Sync Transform WriteToFile with CreateTransformParametersMap #385
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| @@ -159,9 +159,6 @@ DeformationFieldTransform<TElastix>::WriteToFile(const ParametersType & param) c | |||
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| typedef itk::ChangeInformationImageFilter<DeformationFieldType> ChangeInfoFilterType; | |||
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| /** Add some DeformationFieldTransform specific lines. */ | |||
| xout["transpar"] << std::endl << "// DeformationFieldTransform specific" << std::endl; | |||
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Please check that DeformationFieldTransform::WriteToFile cannot be entirely removed!
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@mstaring So is it OK to still have some parameters written to file that are not in the parameter map?
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Or would it be an option to add the parameter "DeformationFieldFileName" (which is now only written to file) to the map as well?
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I guess ideally you would push the whole deformation field to that map. Or at least the filename as you say, so that one can read it in again via disk. Lets discuss over sprint.
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By the way, the "making" of the DeformationFieldFileName throws an exception (std::out_of_range) inside DeformationFieldTransform::WriteToFile when the current TransformParameterFileName is not specified. Would it be OK to suppress (or avoid) the warning and just leave DeformationFieldFileName as an empty string instead? https://github.com/SuperElastix/elastix/blob/5.0.1/Components/Transforms/DeformationFieldTransform/elxDeformationFieldTransform.hxx#L180-L182
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We could assume empty string for lastpart, when TransformParameterFileName is empty.
| normalizeString = "true"; | ||
| } | ||
| xout["transpar"] << "(NormalizeCombinationWeights \"" << normalizeString << "\" )" << std::endl; | ||
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Please check that WeightedCombinationTransform::WriteToFile cannot be entirely removed!
Note: the WeightedCombinationTransform::WriteToFile override may be removed when "SubTransforms" is added to the parameter map!
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Update: "SubTransforms" is now added to the WeightedCombinationTransform parameter map (pull request #391 commit ae9c0fd) And this pull request is adjusted to simply remove the WeightedCombinationTransform::WriteToFile override. 😃 With this force-push
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| @@ -1022,54 +1022,6 @@ BSplineTransformWithDiffusion<TElastix>::WriteToFile(const ParametersType & para | |||
| xl::xout["error"] << excp << std::endl; | |||
| } | |||
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| /** Get the GridSize, GridIndex, GridSpacing and | |||
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Please check that BSplineTransformWithDiffusion::WriteToFile cannot be entirely removed!
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Note that there are still two TODO's from related pull request #379 "Add missing parameters to transform parameter maps" |
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lgtm |
Anticipating pull request #385 "Sync Transform WriteToFile with CreateTransformParametersMap".
Anticipating pull request #385 "Sync Transform WriteToFile with CreateTransformParametersMap".
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Added "MultiBSplineTransformWithNormalLabels" to the transform parameter map of `MultiBSplineTransformWithNormal`, addressing a "TODO" comment. Anticipating pull request #385 "Sync Transform WriteToFile with CreateTransformParametersMap". Also improved the `Test_CreateTransformParametersMap_for_default_transform()` unit test function for `MultiBSplineTransformWithNormal`. Note that this change is not yet completely unit tested, because `MultiBSplineTransformWithNormal::BeforeAll()` throws an exception, saying "ERROR: Missing -labels argument!".
Added "MultiBSplineTransformWithNormalLabels" to the transform parameter map of `MultiBSplineTransformWithNormal`, addressing a "TODO" comment. Anticipating pull request #385 "Sync Transform WriteToFile with CreateTransformParametersMap". Also improved the `Test_CreateTransformParametersMap_for_default_transform()` unit test function for `MultiBSplineTransformWithNormal`. Note that this change is not yet completely unit tested, because `MultiBSplineTransformWithNormal::BeforeAll()` throws an exception, saying "ERROR: Missing -labels argument!".
Synchronized the string representation of double floating point values of transform parameter maps (produced by elastix `CreateTransformParametersMap`) with ITK's .tfm file format (as written by `itk::TransformFileWriter`). Increased the floating point precision from 6 to 16. ITK's `itk::NumberToString` uses a lossless floating point conversion from the Google double-conversion library, https://github.com/google/double-conversion Part of issue #383 "Reconsider string representation of floating points for parameter files and parameter maps"
Added a utility function, which is intended to estimate whether a transform parameter value should be "double quoted", when elastix `Transform::WriteToFile` writes such a value to a TransformParameters .txt file. (A numeric parameter value should not be double quoted.)
Adjusted `TransformBase::WriteToFile` by using the parameter map created by `CreateTransformParametersMap`. Removed 14 out of 16 `WriteToFile` overrides. Ensured that the transform parameter txt file is kept in sync with the corresponding the parameter map. Thereby also adjusted the floating point format for values written to file, as discussed at issue #383, "Reconsider string representation of floating points for parameter files and parameter maps", #383 Addresses issue #217 'the "Origin" precision in TransformParameters is not high enough', reported by GouZi2019, January 5, 2020: #217
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This elastix parameter was mainly intended to allow the user to specify the precision of floating point parameters in the transform parameter file. However, with pull request #385 commit af382ee "ENH: Sync Transform WriteToFile with CreateTransformParametersMap" (related to issue #383 "Reconsider string representation of floating points for parameter files and parameter maps"), this is no longer relevant. Floating point values are now written to transform parameter files in a lossless way.
This elastix parameter was mainly intended to allow the user to specify the precision of floating point parameters in the transform parameter file. However, with pull request #385 commit af382ee "ENH: Sync Transform WriteToFile with CreateTransformParametersMap" (related to issue #383 "Reconsider string representation of floating points for parameter files and parameter maps"), this is no longer relevant. Floating point values are now written to transform parameter files in a lossless way.
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