diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp index fcae2de182..89cd684758 100644 --- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp +++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp @@ -1,294 +1,294 @@ /*=================================================================== 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" #include "mitkImage.h" #include "mitkImageAccessByItk.h" // ITK #include #include #include #include "mitkRegionGrow3DTool.xpm" // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MitkSegmentation_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, bool useValley, int numberOfBins) { //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->SetValleyEmphasis( useValley ); otsuFilter->SetNumberOfBins( numberOfBins ); 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); vtkSmartPointer lookupTable = vtkSmartPointer::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(std::vector regionIDs) { m_MultiLabelResultNode->SetVisibility(false); mitk::Image::Pointer multiLabelSegmentation = dynamic_cast(m_MultiLabelResultNode->GetData()); AccessByItk_1( multiLabelSegmentation, CalculatePreview, regionIDs); } template< typename TPixel, unsigned int VImageDimension> void mitk::OtsuTool3D::CalculatePreview(itk::Image< TPixel, VImageDimension>* itkImage, std::vector regionIDs) { typedef itk::Image< TPixel, VImageDimension > InputImageType; typedef itk::Image< unsigned char, VImageDimension > OutputImageType; typedef itk::BinaryThresholdImageFilter< InputImageType, OutputImageType > FilterType; - FilterType::Pointer filter = FilterType::New(); + typename FilterType::Pointer filter = FilterType::New(); //InputImageType::Pointer itkImage; - OutputImageType::Pointer itkBinaryTempImage1; - OutputImageType::Pointer itkBinaryTempImage2; - OutputImageType::Pointer itkBinaryResultImage; + typename OutputImageType::Pointer itkBinaryTempImage1; + typename OutputImageType::Pointer itkBinaryTempImage2; + typename OutputImageType::Pointer itkBinaryResultImage; //mitk::Image::Pointer multiLabelSegmentation = dynamic_cast(m_MultiLabelResultNode->GetData()); //mitk::CastToItkImage(multiLabelSegmentation, itkImage); filter->SetInput(itkImage); filter->SetLowerThreshold(regionIDs[0]); filter->SetUpperThreshold(regionIDs[0]); filter->SetInsideValue(1); filter->SetOutsideValue(0); filter->Update(); itkBinaryTempImage2 = filter->GetOutput(); itk::OrImageFilter::Pointer orFilter = itk::OrImageFilter::New(); // if more than one region id is used compute the union of all given binary regions for (std::vector::iterator it = regionIDs.begin() ; it != regionIDs.end(); ++it) { filter->SetLowerThreshold(*it); filter->SetUpperThreshold(*it); filter->SetInsideValue(1); filter->SetOutsideValue(0); filter->Update(); itkBinaryTempImage1 = filter->GetOutput(); orFilter->SetInput1(itkBinaryTempImage1); orFilter->SetInput2(itkBinaryTempImage2); orFilter->UpdateLargestPossibleRegion(); itkBinaryResultImage = orFilter->GetOutput(); itkBinaryTempImage2 = itkBinaryResultImage; } //---------------------------------------------------------------------------------------------------- mitk::Image::Pointer binarySegmentation; mitk::CastToMitkImage( itkBinaryResultImage, binarySegmentation); m_BinaryPreviewNode->SetData(binarySegmentation); m_BinaryPreviewNode->SetVisibility(true); m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } //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->SetInsideValue(1); // filter->SetOutsideValue(0); // 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(); }