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fix: FSL FNIRT intensity mapping files #1799

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Merged
merged 6 commits into from
Feb 8, 2017
Merged

fix: FSL FNIRT intensity mapping files #1799

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5b02964
FSL FNIRT: handle multiple intensity map inputs and outputs
cgc Feb 4, 2017
b2888e0
FSL FNIRT: add test for fieldcoeff_file input
cgc Feb 4, 2017
fa5cde8
Address PR comment by making sure exists=True is kwarg for File
cgc Feb 6, 2017
69e178c
FSL FNIRT: ensure txt intensity map file exists
cgc Feb 7, 2017
1a4db10
FSL FNIRT: check list_outputs to increase code coverage
cgc Feb 7, 2017
7a8eb07
FSL FNIRT: fix python3 issue with dict values and map
cgc Feb 7, 2017
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42 changes: 35 additions & 7 deletions nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
from ..base import (TraitedSpec, File, InputMultiPath,
OutputMultiPath, Undefined, traits,
isdefined)
from .base import FSLCommand, FSLCommandInputSpec
from .base import FSLCommand, FSLCommandInputSpec, Info


class BETInputSpec(FSLCommandInputSpec):
Expand Down Expand Up @@ -750,10 +750,12 @@ class FNIRTInputSpec(FSLCommandInputSpec):
desc='name of file containing affine transform')
inwarp_file = File(exists=True, argstr='--inwarp=%s',
desc='name of file containing initial non-linear warps')
in_intensitymap_file = File(exists=True, argstr='--intin=%s',
desc=('name of file/files containing initial '
'intensity maping usually generated by '
'previous fnirt run'))
in_intensitymap_file = traits.List(File(exists=True), argstr='--intin=%s',
copyfiles=False, minlen=1, maxlen=2,
desc=('name of file/files containing '
'initial intensity mapping '
'usually generated by previous '
'fnirt run'))
fieldcoeff_file = traits.Either(
traits.Bool, File, argstr='--cout=%s',
desc='name of output file with field coefficients or true')
Expand Down Expand Up @@ -907,8 +909,9 @@ class FNIRTOutputSpec(TraitedSpec):
field_file = File(desc='file with warp field')
jacobian_file = File(desc='file containing Jacobian of the field')
modulatedref_file = File(desc='file containing intensity modulated --ref')
out_intensitymap_file = File(
desc='file containing info pertaining to intensity mapping')
out_intensitymap_file = traits.List(
File, minlen=2, maxlen=2,
desc='files containing info pertaining to intensity mapping')
log_file = File(desc='Name of log-file')


Expand Down Expand Up @@ -975,9 +978,23 @@ def _list_outputs(self):
change_ext=change_ext)
else:
outputs[key] = os.path.abspath(inval)

if key == 'out_intensitymap_file' and isdefined(outputs[key]):
basename = FNIRT.intensitymap_file_basename(outputs[key])
outputs[key] = [
outputs[key],
'%s.txt' % basename,
]
return outputs

def _format_arg(self, name, spec, value):
if name in ('in_intensitymap_file', 'out_intensitymap_file'):
if name == 'out_intensitymap_file':
value = self._list_outputs()[name]
value = [FNIRT.intensitymap_file_basename(v) for v in value]
assert len(set(value)) == 1, (
'Found different basenames for {}: {}'.format(name, value))
return spec.argstr % value[0]
if name in list(self.filemap.keys()):
return spec.argstr % self._list_outputs()[name]
return super(FNIRT, self)._format_arg(name, spec, value)
Expand Down Expand Up @@ -1005,6 +1022,17 @@ def write_config(self, configfile):
fid.write('%s\n' % (item))
fid.close()

@classmethod
def intensitymap_file_basename(cls, f):
"""Removes valid intensitymap extensions from `f`, returning a basename
that can refer to both intensitymap files.
"""
for ext in list(Info.ftypes.values()) + ['.txt']:
if f.endswith(ext):
return f[:-len(ext)]
# TODO consider warning for this case
return f


class ApplyWarpInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, argstr='--in=%s',
Expand Down
70 changes: 44 additions & 26 deletions nipype/interfaces/fsl/tests/test_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -353,6 +353,7 @@ def test_mcflirt(setup_flirt):
def test_fnirt(setup_flirt):

tmpdir, infile, reffile = setup_flirt
os.chdir(tmpdir)
fnirt = fsl.FNIRT()
assert fnirt.cmd == 'fnirt'

