def test_fslmaths():
std_dir = op.join(platform.fsldir, 'data', 'standard')
mask = op.join(std_dir, 'MNI152_T1_2mm_brain_mask.nii.gz')
assert op.isfile(mask)
img1 = op.join(std_dir, 'MNI152_T1_2mm_b0.nii.gz')
assert op.isfile(img1)
img2 = op.join(std_dir, 'MNI152_T1_2mm.nii.gz')
assert op.isfile(img2)
with tempdir():
cmd = [
'fslmaths', img1, '-add', img2, '-mul', mask, 'reference.nii.gz'
]
runfsl(cmd)
assert op.isfile('reference.nii.gz')
cmd[-2] = 'MASK'
cmd[-1] = 'splitJOBID.nii.gz'
parser = ArgumentParser()
submit.add_to_parser(parser)
args = parser.parse_args(('3', mask, ' '.join(cmd)))
_environ = dict(os.environ)
try:
if 'SGE_ROOT' in os.environ:
del os.environ['SGE_ROOT']
submit.run_from_args(args)
finally:
os.environ.clear()
os.environ.update(_environ)
assert op.isfile('split.nii.gz')
ref = nib.load('reference.nii.gz')
split = nib.load('split.nii.gz')
assert_allclose(ref.get_fdata(), split.get_fdata())
assert (ref.affine == split.affine).all()
assert ref.header == split.header
def robustfov(self):
"""Call ``robustfov`` for the current overlay and set the
:attr:`cropBox` based on the result.
"""
if self.__overlay is None:
return
try:
result = fslrun.runfsl(
'robustfov', '-i', self.__overlay.dataSource)
# robustfov returns two lines, the last
# of which contains the limits, as:
#
# xmin xlen ymin ylen zmin zlen
limits = list(result.strip().split('\n')[-1].split())
limits = [float(l) for l in limits]
# Convert the lens to maxes
limits[1] += limits[0]
limits[3] += limits[2]
limits[5] += limits[4]
self.cropBox[:] = limits
except Exception as e:
log.warning('Call to robustfov failed: {}'.format(str(e)))
def add_to_parser(cls, parser: argparse.ArgumentParser, as_group='fsl_sub commands',
include=('wait_for', 'logdir', 'email', 'mail_options')):
"""
Adds submission parameters to the parser
:param parser: parser that should understand submission commands
:param as_group: add as a new group
:param include: sequence of argument flags/names that should be added to the parser
(set to None to include everything)
:return: the group the arguments got added to
"""
from fsl.utils.run import runfsl, FSLNotPresent
try:
fsl_sub_run, _ = runfsl('fsl_sub', exitcode=True)
except (FileNotFoundError, FSLNotPresent):
warnings.warn('fsl_sub was not found')
return
doc_lines = fsl_sub_run.splitlines()
nspaces = 1
for line in doc_lines:
if len(line.strip()) > 0:
while line.startswith(' ' * nspaces):
nspaces += 1
nspaces -= 1
if as_group:
group = parser.add_argument_group(as_group)
else:
group = parser
def get_explanation(flag):
explanation = None
for line in doc_lines:
if explanation is not None and len(line.strip()) > 0 and line.strip()[0] != '-':
explanation.append(line[nspaces:].strip())
elif explanation is not None:
break
elif line.strip().startswith(flag):
explanation = [line[nspaces:].strip()]
if (explanation is None) or (len(explanation) == 0):
return 'documentation not found'
return ' '.join(explanation)
for flag, value in cls.cmd_line_flags.items():
if include is not None and value not in include and flag not in include:
continue
as_type = {'minutes': float, 'priority': int, 'ram': int, 'verbose': None}
action = 'store_true' if value == 'verbose' else 'store'
group.add_argument(flag, dest='_sub_' + value, help=get_explanation(flag), action=action,
metavar='<' + value + '>', type=as_type.get(value, str))
group.add_argument('-F', dest='_sub_flags', help=get_explanation('-F'), action='store_true')
group.add_argument('-v', dest='_sub_verbose', help=get_explanation('-v'), action='store_true')
group.add_argument('-s', dest='_sub_multi_threaded', help=get_explanation('-s'),
metavar='<pename>,<threads>')
group.add_argument('-j', dest='_sub_wait_for', help=get_explanation('-j'),
metavar='<jid>')
return group
def __call__(self, *command, **kwargs):
"""
Submits the command to the cluster.
