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FIX: Select Eddy command at runtime #1871

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Merged
merged 7 commits into from
Mar 22, 2017
Merged

FIX: Select Eddy command at runtime #1871

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d088cc2
FIX: Make Eddy._use_cuda update instance variable
effigies Mar 9, 2017
c9a3b5e
Dynamically update _cmd property
effigies Mar 9, 2017
772f540
Find eddy command in FSL_BIN
effigies Mar 20, 2017
5ab828d
PEP8 cleanup
effigies Mar 20, 2017
e42d906
Use FSLDIR, warn instead of throwing exception
effigies Mar 20, 2017
84bce14
Revert Eddy cmdline in doctest
effigies Mar 20, 2017
33f5db1
Replace eddy_openmp at runtime if not in FSLDIR
effigies Mar 22, 2017
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85 changes: 53 additions & 32 deletions nipype/interfaces/fsl/epi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
... '../../testing/data'))
>>> os.chdir(datadir)
"""
from __future__ import print_function, division, unicode_literals, absolute_import
from __future__ import print_function, division, unicode_literals, \
absolute_import
from builtins import str

import os
Expand Down Expand Up @@ -106,7 +107,7 @@ def _run_interface(self, runtime):
out_file = self.inputs.out_fieldmap
im = nb.load(out_file, mmap=NUMPY_MMAP)
dumb_img = nb.Nifti1Image(np.zeros(im.shape), im.affine,
im.header)
im.header)
out_nii = nb.funcs.concat_images((im, dumb_img))
nb.save(out_nii, out_file)

Expand Down Expand Up @@ -450,26 +451,25 @@ class EddyInputSpec(FSLCommandInputSpec):


class EddyOutputSpec(TraitedSpec):
out_corrected = File(exists=True,
desc=('4D image file containing all the corrected '
'volumes'))
out_parameter = File(exists=True,
desc=('text file with parameters definining the '
'field and movement for each scan'))
out_rotated_bvecs = File(exists=True,
desc=('File containing rotated b-values for all volumes'))
out_movement_rms = File(exists=True,
desc=('Summary of the "total movement" in each volume'))
out_restricted_movement_rms = File(exists=True,
desc=('Summary of the "total movement" in each volume '
'disregarding translation in the PE direction'))
out_shell_alignment_parameters = File(exists=True,
desc=('File containing rigid body movement parameters '
'between the different shells as estimated by a '
'post-hoc mutual information based registration'))
out_outlier_report = File(exists=True,
desc=('Text-file with a plain language report '
'on what outlier slices eddy has found'))
out_corrected = File(
exists=True, desc='4D image file containing all the corrected volumes')
out_parameter = File(
exists=True, desc=('text file with parameters definining the field and'
'movement for each scan'))
out_rotated_bvecs = File(
exists=True, desc='File containing rotated b-values for all volumes')
out_movement_rms = File(
exists=True, desc='Summary of the "total movement" in each volume')
out_restricted_movement_rms = File(
exists=True, desc=('Summary of the "total movement" in each volume '
'disregarding translation in the PE direction'))
out_shell_alignment_parameters = File(
exists=True, desc=('File containing rigid body movement parameters '
'between the different shells as estimated by a '
'post-hoc mutual information based registration'))
out_outlier_report = File(
exists=True, desc=('Text-file with a plain language report on what '
'outlier slices eddy has found'))


class Eddy(FSLCommand):
Expand All @@ -491,10 +491,16 @@ class Eddy(FSLCommand):
>>> eddy.inputs.in_acqp = 'epi_acqp.txt'
>>> eddy.inputs.in_bvec = 'bvecs.scheme'
>>> eddy.inputs.in_bval = 'bvals.scheme'
>>> eddy.inputs.use_cuda = True
>>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
'eddy_openmp --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
'eddy_cuda --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
--imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
--out=.../eddy_corrected'
>>> eddy.inputs.use_cuda = False
>>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
'eddy_openmp --acqp=epi_acqp.txt --bvals=bvals.scheme \
--bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
--mask=epi_mask.nii --out=.../eddy_corrected'
>>> res = eddy.run() # doctest: +SKIP

"""
Expand All @@ -507,12 +513,13 @@ class Eddy(FSLCommand):
def __init__(self, **inputs):
super(Eddy, self).__init__(**inputs)
self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
if isdefined(self.inputs.use_cuda):
self._use_cuda()
if not isdefined(self.inputs.num_threads):
self.inputs.num_threads = self._num_threads
else:
self._num_threads_update()
self.inputs.on_trait_change(self._use_cuda, 'use_cuda')
if isdefined(self.inputs.use_cuda):
self._use_cuda()

def _num_threads_update(self):
self._num_threads = self.inputs.num_threads
Expand All @@ -524,10 +531,21 @@ def _num_threads_update(self):
self.inputs.num_threads)

def _use_cuda(self):
if self.inputs.use_cuda:
_cmd = 'eddy_cuda'
else:
_cmd = 'eddy_openmp'
self._cmd = 'eddy_cuda' if self.inputs.use_cuda else 'eddy_openmp'

def _run_interface(self, runtime):
# If 'eddy_openmp' is missing, use 'eddy'
FSLDIR = os.getenv('FSLDIR', '')
cmd = self._cmd
if all((FSLDIR != '',
cmd == 'eddy_openmp',
not os.path.exists(os.path.join(FSLDIR, cmd)))):
self._cmd = 'eddy'
runtime = super(Eddy, self)._run_interface(runtime)

# Restore command to avoid side-effects
self._cmd = cmd
return runtime

def _format_arg(self, name, spec, value):
if name == 'in_topup_fieldcoef':
Expand All @@ -551,7 +569,8 @@ def _list_outputs(self):
out_restricted_movement_rms = os.path.abspath(
'%s.eddy_restricted_movement_rms' % self.inputs.out_base)
out_shell_alignment_parameters = os.path.abspath(
'%s.eddy_post_eddy_shell_alignment_parameters' % self.inputs.out_base)
'%s.eddy_post_eddy_shell_alignment_parameters'
% self.inputs.out_base)
out_outlier_report = os.path.abspath(
'%s.eddy_outlier_report' % self.inputs.out_base)

Expand All @@ -560,9 +579,11 @@ def _list_outputs(self):
if os.path.exists(out_movement_rms):
outputs['out_movement_rms'] = out_movement_rms
if os.path.exists(out_restricted_movement_rms):
outputs['out_restricted_movement_rms'] = out_restricted_movement_rms
outputs['out_restricted_movement_rms'] = \
out_restricted_movement_rms
if os.path.exists(out_shell_alignment_parameters):
outputs['out_shell_alignment_parameters'] = out_shell_alignment_parameters
outputs['out_shell_alignment_parameters'] = \
out_shell_alignment_parameters
if os.path.exists(out_outlier_report):
outputs['out_outlier_report'] = out_outlier_report

Expand Down