Expand Down Expand Up @@ -404,64 +405,81 @@ def test_fnirt(setup_flirt):
fnirt.run()
fnirt.inputs.in_file = infile
fnirt.inputs.ref_file = reffile
intmap_basename = '%s_intmap' % fsl.FNIRT.intensitymap_file_basename(infile)
intmap_image = fsl_name(fnirt, intmap_basename)
intmap_txt = '%s.txt' % intmap_basename
# doing this to create the file to pass tests for file existence
with open(intmap_image, 'w'):
pass
with open(intmap_txt, 'w'):
pass

# test files
opt_map = {
'affine_file': ('--aff='),
'inwarp_file': ('--inwarp='),
'in_intensitymap_file': ('--intin='),
'config_file': ('--config='),
'refmask_file': ('--refmask='),
'inmask_file': ('--inmask='),
'field_file': ('--fout='),
'jacobian_file': ('--jout='),
'modulatedref_file': ('--refout='),
'out_intensitymap_file': ('--intout='),
'log_file': ('--logout=')}

for name, settings in list(opt_map.items()):
opt_map = [
('affine_file', '--aff=%s' % infile, infile),
('inwarp_file', '--inwarp=%s' % infile, infile),
('in_intensitymap_file', '--intin=%s' % intmap_basename, [intmap_image]),
('in_intensitymap_file',
'--intin=%s' % intmap_basename,
[intmap_image, intmap_txt]),
('config_file', '--config=%s' % infile, infile),
('refmask_file', '--refmask=%s' % infile, infile),
('inmask_file', '--inmask=%s' % infile, infile),
('field_file', '--fout=%s' % infile, infile),
('jacobian_file', '--jout=%s' % infile, infile),
('modulatedref_file', '--refout=%s' % infile, infile),
('out_intensitymap_file',
'--intout=%s' % intmap_basename, True),
('out_intensitymap_file', '--intout=%s' % intmap_basename, intmap_image),
('fieldcoeff_file', '--cout=%s' % infile, infile),
('log_file', '--logout=%s' % infile, infile)]

for (name, settings, arg) in opt_map:
fnirt = fsl.FNIRT(in_file=infile,
ref_file=reffile,
**{name: infile})
**{name: arg})

if name in ('config_file', 'affine_file', 'field_file'):
cmd = 'fnirt %s%s --in=%s '\
if name in ('config_file', 'affine_file', 'field_file', 'fieldcoeff_file'):
cmd = 'fnirt %s --in=%s '\
'--logout=%s '\
'--ref=%s --iout=%s' % (settings, infile, infile, log,
'--ref=%s --iout=%s' % (settings, infile, log,
reffile, iout)
elif name in ('refmask_file'):
cmd = 'fnirt --in=%s '\
'--logout=%s --ref=%s '\
'%s%s '\
'%s '\
'--iout=%s' % (infile, log,
reffile,
settings, infile,
settings,
iout)
elif name in ('in_intensitymap_file', 'inwarp_file', 'inmask_file', 'jacobian_file'):
cmd = 'fnirt --in=%s '\
'%s%s '\
'%s '\
'--logout=%s --ref=%s '\
'--iout=%s' % (infile,
settings, infile,
settings,
log,
reffile,
iout)
elif name in ('log_file'):
cmd = 'fnirt --in=%s '\
'%s%s --ref=%s '\
'%s --ref=%s '\
'--iout=%s' % (infile,
settings, infile,
settings,
reffile,
iout)
else:
cmd = 'fnirt --in=%s '\
'--logout=%s %s%s '\
'--logout=%s %s '\
'--ref=%s --iout=%s' % (infile, log,
settings, infile,
settings,
reffile, iout)

assert fnirt.cmdline == cmd

if name == 'out_intensitymap_file':
assert fnirt._list_outputs()['out_intensitymap_file'] == [
intmap_image, intmap_txt]

@pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
def test_applywarp(setup_flirt):
Expand Down