diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox index 3d38945f38..d21900ecc1 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginGeneralManualsList.dox @@ -1,32 +1,32 @@ /** \page PluginListGeneralPage List of General Purpose Plugins \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_views_properties - \li \subpage org_mitk_gui_qt_dicom + \li \subpage org_mitk_editors_dicombrowser \li \subpage org_mitk_gui_qt_dicominspector - \li \subpage org_mitk_gui_qt_imagecropper + \li \subpage org_mitk_views_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control \li \subpage org_mitk_gui_qt_matchpoint_evaluator \li \subpage org_mitk_gui_qt_matchpoint_framereg \li \subpage org_mitk_gui_qt_matchpoint_manipulator \li \subpage org_mitk_gui_qt_matchpoint_mapper \li \subpage org_mitk_gui_qt_matchpoint_visualizer \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_views_moviemaker \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_gui_qt_flow_segmentation \li \subpage org_mitk_gui_qt_viewnavigator \li \subpage org_mitk_views_volumevisualization */ diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 26d569a356..2a16c22a1f 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,84 +1,84 @@ /** \page PluginListPage MITK Plugin Manuals The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. \subpage PluginListGeneralPage \subpage PluginListSpecificPage */ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/Basic_ImageCropperView.png b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/Basic_ImageCropperView.png index 7cb45a0828..8dcec773a9 100644 Binary files a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/Basic_ImageCropperView.png and b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/Basic_ImageCropperView.png differ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/BoundingBox_ImageCropperView.png b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/BoundingBox_ImageCropperView.png index af303e721c..f4a6453618 100644 Binary files a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/BoundingBox_ImageCropperView.png and b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/BoundingBox_ImageCropperView.png differ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox index 2bcd21d2bb..ef2b68b13d 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox +++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox @@ -1,37 +1,52 @@ /** -\page org_mitk_gui_qt_imagecropper The Image Cropper +\page org_mitk_views_imagecropper The Image Cropper \imageMacro{crop.svg,"Icon of the Image Cropper Plugin.",20} -\tableofcontents +\section org_mitk_views_imagecropperUsage Usage -\section org_mitk_gui_qt_imagecropperUsage Usage +The Image Cropper Plugin allows to crop and mask subvolumes out of the original image volume by defining a cubic bounding shape. -The Image Cropper Plugin allows to crop subvolumes out of your original image volume by defining a cubic bounding box. +\imageMacro{BoundingBox_ImageCropperView.png,"Bounding Shape.",12.00} -This box can be placed at an arbitrary position in the volume and can be easily adjusted by using the handles on each of the faces. -Touching the handles changes the size of the box whereas touching the box itself changes its position. +A new bounding shape can be created by selecting an image and pressing the 'New' button. The bounding shape appears as a child node in the data manager. Alternatively, an existing bounding shape can be selected. -As soon as the bounding box is placed at the desired position, pressing the button 'Crop' creates a new image assigned to the original image -as child node containing only the selected subvolume. The size of the subvolume equals the size of the bounding box. -Pressing the "Mask" button keeps the original image size but masks out the area not contained within the bounding box bounds. -In case of 3D+t images the whole time series is cropped by default. - -\imageMacro{BoundingBox_ImageCropperView.png,"Bounding Box.",12.00} \imageMacro{Basic_ImageCropperView.png,"Basic Settings.",7.09} -\section org_mitk_gui_qt_imagecropperAdvanced Advanced settings -In the advanced settings view you find additional features to manipulate the bounding box. +This bounding shape can be placed at an arbitrary position in the volume and can be easily adjusted by using the handles on each of the faces. When activated, the handles are shown in red, otherwise, they are colored white. Hovering over either the shape or a single handle allows modifying the bounding shape. Moving the handles changes the respective extent of the bounding shape, whereas moving the shape itself changes its position. + + +As soon as the bounding shape is placed at the desired position, pressing the button 'Crop' creates a new image assigned to the original image as a child node containing only the selected subvolume. The size of the subvolume equals the size of the bounding shape. +Pressing the 'Mask' button keeps the original image size but masks out the area not contained within the bounding shape bounds. +In the case of 3D+t images, the whole time series is cropped by default. + + +\section org_mitk_views_imagecropperAdvanced Advanced settings + +In the advanced settings view you find additional features: \imageMacro{Advanced_ImageCropperView.png,"Advanced Settings.",7.09} -\subsection org_mitk_gui_qt_imagecropperAdvancedOverwrite Overwrite original image +\subsection org_mitk_views_imagecropperMaskOutsidePixel Mask with outside pixel + +Assigns the value of the voxels outside of the bounding shape when 'Mask' is used. + + +\subsection org_mitk_views_imagecropperAdvancedOverwrite