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 94349b9a39..d4ca8f8720 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp @@ -1,532 +1,536 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkImageCropper.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // Includes for image casting between ITK and MITK: added after using Plugin Generator #include #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 *parent) : m_ParentWidget(0), m_ImageNode(nullptr), m_CroppingObject(nullptr), m_CroppingObjectNode(nullptr), m_BoundingShapeInteractor(nullptr), m_CropOutsideValue(0), m_Advanced(0), m_Active(0), m_ScrollEnabled(true) { CreateBoundingShapeInteractor(false); } QmitkImageCropper::~QmitkImageCropper() { //delete pointer objects m_CroppingObjectNode = nullptr; m_CroppingObject = nullptr; //disable interactor if (m_BoundingShapeInteractor != nullptr) { m_BoundingShapeInteractor->SetDataNode(nullptr); m_BoundingShapeInteractor->EnableInteraction(false); } } void QmitkImageCropper::SetFocus() { m_Controls.buttonCreateNewBoundingBox->setFocus(); } void QmitkImageCropper::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.boundingShapeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.boundingShapeSelector->SetPredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); connect(m_Controls.buttonCropping, SIGNAL(clicked()), this, SLOT(DoCropping())); connect(m_Controls.buttonMasking, SIGNAL(clicked()), this, SLOT(DoMasking())); connect(m_Controls.boundingShapeSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnDataSelectionChanged(const mitk::DataNode*))); connect(m_Controls.buttonCreateNewBoundingBox, SIGNAL(clicked()), this, SLOT(DoCreateNewBoundingObject())); connect(m_Controls.buttonAdvancedSettings, SIGNAL(clicked()), this, SLOT(OnAdvancedSettingsButtonToggled())); connect(m_Controls.spinBox, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueChanged(int))); m_Controls.spinBox->setValue(-1000); m_Controls.spinBox->setEnabled(false); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.buttonCropping->setEnabled(false); m_Controls.boundingShapeSelector->setEnabled(false); m_Controls.labelWarningRotation->setVisible(false); m_Controls.buttonAdvancedSettings->setEnabled(false); m_Advanced = false; this->OnAdvancedSettingsButtonToggled(); m_ParentWidget = parent; } void QmitkImageCropper::OnDataSelectionChanged(const mitk::DataNode* node) { m_Controls.boundingShapeSelector->setEnabled(true); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); if (m_CroppingObjectNode.IsNotNull() && dynamic_cast(this->m_CroppingObjectNode->GetData())) { m_Controls.buttonAdvancedSettings->setEnabled(true); m_Controls.labelWarningBB->setText(QString::fromStdString("")); m_CroppingObject = dynamic_cast(m_CroppingObjectNode->GetData()); m_Advanced = true; mitk::RenderingManager::GetInstance()->InitializeViews(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { m_Controls.buttonAdvancedSettings->setEnabled(false); m_CroppingObject = nullptr; m_BoundingShapeInteractor->EnableInteraction(false); m_BoundingShapeInteractor->SetDataNode(nullptr); m_Advanced = false; this->OnAdvancedSettingsButtonToggled(); } } void QmitkImageCropper::OnAdvancedSettingsButtonToggled() { m_Controls.groupImageSettings->setVisible(m_Advanced); m_Advanced = !m_Advanced; } 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() { if (m_ImageNode.IsNotNull()) { bool ok = false; QString name = QInputDialog::getText(QApplication::activeWindow() , "Add cropping shape...", "Enter name for the new cropping shape", QLineEdit::Normal, "BoundingShape", &ok); if (!ok) return; + if (name == "") + { + name = "Bounding Shape"; + } m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.boundingShapeSelector->setEnabled(true); // get current timestep to support 3d+t images auto renderWindowPart = this->GetRenderWindowPart(OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); mitk::BaseGeometry::Pointer imageGeometry = static_cast(m_ImageNode->GetData()->GetGeometry(timeStep)); m_CroppingObject = mitk::GeometryData::New(); m_CroppingObject->SetGeometry(static_cast(this->InitializeWithImageGeometry(imageGeometry))); m_CroppingObjectNode = mitk::DataNode::New(); m_CroppingObjectNode->SetData(m_CroppingObject); m_CroppingObjectNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); m_CroppingObjectNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); m_CroppingObjectNode->SetProperty("opacity", mitk::FloatProperty::New(0.6)); m_CroppingObjectNode->SetProperty("layer", mitk::IntProperty::New(99)); m_CroppingObjectNode->AddProperty("handle size factor", mitk::DoubleProperty::New(1.0 / 40.0)); m_CroppingObjectNode->SetBoolProperty("pickable", true); if (!this->GetDataStorage()->Exists(m_CroppingObjectNode)) { GetDataStorage()->Add(m_CroppingObjectNode, m_ImageNode); m_Controls.boundingShapeSelector->SetSelectedNode(m_CroppingObjectNode); m_CroppingObjectNode->SetVisibility(true); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(this->m_CroppingObjectNode); this->OnDataSelectionChanged(m_CroppingObjectNode); } } // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, m_CroppingObjectNode); //// initialize the views to the bounding geometry //mitk::TimeGeometry::Pointer bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); //mitk::RenderingManager::GetInstance()->InitializeViews(bounds); //mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkImageCropper::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { bool rotationEnabled = false; if (nodes.empty()) { m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("Select an image.")); m_Controls.labelWarningBB->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningBB->setText(QString::fromStdString("Create a bounding shape below.")); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.labelWarningRotation->setVisible(false); return; } m_ParentWidget->setEnabled(true); foreach(mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_ImageNode = nodes[0]; m_Controls.groupBoundingObject->setEnabled(true); m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(0, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("File name: " + m_ImageNode->GetName())); m_Controls.buttonCreateNewBoundingBox->setEnabled(true); mitk::Image::Pointer image = dynamic_cast(m_ImageNode->GetData()); if (image != nullptr) { 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); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); if (m_CroppingObjectNode != nullptr) { this->OnDataSelectionChanged(m_CroppingObjectNode); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(this->m_CroppingObjectNode); m_Controls.boundingShapeSelector->setEnabled(true); } if (image->GetPixelType().GetPixelType() == itk::ImageIOBase::SCALAR) { // Might be changed with the upcoming new image statistics plugin int minPixelValue = static_cast(image->GetScalarValueMinNoRecompute()); //static_castimage->GetStatistics()->GetScalarValueMinNoRecompute(); int maxPixelValue = static_cast(image->GetScalarValueMaxNoRecompute()); //static_castimage->GetStatistics()->GetScalarValueMaxNoRecompute(); m_Controls.spinBox->setEnabled(true); m_Controls.spinBox->setMaximum(maxPixelValue); m_Controls.spinBox->setMinimum(minPixelValue); m_Controls.spinBox->setValue(minPixelValue); } else m_Controls.spinBox->setEnabled(false); unsigned int dim = image->GetDimension(); if (dim < 2 || dim > 4) { m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("Select an image.")); m_ParentWidget->setEnabled(false); } if (m_CroppingObjectNode != nullptr) { m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.boundingShapeSelector->setEnabled(true); m_Controls.labelWarningBB->setVisible(false); } else { m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.boundingShapeSelector->setEnabled(false); m_Controls.labelWarningBB->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningBB->setText(QString::fromStdString("Create a bounding shape below.")); } return; } // iterate all selected objects, adjust warning visibility m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("Select an image.")); m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.boundingShapeSelector->setEnabled(false); m_ParentWidget->setEnabled(true); m_Controls.labelWarningRotation->setVisible(false); } } } void QmitkImageCropper::OnComboBoxSelectionChanged(const mitk::DataNode* node) { mitk::DataNode* selectedNode = const_cast(node); if (selectedNode != nullptr) { if (m_ImageNode.IsNotNull()) selectedNode->SetDataInteractor(m_ImageNode->GetDataInteractor()); // m_ImageNode->GetDataInteractor()->SetDataNode(selectedNode); m_ImageNode = selectedNode; } } 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) { // cropping only possible if valid bounding shape as well as a valid image are loaded QList nodes = this->GetDataManagerSelection(); auto renderWindowPart = this->GetRenderWindowPart(OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); if (nodes.empty()) return; mitk::DataNode* node = nodes[0]; if (node == nullptr) { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); return; } if (m_CroppingObject == nullptr) { QMessageBox::information(nullptr, "Warning", "Please load and select a cropping object before starting image processing."); return; } mitk::BaseData* data = node->GetData(); //get data from node if (data != nullptr) { QString imageName; if (mask) imageName = QString::fromStdString(node->GetName() + "_masked"); else imageName = QString::fromStdString(node->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(m_CroppingObject); // 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) mitk::LabelSetImage* labelsetImageInput = dynamic_cast(data); if (labelsetImageInput != nullptr) { 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 (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, m_ImageNode); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { node->SetData(labelSetImage); node->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, node); // initialize the views to the bounding geometry mitk::TimeGeometry::Pointer bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } else { mitk::Image::Pointer imageInput = dynamic_cast(data); if (imageInput != nullptr) { cutter->SetInput(imageInput); // 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, m_ImageNode); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { node->SetData(cutter->GetOutput()); node->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, node); // initialize the views to the bounding geometry mitk::TimeGeometry::Pointer 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."); } }