diff --git a/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp index 2e8cb3bc26..9f7b209ab8 100644 --- a/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp +++ b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp @@ -1,331 +1,336 @@ /*=================================================================== 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 "mitkBinaryThresholdTool.h" #include "mitkToolManager.h" #include "mitkBoundingObjectToSegmentationFilter.h" #include #include "mitkLevelWindowProperty.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkOrganTypeProperty.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include "mitkImageCast.h" #include "mitkImageAccessByItk.h" #include "mitkImageTimeSelector.h" #include "mitkImageStatisticsHolder.h" #include #include #include "mitkPadImageFilter.h" #include "mitkMaskAndCutRoiImageFilter.h" // us #include "usModule.h" #include "usModuleResource.h" #include "usGetModuleContext.h" namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, BinaryThresholdTool, "Thresholding tool"); } mitk::BinaryThresholdTool::BinaryThresholdTool() :m_SensibleMinimumThresholdValue(-100), m_SensibleMaximumThresholdValue(+100), m_CurrentThresholdValue(0.0), m_IsFloatImage(false) { m_ThresholdFeedbackNode = DataNode::New(); mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties( m_ThresholdFeedbackNode ); m_ThresholdFeedbackNode->SetProperty( "color", ColorProperty::New(0.0, 1.0, 0.0) ); m_ThresholdFeedbackNode->SetProperty( "texture interpolation", BoolProperty::New(false) ); m_ThresholdFeedbackNode->SetProperty( "layer", IntProperty::New( 100 ) ); m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(100, 1) ) ); m_ThresholdFeedbackNode->SetProperty( "name", StringProperty::New("Thresholding feedback") ); m_ThresholdFeedbackNode->SetProperty( "opacity", FloatProperty::New(0.3) ); m_ThresholdFeedbackNode->SetProperty( "helper object", BoolProperty::New(true) ); } mitk::BinaryThresholdTool::~BinaryThresholdTool() { } const char** mitk::BinaryThresholdTool::GetXPM() const { return NULL; } us::ModuleResource mitk::BinaryThresholdTool::GetIconResource() const { us::Module* module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Threshold_48x48.png"); return resource; } const char* mitk::BinaryThresholdTool::GetName() const { return "Threshold"; } void mitk::BinaryThresholdTool::Activated() { m_ToolManager->RoiDataChanged += mitk::MessageDelegate(this, &mitk::BinaryThresholdTool::OnRoiDataChanged); m_OriginalImageNode = m_ToolManager->GetReferenceData(0); m_NodeForThresholding = m_OriginalImageNode; if ( m_NodeForThresholding.IsNotNull() ) { SetupPreviewNodeFor( m_NodeForThresholding ); } else { m_ToolManager->ActivateTool(-1); } } void mitk::BinaryThresholdTool::Deactivated() { m_ToolManager->RoiDataChanged -= mitk::MessageDelegate(this, &mitk::BinaryThresholdTool::OnRoiDataChanged); m_NodeForThresholding = NULL; m_OriginalImageNode = NULL; try { if (DataStorage* storage = m_ToolManager->GetDataStorage()) { storage->Remove( m_ThresholdFeedbackNode ); RenderingManager::GetInstance()->RequestUpdateAll(); } } catch(...) { // don't care } m_ThresholdFeedbackNode->SetData(NULL); } void mitk::BinaryThresholdTool::SetThresholdValue(double value) { if (m_ThresholdFeedbackNode.IsNotNull()) { m_CurrentThresholdValue = value; - m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(m_CurrentThresholdValue, 0.001) ) ); + // Bug 19250: The range of 0.01 is rather random. It was 0.001 before and probably due to rounding error propagation in VTK code + // it leads to strange banding effects on floating point images with a huge range (like -40000 - 40000). 0.01 lowers this effect + // enough to work with our images. Might not work on images with really huge ranges, though. Anyways, still seems to be low enough + // to work for floating point images with a range between 0 and 1. A better solution might be to dynamically calculate the value + // based on the value range of the current image (as big as possible, as small as necessary). + m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(m_CurrentThresholdValue, 0.01) ) ); RenderingManager::GetInstance()->RequestUpdateAll(); } } void mitk::BinaryThresholdTool::AcceptCurrentThresholdValue() { CreateNewSegmentationFromThreshold(m_NodeForThresholding); RenderingManager::GetInstance()->RequestUpdateAll(); m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdTool::CancelThresholding() { m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdTool::SetupPreviewNodeFor( DataNode* nodeForThresholding ) { if (nodeForThresholding) { Image::Pointer image = dynamic_cast( nodeForThresholding->GetData() ); Image::Pointer originalImage = dynamic_cast (m_OriginalImageNode->GetData()); if (image.IsNotNull()) { // initialize and a new node with the