diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
index 7ea7d0a4d4..d96bc4d3ca 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp
@@ -1,1139 +1,1146 @@
/*============================================================================
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 "QmitkSegmentationView.h"
#include "mitkPluginActivator.h"
// blueberry
#include <berryIWorkbenchPage.h>
// mitk
#include <mitkApplicationCursor.h>
#include <mitkBaseApplication.h>
#include <mitkBaseRendererHelper.h>
#include <mitkCameraController.h>
#include <mitkLabelSetImage.h>
#include <mitkLabelSetImageHelper.h>
#include <mitkLabelSetIOHelper.h>
#include <mitkManualPlacementAnnotationRenderer.h>
#include <mitkNodePredicateSubGeometry.h>
#include <mitkSegmentationInteractionEvents.h>
#include <mitkSegmentationObjectFactory.h>
#include <mitkSegTool2D.h>
#include <mitkStatusBar.h>
#include <mitkToolManagerProvider.h>
#include <mitkVtkResliceInterpolationProperty.h>
#include <mitkWorkbenchUtil.h>
// Qmitk
#include <QmitkRenderWindow.h>
#include <QmitkStaticDynamicSegmentationDialog.h>
#include <QmitkNewSegmentationDialog.h>
// us
#include <usModuleResource.h>
#include <usModuleResourceStream.h>
// Qt
#include <QMessageBox>
#include <QShortcut>
#include <QDir>
// vtk
#include <vtkQImageToImageSource.h>
#include <regex>
const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation";
QmitkSegmentationView::QmitkSegmentationView()
: m_Parent(nullptr)
, m_Controls(nullptr)
, m_RenderWindowPart(nullptr)
, m_ToolManager(nullptr)
, m_ReferenceNode(nullptr)
, m_WorkingNode(nullptr)
, m_DrawOutline(true)
, m_SelectionMode(false)
, m_MouseCursorSet(false)
, m_DefaultLabelNaming(true)
, m_SelectionChangeIsAlreadyBeingHandled(false)
{
auto isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
auto isDti = mitk::NodePredicateDataType::New("TensorImage");
auto isOdf = mitk::NodePredicateDataType::New("OdfImage");
auto isSegment = mitk::NodePredicateDataType::New("Segment");
auto validImages = mitk::NodePredicateOr::New();
validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment)));
validImages->AddPredicate(isDwi);
validImages->AddPredicate(isDti);
validImages->AddPredicate(isOdf);
auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
auto isMask = mitk::NodePredicateAnd::New(isBinary, isImage);
auto validSegmentations = mitk::NodePredicateOr::New();
validSegmentations->AddPredicate(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
validSegmentations->AddPredicate(isMask);
m_SegmentationPredicate = mitk::NodePredicateAnd::New();
m_SegmentationPredicate->AddPredicate(validSegmentations);
m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object")));
m_ReferencePredicate = mitk::NodePredicateAnd::New();
m_ReferencePredicate->AddPredicate(validImages);
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate));
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object")));
m_SegmentationInteractor = mitk::SegmentationInteractor::New();
// add observer for the 'SegmentationInteractionEvent'
itk::ReceptorMemberCommand<QmitkSegmentationView>::Pointer geometryNotAlignedCommand =
itk::ReceptorMemberCommand<QmitkSegmentationView>::New();
geometryNotAlignedCommand->SetCallbackFunction(this, &QmitkSegmentationView::ValidateRendererGeometry);
m_SegmentationInteractor->AddObserver(mitk::SegmentationInteractionEvent(nullptr, true), geometryNotAlignedCommand);
m_SegmentationInteractor->Disable();
}
QmitkSegmentationView::~QmitkSegmentationView()
{
if (nullptr != m_Controls)
{
this->LooseLabelSetConnection();
// deactivate all tools
m_ToolManager->ActivateTool(-1);
// removing all observers from working data
for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter)
{
(*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second);
}
m_WorkingDataObserverTags.clear();
// removing all observers from reference data
for (NodeTagMapType::iterator dataIter = m_ReferenceDataObserverTags.begin(); dataIter != m_ReferenceDataObserverTags.end(); ++dataIter)
{
(*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second);
}
m_ReferenceDataObserverTags.clear();
mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag);
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
service->RemoveAllPlanePositions();
context->ungetService(ppmRef);
m_ToolManager->SetReferenceData(nullptr);
m_ToolManager->SetWorkingData(nullptr);
}
m_ToolManager->ActiveToolChanged -=
mitk::MessageDelegate<QmitkSegmentationView>(this, &QmitkSegmentationView::ActiveToolChanged);
delete m_Controls;
}
/**********************************************************************/
/* private Q_SLOTS */
/**********************************************************************/
void QmitkSegmentationView::OnReferenceSelectionChanged(QList<mitk::DataNode::Pointer>)
{
this->OnAnySelectionChanged();
}
void QmitkSegmentationView::OnSegmentationSelectionChanged(QList<mitk::DataNode::Pointer>)
{
this->OnAnySelectionChanged();
}
void QmitkSegmentationView::OnAnySelectionChanged()
{
// When only a segmentation has been selected and the method is then called by a reference image selection,
// the already selected segmentation may not match the geometry predicate of the new reference image anymore.
