mask image if(maskImage.IsNotNull() && referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } mitk::ProgressBar::GetInstance()->Progress(); if( resultImage.IsNull() ) { MITK_ERROR << "Masking failed"; QMessageBox::information( this, "Image and Surface Masking", "Masking failed. For more information please see logging window.", QMessageBox::Ok ); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(4); return; } //Add result to data storage this->AddToDataStorage( dataSelectionWidget->GetDataStorage(), resultImage, dataSelectionWidget->GetSelection(0)->GetName() + "_" + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(); } mitk::Image::Pointer QmitkImageMaskingWidget::MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage ) { mitk::ScalarType backgroundValue = 0.0; if (m_Controls.rbnMinimum->isChecked()) { backgroundValue = referenceImage->GetStatistics()->GetScalarValueMin(); } else if (m_Controls.rbnCustom->isChecked()) { auto warningTitle = QStringLiteral("Invalid custom pixel value"); bool ok = false; auto originalBackgroundValue = m_Controls.txtCustom->text().toDouble(&ok); if (!ok) { // Input is not even a number QMessageBox::warning(nullptr, warningTitle, "Please enter a valid number as custom pixel value."); return nullptr; } else { // Clamp to the numerical limits of the pixel/component type double bottom, top; - AccessByItk_n(referenceImage, GetRange, (bottom, top)); + if (referenceImage->GetDimension() == 4) + { + AccessFixedDimensionByItk_n(referenceImage, GetRange, 4, (bottom, top)); + } + else + { + AccessByItk_n(referenceImage, GetRange, (bottom, top)); + } backgroundValue = std::max(bottom, std::min(originalBackgroundValue, top)); // Get rid of decimals for integral numbers auto type = referenceImage->GetPixelType().GetComponentType(); if (type != itk::ImageIOBase::FLOAT && type != itk::ImageIOBase::DOUBLE) backgroundValue = std::round(backgroundValue); } // Ask the user for permission before correcting their input if (std::abs(originalBackgroundValue - backgroundValue) > 1e-4) { auto warningText = QString( "

The custom pixel value %1 lies not within the range of valid pixel values for the selected image.

" "

Apply the closest valid pixel value %2 instead?

").arg(originalBackgroundValue).arg(backgroundValue); auto ret = QMessageBox::warning( nullptr, warningTitle, warningText, QMessageBox::StandardButton::Apply | QMessageBox::StandardButton::Cancel, QMessageBox::StandardButton::Apply); if (QMessageBox::StandardButton::Apply != ret) return nullptr; m_Controls.txtCustom->setText(QString("%1").arg(backgroundValue)); } } auto maskFilter = mitk::MaskImageFilter::New(); maskFilter->SetInput(referenceImage); maskFilter->SetMask(maskImage); maskFilter->OverrideOutsideValueOn(); maskFilter->SetOutsideValue(backgroundValue); try { maskFilter->Update(); } catch(const itk::ExceptionObject& e) { MITK_ERROR << e.GetDescription(); return nullptr; } return maskFilter->GetOutput(); } mitk::Image::Pointer QmitkImageMaskingWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return nullptr; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = mitk::Image::New(); resultImage = surfaceToImageFilter->GetOutput(); return resultImage; } void QmitkImageMaskingWidget::AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent ) { auto dataNode = mitk::DataNode::New(); dataNode->SetName(name); dataNode->SetData(segmentation); if (parent.IsNotNull()) { mitk::LevelWindow levelWindow; parent->GetLevelWindow(levelWindow); dataNode->SetLevelWindow(levelWindow); } dataStorage->Add(dataNode, parent); }