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Output warp fields and jacobian correction files in TOPUP. #1976

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Merged
merged 4 commits into from
Apr 27, 2017
Merged

Output warp fields and jacobian correction files in TOPUP. #1976

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9707b36
Output warp fields and jacobian correction files in TOPUP.
chrisgorgo Apr 27, 2017
3e69cbe
fixing auto tests
chrisgorgo Apr 27, 2017
83a6782
code readability improvements
chrisgorgo Apr 27, 2017
4ecd866
docstrings fix
chrisgorgo Apr 27, 2017
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24 changes: 22 additions & 2 deletions nipype/interfaces/fsl/epi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@

from ..base import (traits, TraitedSpec, InputMultiPath, File,
isdefined)
from .base import FSLCommand, FSLCommandInputSpec
from .base import FSLCommand, FSLCommandInputSpec, Info


class PrepareFieldmapInputSpec(FSLCommandInputSpec):
Expand Down Expand Up @@ -140,6 +140,13 @@ class TOPUPInputSpec(FSLCommandInputSpec):
out_field = File(argstr='--fout=%s', hash_files=False,
name_source=['in_file'], name_template='%s_field',
desc='name of image file with field (Hz)')
out_warp_prefix = traits.Str("warpfield", argstr='--dfout=%s', hash_files=False,
desc='prefix for the warpfield images (in mm)',
usedefault=True)
out_jac_prefix = traits.Str("jac", argstr='--jacout=%s',
hash_files=False,
desc='prefix for the warpfield images',
usedefault=True)
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Does making these required outputs have the potential to produce large amounts of data?

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I don't thinks so. Those files will also be automatically deleted if no used.

out_corrected = File(argstr='--iout=%s', hash_files=False,
name_source=['in_file'], name_template='%s_corrected',
desc='name of 4D image file with unwarped images')
Expand Down Expand Up @@ -212,6 +219,8 @@ class TOPUPOutputSpec(TraitedSpec):
out_movpar = File(exists=True, desc='movpar.txt output file')
out_enc_file = File(desc='encoding directions file output for applytopup')
out_field = File(desc='name of image file with field (Hz)')
out_warps = traits.List(File(exists=True), desc='warpfield images')
out_jacs = traits.List(File(exists=True), desc='Jacobian images')
out_corrected = File(desc='name of 4D image file with unwarped images')
out_logfile = File(desc='name of log-file')

Expand All @@ -237,7 +246,8 @@ class TOPUP(FSLCommand):
>>> topup.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
'topup --config=b02b0.cnf --datain=topup_encoding.txt \
--imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
--fout=b0_b0rev_field.nii.gz --logout=b0_b0rev_topup.log'
--fout=b0_b0rev_field.nii.gz --jacout=jac --logout=b0_b0rev_topup.log \
--dfout=warpfield'
>>> res = topup.run() # doctest: +SKIP

"""
Expand Down Expand Up @@ -270,6 +280,16 @@ def _list_outputs(self):
outputs['out_movpar'] = self._gen_fname(base, suffix='_movpar',
ext='.txt', cwd=base_path)

n_vols = nb.load(self.inputs.in_file).shape[-1]
ext = Info.output_type_to_ext(self.inputs.output_type)
fmt = os.path.abspath('{prefix}_{i:02d}{ext}').format
outputs['out_warps'] = [
fmt(prefix=self.inputs.out_warp_prefix, i=i, ext=ext)
for i in range(1, n_vols + 1)]
outputs['out_jacs'] = [
fmt(prefix=self.inputs.out_jac_prefix, i=i, ext=ext)
for i in range(1, n_vols + 1)]

if isdefined(self.inputs.encoding_direction):
outputs['out_enc_file'] = self._get_encfilename()
return outputs
Expand Down
10 changes: 10 additions & 0 deletions nipype/interfaces/fsl/tests/test_auto_TOPUP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,14 @@ def test_TOPUP_inputs():
name_source=['in_file'],
name_template='%s_field',
),
out_warp_prefix=dict(argstr='--dfout=%s',
hash_files=False,
usedefault=True,
),
out_jac_prefix=dict(argstr='--jacout=%s',
hash_files=False,
usedefault=True,
),
out_logfile=dict(argstr='--logout=%s',
hash_files=False,
keep_extension=True,
Expand Down Expand Up @@ -98,6 +106,8 @@ def test_TOPUP_outputs():
out_fieldcoef=dict(),
out_logfile=dict(),
out_movpar=dict(),
out_warps=dict(),
out_jacs=dict(),
)
outputs = TOPUP.output_spec()

Expand Down