:param command: string or tuple of strings with the command to submit
:param kwargs: Keyword arguments can override any parameters set in self
:return: job ID
"""
from fsl.utils.run import prepareArgs, runfsl
runner = self.update(**kwargs)
command = prepareArgs(command)
fsl_sub_cmd = ' '.join(('fsl_sub', ) + tuple(runner.as_flags()) + tuple(command))
log.debug(fsl_sub_cmd)
jobid = runfsl(fsl_sub_cmd, env=runner.env).strip()
log.debug('Job submitted as {}'.format(jobid))
return jobid
def robustfov(self):
"""Call ``robustfov`` for the current overlay and set the
:attr:`cropBox` based on the result.
"""
overlay = self.__overlay
if overlay is None:
return
try:
with tempdir.tempdir():
# in-memory image - create and
# save a copy - use a copy
# otherwise the original will
# think that is has been saved
# to disk.
if overlay.dataSource is None:
overlay = fslimage.Image(overlay)
overlay.save('image')
result = fslrun.runfsl('robustfov', '-i', overlay.dataSource)
# robustfov returns two lines, the last
# of which contains the limits, as:
#
# xmin xlen ymin ylen zmin zlen
limits = list(result.strip().split('\n')[-1].split())
limits = [float(l) for l in limits]
# Convert the lens to maxes
limits[1] += limits[0]
limits[3] += limits[2]
limits[5] += limits[4]
self.cropBox[:] = limits
except Exception as e:
log.warning('Call to robustfov failed: {}'.format(str(e)))
import os
import fsl.data.featanalysis as FA
import fsl.utils.run as RUN
# get number of time points using fslinfo (in case of non-uniform runs)
info = RUN.runfsl('fslinfo', snakemake.input.func_file)
info_temp = info.split()
info_dct = {
info_temp[i]: info_temp[i + 1]
for i in range(0, len(info_temp), 2)
}
num_pts = int(info_dct['dim4'])
# get full path to $FSLDIR
FSLDIR = os.path.expandvars('$FSLDIR')
# get path of output design.fsf file
feat_subdir = os.path.split(snakemake.output.design_fsf)[0]
# set variables
# load in design.fsf
design = FA.loadSettings(snakemake.input.feat_dir)
for ev in range(len(snakemake.input.event_files)):
evTemp = ev + 1
evName = design['evtitle%d' % evTemp]
evFile = snakemake.input.event_files[ev]
#evFile = [evf for evf in snakemake.input.event_files if evf == 'trial-%s_onsets.txt'%evName]
custom = [('custom%d' % evTemp, '"%s"' % evFile)]
design.update(custom)
def test_runfsl():
test_script = textwrap.dedent("""
#!/bin/bash
echo {}
exit 0
""").strip()
old_fsldir = fslplatform.fsldir
old_fsldevdir = fslplatform.fsldevdir
try:
with tempdir.tempdir():
make_random_image('image.nii.gz')
# no FSLDIR - should error
fslplatform.fsldir = None
fslplatform.fsldevdir = None
with pytest.raises(run.FSLNotPresent):
run.runfsl('fslhd')
# FSLDIR/bin exists - should be good
fsldir = op.abspath('./fsl')
fslhd = op.join(fsldir, 'bin', 'fslhd')
os.makedirs(op.join(fsldir, 'bin'))
mkexec(fslhd, test_script.format('fsldir'))
fslplatform.fsldir = fsldir
assert run.runfsl('fslhd').strip() == 'fsldir'
# non-FSL command - should error
with pytest.raises(FileNotFoundError):
run.runfsl('ls')
# FSLDEVDIR should take precedence
fsldevdir = './fsldev'
fslhd = op.join(fsldevdir, 'bin', 'fslhd')
shutil.copytree(fsldir, fsldevdir)
mkexec(fslhd, test_script.format('fsldevdir'))
fslplatform.fsldevdir = fsldevdir
fslplatform.fsldir = None
assert run.runfsl('fslhd').strip() == 'fsldevdir'
# FSL_PREFIX should override all
override = './override'
fslhd = op.join(override, 'fslhd')
os.makedirs(override)
mkexec(fslhd, test_script.format('override'))
fslplatform.fsldir = None
fslplatform.fsldevdir = None
run.FSL_PREFIX = override
assert run.runfsl('fslhd').strip() == 'override'
finally:
fslplatform.fsldir = old_fsldir
fslplatform.fsldevdir = old_fsldevdir
run.FSL_PREFIX = None