COMP: Remove global declarations from GenericTransformImage.h

BRAINSia · Sep 12, 2014 · f00678a · f00678a
1 parent 4a80262
commit f00678a
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Showing 35 changed files with 140 additions and 105 deletions.
diff --git a/BRAINSABC/brainseg/AtlasRegistrationMethod.h b/BRAINSABC/brainseg/AtlasRegistrationMethod.h
@@ -98,6 +98,7 @@ class AtlasRegistrationMethod : public itk::Object
   typedef typename ByteImageType::RegionType ByteImageRegionType;
   typedef typename ByteImageType::SizeType   ByteImageSizeType;
 
+  typedef itk::Transform<double, 3, 3>         GenericTransformType;
   typedef std::vector<ProbabilityImagePointer> ProbabilityImageList;
   typedef std::vector<OutputImagePointer>      OutputImageList;
 

diff --git a/BRAINSABC/brainseg/AtlasRegistrationMethod.hxx b/BRAINSABC/brainseg/AtlasRegistrationMethod.hxx
@@ -42,8 +42,9 @@
 
 #include "itkBRAINSROIAutoImageFilter.h"
 
-GenericTransformType::Pointer MakeRigidIdentity(void)
+itk::Transform<double, 3, 3>::Pointer MakeRigidIdentity(void)
 {
+  typedef itk::Transform<double, 3, 3> GenericTransformType;
   // Also append identity matrix for each image
   VersorRigid3DTransformType::Pointer rigidIdentity = VersorRigid3DTransformType::New();
 
@@ -454,7 +455,9 @@ AtlasRegistrationMethod<TOutputPixel, TProbabilityPixel>
     muLogMacro(<< "Registering first atlas images to first subject image." << std::endl);
     // Initialize the outputTransform with the initializer before starting the loop.
     this->m_AtlasToSubjectTransform = this->m_AtlasToSubjectInitialTransform;
-    CompositeTransformType::Pointer atlasToSubjectCompositeTransform = dynamic_cast<CompositeTransformType *>( m_AtlasToSubjectTransform.GetPointer() );
+    typedef itk::CompositeTransform<double, 3>                   CompositeTransformType;
+    CompositeTransformType::Pointer atlasToSubjectCompositeTransform =
+      dynamic_cast<CompositeTransformType *>( m_AtlasToSubjectTransform.GetPointer() );
     if( atlasToSubjectCompositeTransform.IsNull() )
       {
       atlasToSubjectCompositeTransform = CompositeTransformType::New();

diff --git a/BRAINSABC/brainseg/BRAINSABC.cxx b/BRAINSABC/brainseg/BRAINSABC.cxx
@@ -638,6 +638,7 @@ int main(int argc, char * *argv)
   muLogMacro(<< "=== Start ===\n");
   muLogMacro(<< "Registering images using affine transform...\n");
 
+  typedef itk::Transform<double, 3, 3> GenericTransformType;
   GenericTransformType::Pointer atlasToSubjectPreSegmentationTransform = NULL;
 
   AtlasRegType::MapOfFloatImageVectors atlasOriginalImageList;

diff --git a/BRAINSABC/brainseg/EMSegmentationFilter.h b/BRAINSABC/brainseg/EMSegmentationFilter.h
@@ -106,7 +106,10 @@ class EMSegmentationFilter : public itk::ProcessObject
   typedef vnl_matrix<FloatingPrecision>         MatrixType;
   typedef vnl_matrix_inverse<FloatingPrecision> MatrixInverseType;
 
-  typedef BSplineTransformType::Pointer BSplineTransformPointer;
+  typedef itk::BSplineTransform<CoordinateRepType, 3, 3 > BSplineTransformType;
+  typedef BSplineTransformType::Pointer                   BSplineTransformPointer;
+
+  typedef itk::Transform<double, 3, 3>  GenericTransformType;
 
   // Set/Get the maximum polynomial degree of the bias field estimate
   itkSetMacro(MaxBiasDegree, unsigned int);

diff --git a/BRAINSABC/brainseg/EMSegmentationFilter.hxx b/BRAINSABC/brainseg/EMSegmentationFilter.hxx
@@ -1589,6 +1589,7 @@ EMSegmentationFilter<TInputImage, TProbabilityImage>
           std::cerr << "ERROR:  NOT PROPERLY IMPLEMENTED YET HACK:" << std::endl;
           }
 
+        typedef itk::CompositeTransform<double, 3>                   CompositeTransformType;
         CompositeTransformType::Pointer templateGenericCompositeTransform =
                                   dynamic_cast<CompositeTransformType *>( m_TemplateGenericTransform.GetPointer() );
         if( templateGenericCompositeTransform.IsNull() )

diff --git a/BRAINSCommonLib/BRAINSFitHelperTemplate.h b/BRAINSCommonLib/BRAINSFitHelperTemplate.h
@@ -104,6 +104,8 @@ class BRAINSFitHelperTemplate : public Object
   itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
   itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
 
