diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp index 0d34c4616a..f93974900e 100644 --- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp +++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp @@ -1,222 +1,225 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // MITK #include "mitkOtsuTool3D.h" #include "mitkToolManager.h" #include "mitkRenderingManager.h" #include #include #include #include #include #include #include "mitkOtsuSegmentationFilter.h" // ITK #include #include #include "mitkRegionGrow3DTool.xpm" // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(Segmentation_EXPORT, OtsuTool3D, "Otsu Segmentation"); } mitk::OtsuTool3D::OtsuTool3D() { } mitk::OtsuTool3D::~OtsuTool3D() { } void mitk::OtsuTool3D::Activated() { if (m_ToolManager) { m_OriginalImage = dynamic_cast(m_ToolManager->GetReferenceData(0)->GetData()); m_BinaryPreviewNode = mitk::DataNode::New(); m_BinaryPreviewNode->SetName("Binary_Preview"); m_BinaryPreviewNode->SetProperty( "color", ColorProperty::New(0.0, 1.0, 0.0) ); m_BinaryPreviewNode->SetProperty( "opacity", FloatProperty::New(0.3) ); //m_BinaryPreviewNode->SetBoolProperty("helper object", true); //m_BinaryPreviewNode->SetProperty("binary", mitk::BoolProperty::New(true)); m_ToolManager->GetDataStorage()->Add( this->m_BinaryPreviewNode ); m_MultiLabelResultNode = mitk::DataNode::New(); m_MultiLabelResultNode->SetName("Otsu_Preview"); //m_MultiLabelResultNode->SetBoolProperty("helper object", true); m_MultiLabelResultNode->SetVisibility(true); m_MaskedImagePreviewNode = mitk::DataNode::New(); m_MaskedImagePreviewNode->SetName("Volume_Preview"); //m_MultiLabelResultNode->SetBoolProperty("helper object", true); m_MaskedImagePreviewNode->SetVisibility(false); m_ToolManager->GetDataStorage()->Add( this->m_MultiLabelResultNode ); } } void mitk::OtsuTool3D::Deactivated() { m_ToolManager->GetDataStorage()->Remove( this->m_MultiLabelResultNode ); m_MultiLabelResultNode = NULL; m_ToolManager->GetDataStorage()->Remove( this->m_BinaryPreviewNode ); m_BinaryPreviewNode = NULL; + m_ToolManager->GetDataStorage()->Remove( this->m_MaskedImagePreviewNode); + m_MaskedImagePreviewNode = NULL; } const char** mitk::OtsuTool3D::GetXPM() const { return NULL; } us::ModuleResource mitk::OtsuTool3D::GetIconResource() const { us::Module* module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Otsu_48x48.png"); return resource; } void mitk::OtsuTool3D::RunSegmentation(int regions) { //this->m_OtsuSegmentationDialog->setCursor(Qt::WaitCursor); int numberOfThresholds = regions - 1; unsigned int timestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->GetPos(); mitk::Image::Pointer image3D = Get3DImage(m_OriginalImage, timestep); mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New(); otsuFilter->SetNumberOfThresholds( numberOfThresholds ); otsuFilter->SetInput( image3D ); try { otsuFilter->Update(); } catch( ... ) { mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)"; } m_ToolManager->GetDataStorage()->Remove( this->m_MultiLabelResultNode ); m_MultiLabelResultNode = NULL; m_MultiLabelResultNode = mitk::DataNode::New(); m_MultiLabelResultNode->SetName("Otsu_Preview"); m_MultiLabelResultNode->SetVisibility(true); m_ToolManager->GetDataStorage()->Add( this->m_MultiLabelResultNode ); m_MultiLabelResultNode->SetOpacity(1.0); this->m_MultiLabelResultNode->SetData( otsuFilter->GetOutput() ); m_MultiLabelResultNode->SetProperty("binary", mitk::BoolProperty::New(false)); mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New(); renderingMode->SetValue( mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR ); m_MultiLabelResultNode->SetProperty("Image Rendering.Mode", renderingMode); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut); vtkLookupTable *lookupTable = vtkLookupTable::New(); lookupTable->SetHueRange(1.0, 0.0); lookupTable->SetSaturationRange(1.0, 1.0); lookupTable->SetValueRange(1.0, 1.0); lookupTable->SetTableRange(-1.0, 1.0); lookupTable->Build(); lut->SetVtkLookupTable(lookupTable); prop->SetLookupTable(lut); m_MultiLabelResultNode->SetProperty("LookupTable",prop); mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); mitk::LevelWindow levelwindow; levelwindow.SetRangeMinMax(0, numberOfThresholds + 1); levWinProp->SetLevelWindow( levelwindow ); m_MultiLabelResultNode->SetProperty( "levelwindow", levWinProp ); //m_BinaryPreviewNode->SetVisibility(false); // m_MultiLabelResultNode->SetVisibility(true); //this->m_OtsuSegmentationDialog->setCursor(Qt::ArrowCursor); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::OtsuTool3D::ConfirmSegmentation() { GetTargetSegmentationNode()->SetData(dynamic_cast(m_BinaryPreviewNode->GetData())); + m_ToolManager->ActivateTool(-1); } void mitk::OtsuTool3D::UpdateBinaryPreview(int regionID) { m_MultiLabelResultNode->SetVisibility(false); //pixel with regionID -> binary image const unsigned short dim = 3; typedef unsigned char PixelType; typedef itk::Image< PixelType, dim > InputImageType; typedef itk::Image< PixelType, dim > OutputImageType; typedef itk::BinaryThresholdImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); InputImageType::Pointer itkImage; mitk::Image::Pointer multiLabelSegmentation = dynamic_cast(m_MultiLabelResultNode->GetData()); mitk::CastToItkImage(multiLabelSegmentation, itkImage); filter->SetInput(itkImage); filter->SetLowerThreshold(regionID); filter->SetUpperThreshold(regionID); filter->Update(); mitk::Image::Pointer binarySegmentation; mitk::CastToMitkImage( filter->GetOutput(), binarySegmentation); m_BinaryPreviewNode->SetData(binarySegmentation); m_BinaryPreviewNode->SetVisibility(true); m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } const char* mitk::OtsuTool3D::GetName() const { return "Otsu"; } void mitk::OtsuTool3D::UpdateVolumePreview(bool volumeRendering) { if (volumeRendering) { m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", true); m_MaskedImagePreviewNode->SetBoolProperty("volumerendering.uselod", true); } else { m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::OtsuTool3D::ShowMultiLabelResultNode(bool show) { m_MultiLabelResultNode->SetVisibility(show); m_BinaryPreviewNode->SetVisibility(!show); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp index 069e878a19..d1ae564bc4 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp @@ -1,155 +1,154 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkOtsuTool3DGUI.h" #include "QmitkConfirmSegmentationDialog.h" #include #include #include #include #include #include MITK_TOOL_GUI_MACRO(SegmentationUI_EXPORT, QmitkOtsuTool3DGUI, "") QmitkOtsuTool3DGUI::QmitkOtsuTool3DGUI() :QmitkToolGUI(), m_NumberOfRegions(0) { m_Controls.setupUi(this); connect( m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSpinboxValueAccept())); connect(m_Controls.m_selectionListWidget, SIGNAL(itemClicked(QListWidgetItem*)), this, SLOT(OnItemSelectionChanged(QListWidgetItem*))); connect( m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept())); connect( this, SIGNAL(NewToolAssociated(mitk::Tool*)), this, SLOT(OnNewToolAssociated(mitk::Tool*)) ); } QmitkOtsuTool3DGUI::~QmitkOtsuTool3DGUI() { } void QmitkOtsuTool3DGUI::OnItemSelectionChanged(QListWidgetItem* item) { if (m_SelectedItem == item) { m_SelectedItem = 0; m_Controls.m_selectionListWidget->clearSelection(); m_Controls.m_ConfSegButton->setEnabled( false ); m_OtsuTool3DTool->ShowMultiLabelResultNode(true); return; } m_SelectedItem = item; if (m_OtsuTool3DTool.IsNotNull()) { // TODO update preview of region m_OtsuTool3DTool->UpdateBinaryPreview(m_SelectedItem->text().toInt()); if ( !m_Controls.m_selectionListWidget->selectedItems().empty() ) { m_Controls.m_ConfSegButton->setEnabled( true ); } else { m_Controls.m_ConfSegButton->setEnabled( false ); } } } void QmitkOtsuTool3DGUI::OnNewToolAssociated(mitk::Tool* tool) { m_OtsuTool3DTool = dynamic_cast( tool ); } void QmitkOtsuTool3DGUI::OnSegmentationRegionAccept() { QmitkConfirmSegmentationDialog dialog; QString segName = QString::fromStdString(m_OtsuTool3DTool->GetCurrentSegmentationName()); dialog.SetSegmentationName(segName); int result = dialog.exec(); switch(result) { case QmitkConfirmSegmentationDialog::CREATE_NEW_SEGMENTATION: m_OtsuTool3DTool->SetOverwriteExistingSegmentation(false); break; case QmitkConfirmSegmentationDialog::OVERWRITE_SEGMENTATION: m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true); break; case QmitkConfirmSegmentationDialog::CANCEL_SEGMENTATION: return; } if (m_OtsuTool3DTool.IsNotNull() && m_Controls.m_selectionListWidget->currentItem() != NULL) { m_OtsuTool3DTool->ConfirmSegmentation(); - m_OtsuTool3DTool->Deactivated(); } } void QmitkOtsuTool3DGUI::OnSpinboxValueAccept() { if( m_NumberOfRegions == m_Controls.m_Spinbox->value() ) return; if (m_OtsuTool3DTool.IsNotNull()) { try { m_NumberOfRegions = m_Controls.m_Spinbox->value(); int proceed; QMessageBox* messageBox = new QMessageBox(QMessageBox::Question, NULL, "The otsu segmentation computation may take several minutes depending on the number of Regions you selected. Proceed anyway?", QMessageBox::Ok | QMessageBox::Cancel); if (m_NumberOfRegions >= 5) { proceed = messageBox->exec(); if (proceed != QMessageBox::Ok) return; } this->setCursor(Qt::WaitCursor); m_OtsuTool3DTool->RunSegmentation( m_NumberOfRegions ); this->setCursor(Qt::ArrowCursor); } catch( ... ) { this->setCursor(Qt::ArrowCursor); QMessageBox* messageBox = new QMessageBox(QMessageBox::Critical, NULL, "itkOtsuFilter error: image dimension must be in {2, 3} and no RGB images can be handled."); messageBox->exec(); delete messageBox; return; } //insert regions into widget QString itemName; QListWidgetItem* item; m_Controls.m_selectionListWidget->clear(); for(int i=0; ivalue(); ++i) { itemName = QString::number(i); item = new QListWidgetItem(itemName); m_Controls.m_selectionListWidget->addItem(item); } } } void QmitkOtsuTool3DGUI::OnVolumePreviewChecked(int state) { if (state == 1) { } }