[ENH/WIP] Add SPM Fieldmap Tool wrapper #1905
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| # Local imports | ||
| from ...utils.filemanip import (fname_presuffix, filename_to_list, | ||
| list_to_filename, split_filename) | ||
| from ..base import (OutputMultiPath, TraitedSpec, isdefined, | ||
| traits, InputMultiPath, File, Str) | ||
| from .base import (SPMCommand, scans_for_fname, func_is_3d, | ||
| scans_for_fnames, SPMCommandInputSpec, ImageFileSPM) | ||
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| __docformat__ = 'restructuredtext' | ||
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| class FieldMapInputSpec(SPMCommandInputSpec): | ||
| jobtype = traits.Enum('calculatevdm', 'applyvdm', usedefault=True, | ||
| desc='one of: calculatevdm, applyvdm') | ||
| phase = File(mandatory=True, exists=True, copyfile=False, | ||
| field='subj.data.presubphasemag.phase', | ||
| desc='presubstracted phase file') | ||
| magnitude = File(mandatory=True, exists=True, copyfile=False, | ||
| field='subj.data.presubphasemag.magnitude', | ||
| desc='presubstracted magnitude file') | ||
| et = traits.Tuple(traits.Float, traits.Float, mandatory=True, | ||
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There was a problem hiding this comment. I see this is matches the final part of the field name, so it may be that SPM users will find this intuitive, but you may want to consider |
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| field='subj.defaults.defaultsval.et', | ||
| desc='short and long echo times') | ||
| maskbrain = traits.Bool(True, usedefault=True, | ||
| field='subj.defaults.defaultsval.maskbrain', | ||
| desc='masking or no masking of the brain') | ||
| blipdir = traits.Enum(1, -1, mandatory=True, | ||
| field='subj.defaults.defaultsval.blipdir', | ||
| desc='polarity of the phase-encode blips') | ||
| tert = traits.Float(mandatory=True, | ||
| field='subj.defaults.defaultsval.tert', | ||
| desc='total EPI readout time') | ||
| epifm = traits.Bool(False, usedefault=True, | ||
| field='subj.defaults.defaultsval.epifm', | ||
| desc='epi-based field map'); | ||
| ajm = traits.Bool(False, usedefault=True, | ||
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There was a problem hiding this comment. Here, again, I would consider |
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| field='subj.defaults.defaultsval.ajm', | ||
| desc='jacobian modulation'); | ||
| # Unwarping defaults parameters | ||
| method = traits.Enum('Mark3D', 'Mark2D', 'Huttonish', usedefault=True, | ||
| desc='One of: Mark3D, Mark2D, Huttonish', | ||
| field='subj.defaults.defaultsval.uflags.method'); | ||
| fwhm = traits.Range(low=0, value=10, usedefault=True, | ||
| field='subj.defaults.defaultsval.uflags.fwhm', | ||
| desc='gaussian smoothing kernel width'); | ||
| pad = traits.Range(low=0, value=0, usedefault=True, | ||
| field='subj.defaults.defaultsval.uflags.pad', | ||
| desc='padding kernel width'); | ||
| ws = traits.Bool(True, usedefault=True, | ||
| field='subj.defaults.defaultsval.uflags.ws', | ||
| desc='weighted smoothing'); | ||
| # Brain mask defaults parameters | ||
| template = File(copyfile=False, exists=True, | ||
| field='subj.defaults.defaultsval.mflags.template', | ||
| desc='template image for brain masking'); | ||
| fwhm = traits.Range(low=0, value=5, usedefault=True, | ||
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There was a problem hiding this comment. You've got |
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| field='subj.defaults.defaultsval.mflags.fwhm', | ||
| desc='gaussian smoothing kernel width'); | ||
| nerode = traits.Range(low=0, value=2, usedefault=True, | ||
| field='subj.defaults.defaultsval.mflags.nerode', | ||
| desc='number of erosions'); | ||
| ndilate = traits.Range(low=0, value=4, usedefault=True, | ||
| field='subj.defaults.defaultsval.mflags.ndilate', | ||
| desc='number of erosions'); | ||
| thresh = traits.Float(0.5, usedefault=True, | ||
| field='subj.defaults.defaultsval.mflags.thresh', | ||
| desc='threshold used to create brain mask from segmented data'); | ||
| reg = traits.Float(0.02, usedefault=True, | ||
| field='subj.defaults.defaultsval.mflags.reg', | ||
| desc='regularization value used in the segmentation'); | ||
| # EPI unwarping for quality check | ||
| epi = File(copyfile=False, exists=True, mandatory=True, | ||
| field='subj.session.epi', | ||
| desc='EPI to unwarp'); | ||
| matchvdm = traits.Bool(True, usedefault=True, | ||
| field='subj.matchvdm', | ||