// This will trigger a recursive call of this method further below. While it would be resolved gracefully, we
// can spare the extra call with an early-out. The original call of this method will handle the segmentation
// selection change afterwards anyway.
if (m_SelectionChangeIsAlreadyBeingHandled)
return;
auto selectedReferenceNode = m_Controls->referenceNodeSelector->GetSelectedNode();
bool referenceNodeChanged = false;
m_ToolManager->ActivateTool(-1);
if (m_ReferenceNode != selectedReferenceNode)
{
referenceNodeChanged = true;
// Remove visibility observer for the current reference node
if (m_ReferenceDataObserverTags.find(m_ReferenceNode) != m_ReferenceDataObserverTags.end())
{
m_ReferenceNode->GetProperty("visible")->RemoveObserver(m_ReferenceDataObserverTags[m_ReferenceNode]);
m_ReferenceDataObserverTags.erase(m_ReferenceNode);
}
// Set new reference node
m_ReferenceNode = selectedReferenceNode;
m_ToolManager->SetReferenceData(m_ReferenceNode);
// Prepare for a potential recursive call when changing node predicates of the working node selector
m_SelectionChangeIsAlreadyBeingHandled = true;
if (m_ReferenceNode.IsNull())
{
// Without a reference image, allow all segmentations to be selected
m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate);
m_SelectionChangeIsAlreadyBeingHandled = false;
}
else
{
// With a reference image, only allow segmentations that fit the geometry of the reference image to be selected.
m_Controls->workingNodeSelector->SetNodePredicate(mitk::NodePredicateAnd::New(
mitk::NodePredicateSubGeometry::New(m_ReferenceNode->GetData()->GetGeometry()),
m_SegmentationPredicate.GetPointer()));
m_SelectionChangeIsAlreadyBeingHandled = false;
this->ApplySelectionModeOnReferenceNode();
// Add visibility observer for the new reference node
auto command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput);
m_ReferenceDataObserverTags[m_ReferenceNode] =
m_ReferenceNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command);
}
}
auto selectedWorkingNode = m_Controls->workingNodeSelector->GetSelectedNode();
bool workingNodeChanged = false;
if (m_WorkingNode != selectedWorkingNode)
{
workingNodeChanged = true;
// Remove visibility observer for the current working node
if (m_WorkingDataObserverTags.find(m_WorkingNode) != m_WorkingDataObserverTags.end())
{
m_WorkingNode->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[m_WorkingNode]);
m_WorkingDataObserverTags.erase(m_WorkingNode);
}
// Disconnect from current label set image
this->LooseLabelSetConnection();
// Set new working node
m_WorkingNode = selectedWorkingNode;
m_ToolManager->SetWorkingData(m_WorkingNode);
if (m_WorkingNode.IsNotNull())
{
this->ApplySelectionModeOnWorkingNode();
// Connect to new label set image
this->EstablishLabelSetConnection();
m_Controls->labelSetWidget->ResetAllTableWidgetItems();
// Add visibility observer for the new segmentation node
auto command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput);
m_WorkingDataObserverTags[m_WorkingNode] =
m_WorkingNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command);
}
}
// Reset camera if any selection changed but only if both reference node and working node are set
if ((referenceNodeChanged || workingNodeChanged) && (m_ReferenceNode.IsNotNull() && m_WorkingNode.IsNotNull()))
{
if (nullptr != m_RenderWindowPart)
{
m_RenderWindowPart->SetReferenceGeometry(m_ReferenceNode->GetData()->GetTimeGeometry(), false);
}
}
this->UpdateGUI();
}
void QmitkSegmentationView::OnVisibilityShortcutActivated()
{
if (m_WorkingNode.IsNull())
{
return;
}
bool isVisible = false;
m_WorkingNode->GetBoolProperty("visible", isVisible);
m_WorkingNode->SetVisibility(!isVisible);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkSegmentationView::OnLabelToggleShortcutActivated()
{
if (m_WorkingNode.IsNull())
{
return;
}
auto workingImage = dynamic_cast<mitk::LabelSetImage*>(m_WorkingNode->GetData());
if (nullptr == workingImage)
{
return;
}
this->WaitCursorOn();
workingImage->GetActiveLabelSet()->SetNextActiveLabel();
workingImage->Modified();