+
+  typedef typename itk::CompositeTransform<double, 3>               CompositeTransformType;
   typedef typename CompositeTransformType::Pointer                  CompositeTransformPointer;
   typedef IdentityTransform<double, MovingImageDimension>           IdentityTransformType;
 

diff --git a/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx b/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx
@@ -789,7 +789,7 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           itkGenericExceptionMacro("Linear initial composite transform should have only one component \
                                    as all linaear transforms are collapsed together.");
           }
-        const GenericTransformType::ConstPointer currInitTransformFormGenericComposite =
+        const itk::Transform<double, 3, 3>::ConstPointer currInitTransformFormGenericComposite =
                                                   m_CurrentGenericTransform->GetFrontTransform();
         try
           {
@@ -878,7 +878,7 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           itkGenericExceptionMacro("Linear initial composite transform should have only one component \
                                    as all linaear transforms are collapsed together.");
           }
-        const GenericTransformType::ConstPointer currInitTransformFormGenericComposite =
+        const itk::Transform<double, 3, 3>::ConstPointer currInitTransformFormGenericComposite =
                                                   m_CurrentGenericTransform->GetFrontTransform();
         try
           {
@@ -980,7 +980,7 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           itkGenericExceptionMacro("Linear initial composite transform should have only one component \
                                    as all linaear transforms are collapsed together.");
           }
-        const GenericTransformType::ConstPointer currInitTransformFormGenericComposite =
+        const itk::Transform<double, 3, 3>::ConstPointer currInitTransformFormGenericComposite =
                                                   m_CurrentGenericTransform->GetFrontTransform();
         try
           {
@@ -1088,7 +1088,7 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           itkGenericExceptionMacro("Linear initial composite transform should have only one component \
                                    as all linaear transforms are collapsed together.");
           }
-        const GenericTransformType::ConstPointer currInitTransformFormGenericComposite =
+        const itk::Transform<double, 3, 3>::ConstPointer currInitTransformFormGenericComposite =
                                                   m_CurrentGenericTransform->GetFrontTransform();
         try
           {
@@ -1372,8 +1372,8 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           std::cout << "\nMoving image is warped by initial transform, "
                     << "before it is passed to the BSpline registration.\n" << std::endl;
           typedef float                                                                     VectorComponentType;
-          typedef itk::Vector<VectorComponentType, GenericTransformImageNS::SpaceDimension> VectorPixelType;
-          typedef itk::Image<VectorPixelType,  GenericTransformImageNS::SpaceDimension>     DisplacementFieldType;
+          typedef itk::Vector<VectorComponentType, 3> VectorPixelType;
+          typedef itk::Image<VectorPixelType,  3>     DisplacementFieldType;
           typename MovingImageType::Pointer warpedMoving =
                                               GenericTransformImage<
                                                      MovingImageType,
@@ -1513,7 +1513,7 @@ BRAINSFitHelperTemplate<FixedImageType, MovingImageType>::Update(void)
           itkGenericExceptionMacro("Linear initial composite transform should have only one component \
                                    as all linaear transforms are collapsed together.");
           }
-        const GenericTransformType::ConstPointer currInitTransformFormGenericComposite =
+        const itk::Transform<double, 3, 3>::ConstPointer currInitTransformFormGenericComposite =
                                                   m_CurrentGenericTransform->GetFrontTransform();
         const std::string transformFileType = currInitTransformFormGenericComposite->GetNameOfClass();
 

diff --git a/BRAINSCommonLib/BRAINSFitSyN.h b/BRAINSCommonLib/BRAINSFitSyN.h
@@ -30,10 +30,10 @@ typedef  SyNRegistrationHelperType::ImageType              ImageType;
 }
 
 template <class FixedImageType, class MovingimageType>
-typename BRAINSCompositeTransformType::Pointer
+typename itk::CompositeTransform<double,3>::Pointer
 simpleSynReg( typename FixedImageType::Pointer & infixedImage,
               typename MovingimageType::Pointer & inmovingImage,
-              typename BRAINSCompositeTransformType::Pointer compositeInitialTransform )
+              typename itk::CompositeTransform<double,3>::Pointer compositeInitialTransform )
 {
   typename SyNRegistrationHelperType::Pointer regHelper = SyNRegistrationHelperType::New();
     {
@@ -148,7 +148,8 @@ simpleSynReg( typename FixedImageType::Pointer & infixedImage,
     std::cerr << "Finshed SyN stage" << std::endl;
     }
   // Get the output transform
-  typename BRAINSCompositeTransformType::Pointer outputCompositeTransform = regHelper->GetModifiableCompositeTransform();
+  typename itk::CompositeTransform<double,3>::Pointer outputCompositeTransform =
+    regHelper->GetModifiableCompositeTransform();
   // return composite result Transform;
   return outputCompositeTransform;
 }

