2D similarity transform parameter map doesn't keep "CenterOfRotationPoint" parameter

Hi all, thanks for putting together this package, I’m really enjoying the ease of installation.

It seems the similarity transform as wrapped in ITKElastix doesn’t return the CenterOfRotationPoint transform parameter (although it is written to file) when doing 2D to 2D registration.

I encountered this issue using SimpleElastix as well so it may be in elastix codebase itself.

import numpy as np
import itk

zero_image = np.zeros([1024,1024])

similarity_parameter_map = parameter_object.GetDefaultParameterMap("rigid")

# set method to similarity & 2D
similarity_parameter_map["Transform"] = ["SimilarityTransform"]
similarity_parameter_map["MovingImageDimension"] = ["2"]
similarity_parameter_map["FixedImageDimension"] = ["2"]

parameter_object = itk.ParameterObject.New()
parameter_object.AddParameterMap(similarity_parameter_map)

sim_result_image, sim_params = itk.elastix_registration_method(
    zero_image.astype(np.float32),
    zero_image.astype(np.float32),
    parameter_object=parameter_object,
    log_to_console=True,
    output_directory="./transforms_similarity",
)

transform_cent_rot = np.array(
    sim_params.GetParameter(0, "CenterOfRotationPoint")
).astype(np.float32)[::-1]

assert len(transform_cent_rot) == 2

print(sim_params)

ParameterObject (0000028751D7CE00)
  RTTI typeinfo:   class elastix::ParameterObject
  Reference Count: 1
  Modified Time: 2007229
  Debug: Off
  Object Name: 
  Observers: 
    none
ParameterMap 0: 
  (CenterOfRotationPoint)
  (CompressResultImage "false")
  (DefaultPixelValue 0)
  (Direction 1 0 0 1)
  (FinalBSplineInterpolationOrder 3)
  (FixedImageDimension 2)
  (FixedInternalImagePixelType "float")
  (HowToCombineTransforms "Compose")
  (Index 0 0)
  (InitialTransformParametersFileName "NoInitialTransform")
  (MovingImageDimension 2)
  (MovingInternalImagePixelType "float")
  (NumberOfParameters 4)
  (Origin 0 0)
  (ResampleInterpolator "FinalBSplineInterpolator")
  (Resampler "DefaultResampler")
  (ResultImageFormat "nii")
  (ResultImagePixelType "float")
  (Size 1024 1024)
  (Spacing 1 1)
  (Transform "SimilarityTransform")
  (TransformParameters 1 0 0 0)
  (UseDirectionCosines "true")

file on disk

(Transform "SimilarityTransform")
(NumberOfParameters 4)
(TransformParameters 1.000000 0.000000 0.000000 0.000000)
(InitialTransformParametersFileName "NoInitialTransform")
(UseBinaryFormatForTransformationParameters "false")
(HowToCombineTransforms "Compose")

// Image specific
(FixedImageDimension 2)
(MovingImageDimension 2)
(FixedInternalImagePixelType "float")
(MovingInternalImagePixelType "float")
(Size 1024 1024)
(Index 0 0)
(Spacing 1.0000000000 1.0000000000)
(Origin 0.0000000000 0.0000000000)
(Direction 1.0000000000 0.0000000000 0.0000000000 1.0000000000)
(UseDirectionCosines "true")

// SimilarityTransform specific
(CenterOfRotationPoint 511.5000000000 511.5000000000)

// ResampleInterpolator specific
(ResampleInterpolator "FinalBSplineInterpolator")
(FinalBSplineInterpolationOrder 3)

// Resampler specific
(Resampler "DefaultResampler")
(DefaultPixelValue 0.000000)
(ResultImageFormat "nii")
(ResultImagePixelType "float")
(CompressResultImage "false")

[N-Dekker]

@NHPatterson Thanks for reporting this issue, Heath. Stefan (@stefanklein), Viktor (@ViktorvdValk) and I just discussed the issue. It appears that elastix::SimilarityTransformElastix should override CreateTransformParametersMap, in order to fix this issue. I will try to fix it soon!

[N-Dekker]

@NHPatterson Hi Heath! I’m closing the issue now, as I think we got it fixed 😃 By pull request https://github.com/SuperElastix/elastix/pull/379 “Add missing parameters to transform parameter maps”, which is just merged onto the https://github.com/SuperElastix/elastix develop branch. If you have the time, please check it out! And of course, if you think the issue is not entirely fixed, please feel free to reopen the issue, or submit another one. Thanks again!