diff --git a/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp b/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp index e630aef6cf..fd3b295c64 100644 --- a/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp +++ b/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp @@ -1,384 +1,418 @@ /*=================================================================== 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 "mitkMorphologicalOperations.h" #include #include #include #include #include #include #include #include #include #include #include void mitk::MorphologicalOperations::Closing(mitk::Image::Pointer &image, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElement) { MITK_INFO << "Start Closing..."; auto timeSteps = static_cast(image->GetTimeSteps()); if (timeSteps > 1) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(image); for (int t = 0; t < timeSteps; ++t) { MITK_INFO << " Processing time step " << t; timeSelector->SetTimeNr(t); timeSelector->Update(); mitk::Image::Pointer img3D = timeSelector->GetOutput(); img3D->DisconnectPipeline(); AccessByItk_3(img3D, itkClosing, img3D, factor, structuralElement); mitk::ImageReadAccessor accessor(img3D); image->SetVolume(accessor.GetData(), t); } } else { AccessByItk_3(image, itkClosing, image, factor, structuralElement); } MITK_INFO << "Finished Closing"; } void mitk::MorphologicalOperations::Erode(mitk::Image::Pointer &image, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElement) { MITK_INFO << "Start Erode..."; auto timeSteps = static_cast(image->GetTimeSteps()); if (timeSteps > 1) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(image); for (int t = 0; t < timeSteps; ++t) { MITK_INFO << " Processing time step " << t; timeSelector->SetTimeNr(t); timeSelector->Update(); mitk::Image::Pointer img3D = timeSelector->GetOutput(); img3D->DisconnectPipeline(); AccessByItk_3(img3D, itkErode, img3D, factor, structuralElement); mitk::ImageReadAccessor accessor(img3D); image->SetVolume(accessor.GetData(), t); } } else { AccessByItk_3(image, itkErode, image, factor, structuralElement); } MITK_INFO << "Finished Erode"; } void mitk::MorphologicalOperations::Dilate(mitk::Image::Pointer &image, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElement) { MITK_INFO << "Start Dilate..."; auto timeSteps = static_cast(image->GetTimeSteps()); if (timeSteps > 1) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(image); for (int t = 0; t < timeSteps; ++t) { MITK_INFO << " Processing time step " << t; timeSelector->SetTimeNr(t); timeSelector->Update(); mitk::Image::Pointer img3D = timeSelector->GetOutput(); img3D->DisconnectPipeline(); AccessByItk_3(img3D, itkDilate, img3D, factor, structuralElement); mitk::ImageReadAccessor accessor(img3D); image->SetVolume(accessor.GetData(), t); } } else { AccessByItk_3(image, itkDilate, image, factor, structuralElement); } MITK_INFO << "Finished Dilate"; } void mitk::MorphologicalOperations::Opening(mitk::Image::Pointer &image, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElement) { MITK_INFO << "Start Opening..."; auto timeSteps = static_cast(image->GetTimeSteps()); if (timeSteps > 1) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(image); for (int t = 0; t < timeSteps; ++t) { MITK_INFO << " Processing time step " << t; timeSelector->SetTimeNr(t); timeSelector->Update(); mitk::Image::Pointer img3D = timeSelector->GetOutput(); img3D->DisconnectPipeline(); AccessByItk_3(img3D, itkOpening, img3D, factor, structuralElement); mitk::ImageReadAccessor accessor(img3D); image->SetVolume(accessor.GetData(), t); } } else { AccessByItk_3(image, itkOpening, image, factor, structuralElement); } MITK_INFO << "Finished Opening"; } void mitk::MorphologicalOperations::FillHoles(mitk::Image::Pointer &image) { MITK_INFO << "Start FillHole..."; auto timeSteps = static_cast(image->GetTimeSteps()); if (timeSteps > 1) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(image); for (int t = 0; t < timeSteps; ++t) { MITK_INFO << " Processing time step " << t; timeSelector->SetTimeNr(t); timeSelector->Update(); mitk::Image::Pointer img3D = timeSelector->GetOutput(); img3D->DisconnectPipeline(); AccessByItk_1(img3D, itkFillHoles, img3D); mitk::ImageReadAccessor accessor(img3D); image->SetVolume(accessor.GetData(), t); } } else { AccessByItk_1(image, itkFillHoles, image); } MITK_INFO << "Finished FillHole"; } template void mitk::MorphologicalOperations::itkClosing( itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElementFlags) { typedef itk::Image ImageType; typedef itk::BinaryBallStructuringElement BallType; typedef itk::BinaryCrossStructuringElement