Merge branch 'T27417-FixReaders'

MIC-DKFZ · May 14, 2020 · 0653d49 · 0653d49
2 parents 3f11466 + e11dd61
commit 0653d49
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Showing 31 changed files with 61 additions and 61 deletions.
diff --git a/Modules/DiffusionIO/ReaderWriter/mitkConnectomicsNetworkReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkConnectomicsNetworkReader.cpp
@@ -41,7 +41,7 @@ namespace mitk
   {
   }
 
-  std::vector<itk::SmartPointer<BaseData> > ConnectomicsNetworkReader::Read()
+  std::vector<itk::SmartPointer<BaseData> > ConnectomicsNetworkReader::DoRead()
   {
     std::vector<itk::SmartPointer<mitk::BaseData> > result;
     std::string location = GetInputLocation();

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkConnectomicsNetworkReader.h b/Modules/DiffusionIO/ReaderWriter/mitkConnectomicsNetworkReader.h
@@ -39,8 +39,8 @@ namespace mitk
     ConnectomicsNetworkReader();
     ~ConnectomicsNetworkReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
     ConnectomicsNetworkReader* Clone() const override;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageDicomReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageDicomReader.cpp
@@ -86,7 +86,7 @@ DiffusionImageDicomReader()
 }
 
 std::vector<itk::SmartPointer<mitk::BaseData> >
-DiffusionImageDicomReader::Read()
+DiffusionImageDicomReader::DoRead()
 {
   return InternalRead();
 }

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageDicomReader.h b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageDicomReader.h
@@ -45,8 +45,8 @@ namespace mitk
     DiffusionImageDicomReader();
     ~DiffusionImageDicomReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
     typedef short                                                           DiffusionPixelType;
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNiftiReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNiftiReader.cpp
@@ -84,7 +84,7 @@ DiffusionImageNiftiReader()
 
 std::vector<itk::SmartPointer<mitk::BaseData> >
 DiffusionImageNiftiReader::
-Read()
+DoRead()
 {
   std::vector<itk::SmartPointer<mitk::BaseData> > result;
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNiftiReader.h b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNiftiReader.h
@@ -45,8 +45,8 @@ namespace mitk
     DiffusionImageNiftiReader();
     ~DiffusionImageNiftiReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
     typedef short                                                           DiffusionPixelType;
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNrrdReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNrrdReader.cpp
@@ -78,7 +78,7 @@ namespace mitk
 
   std::vector<itk::SmartPointer<mitk::BaseData> >
   DiffusionImageNrrdReader::
-  Read()
+  DoRead()
   {
     std::vector<itk::SmartPointer<mitk::BaseData> > result;
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNrrdReader.h b/Modules/DiffusionIO/ReaderWriter/mitkDiffusionImageNrrdReader.h
@@ -45,8 +45,8 @@ namespace mitk
     DiffusionImageNrrdReader();
     ~DiffusionImageNrrdReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
     typedef short                                                           DiffusionPixelType;
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleDicomReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleDicomReader.cpp
@@ -55,7 +55,7 @@ mitk::FiberBundleDicomReader * mitk::FiberBundleDicomReader::Clone() const
   return new FiberBundleDicomReader(*this);
 }
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleDicomReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleDicomReader::DoRead()
 {
 
   std::vector<itk::SmartPointer<mitk::BaseData> > output_fibs;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleDicomReader.h b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleDicomReader.h
@@ -39,8 +39,8 @@ namespace mitk
     FiberBundleDicomReader(const FiberBundleDicomReader& other);
     FiberBundleDicomReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTckReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTckReader.cpp
@@ -52,7 +52,7 @@ mitk::FiberBundleTckReader * mitk::FiberBundleTckReader::Clone() const
   return new FiberBundleTckReader(*this);
 }
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTckReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTckReader::DoRead()
 {
 