this->WaitCursorOff();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkSegmentationView::OnNewSegmentation()
{
m_ToolManager->ActivateTool(-1);
if (m_ReferenceNode.IsNull())
{
MITK_ERROR << "'Create new segmentation' button should never be clickable unless a reference image is selected.";
return;
}
mitk::Image::ConstPointer referenceImage = dynamic_cast<mitk::Image*>(m_ReferenceNode->GetData());
if (referenceImage.IsNull())
{
QMessageBox::information(
m_Parent, "New segmentation", "Please load and select an image before starting some action.");
return;
}
if (referenceImage->GetDimension() <= 1)
{
QMessageBox::information(
m_Parent, "New segmentation", "Segmentation is currently not supported for 2D images");
return;
}
auto segTemplateImage = referenceImage;
if (referenceImage->GetDimension() > 3)
{
QmitkStaticDynamicSegmentationDialog dialog(m_Parent);
dialog.SetReferenceImage(referenceImage.GetPointer());
dialog.exec();
segTemplateImage = dialog.GetSegmentationTemplate();
}
mitk::DataNode::Pointer newSegmentationNode;
try
{
this->WaitCursorOn();
newSegmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(m_ReferenceNode, segTemplateImage);
this->WaitCursorOff();
}
catch (mitk::Exception& e)
{
this->WaitCursorOff();
MITK_ERROR << "Exception caught: " << e.GetDescription();
QMessageBox::warning(m_Parent, "New segmentation", "Could not create a new segmentation.");
return;
}
auto newLabelSetImage = dynamic_cast<mitk::LabelSetImage*>(newSegmentationNode->GetData());
if (nullptr == newLabelSetImage)
{
// something went wrong
return;
}
const auto labelSetPreset = this->GetDefaultLabelSetPreset();
if (labelSetPreset.empty() || !mitk::LabelSetIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage))
{
auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage);
if (!m_DefaultLabelNaming)
{
QmitkNewSegmentationDialog dialog(m_Parent);
dialog.SetName(QString::fromStdString(newLabel->GetName()));
dialog.SetColor(newLabel->GetColor());
if (QDialog::Rejected == dialog.exec())
return;
auto name = dialog.GetName();
if (!name.isEmpty())
newLabel->SetName(name.toStdString());
newLabel->SetColor(dialog.GetColor());
}
newLabelSetImage->GetActiveLabelSet()->AddLabel(newLabel);
}
if (!this->GetDataStorage()->Exists(newSegmentationNode))
{
this->GetDataStorage()->Add(newSegmentationNode, m_ReferenceNode);
}
if (m_ToolManager->GetWorkingData(0))
{
m_ToolManager->GetWorkingData(0)->SetSelected(false);
}
newSegmentationNode->SetSelected(true);
m_Controls->workingNodeSelector->SetCurrentSelectedNode(newSegmentationNode);
}
std::string QmitkSegmentationView::GetDefaultLabelSetPreset() const
{
auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), "");
if (labelSetPreset.empty())
labelSetPreset = m_LabelSetPresetPreference.toStdString();
return labelSetPreset;
}
void QmitkSegmentationView::OnManualTool2DSelected(int id)
{
this->ResetMouseCursor();
mitk::StatusBar::GetInstance()->DisplayText("");
if (id >= 0)
{
std::string text = "Active Tool: \"";
text += m_ToolManager->GetToolById(id)->GetName();
text += "\"";
mitk::StatusBar::GetInstance()->DisplayText(text.c_str());
us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource();
this->SetMouseCursor(resource, 0, 0);
}
}
void QmitkSegmentationView::OnShowMarkerNodes(bool state)
{
mitk::SegTool2D::Pointer manualSegmentationTool;
unsigned int numberOfExistingTools = m_ToolManager->GetTools().size();
for (unsigned int i = 0; i < numberOfExistingTools; i++)
{
manualSegmentationTool = dynamic_cast<mitk::SegTool2D*>(m_ToolManager->GetToolById(i));
if (nullptr == manualSegmentationTool)
{
continue;
}
manualSegmentationTool->SetShowMarkerNodes(state);
}
}
void QmitkSegmentationView::OnLayersChanged()
{
this->EstablishLabelSetConnection();
m_Controls->labelSetWidget->ResetAllTableWidgetItems();
}
void QmitkSegmentationView::OnShowLabelTable(bool value)
{
m_Controls->labelSetWidget->setVisible(value);
}
void QmitkSegmentationView::OnGoToLabel(const mitk::Point3D& pos)
{
if (m_RenderWindowPart)
{
m_RenderWindowPart->SetSelectedPosition(pos);
}
}
void QmitkSegmentationView::OnLabelSetWidgetReset()
