diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp index 340396bd06..0502d60a82 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp @@ -1,484 +1,484 @@ /*============================================================================ 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 "QmitkImageCropper.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkImageCropper::VIEW_ID = "org.mitk.views.qmitkimagecropper"; QmitkImageCropper::QmitkImageCropper(QObject *) : m_ParentWidget(nullptr) , m_BoundingShapeInteractor(nullptr) , m_CropOutsideValue(0) { CreateBoundingShapeInteractor(false); } QmitkImageCropper::~QmitkImageCropper() { //disable interactor if (m_BoundingShapeInteractor != nullptr) { m_BoundingShapeInteractor->SetDataNode(nullptr); m_BoundingShapeInteractor->EnableInteraction(false); } } void QmitkImageCropper::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.imageSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls.imageSelectionWidget->SetNodePredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_Controls.imageSelectionWidget->SetSelectionIsOptional(true); m_Controls.imageSelectionWidget->SetEmptyInfo(QString("Please select an image node")); m_Controls.imageSelectionWidget->SetPopUpTitel(QString("Select image node")); connect(m_Controls.imageSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageCropper::OnImageSelectionChanged); m_Controls.boundingBoxSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls.boundingBoxSelectionWidget->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); m_Controls.boundingBoxSelectionWidget->SetSelectionIsOptional(true); m_Controls.boundingBoxSelectionWidget->SetEmptyInfo(QString("Please select a bounding box")); m_Controls.boundingBoxSelectionWidget->SetPopUpTitel(QString("Select bounding box node")); connect(m_Controls.boundingBoxSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageCropper::OnBoundingBoxSelectionChanged); connect(m_Controls.buttonCreateNewBoundingBox, SIGNAL(clicked()), this, SLOT(DoCreateNewBoundingObject())); connect(m_Controls.buttonCropping, SIGNAL(clicked()), this, SLOT(DoCropping())); connect(m_Controls.buttonMasking, SIGNAL(clicked()), this, SLOT(DoMasking())); auto lambda = [this]() { m_Controls.groupImageSettings->setVisible(!m_Controls.groupImageSettings->isVisible()); }; connect(m_Controls.buttonAdvancedSettings, &ctkExpandButton::clicked, this, lambda); connect(m_Controls.spinBoxOutsidePixelValue, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueChanged(int))); SetDefaultGUI(); m_ParentWidget = parent; } +void QmitkImageCropper::OnImageSelectionChanged(QList) +{ + bool rotationEnabled = false; + auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); + if (imageNode.IsNull()) + { + SetDefaultGUI(); + return; + } + + auto image = dynamic_cast(imageNode->GetData()); + if (nullptr != image) + { + if (image->GetDimension() < 3) + { + QMessageBox::warning(nullptr, + tr("Invalid image selected"), + tr("ImageCropper only works with 3 or more dimensions."), + QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); + SetDefaultGUI(); + return; + } + + m_ParentWidget->setEnabled(true); + m_Controls.buttonCreateNewBoundingBox->setEnabled(true); + + vtkSmartPointer imageMat = image->GetGeometry()->GetVtkMatrix(); + // check whether the image geometry is rotated; if so, no pixel aligned cropping or masking can be performed + if ((imageMat->GetElement(1, 0) == 0.0) && (imageMat->GetElement(0, 1) == 0.0) && + (imageMat->GetElement(1, 2) == 0.0) && (imageMat->GetElement(2, 1) == 0.0) && + (imageMat->GetElement(2, 0) == 0.0) && (imageMat->GetElement(0, 2) == 0.0)) + { + rotationEnabled = false; + m_Controls.labelWarningRotation->setVisible(false); + } + else + { + rotationEnabled = true; + m_Controls.labelWarningRotation->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); + m_Controls.labelWarningRotation->setVisible(true); + } + + this->CreateBoundingShapeInteractor(rotationEnabled); + + if (itk::ImageIOBase::SCALAR == image->GetPixelType().GetPixelType()) + { + // Might be changed with the upcoming new image statistics plugin + //(recomputation might be very expensive for large images ;) ) + auto statistics = image->GetStatistics(); + auto minPixelValue = statistics->GetScalarValueMin(); + auto maxPixelValue = statistics->GetScalarValueMax(); + + if (minPixelValue < std::numeric_limits::min()) + { + minPixelValue = std::numeric_limits::min(); + } + if (maxPixelValue > std::numeric_limits::max()) + { + maxPixelValue = std::numeric_limits::max(); + } + + m_Controls.spinBoxOutsidePixelValue->setEnabled(true); + m_Controls.spinBoxOutsidePixelValue->setMaximum(static_cast(maxPixelValue)); + m_Controls.spinBoxOutsidePixelValue->setMinimum(static_cast(minPixelValue)); + m_Controls.spinBoxOutsidePixelValue->setValue(static_cast(minPixelValue)); + } + else + { + m_Controls.spinBoxOutsidePixelValue->setEnabled(false); + } + + unsigned int dim = image->GetDimension(); + if (dim < 2 || dim > 4) + { + m_ParentWidget->setEnabled(false); + } + + if (m_Controls.boundingBoxSelectionWidget->GetSelectedNode().IsNotNull()) + { + m_Controls.buttonCropping->setEnabled(true); + m_Controls.buttonMasking->setEnabled(true); + m_Controls.buttonAdvancedSettings->setEnabled(true); + m_Controls.groupImageSettings->setEnabled(true); + } + } +} + void QmitkImageCropper::OnBoundingBoxSelectionChanged(QList) { auto boundingBoxNode = m_Controls.boundingBoxSelectionWidget->GetSelectedNode(); if (boundingBoxNode.IsNull()) { SetDefaultGUI(); m_BoundingShapeInteractor->EnableInteraction(false); m_BoundingShapeInteractor->SetDataNode(nullptr); if (m_Controls.imageSelectionWidget->GetSelectedNode().IsNotNull()) { m_Controls.buttonCreateNewBoundingBox->setEnabled(true); } return; } auto boundingBox = dynamic_cast(boundingBoxNode->GetData()); if (nullptr != boundingBox) { // node newly selected boundingBoxNode->SetVisibility(true); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(boundingBoxNode); mitk::RenderingManager::GetInstance()->InitializeViews(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls.imageSelectionWidget->GetSelectedNode().IsNotNull()) { m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.buttonAdvancedSettings->setEnabled(true); m_Controls.groupImageSettings->setEnabled(true); } } } void QmitkImageCropper::CreateBoundingShapeInteractor(bool rotationEnabled) { if (m_BoundingShapeInteractor.IsNull()) { m_BoundingShapeInteractor = mitk::BoundingShapeInteractor::New(); m_BoundingShapeInteractor->LoadStateMachine("BoundingShapeInteraction.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); m_BoundingShapeInteractor->SetEventConfig("BoundingShapeMouseConfig.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); } m_BoundingShapeInteractor->SetRotationEnabled(rotationEnabled); } mitk::Geometry3D::Pointer QmitkImageCropper::InitializeWithImageGeometry(mitk::BaseGeometry::Pointer geometry) { // convert a BaseGeometry into a Geometry3D (otherwise IO is not working properly) if (geometry == nullptr) mitkThrow() << "Geometry is not valid."; auto boundingGeometry = mitk::Geometry3D::New(); boundingGeometry->SetBounds(geometry->GetBounds()); boundingGeometry->SetImageGeometry(geometry->GetImageGeometry()); boundingGeometry->SetOrigin(geometry->GetOrigin()); boundingGeometry->SetSpacing(geometry->GetSpacing()); boundingGeometry->SetIndexToWorldTransform(geometry->GetIndexToWorldTransform()); boundingGeometry->Modified(); return boundingGeometry; } void QmitkImageCropper::DoCreateNewBoundingObject() { auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { return; } QString name = QString::fromStdString(imageNode->GetName() + " Bounding Shape"); auto boundingShape = this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&name](const mitk::DataNode *node) { return 0 == node->GetName().compare(name.toStdString()); })); if (nullptr != boundingShape) { name = this->AdaptBoundingObjectName(name); } // get current timestep to support 3d+t images auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); auto imageGeometry = static_cast(imageNode->GetData()->GetGeometry(timeStep)); auto boundingBox = mitk::GeometryData::New(); boundingBox->SetGeometry(static_cast(this->InitializeWithImageGeometry(imageGeometry))); auto boundingBoxNode = mitk::DataNode::New(); boundingBoxNode->SetData(boundingBox); boundingBoxNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); boundingBoxNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); boundingBoxNode->SetProperty("opacity", mitk::FloatProperty::New(0.6)); boundingBoxNode->SetProperty("layer", mitk::IntProperty::New(99)); boundingBoxNode->AddProperty("handle size factor", mitk::DoubleProperty::New(1.0 / 40.0)); boundingBoxNode->SetBoolProperty("pickable", true); if (!this->GetDataStorage()->Exists(boundingBoxNode)) { GetDataStorage()->Add(boundingBoxNode, imageNode); } m_Controls.boundingBoxSelectionWidget->SetCurrentSelectedNode(boundingBoxNode); } -void