ENH: Update to support ITK >= 5.4 and MetaIO versioning (#163)

Updated to ITKv5.4 include:
* ITK_NULLPTR -> nullptr
* ITK_OVERRIDE -> override

MetaIO updates include
* use of itksys instead of std for ifstream/ofstream
* use of metaio version 1 features with spatial objects

examples/Applications/ComputeTubeProbability/ComputeTubeProbability.cxx

@@ -92,7 +92,7 @@ int DoIt( int argc, char * argv[] )
     itk::Point<double, VDimension> pnt;
     itk::Index< VDimension > indx;
     tube->Update();
-   
+
     for( unsigned int i=0; i<tube->GetNumberOfPoints(); i++ )
       {
       // Get point
@@ -102,8 +102,13 @@ int DoIt( int argc, char * argv[] )
       pnt = tubePoint.GetPositionInWorldSpace();
 
       // Get closest voxel
-      meanImage->TransformPhysicalPointToIndex( pnt, indx );
-
+      bool success = meanImage->TransformPhysicalPointToIndex( pnt, indx );
+      if( !success )
+        {
+        ::tube::WarningMessage("Point is outside of image bounds.");
+        continue;
+        }
+
       // Write value of ATLAS EMD file at voxel
       writeStream << meanImage->GetPixel( indx ) << std::endl;
       }

examples/Applications/ConvertTubesToImage/Testing/ConvertTubesToImageTest.py

@@ -5,7 +5,7 @@
 # Append ITK libs
 sys.path.append(os.path.join(os.environ['ITK_BUILD_DIR'],
                              'Wrapping/Generators/Python'))
-sys.path.append(os.path.join(os.environ['ITK_BUILD_DIR'], 'lib')
+sys.path.append(os.path.join(os.environ['ITK_BUILD_DIR'], 'lib'))
 
 # Append TubeTK libs :
 sys.path.append(os.environ['TUBETK_BUILD_DIR'], 'TubeTK-build/lib/TubeTK')

include/tubeShrinkImageWithBlending.hxx

@@ -87,7 +87,7 @@ ShrinkImageWithBlending< TInputImage, TOutputImage >
   os << indent << "UseLog:"
      << m_Filter->GetUseLog() << std::endl;
 
-  if( m_Filter->GetInputMipPointImage() != ITK_NULLPTR )
+  if( m_Filter->GetInputMipPointImage() != nullptr )
     {
     os << indent << "Input MIP Point Image: "
        << m_Filter->GetInputMipPointImage() << std::endl;
@@ -97,7 +97,7 @@ ShrinkImageWithBlending< TInputImage, TOutputImage >
     os << indent << "Input MIP Point Image: NULL" << std::endl;
     }
 
-  if( m_Filter->GetOutputMipPointImage() != ITK_NULLPTR )
+  if( m_Filter->GetOutputMipPointImage() != nullptr )
     {
     os << indent << "Output MIP Point Image: "
        << m_Filter->GetOutputMipPointImage() << std::endl;

src/Filtering.cmake

@@ -22,6 +22,7 @@
 
 set( TubeTK_Filtering_H_Files
   Filtering/itkGeneralizedDistanceTransformImageFilter.h
+  Filtering/itkImageRegionSplitter.h
   Filtering/itktubeAnisotropicCoherenceEnhancingDiffusionImageFilter.h
   Filtering/itktubeAnisotropicDiffusionTensorFunction.h
   Filtering/itktubeAnisotropicDiffusionTensorImageFilter.h
@@ -65,6 +66,7 @@ set( TubeTK_Filtering_H_Files
 
 set( TubeTK_Filtering_HXX_Files
   Filtering/itkGeneralizedDistanceTransformImageFilter.txx
+  Filtering/itkImageRegionSplitter.hxx
   Filtering/itktubeAnisotropicCoherenceEnhancingDiffusionImageFilter.hxx
   Filtering/itktubeAnisotropicDiffusionTensorFunction.hxx
   Filtering/itktubeAnisotropicDiffusionTensorImageFilter.hxx

src/Filtering/itkImageRegionSplitter.h

@@ -119,7 +119,7 @@ class ImageRegionSplitter:public ImageRegionSplitterBase
 
   virtual unsigned int GetNumberOfSplitsInternal( unsigned int,
     const IndexValueType regionIndex[], const SizeValueType regionSize[],
-    unsigned int requestedNumber ) const ITK_OVERRIDE
+    unsigned int requestedNumber ) const override
     {
     // this function adapts the legecy method, defined in this class
     // be used by the ImageRegionSplitterBase.
@@ -137,7 +137,7 @@ class ImageRegionSplitter:public ImageRegionSplitterBase
                                 unsigned int i,
                                 unsigned int numberOfPieces,
                                 IndexValueType regionIndex[],
-                                SizeValueType regionSize[] ) const ITK_OVERRIDE
+                                SizeValueType regionSize[] ) const override
     {
     // this function adapts the legecy method, defined in this class
     // be used by the ImageRegionSplitterBase.

src/Filtering/itktubeShrinkWithBlendingImageFilter.hxx

@@ -38,8 +38,8 @@ template< class TInputImage, class TOutputImage >
 ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
 ::ShrinkWithBlendingImageFilter( void )
 {
-  m_InputMipPointImage = ITK_NULLPTR;
-  m_OutputMipPointImage = ITK_NULLPTR;
+  m_InputMipPointImage = nullptr;
+  m_OutputMipPointImage = nullptr;
 
   m_Overlap.Fill( 0 );
 
@@ -357,7 +357,7 @@ ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
     progress.CompletedPixel();
     }
 
-  if( inputMipPointItPtr != ITK_NULLPTR )
+  if( inputMipPointItPtr != nullptr )
     {
     delete inputMipPointItPtr;
     }

src/IO/itktubePDFSegmenterParzenIO.hxx

@@ -198,8 +198,6 @@ Read( const char * _headerName )
     std::cout << "MetaClassPDF: M_SetupReadFields" << std::endl;
     }
 
-  MetaClassPDF classPDFReader;
-
   std::vector< MET_FieldRecordType * > metaFields;
 
   MET_FieldRecordType * mF;
@@ -485,6 +483,9 @@ Read( const char * _headerName )
         0.005 * spacing[j] )
         {
         std::cout << "ERROR: Spacing mismatch" << std::endl;
+        std::cout << "   Spacing[" << j << "] = " << spacing[j] << std::endl;
+        std::cout << "   PDFSpacing[" << j << "] = "
+          << m_PDFSegmenter->GetBinSize()[j] << std::endl;
         for( unsigned int f=0; f<metaFields.size(); ++f )
           {
           delete metaFields[f];