{
this->ValidateSelectionInput();
}
/**********************************************************************/
/* private */
/**********************************************************************/
void QmitkSegmentationView::CreateQtPartControl(QWidget* parent)
{
m_Parent = parent;
m_Controls = new Ui::QmitkSegmentationViewControls;
m_Controls->setupUi(parent);
// *------------------------
// * SHORTCUTS
// *------------------------
QShortcut* visibilityShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_H), parent);
connect(visibilityShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnVisibilityShortcutActivated);
QShortcut* labelToggleShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_L, Qt::CTRL | Qt::Key::Key_I), parent);
connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnLabelToggleShortcutActivated);
// *------------------------
// * DATA SELECTION WIDGETS
// *------------------------
m_Controls->referenceNodeSelector->SetDataStorage(GetDataStorage());
m_Controls->referenceNodeSelector->SetNodePredicate(m_ReferencePredicate);
m_Controls->referenceNodeSelector->SetInvalidInfo("Select an image");
m_Controls->referenceNodeSelector->SetPopUpTitel("Select an image");
m_Controls->referenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation.");
m_Controls->workingNodeSelector->SetDataStorage(GetDataStorage());
m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate);
m_Controls->workingNodeSelector->SetInvalidInfo("Select a segmentation");
m_Controls->workingNodeSelector->SetPopUpTitel("Select a segmentation");
m_Controls->workingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected.");
connect(m_Controls->referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this, &QmitkSegmentationView::OnReferenceSelectionChanged);
connect(m_Controls->workingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this, &QmitkSegmentationView::OnSegmentationSelectionChanged);
// *------------------------
// * TOOLMANAGER
// *------------------------
m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager();
m_ToolManager->SetDataStorage(*(this->GetDataStorage()));
m_ToolManager->InitializeTools();
QString segTools2D = tr("Add Subtract Lasso Fill Erase Close Paint Wipe 'Region Growing' 'Live Wire'");
QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking GrowCut");
#ifdef __linux__
segTools3D.append(" nnUNet"); // plugin not enabled for MacOS / Windows
#endif
std::regex extSegTool2DRegEx("SegTool2D$");
std::regex extSegTool3DRegEx("SegTool3D$");
auto tools = m_ToolManager->GetTools();
for (const auto &tool : tools)
{
if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx))
{
segTools2D.append(QString(" '%1'").arg(tool->GetName()));
}
else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx))
{
segTools3D.append(QString(" '%1'").arg(tool->GetName()));
}
}
// setup 2D tools
m_Controls->toolSelectionBox2D->SetToolManager(*m_ToolManager);
m_Controls->toolSelectionBox2D->SetGenerateAccelerators(true);
m_Controls->toolSelectionBox2D->SetToolGUIArea(m_Controls->toolGUIArea2D);
m_Controls->toolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString());
m_Controls->toolSelectionBox2D->SetLayoutColumns(3);
connect(m_Controls->toolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected,
this, &QmitkSegmentationView::OnManualTool2DSelected);
// setup 3D Tools
m_Controls->toolSelectionBox3D->SetToolManager(*m_ToolManager);
m_Controls->toolSelectionBox3D->SetGenerateAccelerators(true);
m_Controls->toolSelectionBox3D->SetToolGUIArea(m_Controls->toolGUIArea3D);
m_Controls->toolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString());
m_Controls->toolSelectionBox3D->SetLayoutColumns(3);
m_Controls->slicesInterpolator->SetDataStorage(this->GetDataStorage());
// create general signal / slot connections
connect(m_Controls->newSegmentationButton, &QToolButton::clicked, this, &QmitkSegmentationView::OnNewSegmentation);
connect(m_Controls->slicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes);
connect(m_Controls->layersWidget, &QmitkLayersWidget::LayersChanged, this, &QmitkSegmentationView::OnLayersChanged);