| desc='match VDM to EPI'); | ||
| sessname = Str('_run-', usedefault=True, | ||
| field='subj.sessname', | ||
| desc='VDM filename extension'); | ||
| writeunwarped = traits.Bool(False, usedefault=True, | ||
| field='subj.writeunwarped', | ||
| desc='write unwarped EPI'); | ||
| anat = File(copyfile=False, exists=True, | ||
| field='subj.anat', | ||
| desc='anatomical image for comparison'); | ||
| matchanat = traits.Bool(True, usedefault=True, | ||
| field='subj.matchanat', | ||
| desc='match anatomical image to EPI'); | ||
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| class FieldMapOutputSpec(TraitedSpec): | ||
| vdm = File(exists=True, desc='voxel difference map') | ||
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| class FieldMap(SPMCommand): | ||
| """Use the fieldmap toolbox from spm to calculate the voxel displacement map (VDM). | ||
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| http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#page=173 | ||
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| To do | ||
| ----- | ||
| Deal with real/imag magnitude images and with the two phase files case. | ||
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| Examples | ||
| -------- | ||
| >>> from nipype.interfaces.spm import FieldMap | ||
| >>> fm = FieldMap() | ||
| >>> fm.inputs.phase = 'phasediff.nii' | ||
| >>> fm.inputs.magnitude = 'magnitude1.nii' | ||
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There was a problem hiding this comment.
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| >>> fm.inputs.et = [5.19, 7.65] | ||
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There was a problem hiding this comment. This should be a tuple, not a list. |
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| >>> fm.inputs.blipdir = 1 | ||
| >>> fm.inputs.tert = 15.6 | ||
| >>> fm.inputs.epi = 'bold.nii' | ||
| >>> fm.run() # doctest: +SKIP | ||
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| """ | ||
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| input_spec = FieldMapInputSpec | ||
| output_spec = FieldMapOutputSpec | ||
| _jobtype = 'tools' | ||
| _jobname = 'fieldmap' | ||
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| def _format_arg(self, opt, spec, val): | ||
| """Convert input to appropriate format for spm | ||
| """ | ||
| if opt in ['phase', 'magnitude', 'anat', 'epi']: | ||
| return scans_for_fname(filename_to_list(val)) | ||
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| return super(FieldMap, self)._format_arg(opt, spec, val) | ||
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| def _parse_inputs(self): | ||
| """validate spm fieldmap options if set to None ignore | ||
| """ | ||
| einputs = super(FieldMap, self)._parse_inputs() | ||
| jobtype = self.inputs.jobtype | ||
| return [{'%s' % (jobtype): einputs[0]}] | ||
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There was a problem hiding this comment. What's the advantage of this over the following? return [{self.inputs.jobtype: einputs[0]}]There was a problem hiding this comment. I like better your style, but I originally used the syntax of another wrapper (typically |
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| def _list_outputs(self): | ||
| outputs = self._outputs().get() | ||
| jobtype = self.inputs.jobtype | ||
| if jobtype == "calculatevdm": | ||
| outputs['vdm'] = [] | ||
| for phase in filename_to_list(self.inputs.phase): | ||
| outputs['vdm'].append(fname_presuffix(phase, prefix='vdm5_sc')) | ||
| outputs['vdm'] = list_to_filename(outputs['vdm']) | ||
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There was a problem hiding this comment. I'm a bit confused by this. if self.inputs.jobtype == 'calculatevdm':
outputs['vdm'] = fname_presuffix(self.inputs.phase, prefix='vdm5_sc')Or am I missing something? There was a problem hiding this comment. You're not, I just adapted another more complicated wrapper's piece of code without thinking about making it clearer. Thanks for noticing! |
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| return outputs | ||
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| class SliceTimingInputSpec(SPMCommandInputSpec): | ||
| in_files = InputMultiPath( | ||
| traits.Either( | ||
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We often use the suffix
_fileto indicate inputs that should be files. So consider making thisphase_file. Similarly below withmagnitude_file.Not a big deal, if you think that would be disorienting to SPM users.