CrossType; typedef typename itk::BinaryMorphologicalClosingImageFilter BallClosingFilterType; typedef typename itk::BinaryMorphologicalClosingImageFilter CrossClosingFilterType; if (structuralElementFlags & (Ball_Axial | Ball_Coronal | Ball_Sagital)) { BallType ball = CreateStructuringElement(structuralElementFlags, factor); typename BallClosingFilterType::Pointer closingFilter = BallClosingFilterType::New(); closingFilter->SetKernel(ball); closingFilter->SetInput(sourceImage); closingFilter->SetForegroundValue(1); closingFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(closingFilter->GetOutput(), resultImage); } else { CrossType cross = CreateStructuringElement(structuralElementFlags, factor); typename CrossClosingFilterType::Pointer closingFilter = CrossClosingFilterType::New(); closingFilter->SetKernel(cross); closingFilter->SetInput(sourceImage); closingFilter->SetForegroundValue(1); closingFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(closingFilter->GetOutput(), resultImage); } } template void mitk::MorphologicalOperations::itkErode( itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElementFlags) { typedef itk::Image ImageType; typedef itk::BinaryBallStructuringElement BallType; typedef itk::BinaryCrossStructuringElement CrossType; typedef typename itk::BinaryErodeImageFilter BallErodeFilterType; typedef typename itk::BinaryErodeImageFilter CrossErodeFilterType; if (structuralElementFlags & (Ball_Axial | Ball_Coronal | Ball_Sagital)) { BallType ball = CreateStructuringElement(structuralElementFlags, factor); typename BallErodeFilterType::Pointer erodeFilter = BallErodeFilterType::New(); erodeFilter->SetKernel(ball); erodeFilter->SetInput(sourceImage); erodeFilter->SetErodeValue(1); erodeFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(erodeFilter->GetOutput(), resultImage); } else { CrossType cross = CreateStructuringElement(structuralElementFlags, factor); typename CrossErodeFilterType::Pointer erodeFilter = CrossErodeFilterType::New(); erodeFilter->SetKernel(cross); erodeFilter->SetInput(sourceImage); erodeFilter->SetErodeValue(1); erodeFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(erodeFilter->GetOutput(), resultImage); } } template void mitk::MorphologicalOperations::itkDilate( itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElementFlags) { typedef itk::Image ImageType; typedef itk::BinaryBallStructuringElement BallType; typedef itk::BinaryCrossStructuringElement CrossType; typedef typename itk::BinaryDilateImageFilter BallDilateFilterType; typedef typename itk::BinaryDilateImageFilter CrossDilateFilterType; if (structuralElementFlags & (Ball_Axial | Ball_Coronal | Ball_Sagital)) { BallType ball = CreateStructuringElement(structuralElementFlags, factor); typename BallDilateFilterType::Pointer dilateFilter = BallDilateFilterType::New(); dilateFilter->SetKernel(ball); dilateFilter->SetInput(sourceImage); dilateFilter->SetDilateValue(1); dilateFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(dilateFilter->GetOutput(), resultImage); } else { CrossType cross = CreateStructuringElement(structuralElementFlags, factor); typename CrossDilateFilterType::Pointer dilateFilter = CrossDilateFilterType::New(); dilateFilter->SetKernel(cross); dilateFilter->SetInput(sourceImage); dilateFilter->SetDilateValue(1); dilateFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(dilateFilter->GetOutput(), resultImage); } } template void mitk::MorphologicalOperations::itkOpening( itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, mitk::MorphologicalOperations::StructuralElementType structuralElementFlags) { typedef itk::Image ImageType; typedef itk::BinaryBallStructuringElement BallType; typedef itk::BinaryCrossStructuringElement CrossType; typedef typename itk::BinaryMorphologicalOpeningImageFilter BallOpeningFiltertype; typedef typename itk::BinaryMorphologicalOpeningImageFilter CrossOpeningFiltertype; if (structuralElementFlags & (Ball_Axial | Ball_Coronal | Ball_Sagital)) { BallType ball = CreateStructuringElement(structuralElementFlags, factor); typename BallOpeningFiltertype::Pointer openingFilter = BallOpeningFiltertype::New(); openingFilter->SetKernel(ball); openingFilter->SetInput(sourceImage); openingFilter->SetForegroundValue(1); openingFilter->SetBackgroundValue(0); openingFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(openingFilter->GetOutput(), resultImage); } else { CrossType cross = CreateStructuringElement(structuralElementFlags, factor); typename CrossOpeningFiltertype::Pointer openingFilter = CrossOpeningFiltertype::New(); openingFilter->SetKernel(cross); openingFilter->SetInput(sourceImage); openingFilter->SetForegroundValue(1); openingFilter->SetBackgroundValue(0); openingFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(openingFilter->GetOutput(), resultImage); } } template void mitk::MorphologicalOperations::itkFillHoles(itk::Image *sourceImage, mitk::Image::Pointer &resultImage) { typedef itk::Image ImageType; typedef typename itk::BinaryFillholeImageFilter FillHoleFilterType; typename FillHoleFilterType::Pointer fillHoleFilter = FillHoleFilterType::New(); fillHoleFilter->SetInput(sourceImage); fillHoleFilter->SetForegroundValue(1); fillHoleFilter->UpdateLargestPossibleRegion(); mitk::CastToMitkImage(fillHoleFilter->GetOutput(), resultImage); } + +template +TStructuringElement mitk::MorphologicalOperations::CreateStructuringElement(StructuralElementType structuralElementFlag, int factor) +{ + TStructuringElement strElem; + typename TStructuringElement::SizeType size; + size.Fill(0); + switch (structuralElementFlag) + { + case Ball_Axial: + case Cross_Axial: + size.SetElement(0, factor); + size.SetElement(1, factor); + break; + case Ball_Coronal: + case Cross_Coronal: + size.SetElement(0, factor); + size.SetElement(2, factor); + break; + case Ball_Sagital: + case Cross_Sagital: + size.SetElement(1, factor); + size.SetElement(2, factor); + break; + case Ball: + case Cross: + size.Fill(factor); + break; + } + + strElem.SetRadius(size); + strElem.CreateStructuringElement(); + return strElem; +} \ No newline at end of file diff --git a/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.h b/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.h index 24bdeabc1d..a615a73820 100644 --- a/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.h +++ b/Modules/Segmentation/SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.h @@ -1,124 +1,93 @@ /*=================================================================== 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. ===================================================================*/ #ifndef mitkMorphologicalOperations_h #define mitkMorphologicalOperations_h #include #include namespace mitk { /** \brief Encapsulates several morphological operations that can be performed on segmentations. */ class MITKSEGMENTATION_EXPORT MorphologicalOperations { public: enum StructuralElementType { Ball = 7, Ball_Axial = 1, Ball_Sagital = 2, Ball_Coronal = 4, Cross = 56, Cross_Axial = 8, Cross_Sagital = 16, Cross_Coronal = 32 }; ///@{ /** \brief Perform morphological operation on 2D, 3D or 3D+t segmentation. */ static void Closing(mitk::Image::Pointer &image, int factor, StructuralElementType structuralElement); static void Erode(mitk::Image::Pointer &image, int factor, StructuralElementType structuralElement); static void Dilate(mitk::Image::Pointer &image, int factor, StructuralElementType structuralElement); static void Opening(mitk::Image::Pointer &image, int factor, StructuralElementType structuralElement); static void FillHoles(mitk::Image::Pointer &image); ///@} private: MorphologicalOperations(); template - static TStructuringElement CreateStructuringElement(StructuralElementType structuralElementFlag, int factor) - { - TStructuringElement strElem; - typename TStructuringElement::SizeType size; - size.Fill(0); - switch (structuralElementFlag) - { - case Ball_Axial: - case Cross_Axial: - size.SetElement(0, factor); - size.SetElement(1, factor); - break; - case Ball_Coronal: - case Cross_Coronal: - size.SetElement(0, factor); - size.SetElement(2, factor); - break; - case Ball_Sagital: - case Cross_Sagital: - size.SetElement(1, factor); - size.SetElement(2, factor); - break; - case Ball: - case Cross: - size.Fill(factor); - break; - } - - strElem.SetRadius(size); - strElem.CreateStructuringElement(); - return strElem; - } + static TStructuringElement CreateStructuringElement(StructuralElementType structuralElementFlag, int factor); ///@{ /** \brief Perform morphological operation by using corresponding ITK filter. */ template static void itkClosing(itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, StructuralElementType structuralElement); template static void itkErode(itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, StructuralElementType structuralElement); template static void itkDilate(itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, StructuralElementType structuralElement); template static void itkOpening(itk::Image *sourceImage, mitk::Image::Pointer &resultImage, int factor, StructuralElementType structuralElement); template static void itkFillHoles(itk::Image *sourceImage, mitk::Image::Pointer &resultImage); ///@} }; } #endif