merge_changes

CemrgApp/Modules/CemrgAppModule/files.cmake

@@ -8,6 +8,7 @@ set(CPP_FILES
     CemrgAtriaClipper.cpp
     CemrgAtrialTools.cpp
     CemrgScarAdvanced.cpp
+    CemrgMultilabelSegmentationUtils.cpp
     CemrgTests.cpp
 )
 
@@ -24,6 +25,7 @@ set(MOC_H_FILES
   include/CemrgStrains.h
   include/CemrgPower.h
   include/CemrgScarAdvanced.h
+  include/CemrgMultilabelSegmentationUtils.h
 )
 
 set(RESOURCE_FILES

CemrgApp/Modules/CemrgAppModule/include/CemrgMultilabelSegmentationUtils.h

@@ -0,0 +1,100 @@
+/*=========================================================================
+
+Program:   Medical Imaging & Interaction Toolkit
+Language:  C++
+Date:      $Date$
+Version:   $Revision$
+
+Copyright (c) German Cancer Research Center, Division of Medical and
+Biological Informatics. All rights reserved.
+See MITKCopyright.txt or http://www.mitk.org/copyright.html for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+/*=========================================================================
+ *
+ * Four Chamber Tools (inherits CemrgCommandLine)
+ *
+ * Cardiac Electromechanics Research Group
+ * http://www.cemrgapp.com
+ * [email protected]
+ *
+ * This software is distributed WITHOUT ANY WARRANTY or SUPPORT!
+ *
+=========================================================================*/
+
+#ifndef CemrgMultilabelSegmentationUtils_h
+#define CemrgMultilabelSegmentationUtils_h
+
+#include <QString>
+#include <QJsonObject>
+
+#include <mitkIOUtil.h>
+#include <mitkImage.h>
+#include <mitkCommon.h>
+
+// VTK
+#include <vtkSmartPointer.h>
+#include <vtkConnectivityFilter.h>
+#include <vtkIdList.h>
+#include <vtkRegularPolygonSource.h>
+
+// ITK
+#include <itkImage.h>
+#include <itkImageRegionIterator.h>
+
+#include "CemrgCommandLine.h"
+
+class MITKCEMRGAPPMODULE_EXPORT CemrgMultilabelSegmentationUtils {
+    typedef itk::Image<uint8_t, 3> ImageType;
+    typedef itk::ImageRegionIterator<ImageType> IteratorType;
+
+    public:
+        CemrgMultilabelSegmentationUtils();
+        ~CemrgMultilabelSegmentationUtils();
+
+        // Segmentation Utilities
+        bool CheckExisting(mitk::Image::Pointer seg, int queryLabel);
+        void ExploreLabelsToSplit(mitk::Image::Pointer seg, std::vector<int>& labels); 
+        mitk::Image::Pointer SplitLabelsOnRepeat(mitk::Image::Pointer seg, int label, unsigned int radius=3);
+
+        mitk::Image::Pointer ReplaceLabel(mitk::Image::Pointer seg, int oldLabel, int newLabel);
+        inline mitk::Image::Pointer RemoveLabel(mitk::Image::Pointer seg, int label) { return ReplaceLabel(seg, label, 0); };
+
+        mitk::Image::Pointer ResampleSmoothLabel(mitk::Image::Pointer image, std::vector<double> spacing, double sigmaFraction=0.5, double alphaFraction=3.0);
+
+        mitk::Image::Pointer LabelMaskAndOperation(mitk::Image::Pointer seg, mitk::Image::Pointer mask, int oldLabel, int newLabel);
+        mitk::Image::Pointer ConnectedComponent(mitk::Image::Pointer seg, std::vector<unsigned int> seedIdx, int label, bool keep=false);
+        inline mitk::Image::Pointer ConnectedComponentKeep(mitk::Image::Pointer seg, std::vector<unsigned int> seedIdx, int label) { return ConnectedComponent(seg, seedIdx, label, true); };
+        mitk::Image::Pointer ExtractLargestComponent(mitk::Image::Pointer seg, int numLabels=1, int outputLabel=1);
+        mitk::Image::Pointer CleanMultilabelSegmentation(mitk::Image::Pointer seg, int background=0);
+
+        mitk::Image::Pointer DistanceMap(mitk::Image::Pointer seg, int label);
+        mitk::Image::Pointer Threshold(mitk::Image::Pointer seg, int label, int lower, int upper);
+
+        mitk::Image::Pointer ZerosLike(mitk::Image::Pointer image);
+
+        // helper functions
+        void GetLabels(mitk::Image::Pointer seg, std::vector<int>& labels, int background=0);
+        mitk::Image::Pointer ExtractSingleLabel(mitk::Image::Pointer seg, int label, bool binarise=true);
+        mitk::Image::Pointer ExtractSetOfLabels(mitk::Image::Pointer seg, std::vector<int> labels, bool binarise=true);
+        mitk::Image::Pointer BwLabelN(mitk::Image::Pointer seg, std::vector<int>& labels, bool openImage=false);
+        ImageType::Pointer ItkBwLabelN(mitk::Image::Pointer seg, std::vector<int>& labels, bool openImage=false);
+
+        bool GetLabelCentreOfMassIndex(mitk::Image::Pointer seg, int label, std::vector<unsigned int> &cogIndx);
+        bool GetLabelCentreOfMass(mitk::Image::Pointer seg, int label, std::vector<double> &cog);
+
+        void WorldToIndex(mitk::Image::Pointer image, std::vector<double> world, std::vector<unsigned int>& index);
+        void IndexToWorld(mitk::Image::Pointer image, std::vector<unsigned int> index, std::vector<double> &world);
+
+        void WorldToIndexOriginSpacing(std::vector<double> world, std::vector<unsigned int>& index, std::vector<double> origin, std::vector<double> spacing);
+        void IndexToWorldOriginSpacing(std::vector<unsigned int> index, std::vector<double> &world, std::vector<double> origin, std::vector<double> spacing);
+
+    protected:
+
+    private : 
+};
+#endif // CemrgMultilabelSegmentationUtils_h