ITKElastix: External initial transform causes a failure in ConvertToItkTransform

elastix_object = itk.ElastixRegistrationMethod.New(fixed_image, moving_image)
elastix_object.SetExternalInitialTransform(initial_transform)
...
comb_transform = elastix_object.GetCombinationTransform()
itk_transform = elastix_object.ConvertToItkTransform(comb_transform)  # error

produces:

RuntimeError: D:\a\im\_skbuild\win-amd64-3.9\cmake-build\_deps\elx-src\Core\Main\itkElastixRegistrationMethod.hxx:1019:
ITK ERROR: Failed to convert transform object SimilarityTransformElastix (000001A9A7B0E0B0)
  RTTI typeinfo:   class elastix::SimilarityTransformElastix<class elastix::ElastixTemplate<class itk::Image<float,3>,class itk::Image<float,3> > >
  Reference Count: 12
  Modified Time: 50477
  Debug: Off
  Object Name: 
  Observers: 
    none

The code does not crash if elastix_object.SetInitialTransform(initial_transform) or elastix_object.SetInitialTransformParameterFileName(initial_transform_txt_path) is invoked instead.

About this issue

Original URL
State: open
Created 10 months ago
Comments: 16 (8 by maintainers)

Most upvoted comments

Thansk @dzenanz Looks like it can be further reduced to:

import itk
fixed_image = itk.imread('data/CT_2D_head_fixed.mha', itk.F)
moving_image = itk.imread('data/CT_2D_head_moving.mha', itk.F)
parameter_object = itk.ParameterObject.New()
parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')
parameter_object.AddParameterMap(parameter_map_rigid)
elastix_object = itk.ElastixRegistrationMethod.New(fixed_image,moving_image)
elastix_object.SetParameterObject(parameter_object)
initial_transform = itk.Similarity2DTransform[itk.D].New()
elastix_object.SetExternalInitialTransform(initial_transform)
elastix_object.Update()
comb_transform = elastix_object.GetCombinationTransform()
itk_transform = elastix_object.ConvertToItkTransform(comb_transform)

Right? Which produces:

RuntimeError: D:\a\im_skbuild\win-amd64-3.8\cmake-build_deps\elx-src\Core\Main\itkElastixRegistrationMethod.hxx:1020: ITK ERROR: Failed to convert transform object EulerTransformElastix (00000202831CCF10) RTTI typeinfo: class elastix::EulerTransformElastix<class elastix::ElastixTemplate<class itk::Image<float,2>,class itk::Image<float,2> > >

N-Dekker on Sep 15, 2023

Below is the code which triggers the error. To be used from a jupyter notebook or a script in examples directory. I based it on https://github.com/InsightSoftwareConsortium/ITKElastix/blob/4fbdc9c9ca32aa740d8842c0892b817cf8ef0f41/examples/ITK_Example04_InitialTransformAndMultiThreading.ipynb.

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[1], line 27
     25 result_image = elastix_object.GetOutput()
     26 comb_transform = elastix_object.GetCombinationTransform()
---> 27 itk_transform = elastix_object.ConvertToItkTransform(comb_transform)
     28 elastix_transform_parameters = elastix_object.GetTransformParameterObject()

RuntimeError: D:\a\im\_skbuild\win-amd64-3.9\cmake-build\_deps\elx-src\Core\Main\itkElastixRegistrationMethod.hxx:1019:
ITK ERROR: Failed to convert transform object SimilarityTransformElastix (000001D6E5473250)
  RTTI typeinfo:   class elastix::SimilarityTransformElastix<class elastix::ElastixTemplate<class itk::Image<float,2>,class itk::Image<float,2> > >
  Reference Count: 9
  Modified Time: 36004
  Debug: Off
  Object Name: 
  Observers: 
    none

import itk

# Import Images
fixed_image = itk.imread('data/CT_2D_head_fixed.mha', itk.F)
moving_image = itk.imread('data/CT_2D_head_moving.mha', itk.F)

# Import Default Parameter Map
parameter_object = itk.ParameterObject.New()
parameter_map_rigid = parameter_object.GetDefaultParameterMap('rigid')
parameter_map_rigid['Transform'] = ['SimilarityTransform']
parameter_object.AddParameterMap(parameter_map_rigid)

# Load Elastix Image Filter Object with initial transfrom and number of threads
elastix_object = itk.ElastixRegistrationMethod.New(fixed_image,moving_image)
elastix_object.SetParameterObject(parameter_object)
initial_transform = itk.Similarity2DTransform[itk.D].New()
elastix_object.SetExternalInitialTransform(initial_transform)
# Set additional options
elastix_object.SetLogToConsole(False)

# Update filter object (required)
elastix_object.UpdateLargestPossibleRegion()

# Results of Registration
result_image = elastix_object.GetOutput()
comb_transform = elastix_object.GetCombinationTransform()
itk_transform = elastix_object.ConvertToItkTransform(comb_transform)
elastix_transform_parameters = elastix_object.GetTransformParameterObject()

dzenanz on Sep 15, 2023

perhaps documentation could be improved. What is the difference between SetExternalInitialTransform and SetInitialTransform?

Thanks @dzenanz I made that an issue:

https://github.com/SuperElastix/elastix/issues/961

N-Dekker on Sep 13, 2023