connect(m_Controls->labelsWidget, &QmitkLabelsWidget::ShowLabelTable, this, &QmitkSegmentationView::OnShowLabelTable);
// *------------------------
// * LABELSETWIDGET
// *------------------------
connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::goToLabel, this, &QmitkSegmentationView::OnGoToLabel);
connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::LabelSetWidgetReset, this, &QmitkSegmentationView::OnLabelSetWidgetReset);
m_Controls->labelSetWidget->SetDataStorage(this->GetDataStorage());
m_Controls->labelSetWidget->hide();
auto command = itk::SimpleMemberCommand<QmitkSegmentationView>::New();
command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput);
m_RenderingManagerObserverTag =
mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command);
m_RenderWindowPart = this->GetRenderWindowPart();
if (nullptr != m_RenderWindowPart)
{
this->RenderWindowPartActivated(m_RenderWindowPart);
}
// Make sure the GUI notices if appropriate data is already present on creation.
// Should be done last, if everything else is configured because it triggers the autoselection of data.
m_Controls->referenceNodeSelector->SetAutoSelectNewNodes(true);
m_Controls->workingNodeSelector->SetAutoSelectNewNodes(true);
this->UpdateGUI();
}
void QmitkSegmentationView::ActiveToolChanged()
{
auto activeTool = m_ToolManager->GetActiveTool();
if (nullptr == activeTool)
{
// no tool activated, deactivate the segmentation interactor
m_SegmentationInteractor->Disable();
return;
}
// activate segmentation interactor to get informed about render window entered / left events
m_SegmentationInteractor->Enable();
}
void QmitkSegmentationView::ValidateRendererGeometry(const itk::EventObject& event)
{
if (!mitk::SegmentationInteractionEvent().CheckEvent(&event))
{
return;
}
const auto* segmentationInteractionEvent =
dynamic_cast<const mitk::SegmentationInteractionEvent*>(&event);
const mitk::BaseRenderer::Pointer sendingRenderer = segmentationInteractionEvent->GetSender();
if (nullptr == sendingRenderer)
{
return;
}
bool entered = segmentationInteractionEvent->HasEnteredRenderWindow();
if (entered)
{
// mouse cursor of tool inside render window
// check if tool can be used: reference geometry needs to be aligned with renderer geometry
const auto* referenceDataNode = m_ToolManager->GetReferenceData(0);
if (nullptr != referenceDataNode)
{
const auto workingImage = dynamic_cast<mitk::Image*>(referenceDataNode->GetData());
if (nullptr != workingImage)
{
const mitk::TimeGeometry* workingImageGeometry = workingImage->GetTimeGeometry();
if (nullptr != workingImageGeometry)
{
bool isGeometryAligned = false;
try
{
isGeometryAligned =
mitk::BaseRendererHelper::IsRendererAlignedWithSegmentation(sendingRenderer, workingImageGeometry);
}
catch (const mitk::Exception& e)
{
MITK_ERROR << "Unable to validate renderer geometry\n"
<< "Reason: " << e.GetDescription();
this->ShowRenderWindowWarning(sendingRenderer, true);
this->UpdateWarningLabel(
tr("Unable to validate renderer geometry. Please see log!"));
return;
}
if (!isGeometryAligned)
{
this->ShowRenderWindowWarning(sendingRenderer, true);
this->UpdateWarningLabel(
tr("Please perform a reinit on the segmentation image inside the entered Render Window!"));
return;
}
}
}
}
}
this->ShowRenderWindowWarning(sendingRenderer, false);
this->UpdateWarningLabel(tr(""));
}
void QmitkSegmentationView::ShowRenderWindowWarning(mitk::BaseRenderer* baseRenderer, bool show)
{
const auto* rendererName = baseRenderer->GetName();
auto* renderWindow = m_RenderWindowPart->GetQmitkRenderWindow(rendererName);
renderWindow->ShowOverlayMessage(show);
}
void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)
{
if (m_RenderWindowPart != renderWindowPart)
{
m_RenderWindowPart = renderWindowPart;
}
if (nullptr != m_Parent)
{
m_Parent->setEnabled(true);
}
if (nullptr == m_Controls)
{
return;
}
if (nullptr != m_RenderWindowPart)
{
// tell the interpolation about tool manager, data storage and render window part
QList<mitk::SliceNavigationController*> controllers;
controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
m_Controls->slicesInterpolator->Initialize(m_ToolManager, controllers);
if (!m_RenderWindowPart->HasCoupledRenderWindows())
{
// react if the active tool changed, only if a render window part with decoupled render windows is used
m_ToolManager->ActiveToolChanged +=
mitk::MessageDelegate<QmitkSegmentationView>(this, &QmitkSegmentationView::ActiveToolChanged);
}
}
}
void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/)
{
m_RenderWindowPart = nullptr;
if (nullptr != m_Parent)
{
m_Parent->setEnabled(false);
}
// remove message-connection to make sure no message is processed if no render window part is available
m_ToolManager->ActiveToolChanged -=
mitk::MessageDelegate<QmitkSegmentationView>(this, &QmitkSegmentationView::ActiveToolChanged);
m_Controls->slicesInterpolator->Uninitialize();
}
void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs)
{
auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), "");
m_DefaultLabelNaming = labelSuggestions.empty()
? prefs->GetBool("default label naming", true)
: false; // No default label naming when label suggestions are enforced via command-line argument
if (nullptr != m_Controls)
{
m_Controls->labelsWidget->SetDefaultLabelNaming(m_DefaultLabelNaming);
bool slimView = prefs->GetBool("slim view", false);
m_Controls->toolSelectionBox2D->SetShowNames(!slimView);
m_Controls->toolSelectionBox3D->SetShowNames(!slimView);
}
m_DrawOutline = prefs->GetBool("draw outline", true);
m_SelectionMode = prefs->GetBool("selection mode", false);
m_LabelSetPresetPreference = prefs->Get("label set preset", "");
this->ApplyDisplayOptions();
this->ApplySelectionMode();
}
void QmitkSegmentationView::NodeAdded(const mitk::DataNode* node)
{
if (m_SegmentationPredicate->CheckNode(node))
this->ApplyDisplayOptions(const_cast<mitk::DataNode*>(node));
this->ApplySelectionMode();
}
void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node)
{
if (!m_SegmentationPredicate->CheckNode(node))
{
return;
}
// remove all possible contour markers of the segmentation
mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(
node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true)));
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it)
{
std::string nodeName = node->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1;
service->RemovePlanePosition(id);
this->GetDataStorage()->Remove(it->Value());
}
context->ungetService(ppmRef);
service = nullptr;
mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image);
}
void QmitkSegmentationView::EstablishLabelSetConnection()
{
if (m_WorkingNode.IsNull())
return;
auto workingImage = dynamic_cast<mitk::LabelSetImage*>(m_WorkingNode->GetData());
+ if (nullptr == workingImage)
+ return;
workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1<QmitkLabelSetWidget,
mitk::Label::PixelType>(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue);
workingImage->AfterChangeLayerEvent += mitk::MessageDelegate<QmitkSegmentationView>(
this, &QmitkSegmentationView::UpdateGUI);
}
void QmitkSegmentationView::LooseLabelSetConnection()
{
if (m_WorkingNode.IsNull())
return;
auto workingImage = dynamic_cast<mitk::LabelSetImage*>(m_WorkingNode->GetData());
+ if (nullptr == workingImage)
+ return;
workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1<QmitkLabelSetWidget,
mitk::Label::PixelType>(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue);
workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate<QmitkSegmentationView>(
this, &QmitkSegmentationView::UpdateGUI);
}
void QmitkSegmentationView::ApplyDisplayOptions()
{
if (nullptr == m_Parent)
{
return;
}
if (nullptr == m_Controls)
{
return; // might happen on initialization (preferences loaded)
}
mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter)
{
this->ApplyDisplayOptions(*iter);
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node)
{
if (nullptr == node)
{
return;
}
auto labelSetImage = dynamic_cast<mitk::LabelSetImage*>(node->GetData());
if (nullptr != labelSetImage)
{
// node is a multi label segmentation