QmitkImageCropper::OnImageSelectionChanged(QList) -{ - bool rotationEnabled = false; - auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); - if (imageNode.IsNull()) - { - SetDefaultGUI(); - return; - } - - auto image = dynamic_cast(imageNode->GetData()); - if (nullptr != image) - { - if (image->GetDimension() < 3) - { - QMessageBox::warning(nullptr, - tr("Invalid image selected"), - tr("ImageCropper only works with 3 or more dimensions."), - QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); - SetDefaultGUI(); - return; - } - - m_ParentWidget->setEnabled(true); - m_Controls.buttonCreateNewBoundingBox->setEnabled(true); - - vtkSmartPointer imageMat = image->GetGeometry()->GetVtkMatrix(); - // check whether the image geometry is rotated; if so, no pixel aligned cropping or masking can be performed - if ((imageMat->GetElement(1, 0) == 0.0) && (imageMat->GetElement(0, 1) == 0.0) && - (imageMat->GetElement(1, 2) == 0.0) && (imageMat->GetElement(2, 1) == 0.0) && - (imageMat->GetElement(2, 0) == 0.0) && (imageMat->GetElement(0, 2) == 0.0)) - { - rotationEnabled = false; - m_Controls.labelWarningRotation->setVisible(false); - } - else - { - rotationEnabled = true; - m_Controls.labelWarningRotation->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); - m_Controls.labelWarningRotation->setVisible(true); - } - - this->CreateBoundingShapeInteractor(rotationEnabled); - - if (itk::ImageIOBase::SCALAR == image->GetPixelType().GetPixelType()) - { - // Might be changed with the upcoming new image statistics plugin - //(recomputation might be very expensive for large images ;) ) - auto statistics = image->GetStatistics(); - auto minPixelValue = statistics->GetScalarValueMin(); - auto maxPixelValue = statistics->GetScalarValueMax(); - - if (minPixelValue < std::numeric_limits::min()) - { - minPixelValue = std::numeric_limits::min(); - } - if (maxPixelValue > std::numeric_limits::max()) - { - maxPixelValue = std::numeric_limits::max(); - } - - m_Controls.spinBoxOutsidePixelValue->setEnabled(true); - m_Controls.spinBoxOutsidePixelValue->setMaximum(static_cast(maxPixelValue)); - m_Controls.spinBoxOutsidePixelValue->setMinimum(static_cast(minPixelValue)); - m_Controls.spinBoxOutsidePixelValue->setValue(static_cast(minPixelValue)); - } - else - { - m_Controls.spinBoxOutsidePixelValue->setEnabled(false); - } - - unsigned int dim = image->GetDimension(); - if (dim < 2 || dim > 4) - { - m_ParentWidget->setEnabled(false); - } - - if (m_Controls.boundingBoxSelectionWidget->GetSelectedNode().IsNotNull()) - { - m_Controls.buttonCropping->setEnabled(true); - m_Controls.buttonMasking->setEnabled(true); - m_Controls.buttonAdvancedSettings->setEnabled(true); - m_Controls.groupImageSettings->setEnabled(true); - } - } -} - void QmitkImageCropper::OnSliderValueChanged(int slidervalue) { m_CropOutsideValue = slidervalue; } void QmitkImageCropper::DoMasking() { this->ProcessImage(true); } void QmitkImageCropper::DoCropping() { this->ProcessImage(false); } void QmitkImageCropper::ProcessImage(bool mask) { auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); return; } auto boundingBoxNode = m_Controls.boundingBoxSelectionWidget->GetSelectedNode(); if (boundingBoxNode.IsNull()) { QMessageBox::information(nullptr, "Warning", "Please load and select a cropping object before starting image processing."); return; } auto image = dynamic_cast(imageNode->GetData()); auto boundingBox = dynamic_cast(boundingBoxNode->GetData()); if (nullptr != image && nullptr != boundingBox) { QString imageName; if (mask) { imageName = QString::fromStdString(imageNode->GetName() + "_" + boundingBoxNode->GetName() + "_masked"); } else { imageName = QString::fromStdString(imageNode->GetName() + "_" + boundingBoxNode->GetName() + "_cropped"); } if (m_Controls.checkBoxCropTimeStepOnly->isChecked()) { imageName = imageName + "_T" + QString::number(timeStep); } // image and bounding shape ok, set as input auto croppedImageNode = mitk::DataNode::New(); auto cutter = mitk::BoundingShapeCropper::New(); cutter->SetGeometry(boundingBox); // adjustable in advanced settings cutter->SetUseWholeInputRegion(mask); //either mask (mask=true) or crop (mask=false) cutter->SetOutsideValue(m_CropOutsideValue); cutter->SetUseCropTimeStepOnly(m_Controls.checkBoxCropTimeStepOnly->isChecked()); cutter->SetCurrentTimeStep(timeStep); // TODO: Add support for MultiLayer (right now only Mulitlabel support) auto labelsetImageInput = dynamic_cast(image); if (nullptr != labelsetImageInput) { cutter->SetInput(labelsetImageInput); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } auto labelSetImage = mitk::LabelSetImage::New(); labelSetImage->InitializeByLabeledImage(cutter->GetOutput()); for (unsigned int i = 0; i < labelsetImageInput->GetNumberOfLayers(); i++) { labelSetImage->AddLabelSetToLayer(i, labelsetImageInput->GetLabelSet(i)); } croppedImageNode->SetData(labelSetImage); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, imageNode); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { imageNode->SetData(labelSetImage); imageNode->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, imageNode); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } else { cutter->SetInput(image); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { croppedImageNode->SetData(cutter->GetOutput()); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); croppedImageNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); croppedImageNode->SetProperty("layer", mitk::IntProperty::New(99)); // arbitrary, copied from segmentation functionality if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, imageNode); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { imageNode->SetData(cutter->GetOutput()); imageNode->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, imageNode); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } else { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); } } void QmitkImageCropper::SetDefaultGUI() { m_Controls.labelWarningRotation->setVisible(false); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.buttonAdvancedSettings->setEnabled(false); m_Controls.groupImageSettings->setEnabled(false); m_Controls.groupImageSettings->setVisible(false); m_Controls.checkOverwriteImage->setChecked(false); m_Controls.checkBoxCropTimeStepOnly->setChecked(false); } QString QmitkImageCropper::AdaptBoundingObjectName(const QString& name) const { unsigned int counter = 2; QString newName = QString("%1 %2").arg(name).arg(counter); while (nullptr != this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&newName](const mitk::DataNode *node) { return 0 == node->GetName().compare(newName.toStdString()); }))) { newName = QString("%1 %2").arg(name).arg(++counter); } return newName; } diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.h b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.h index 5e5628a586..931cb34ac4 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.h +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.h @@ -1,94 +1,97 @@ /*============================================================================ 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 QmitkImageCropper_h #define QmitkImageCropper_h #include #include #include "ui_QmitkImageCropperViewControls.h" class QmitkImageCropper : public QmitkAbstractView { Q_OBJECT public: QmitkImageCropper(QObject *parent = nullptr); ~QmitkImageCropper() override; static const std::string VIEW_ID; void CreateQtPartControl(QWidget *parent) override; void SetFocus() override { }; protected Q_SLOTS: /*! * @brief Creates a new bounding object */ virtual void DoCreateNewBoundingObject(); /*! * @brief Whenever Crop button is pressed, issue a cropping action */ void DoCropping(); /*! * @brief Whenever Mask button is pressed, issue a masking action */ void DoMasking(); /*! +* @brief Updates current selection of the image to crop +*/ + void OnImageSelectionChanged(QList nodes); + /*! * @brief Updates current selection of the bounding object */ void OnBoundingBoxSelectionChanged(QList nodes); /*! * @brief Sets the scalar value for outside pixels in case of masking */ void OnSliderValueChanged(int slidervalue); protected: - void OnImageSelectionChanged(QList nodes); /*! * @brief Initializes a new bounding shape using the selected image geometry. */ mitk::Geometry3D::Pointer InitializeWithImageGeometry(mitk::BaseGeometry::Pointer geometry); void CreateBoundingShapeInteractor(bool rotationEnabled); private: QWidget* m_ParentWidget; /*! * @brief Interactor for moving and scaling the cuboid */ mitk::BoundingShapeInteractor::Pointer m_BoundingShapeInteractor; void ProcessImage(bool crop); /*! * @brief Resets GUI to default */ void SetDefaultGUI(); QString AdaptBoundingObjectName(const QString& name) const; // cropping parameter mitk::ScalarType m_CropOutsideValue; Ui::QmitkImageCropperViewControls m_Controls; }; #endif // QmitkImageCropper_h