   std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTckReader.h b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTckReader.h
@@ -39,8 +39,8 @@ namespace mitk
     FiberBundleTckReader(const FiberBundleTckReader& other);
     FiberBundleTckReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
@@ -55,7 +55,7 @@ mitk::FiberBundleTrackVisReader * mitk::FiberBundleTrackVisReader::Clone() const
   return new FiberBundleTrackVisReader(*this);
 }
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTrackVisReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTrackVisReader::DoRead()
 {
 
   std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.h b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.h
@@ -39,8 +39,8 @@ namespace mitk
     FiberBundleTrackVisReader(const FiberBundleTrackVisReader& other);
     FiberBundleTrackVisReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleVtkReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleVtkReader.cpp
@@ -53,7 +53,7 @@ mitk::FiberBundleVtkReader * mitk::FiberBundleVtkReader::Clone() const
 }
 
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleVtkReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleVtkReader::DoRead()
 {
 
   std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleVtkReader.h b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleVtkReader.h
@@ -39,8 +39,8 @@ namespace mitk
     FiberBundleVtkReader(const FiberBundleVtkReader& other);
     FiberBundleVtkReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkNrrdOdfImageReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkNrrdOdfImageReader.cpp
@@ -43,7 +43,7 @@ namespace mitk
   {
   }
 
-  std::vector<itk::SmartPointer<BaseData> > NrrdOdfImageReader::Read()
+  std::vector<itk::SmartPointer<BaseData> > NrrdOdfImageReader::DoRead()
   {
     std::vector<itk::SmartPointer<mitk::BaseData> > result;
     std::string location = GetInputLocation();

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkNrrdOdfImageReader.h b/Modules/DiffusionIO/ReaderWriter/mitkNrrdOdfImageReader.h
@@ -42,8 +42,8 @@ namespace mitk
     NrrdOdfImageReader();
     ~NrrdOdfImageReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   protected:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkNrrdTensorImageReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkNrrdTensorImageReader.cpp
@@ -48,7 +48,7 @@ namespace mitk
   {
   }
 
-  std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::Read()
+  std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::DoRead()
   {
     std::vector<itk::SmartPointer<mitk::BaseData> > result;
     std::string location = GetInputLocation();

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkNrrdTensorImageReader.h b/Modules/DiffusionIO/ReaderWriter/mitkNrrdTensorImageReader.h
@@ -44,8 +44,8 @@ namespace mitk
     NrrdTensorImageReader();
     ~NrrdTensorImageReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   protected:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkPeakImageReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkPeakImageReader.cpp
@@ -46,7 +46,7 @@ namespace mitk
   {
   }
 
-  std::vector<itk::SmartPointer<BaseData> > PeakImageReader::Read()
+  std::vector<itk::SmartPointer<BaseData> > PeakImageReader::DoRead()
   {
     mitk::LocaleSwitch localeSwitch("C");
     std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkPeakImageReader.h b/Modules/DiffusionIO/ReaderWriter/mitkPeakImageReader.h
@@ -36,8 +36,8 @@ namespace mitk
     PeakImageReader();
     ~PeakImageReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   protected:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkPlanarFigureCompositeReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkPlanarFigureCompositeReader.cpp
@@ -47,7 +47,7 @@ mitk::PlanarFigureCompositeReader * mitk::PlanarFigureCompositeReader::Clone() c
 }
 
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::PlanarFigureCompositeReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::PlanarFigureCompositeReader::DoRead()
 {
 
     std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkPlanarFigureCompositeReader.h b/Modules/DiffusionIO/ReaderWriter/mitkPlanarFigureCompositeReader.h
@@ -39,8 +39,8 @@ namespace mitk
     PlanarFigureCompositeReader(const PlanarFigureCompositeReader& other);
     PlanarFigureCompositeReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkShImageReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkShImageReader.cpp
@@ -71,7 +71,7 @@ namespace mitk
     return resultImage;
   }
 
-  std::vector<itk::SmartPointer<BaseData> > ShImageReader::Read()
+  std::vector<itk::SmartPointer<BaseData> > ShImageReader::DoRead()
   {
     mitk::LocaleSwitch localeSwitch("C");
     std::vector<itk::SmartPointer<mitk::BaseData> > result;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkShImageReader.h b/Modules/DiffusionIO/ReaderWriter/mitkShImageReader.h
@@ -43,8 +43,8 @@ namespace mitk
     ShImageReader();
     ~ShImageReader() override;
 