same image as our reference image // use the level window property of this image copy to display the result of a thresholding operation m_ThresholdFeedbackNode->SetData( image ); int layer(50); nodeForThresholding->GetIntProperty("layer", layer); m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1); if (DataStorage* storage = m_ToolManager->GetDataStorage()) { if (storage->Exists(m_ThresholdFeedbackNode)) storage->Remove(m_ThresholdFeedbackNode); storage->Add( m_ThresholdFeedbackNode, m_OriginalImageNode ); } if (image.GetPointer() == originalImage.GetPointer()) { if ((originalImage->GetPixelType().GetPixelType() == itk::ImageIOBase::SCALAR) &&(originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT || originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE)) m_IsFloatImage = true; else m_IsFloatImage = false; Image::StatisticsHolderPointer statistics = originalImage->GetStatistics(); m_SensibleMinimumThresholdValue = static_cast( statistics->GetScalarValueMin() ); m_SensibleMaximumThresholdValue = static_cast( statistics->GetScalarValueMax() ); } LevelWindowProperty::Pointer lwp = dynamic_cast( m_ThresholdFeedbackNode->GetProperty( "levelwindow" )); if (lwp && !m_IsFloatImage ) { m_CurrentThresholdValue = static_cast( lwp->GetLevelWindow().GetLevel() ); } else { m_CurrentThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 2.0; } IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue, m_IsFloatImage); ThresholdingValueChanged.Send(m_CurrentThresholdValue); } } } void mitk::BinaryThresholdTool::CreateNewSegmentationFromThreshold(DataNode* node) { if (node) { Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNotNull()) { DataNode::Pointer emptySegmentation = GetTargetSegmentationNode(); if (emptySegmentation) { // actually perform a thresholding and ask for an organ type for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep) { try { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( image ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer image3D = timeSelector->GetOutput(); if (image3D->GetDimension() == 2) { AccessFixedDimensionByItk_2( image3D, ITKThresholding, 2, dynamic_cast(emptySegmentation->GetData()), timeStep ); } else { AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast(emptySegmentation->GetData()), timeStep ); } } catch(...) { Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation."); } } if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer()) { mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, dynamic_cast (emptySegmentation->GetData())); padFilter->SetInput(1, dynamic_cast (m_OriginalImageNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); emptySegmentation->SetData(padFilter->GetOutput()); } m_ToolManager->SetWorkingData( emptySegmentation ); m_ToolManager->GetWorkingData(0)->Modified(); } } } } template void mitk::BinaryThresholdTool::ITKThresholding( itk::Image* originalImage, Image* segmentation, unsigned int timeStep ) { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( segmentation ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer segmentation3D = timeSelector->GetOutput(); typedef itk::Image< Tool::DefaultSegmentationDataType, 3> SegmentationType; // this is sure for new segmentations SegmentationType::Pointer itkSegmentation; CastToItkImage( segmentation3D, itkSegmentation ); // iterate over original and segmentation typedef itk::ImageRegionConstIterator< itk::Image > InputIteratorType; typedef itk::ImageRegionIterator< SegmentationType > SegmentationIteratorType; InputIteratorType inputIterator( originalImage, originalImage->GetLargestPossibleRegion() ); SegmentationIteratorType outputIterator( itkSegmentation, itkSegmentation->GetLargestPossibleRegion() ); inputIterator.GoToBegin(); outputIterator.GoToBegin(); while (!outputIterator.IsAtEnd()) { if ( inputIterator.Get() >= m_CurrentThresholdValue ) outputIterator.Set( 1 ); else outputIterator.Set( 0 ); ++inputIterator; ++outputIterator; } } void mitk::BinaryThresholdTool::OnRoiDataChanged() { mitk::DataNode::Pointer node = m_ToolManager->GetRoiData(0); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast (m_NodeForThresholding->GetData()); if (image.IsNull()) return; mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New(); roiFilter->SetInput(image); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); mitk::DataNode::Pointer tmpNode = mitk::DataNode::New(); mitk::Image::Pointer tmpImage = roiFilter->GetOutput(); tmpNode->SetData(tmpImage); m_SensibleMaximumThresholdValue = static_cast (roiFilter->GetMaxValue()); m_SensibleMinimumThresholdValue = static_cast (roiFilter->GetMinValue()); SetupPreviewNodeFor( tmpNode ); m_NodeForThresholding = tmpNode; return; } else { this->SetupPreviewNodeFor(m_OriginalImageNode); m_NodeForThresholding = m_OriginalImageNode; return; } }