Overwrite original image + By enabling this checkbox the image is replaced by the cropped subvolume. Be careful to use this option since there is no undo action available. -\subsection org_mitk_gui_qt_imagecropperAdvancedTimestep Crop current time step only -If this checkbox is enabled the xD + t image is reduced to a xD image (e.g., 3D+t --> 3D) with the time step visible in the widget. This is useful if you want to extract a single image or its corresponding subvolume of the time series. The whole time series is cropped by default using the timeGeometry of the time step visible in the widget. +\subsection org_mitk_views_imagecropperAdvancedTimestep Crop current time step only + +If you have an xD + t image, the whole time series (all timesteps) is cropped by default. In this case, the 'time geometry' of the current time step is used. + +If the checkbox 'Only crop current time step' is ticked, the xD + t image is reduced to an xD image (e.g., 3D+t --> 3D) with the current time step only. That can be useful if you want to extract a single image or its corresponding subvolume of the time series. + +\section org_mitk_views_imagecropperIssues Current issues -\section org_mitk_gui_qt_imagecropperIssues Current issues Cropping 2D images is not supported unless the are 3D images containing only a single slice. The user will be notified by a warning and the input is handled as a single label image. -Right now changing the shape or rotation of the bounding box is not supported but might be integrated in the future. -*/ \ No newline at end of file +Right now changing the shape or rotation of the bounding shape is not supported but might be integrated in the future. + +Furthermore, a warning appears when the bounding shape is not aligned with the image. In this case, the handles can not be used correctly and get deactivated. You can continue to alter them by performing a 'Reinit' on the image. + +*/ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper_Icon.png b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper_Icon.png deleted file mode 100644 index 221f3f7ac1..0000000000 Binary files a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper_Icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp index 84835e20fd..3594ac014f 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp @@ -1,494 +1,496 @@ /*============================================================================ 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 "QmitkImageCropperView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkImageCropperView::VIEW_ID = "org.mitk.views.qmitkimagecropper"; QmitkImageCropperView::QmitkImageCropperView(QObject *) : m_ParentWidget(nullptr) , m_BoundingShapeInteractor(nullptr) , m_CropOutsideValue(0) { CreateBoundingShapeInteractor(false); } QmitkImageCropperView::~QmitkImageCropperView() { //disable interactor if (m_BoundingShapeInteractor != nullptr) { m_BoundingShapeInteractor->SetDataNode(nullptr); m_BoundingShapeInteractor->EnableInteraction(false); } } void QmitkImageCropperView::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->SetAutoSelectNewNodes(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, &QmitkImageCropperView::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->SetAutoSelectNewNodes(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, &QmitkImageCropperView::OnBoundingBoxSelectionChanged); connect(m_Controls.buttonCreateNewBoundingBox, SIGNAL(clicked()), this, SLOT(OnCreateNewBoundingBox())); connect(m_Controls.buttonCropping, SIGNAL(clicked()), this, SLOT(OnCropping())); connect(m_Controls.buttonMasking, SIGNAL(clicked()), this, SLOT(OnMasking())); 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 QmitkImageCropperView::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 QmitkImageCropperView::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 QmitkImageCropperView::OnCreateNewBoundingBox() { auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { return; } if (nullptr == imageNode->GetData()) { 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); const auto timePoint = renderWindowPart->GetSelectedTimePoint(); const auto imageGeometry = imageNode->GetData()->GetTimeGeometry()->GetGeometryForTimePoint(timePoint); 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 QmitkImageCropperView::OnCropping() { this->ProcessImage(false); } void QmitkImageCropperView::OnMasking() { this->ProcessImage(true); } void QmitkImageCropperView::OnSliderValueChanged(int slidervalue) { m_CropOutsideValue = slidervalue; } void QmitkImageCropperView::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 QmitkImageCropperView::InitializeWithImageGeometry(const mitk::BaseGeometry* geometry) const { // 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()->Clone()); boundingGeometry->Modified(); return boundingGeometry; } void QmitkImageCropperView::ProcessImage(bool mask) { auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); const auto timePoint = renderWindowPart->GetSelectedTimePoint(); 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; } if (!imageNode->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) { QMessageBox::information(nullptr, "Warning", "Please select a time point that is within the time bounds of the selected image."); return; } const auto timeStep = imageNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(timePoint); 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 QmitkImageCropperView::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 QmitkImageCropperView::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; }