-    using AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   protected:
 

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkTractographyForestReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkTractographyForestReader.cpp
@@ -42,7 +42,7 @@ mitk::TractographyForestReader * mitk::TractographyForestReader::Clone() const
 }
 
 
-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::TractographyForestReader::Read()
+std::vector<itk::SmartPointer<mitk::BaseData> > mitk::TractographyForestReader::DoRead()
 {
   std::vector<itk::SmartPointer<mitk::BaseData> > result;
   std::shared_ptr< vigra::RandomForest<int> > forest;

diff --git a/Modules/DiffusionIO/ReaderWriter/mitkTractographyForestReader.h b/Modules/DiffusionIO/ReaderWriter/mitkTractographyForestReader.h
@@ -37,8 +37,8 @@ namespace mitk
     TractographyForestReader(const TractographyForestReader& other);
     TractographyForestReader * Clone() const override;
 
-    using mitk::AbstractFileReader::Read;
-    std::vector<itk::SmartPointer<BaseData> > Read() override;
+    using mitk::AbstractFileReader::DoRead;
+    std::vector<itk::SmartPointer<BaseData> > DoRead() override;
 
   private:
 

diff --git a/...onimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/...onimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox
@@ -1,7 +1,7 @@
 /**
 \page org_mitk_views_fiberprocessing Fiber Processing
 
-This view provides tools to extract subbundles from a given fiber bundle, to remove unwanted fibers (e.g. via length, curvature, directional and fiber weight constraints) and to modify the properties of a fiber bundles such as coloring or fiber sampling.
+This view provides tools to extract subbundles from a given fiber bundle, to remove unwanted fibers (e.g. via length, curvature, directional and fiber weight constraints) and to modify the properties of a fiber bundles such as coloring, fiber weights or fiber sampling.
 
 <b>Fiber Extraction:</b>
 Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. The extraction can also be performed using 3D ROIs represented as binary mask images. In this extraction method, the logical operations are not implemented at the moment.

diff --git a/...rg.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp b/...rg.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
@@ -189,17 +189,17 @@ void QmitkFiberProcessingView::Modify()
   }
   case 3:
   {
-    DoImageColorCoding();
+    MirrorFibers();
     break;
   }
   case 4:
   {
-    MirrorFibers();
+    WeightFibers();
     break;
   }
   case 5:
   {
-    WeightFibers();
+    DoWeightColorCoding();
     break;
   }
   case 6:
@@ -209,12 +209,12 @@ void QmitkFiberProcessingView::Modify()
   }
   case 7:
   {
-    DoWeightColorCoding();
+    DoLengthColorCoding();
     break;
   }
   case 8:
   {
-    DoLengthColorCoding();
+    DoImageColorCoding();
     break;
   }
   }
@@ -1083,28 +1083,28 @@ void QmitkFiberProcessingView::UpdateGui()
     m_Controls->m_CompressFibersFrame->setVisible(true);
     break;
   case 3:
-    m_Controls->m_ValueAsWeightBox->setVisible(true);
-    m_Controls->m_ColorFibersFrame->setVisible(true);
-    m_Controls->m_ColorMapBox->setVisible(true);
-    break;
-  case 4:
     m_Controls->m_MirrorFibersFrame->setVisible(true);
     if (m_SelectedSurfaces.size()>0)
       m_Controls->m_ModifyButton->setEnabled(true);
     break;
-  case 5:
+  case 4:
     m_Controls->m_BundleWeightFrame->setVisible(true);
     break;
+  case 5:
+    m_Controls->m_ColorFibersFrame->setVisible(true);
+    break;
   case 6:
     m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
     break;
   case 7:
+    m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
     break;
   case 8:
     m_Controls->m_ValueAsWeightBox->setVisible(true);
     m_Controls->m_ColorFibersFrame->setVisible(true);
+    m_Controls->m_ColorMapBox->setVisible(true);
     break;
   }