STYLE: ITKv4 no longer needs transform registratoin

Removed ITKv3 work-arounds for specialized transform
registrations.

BRAINSCommonLib/GenericTransformImage.cxx

@@ -541,83 +541,4 @@ void WriteTransformToDisk(GenericTransformType const *const MyTransform, const s
     }
 }
 
-// HACK:  This can now be removed!
-//  * COMMENT: The above comment says this is a hack and can be removed, but
-//  as of 30 Sep 2011, there is still code calling it.
-// Adding a single new transform require registering all the transform types.
-void AddExtraTransformRegister(void)
-{
-#if (ITK_VERSION_MAJOR < 4)
-  // This is needed in order to read and write ScaleVersor3D TransformTypes.
-  // Hopefully in ITK-3-19 this will become part of the non-review transform
-  // types.
-  itk::TransformFactory<itk::ScaleVersor3DTransform<float> >::RegisterDefaultTransforms();
-  itk::TransformFactory<itk::ScaleVersor3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleVersor3DTransform<float> >::RegisterTransform();
-
-  itk::TransformFactory<itk::AffineTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::AffineTransform<double, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::BSplineDeformableTransform<double, 2, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::BSplineDeformableTransform<double, 3, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredAffineTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredAffineTransform<double, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredEuler3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredRigid2DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredSimilarity2DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::Similarity2DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::Euler2DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::Euler3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::FixedCenterOfRotationAffineTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::IdentityTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::IdentityTransform<double, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::QuaternionRigidTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::Rigid2DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::Rigid3DPerspectiveTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScalableAffineTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleLogarithmicTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleSkewVersor3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<double, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::TranslationTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::VersorRigid3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::VersorTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::AffineTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::AffineTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::BSplineDeformableTransform<float, 2, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::BSplineDeformableTransform<float, 3, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredAffineTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredAffineTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredEuler3DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredRigid2DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::CenteredSimilarity2DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::Similarity2DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::Euler2DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::Euler3DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::FixedCenterOfRotationAffineTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::IdentityTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::IdentityTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::QuaternionRigidTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::Rigid2DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::Rigid3DPerspectiveTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::ScalableAffineTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleLogarithmicTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleSkewVersor3DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::TranslationTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::VersorRigid3DTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::VersorTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::VersorTransform<float> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateR2LogRSplineKernelTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateR2LogRSplineKernelTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateSplineKernelTransform<float, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateSplineKernelTransform<float, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateR2LogRSplineKernelTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateR2LogRSplineKernelTransform<double, 3> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateSplineKernelTransform<double, 2> >::RegisterTransform();
-  itk::TransformFactory<itk::ThinPlateSplineKernelTransform<double, 3> >::RegisterTransform();
-#endif
-}
 } // end namespace itk

BRAINSCommonLib/GenericTransformImage.h

@@ -155,8 +155,6 @@ extern int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer ge
   */
 extern int WriteStrippedRigidTransformToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
                                              const std::string & strippedOutputTransform);
-
-extern void AddExtraTransformRegister(void);
 }
 
 /**

BRAINSCut/BRAINSCut.cxx

@@ -19,12 +19,6 @@ int main(int argc, char * *argv)
 {
   PARSE_ARGS;
 
-  /* Solution from Kent
-   * ITK4 resigration initilization
-   */
-  // Call register default transforms
-  // itk::TransformFactoryBase::RegisterDefaultTransforms();
-
   if( !netConfiguration.empty() && modelConfigurationFilename.empty() )
     {
     modelConfigurationFilename = netConfiguration;

BRAINSDemonWarp/BRAINSDemonWarp.cxx

@@ -18,10 +18,6 @@ DebugImageViewerClient DebugImageDisplaySender;
 
 int main(int argc, char *argv[])
 {
-  // Apparently when you register one transform, you need to register all your
-  // transforms.
-  itk::AddExtraTransformRegister();
-
   struct BRAINSDemonWarpAppParameters command;
 
     {

BRAINSDemonWarp/ValidationInputParser.hxx

@@ -113,14 +113,6 @@ ValidationInputParser<TImage>
     // within
     //      the regression test suite.
 
