Ants brain extraction interface #1231
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please rebase/merge master - we have fixed the CircleCI tests |
MartinPerez
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Sorry for the delay. I rebased... |
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tests still failing after rebase :S |
| >>> brainextraction.inputs.brain_template = 'study_template.nii.gz' | ||
| >>> brainextraction.inputs.brain_probability_mask ='ProbabilityMaskOfStudyTemplate.nii.gz' | ||
| >>> brainextraction.cmdline | ||
| 'antsBrainExtraction.sh -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -d 3 -s nii.gz -o highres001_ |
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You are missing a quotation mark at the end. This makes one of the tests to fail: https://travis-ci.org/nipy/nipype/jobs/87317019#L4110
| output_spec = antsBrainExtractionOutputSpec | ||
| _cmd = 'antsBrainExtraction.sh' | ||
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| def _format_arg(self, opt, spec, val): |
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There shouldn't be any need to overload format_args for these inputs as they are pretty straight forward. I would recommend removing this for code clarity.
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you are right. got rid of the unnecessary overload!
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still seeing the overloaded _format_arg .
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I think all is fine now. |
| def _format_arg(self, opt, spec, val): | ||
| return super(ANTSCommand, self)._format_arg(opt, spec, val) | ||
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| def _run_interface(self, runtime, correct_return_codes=[0]): |
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this function is also not necessary
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good to go? |
| '(default = 1)')) | ||
| keep_temporary_files = traits.Int(argstr='-k %d', | ||
| desc='Keep brain extraction/segmentation warps, etc (default = 0).') | ||
| use_floatingpoint_precision = traits.Enum(0, 1, argstr='-q %d', |
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@hjmjohnson - do all ants commands now have this option, if so should this be moved to the base class?
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@satra all of ANTs does not have this command. It is being implemented one program at a time. :( Sorry. |
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@hjmjohnson is this true for the |
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This depends on what you consider an "ANTs" program. There is no formal mechanism for tools build as part of the ANTs package to maintain a consistent interface. There is an attempt to keep similar items consistent (via copy-n-paste coding) across tools, but it is not rigorously enforced. I honestly do not know how uniform the --verbose option is across tools, that would require a review of the ANTs code base. |
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Should we merge this as is then? |
Ants brain extraction interface
Here is a wrapper for the ants brain extraction script , #1230. Hope it will be useful to others as well. I provide test and also made a very small modification to antsCorticalThicknessoutputSpec not following the capital O in Output convention.