diff --git a/BRAINSCommonLib/GenericTransformImage.cxx b/BRAINSCommonLib/GenericTransformImage.cxx
@@ -51,11 +51,14 @@
 
 namespace itk
 {
-VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
-  const GenericTransformType::ConstPointer genericTransformToWrite)
+itk::VersorRigid3DTransform<double>::Pointer
+ComputeRigidTransformFromGeneric(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite)
 {
-  typedef VersorRigid3DTransformType          VersorRigidTransformType;
-  VersorRigidTransformType::Pointer versorRigid = VersorRigidTransformType::New();
+  typedef itk::VersorRigid3DTransform<double>     VersorRigid3DTransformType;
+  typedef itk::ScaleVersor3DTransform<double>     ScaleVersor3DTransformType;
+  typedef itk::ScaleSkewVersor3DTransform<double> ScaleSkewVersor3DTransformType;
+
+  VersorRigid3DTransformType::Pointer versorRigid = VersorRigid3DTransformType::New();
   versorRigid->SetIdentity();
   // //////////////////////////////////////////////////////////////////////////
   // ConvertTransforms
@@ -96,6 +99,7 @@ VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
         }
       else if( transformFileType == "AffineTransform" )
         {
+        typedef itk::AffineTransform<double, 3> AffineTransformType;
         const AffineTransformType::ConstPointer tempInitializerITKTransform =
           dynamic_cast<AffineTransformType const *>( genericTransformToWrite.GetPointer() );
         if( tempInitializerITKTransform.IsNull() )
@@ -129,10 +133,12 @@ VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
   return versorRigid;
 }
 
-int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+int WriteBothTransformsToDisk(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite,
                               const std::string & outputTransform,
                               const std::string & strippedOutputTransform)
 {
+  typedef itk::VersorRigid3DTransform<double>  VersorRigid3DTransformType;
+  typedef itk::CompositeTransform<double, 3> CompositeTransformType;
   // //////////////////////////////////////////////////////////////////////////
   // Write out tranfoms for BRAINSFit.
   /*
@@ -183,6 +189,10 @@ int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTr
         }
       else if( transformFileType == "BSplineTransform" )
         {
+        typedef itk::BSplineTransform<double,
+                                      3,
+                                      3> BSplineTransformType;
+
         const BSplineTransformType::ConstPointer tempInitializerITKTransform =
                                                   dynamic_cast<BSplineTransformType  const *>( genericComponent.GetPointer() );
         if( tempInitializerITKTransform.IsNull() )
@@ -217,8 +227,8 @@ int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTr
         // Should just write out the rigid transform here.
       if( strippedOutputTransform.size() > 0  )
         {
-        typedef VersorRigid3DTransformType VersorRigidTransformType;
-        VersorRigidTransformType::Pointer versorRigid = itk::ComputeRigidTransformFromGeneric( genericComponent.GetPointer() );
+        VersorRigid3DTransformType::Pointer versorRigid =
+          itk::ComputeRigidTransformFromGeneric( genericComponent.GetPointer() );
         if( versorRigid.IsNotNull() )
           {
           itk::WriteTransformToDisk<double>(versorRigid.GetPointer(), strippedOutputTransform);
@@ -233,19 +243,31 @@ int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTr
   return 0;
 }
 
-int WriteStrippedRigidTransformToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+int WriteStrippedRigidTransformToDisk(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite,
                                       const std::string & strippedOutputTransform)
 {
   return WriteBothTransformsToDisk(genericTransformToWrite, std::string(""), strippedOutputTransform);
 }
 
-GenericTransformType::Pointer ReadTransformFromDisk(const std::string & initialTransform)
+itk::Transform<double, 3, 3>::Pointer ReadTransformFromDisk(const std::string & initialTransform)
 {
-  GenericTransformType::Pointer genericTransform = NULL;
-  // read in the initial ITKTransform
-  TransformReaderType::Pointer      transformListReader =  TransformReaderType::New();
-  TransformListType                 currentTransformList;
-  TransformListType::const_iterator currentTransformListIterator;
+  itk::Transform<double, 3, 3>::Pointer genericTransform = NULL;
+
+  typedef itk::ThinPlateR2LogRSplineKernelTransform<double, 3> ThinPlateSpline3DTransformType;
+  typedef itk::ScaleVersor3DTransform<double>                  ScaleVersor3DTransformType;
+  typedef itk::ScaleSkewVersor3DTransform<double>              ScaleSkewVersor3DTransformType;
+  typedef itk::VersorRigid3DTransform<double>                  VersorRigid3DTransformType;
+  typedef itk::AffineTransform<double, 3>                      AffineTransformType;
+  typedef itk::BSplineTransform<double, 3, 3>                  BSplineTransformType;
+  typedef itk::CompositeTransform<double, 3>                   BRAINSCompositeTransformType;
+
+  TransformFileReader::Pointer transformListReader = TransformFileReader::New();
+
+  typedef TransformFileReader::TransformListType TransformListType;
+
+  TransformListType currentTransformList;
+
+  TransformFileReader::TransformListType::const_iterator currentTransformListIterator;
 