-    // VBRAINSDemonWarpPrimary.cxx
-    // Review reading of transform files from BRAINSFit code for
-    // reading Versor/Euler/Affine file from
-    // Apparently when you register one transform, you need to register all your
-    // transforms.
-    //
-    AddExtraTransformRegister();
-
     //  #######Now use TransformToDisplacementFieldSource
 #if (ITK_VERSION_MAJOR < 4)
     typedef itk::TransformToDeformationFieldSource<TDisplacementField, double> DisplacementFieldGeneratorType;

BRAINSFit/BRAINSFit.cxx

@@ -107,16 +107,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
 
-  itk::AddExtraTransformRegister();
-  // Apparently when you register one transform, you need to register all your
-  // transforms.
-  itk::TransformFactory<VersorRigid3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleSkewVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<AffineTransformType>::RegisterTransform();
-  itk::TransformFactory<BSplineTransformType>::RegisterTransform();
-  itk::TransformFactory<CompositeTransformType>::RegisterTransform(); // added by Ali
-
 #ifdef USE_DebugImageViewer
   if( UseDebugImageViewer )
     {

BRAINSFit/BRAINSFitEZ.cxx

@@ -109,16 +109,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
 
-  itk::AddExtraTransformRegister();
-  // Apparently when you register one transform, you need to register all your
-  // transforms.
-  itk::TransformFactory<VersorRigid3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleSkewVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<AffineTransformType>::RegisterTransform();
-  itk::TransformFactory<BSplineTransformType>::RegisterTransform();
-  itk::TransformFactory<CompositeTransformType>::RegisterTransform(); // added by Ali
-
 #ifdef USE_DebugImageViewer
   if( UseDebugImageViewer )
     {

BRAINSResample/BRAINSResample.cxx

@@ -49,10 +49,6 @@ void PrintImageMinAndMax(TImage *inputImage)
 int main(int argc, char *argv[])
 {
   PARSE_ARGS;
-#if ITK_VERSION_MAJOR > 3
-  // Call register default transforms
-  itk::TransformFactoryBase::RegisterDefaultTransforms();
-#endif
   itk::Object::SetGlobalWarningDisplay(false); // itk warnings aren't thread safe and in
   // this program cause intermittent crashes.
 

GTRACT/Cmdline/future_work/gtractCoRegAnatomyRigid.cxx

@@ -31,7 +31,6 @@
 int main(int argc, char * *argv)
 {
   PARSE_ARGS;
-  itk::AddExtraTransformRegister();
 
   bool debug = true;
   if( debug )

GTRACT/Cmdline/gtractCoRegAnatomy.cxx

@@ -35,9 +35,6 @@ int main(int argc, char *argv[])
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
 
-  itk::TransformFactory<itk::ScaleVersor3DTransform<double> >::RegisterTransform();
-  itk::TransformFactory<itk::ScaleVersor3DTransform<float> >::RegisterTransform();
-
   std::vector<int> GridSize;
   GridSize.push_back( gridSize[0] );
   GridSize.push_back( gridSize[1] );

GTRACT/Cmdline/gtractCoRegAnatomyBspline.cxx

@@ -33,7 +33,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   std::vector<int> GridSize;
   GridSize.push_back( gridSize[0] );

GTRACT/Cmdline/gtractCopyImageOrientation.cxx

@@ -30,7 +30,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   bool debug = true;
   if( debug )

GTRACT/Cmdline/gtractImageConformity.cxx

@@ -30,7 +30,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   bool debug = true;
   if( debug )

GTRACT/Cmdline/gtractInvertBSplineTransform.cxx

@@ -36,7 +36,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   int xSize = landmarkDensity[0];
   int ySize = landmarkDensity[1];
@@ -60,9 +59,6 @@ int main(int argc, char *argv[])
   typedef itk::ThinPlateR2LogRSplineKernelTransform<
       BSplineCoordinateRepType, 3>     ThinPlateSplineTransformType;
 
-  itk::AddExtraTransformRegister();
-
-  typedef signed short PixelType;
 
   typedef signed short PixelType;
 

GTRACT/Cmdline/gtractInvertRigidTransform.cxx

@@ -35,7 +35,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   bool debug = true;
   if( debug )

GTRACT/Cmdline/gtractResampleAnisotropy.cxx

@@ -34,7 +34,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   typedef double                                                          BSplineCoordinateRepType;
   typedef itk::VersorRigid3DTransform<double>                             RigidTransformType;

GTRACT/Cmdline/gtractResampleB0.cxx

@@ -36,7 +36,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   typedef double                                                          BSplineCoordinateRepType;
   typedef itk::VersorRigid3DTransform<double>                             RigidTransformType;

