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Make itk.ParameterObject
and parameter maps serializable
#257
Comments
Could/should |
Possibly. Given that Elastix parameter maps nearly implement the Python For instance, to convert a single parameter map to a pickleable Python >>> dict(po.GetDefaultParameterMap('rigid'))
{'AutomaticParameterEstimation': ('true',), 'AutomaticScalesEstimation': ('true',), 'CheckNumberOfSamples': ('true',), 'DefaultPixelValue': ('0',), 'FinalBSplineInterpolationOrder': ('3',), 'FixedImagePyramid': ('FixedSmoothingImagePyramid',), 'ImageSampler': ('RandomCoordinate',), 'Interpolator': ('LinearInterpolator',), 'MaximumNumberOfIterations': ('256',), 'MaximumNumberOfSamplingAttempts': ('8',), 'Metric': ('AdvancedMattesMutualInformation',), 'MovingImagePyramid': ('MovingSmoothingImagePyramid',), 'NewSamplesEveryIteration': ('true',), 'NumberOfResolutions': ('4',), 'NumberOfSamplesForExactGradient': ('4096',), 'NumberOfSpatialSamples': ('2048',), 'Optimizer': ('AdaptiveStochasticGradientDescent',), 'Registration': ('MultiResolutionRegistration',), 'ResampleInterpolator': ('FinalBSplineInterpolator',), 'Resampler': ('DefaultResampler',), 'ResultImageFormat': ('nii',), 'Transform': ('EulerTransform',), 'WriteIterationInfo': ('false',), 'WriteResultImage': ('true',)} To convert a parameter object to a pickleable >>> [dict(parameter_object.GetParameterMap(map_index)) for map_index in range(parameter_object.GetNumberOfParameterMaps())]
[{'AutomaticParameterEstimation': ('true',), 'AutomaticScalesEstimation': ('true',), 'CheckNumberOfSamples': ('true',), 'DefaultPixelValue': ('0',), 'FinalBSplineInterpolationOrder': ('3',), 'FixedImagePyramid': ('FixedSmoothingImagePyramid',), 'ImageSampler': ('RandomCoordinate',), 'Interpolator': ('LinearInterpolator',), 'MaximumNumberOfIterations': ('256',), 'MaximumNumberOfSamplingAttempts': ('8',), 'Metric': ('AdvancedMattesMutualInformation',), 'MovingImagePyramid': ('MovingSmoothingImagePyramid',), 'NewSamplesEveryIteration': ('true',), 'NumberOfResolutions': ('4',), 'NumberOfSamplesForExactGradient': ('4096',), 'NumberOfSpatialSamples': ('2048',), 'Optimizer': ('AdaptiveStochasticGradientDescent',), 'Registration': ('MultiResolutionRegistration',), 'ResampleInterpolator': ('FinalBSplineInterpolator',), 'Resampler': ('DefaultResampler',), 'ResultImageFormat': ('nii',), 'Transform': ('EulerTransform',), 'WriteIterationInfo': ('false',), 'WriteResultImage': ('true',)}] |
We can create these function in itk-dreg for now, apply before returning and when entering the block registration method, and integrate into itk-elastix as a later step. |
Agreed, this issue is not holding up |
With #278, it is much easier to add pure python modules to the package. |
Background
itk.ParameterObject
acts as an ordered collection of Elastix parameter map dictionaries. We should make these C++ wrapper objects serializable to facilitate interactions withdask.distributed
and other cases where registration may occur in a worker other than where Elastix parameters are originally specified.Steps to Reproduce
Expected behavior
Parameter object is serialized and can be reconstructed with
pickle.loads(bytestring)
Observed behavior
Additional Notes
As a minimum effort it may be sufficient to package
itk-elastix
with Python helper methods to convert parameter maps and objects to and from Python types such asdict
andlist
that already support serialization.For a complete implementation we should wrap
itk.ParameterObject
anditk.elxParameterObjectPython.mapstringvectorstring
with__setstate__
and__getstate__
methods. See Python's pickle documentation.Related to work in https://github.com/InsightSoftwareConsortium/itk-dreg (cc @thewtex )
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