// its outline property can be set in the segmentation preference page
node->SetProperty("labelset.contour.active", mitk::BoolProperty::New(m_DrawOutline));
// force render window update to show outline
node->GetData()->Modified();
}
else if (nullptr != node->GetData())
{
// node is a legacy binary segmentation
bool isBinary = false;
node->GetBoolProperty("binary", isBinary);
if (isBinary)
{
node->SetProperty("outline binary", mitk::BoolProperty::New(m_DrawOutline));
node->SetProperty("outline width", mitk::FloatProperty::New(2.0));
// force render window update to show outline
node->GetData()->Modified();
}
}
}
void QmitkSegmentationView::ApplySelectionMode()
{
if (!m_SelectionMode)
return;
this->ApplySelectionModeOnReferenceNode();
this->ApplySelectionModeOnWorkingNode();
}
void QmitkSegmentationView::ApplySelectionModeOnReferenceNode()
{
this->ApplySelectionMode(m_ReferenceNode, m_ReferencePredicate);
}
void QmitkSegmentationView::ApplySelectionModeOnWorkingNode()
{
this->ApplySelectionMode(m_WorkingNode, m_SegmentationPredicate);
}
void QmitkSegmentationView::ApplySelectionMode(mitk::DataNode* node, mitk::NodePredicateBase* predicate)
{
if (!m_SelectionMode || node == nullptr || predicate == nullptr)
return;
auto nodes = this->GetDataStorage()->GetSubset(predicate);
for (auto iter = nodes->begin(); iter != nodes->end(); ++iter)
(*iter)->SetVisibility(*iter == node);
}
void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode* node)
{
QmitkRenderWindow* selectedRenderWindow = nullptr;
auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN);
auto* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial");
auto* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal");
auto* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal");
auto* threeDRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d");
bool PlanarFigureInitializedWindow = false;
// find initialized renderwindow
if (node->GetBoolProperty("PlanarFigureInitializedWindow",
PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer()))
{
selectedRenderWindow = axialRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
sagittalRenderWindow->GetRenderer()))
{
selectedRenderWindow = sagittalRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
coronalRenderWindow->GetRenderer()))
{
selectedRenderWindow = coronalRenderWindow;
}
if (!selectedRenderWindow && node->GetBoolProperty(
"PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
threeDRenderWindow->GetRenderer()))
{
selectedRenderWindow = threeDRenderWindow;
}
// make node visible
if (nullptr != selectedRenderWindow)
{
std::string nodeName = node->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1;
ctkPluginContext* context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id));
context->ungetService(ppmRef);
selectedRenderWindow->GetRenderer()->GetCameraController()->Fit();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes)
{
if (0 == nodes.size())
{
return;
}
std::string markerName = "Position";
unsigned int numberOfNodes = nodes.size();
std::string nodeName = nodes.at(0)->GetName();
if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0))
{
this->OnContourMarkerSelected(nodes.at(0));
return;
}
}
void QmitkSegmentationView::ResetMouseCursor()
{
if (m_MouseCursorSet)
{
mitk::ApplicationCursor::GetInstance()->PopCursor();
m_MouseCursorSet = false;
}
}
void QmitkSegmentationView::SetMouseCursor(const us::ModuleResource& resource, int hotspotX, int hotspotY)
{
// Remove previously set mouse cursor
if (m_MouseCursorSet)
{
this->ResetMouseCursor();
}
if (resource)
{
us::ModuleResourceStream cursor(resource, std::ios::binary);
mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY);
m_MouseCursorSet = true;
}
}
void QmitkSegmentationView::UpdateGUI()
{
mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0);
bool hasReferenceNode = referenceNode != nullptr;
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
bool hasWorkingNode = workingNode != nullptr;
m_Controls->newSegmentationButton->setEnabled(false);
if (hasReferenceNode)
{
m_Controls->newSegmentationButton->setEnabled(true);