GTRACT/Cmdline/gtractResampleCodeImage.cxx

@@ -36,7 +36,7 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
+
   typedef double                              BSplineCoordinateRepType;
   typedef itk::VersorRigid3DTransform<double> RigidTransformType;
   typedef itk::BSplineDeformableTransform<BSplineCoordinateRepType, 3, 3>

GTRACT/Cmdline/gtractResampleDWIInPlace.cxx

@@ -85,7 +85,6 @@ int main(int argc, char *argv[])
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
   itk::NumberToString<double>                                        doubleConvert;
-  itk::AddExtraTransformRegister();
 
   bool debug = true;
   if( debug )

GTRACT/Cmdline/gtractResampleFibers.cxx

@@ -113,7 +113,6 @@ int main( int argc, char *argv[] )
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-// itk::AddExtraTransformRegister();
 
   const unsigned int Dimension = 3;
   typedef unsigned short                      PixelType;

GTRACT/Cmdline/gtractTensor.cxx

@@ -54,7 +54,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   typedef signed short                   PixelType;
   typedef double                         TensorPixelType;

GTRACT/Cmdline/gtractTransformToDisplacementField.cxx

@@ -52,7 +52,6 @@ int main(int argc, char *argv[])
 {
   PARSE_ARGS;
   const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
-  itk::AddExtraTransformRegister();
 
   std::cout << "Input Transform: " <<  inputTransform << std::endl;
   std::cout << "Reference Image: " <<  inputReferenceVolume << std::endl;
@@ -65,8 +64,6 @@ int main(int argc, char *argv[])
   typedef itk::Image<signed short, 3>              ReferenceImageType;
   typedef itk::ImageFileReader<ReferenceImageType> ReferenceReaderType;
 
-  // TODO:  May need to add the TPS transform type to
-  // "AddExtraTransformRegister"
   typedef itk::ThinPlateR2LogRSplineKernelTransform<double, 3> ThinPlateSplineTransformType;
 
 #if (ITK_VERSION_MAJOR < 4)
@@ -76,8 +73,6 @@ int main(int argc, char *argv[])
 #endif
   typedef DisplacementFieldGeneratorType::TransformType TransformType;
 
-  itk::AddExtraTransformRegister();
-
   // Read the Reference file
   ReferenceReaderType::Pointer referenceReader = ReferenceReaderType::New();
   referenceReader->SetFileName(inputReferenceVolume);

ICCDEF/ApplyWarp.cxx

@@ -387,17 +387,6 @@ int main( int argc, char *argv[] )
   std::cout << "This program has been replaced by BRAINSResample.  PLEASE TRY TO AVOID USING THIS!" << std::endl;
   std::cout << "This program has been replaced by BRAINSResample.  PLEASE TRY TO AVOID USING THIS!" << std::endl;
   std::cout << "This program has been replaced by BRAINSResample.  PLEASE TRY TO AVOID USING THIS!" << std::endl;
-  // HACK:  BRAINS2 Masks are currently broken
-  // The direction cosines are and the direction labels are not consistently being set.
-  // itk::Brains2MaskImageIOFactory::RegisterOneFactory();
-
-  // Apparently when you register one transform, you need to register all your
-  // transforms.
-  itk::TransformFactory<VersorRigid3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<ScaleSkewVersor3DTransformType>::RegisterTransform();
-  itk::TransformFactory<AffineTransformType>::RegisterTransform();
-  itk::TransformFactory<BSplineTransformType>::RegisterTransform();
 
   return ApplyWarp(argc, argv);
 }

ICCDEF/IccdefPreprocessor.hxx

@@ -132,14 +132,6 @@ IccdefPreprocessor<TInputImage, TOutputImage>
 
   if( m_InitialTransformFilename != "" )
     {
-    // Review reading of transform files from BRAINSFit code for
-    // reading Versor/Euler/Affine file from
-
-    itk::TransformFactory<VersorRigid3DTransformType>::RegisterTransform();
-    itk::TransformFactory<ScaleSkewVersor3DTransformType>::RegisterTransform();
-    itk::TransformFactory<AffineTransformType>::RegisterTransform();
-    itk::TransformFactory<BSplineTransformType>::RegisterTransform();
-
     //
     // read in the initial ITKTransform
     //