   try
     {

diff --git a/BRAINSCommonLib/GenericTransformImage.h b/BRAINSCommonLib/GenericTransformImage.h
@@ -48,34 +48,6 @@
 #include "itkTransformFactory.h"
 #include "itkTransformFileReader.h"
 #include "itkTransformFileWriter.h"
-//
-// TODO:  The next two should be hidden in the cxx files again.
-typedef itk::TransformFileReader                    TransformReaderType;
-typedef itk::TransformFileReader::TransformListType TransformListType;
-
-// TODO:  These should be hidden in the BRAINSFit namespace.
-typedef itk::Transform<double, 3, 3> GenericTransformType;
-
-namespace GenericTransformImageNS
-{
-static const unsigned int SpaceDimension = 3;
-static const unsigned int SplineOrder = 3;
-}
-
-typedef double CoordinateRepType;
-
-typedef itk::BSplineTransform<CoordinateRepType,
-                                        GenericTransformImageNS::SpaceDimension,
-                                        GenericTransformImageNS::SplineOrder>       BSplineTransformType;
-
-typedef itk::CompositeTransform<double, 3>                   CompositeTransformType;
-typedef itk::AffineTransform<double, 3>                      AffineTransformType;
-typedef itk::VersorRigid3DTransform<double>                  VersorRigid3DTransformType;
-typedef itk::ScaleVersor3DTransform<double>                  ScaleVersor3DTransformType;
-typedef itk::ScaleSkewVersor3DTransform<double>              ScaleSkewVersor3DTransformType;
-typedef itk::ThinPlateR2LogRSplineKernelTransform<double, 3> ThinPlateSpline3DTransformType;
-
-typedef itk::CompositeTransform<double, 3> BRAINSCompositeTransformType;
 
 namespace itk
 {
@@ -133,7 +105,8 @@ extern void WriteTransformToDisk( itk::Transform<TScalarType, 3, 3> const *const
   * }
   * \endcode
   */
-extern GenericTransformType::Pointer ReadTransformFromDisk(const std::string & initialTransform);
+
+extern itk::Transform<double, 3, 3>::Pointer ReadTransformFromDisk(const std::string & initialTransform);
 
 /**
   * \author Hans J. Johnson
@@ -152,23 +125,23 @@ extern GenericTransformType::Pointer ReadTransformFromDisk(const std::string & i
   * WriteTransformToDisk<TScalarType>(myAffine.GetPointer(), "myAffineFile.mat");
   * \endcode
   */
-extern VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
-  const GenericTransformType::ConstPointer genericTransformToWrite);
+extern itk::VersorRigid3DTransform<double>::Pointer
+ComputeRigidTransformFromGeneric(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite);
 
 /**
   * \author Hans J. Johnson
   * \brief Special purpose convenience function -- should not have a public
   *interface.
   */
-extern int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+extern int WriteBothTransformsToDisk(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite,
                                      const std::string & outputTransform, const std::string & strippedOutputTransform);
 
 /**
   * \author Hans J. Johnson
   * \brief Special purpose convenience function -- should not have a public
   *interface.
   */
-extern int WriteStrippedRigidTransformToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+extern int WriteStrippedRigidTransformToDisk(const itk::Transform<double, 3, 3>::ConstPointer genericTransformToWrite,
                                              const std::string & strippedOutputTransform);
 }
 
@@ -184,7 +157,7 @@ TransformResample(
   const typename InputImageType::PixelType defaultValue,
   typename itk::InterpolateImageFunction<InputImageType,
   typename itk::NumericTraits<typename InputImageType::PixelType>::RealType>::Pointer interp,
-  typename GenericTransformType::ConstPointer transform);
+  typename itk::Transform<double, 3, 3>::ConstPointer transform);
 
 /**
   * \author Hans J. Johnson
@@ -211,7 +184,7 @@ typename OutputImageType::Pointer GenericTransformImage(
   InputImageType const *const OperandImage,
   const itk::ImageBase<InputImageType::ImageDimension> *ReferenceImage,
   // typename DisplacementImageType::Pointer DisplacementField,
-  typename GenericTransformType::Pointer genericTransform,
+  typename itk::Transform<double, 3, 3>::Pointer genericTransform,
   typename InputImageType::PixelType suggestedDefaultValue, // NOTE:  This is
                                                             // ignored in the
                                                             // case of binary