}
if (hasWorkingNode && hasReferenceNode)
{
int layer = -1;
referenceNode->GetIntProperty("layer", layer);
workingNode->SetIntProperty("layer", layer + 1);
}
m_Controls->layersWidget->UpdateGUI();
m_Controls->labelsWidget->UpdateGUI();
this->ValidateSelectionInput();
}
void QmitkSegmentationView::ValidateSelectionInput()
{
auto referenceNode = m_Controls->referenceNodeSelector->GetSelectedNode();
auto workingNode = m_Controls->workingNodeSelector->GetSelectedNode();
bool hasReferenceNode = referenceNode.IsNotNull();
bool hasWorkingNode = workingNode.IsNotNull();
bool hasBothNodes = hasReferenceNode && hasWorkingNode;
QString warning;
bool toolSelectionBoxesEnabled = hasReferenceNode && hasWorkingNode;
unsigned int numberOfLabels = 0;
m_Controls->layersWidget->setEnabled(hasWorkingNode);
m_Controls->labelsWidget->setEnabled(hasWorkingNode);
m_Controls->labelSetWidget->setEnabled(hasWorkingNode);
m_Controls->toolSelectionBox2D->setEnabled(hasBothNodes);
m_Controls->toolSelectionBox3D->setEnabled(hasBothNodes);
m_Controls->slicesInterpolator->setEnabled(false);
m_Controls->interpolatorWarningLabel->hide();
if (hasReferenceNode)
{
if (!referenceNode->IsVisible(nullptr))
{
warning += tr("The selected reference image is currently not visible!");
toolSelectionBoxesEnabled = false;
}
}
if (hasWorkingNode)
{
if (!workingNode->IsVisible(nullptr))
{
warning += (!warning.isEmpty() ? "<br>" : "") + tr("The selected segmentation is currently not visible!");
toolSelectionBoxesEnabled = false;
}
auto labelSetImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
- auto activeLayer = labelSetImage->GetActiveLayer();
- numberOfLabels = labelSetImage->GetNumberOfLabels(activeLayer);
-
- if (2 == numberOfLabels)
- {
- m_Controls->slicesInterpolator->setEnabled(true);
- }
- else if (2 < numberOfLabels)
+ if (nullptr != labelSetImage)
{
- m_Controls->interpolatorWarningLabel->setText(
- "<font color=\"red\">Interpolation only works for single label segmentations.</font>");
- m_Controls->interpolatorWarningLabel->show();
+ auto activeLayer = labelSetImage->GetActiveLayer();
+ numberOfLabels = labelSetImage->GetNumberOfLabels(activeLayer);
+
+ if (2 == numberOfLabels)
+ {
+ m_Controls->slicesInterpolator->setEnabled(true);
+ }
+ else if (2 < numberOfLabels)
+ {
+ m_Controls->interpolatorWarningLabel->setText(
+ "<font color=\"red\">Interpolation only works for single label segmentations.</font>");
+ m_Controls->interpolatorWarningLabel->show();
+ }
}
}
toolSelectionBoxesEnabled &= numberOfLabels > 1;
// Here we need to check whether the geometry of the selected segmentation image (working image geometry)
// is aligned with the geometry of the 3D render window.
// It is not allowed to use a geometry different from the working image geometry for segmenting.
// We only need to this if the tool selection box would be enabled without this check.
if (toolSelectionBoxesEnabled && nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows())
{
const mitk::BaseGeometry* workingNodeGeometry = workingNode->GetData()->GetGeometry();
const mitk::BaseGeometry* renderWindowGeometry =
m_RenderWindowPart->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D();
if (nullptr != workingNodeGeometry && nullptr != renderWindowGeometry)
{
if (!mitk::Equal(*workingNodeGeometry->GetBoundingBox(), *renderWindowGeometry->GetBoundingBox(), mitk::eps, true))
{
warning += (!warning.isEmpty() ? "<br>" : "") + tr("Please reinitialize the selected segmentation image!");
toolSelectionBoxesEnabled = false;
}
}
}
m_Controls->toolSelectionBox2D->setEnabled(toolSelectionBoxesEnabled);
m_Controls->toolSelectionBox3D->setEnabled(toolSelectionBoxesEnabled);
this->UpdateWarningLabel(warning);
m_ToolManager->SetReferenceData(referenceNode);
m_ToolManager->SetWorkingData(workingNode);
}
void QmitkSegmentationView::UpdateWarningLabel(QString text)
{
if (text.isEmpty())
{
m_Controls->selectionWarningLabel->hide();
}
else
{
m_Controls->selectionWarningLabel->setText("<font color=\"red\">" + text + "</font>");
m_Controls->selectionWarningLabel->show();
}
}