def _get_fsl_slice_output_files(out_base_name, output_type):
ext = Info.output_type_to_ext(output_type)
suffix = '_slice_*' + ext
exact_pattern = '_slice_[0-9][0-9][0-9][0-9]' + ext
fname_template = os.path.abspath(out_base_name + suffix)
fname_exact_pattern = os.path.abspath(out_base_name + exact_pattern)
sliced_files = fnmatch.filter(sorted(glob.glob(fname_template)),
fname_exact_pattern)
return sliced_files
def _gen_fname(self,
basename,
cwd=None,
suffix=None,
change_ext=True,
ext=None):
"""Generate a filename based on the given parameters.
The filename will take the form: cwd/basename<suffix><ext>.
If change_ext is True, it will use the extentions specified in
<instance>intputs.output_type.
Parameters
----------
basename : str
Filename to base the new filename on.
cwd : str
Path to prefix to the new filename. (default is os.getcwd())
suffix : str
Suffix to add to the `basename`. (defaults is '' )
change_ext : bool
Flag to change the filename extension to the FSL output type.
(default True)
Returns
-------
fname : str
New filename based on given parameters.
"""
if basename == '':
msg = 'Unable to generate filename for command %s. ' % self.cmd
msg += 'basename is not set!'
raise ValueError(msg)
if cwd is None:
cwd = os.getcwd()
if ext is None:
ext = Info.output_type_to_ext(self.inputs.output_type)
if change_ext:
if suffix:
suffix = ''.join((suffix, ext))
else:
suffix = ext
if suffix is None:
suffix = ''
fname = fname_presuffix(basename,
suffix=suffix,
use_ext=False,
newpath=cwd)
return fname
def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
ext=None):
"""Generate a filename based on the given parameters.
The filename will take the form: cwd/basename<suffix><ext>.
If change_ext is True, it will use the extentions specified in
<instance>intputs.output_type.
Parameters
----------
basename : str
Filename to base the new filename on.
cwd : str
Path to prefix to the new filename. (default is os.getcwd())
suffix : str
Suffix to add to the `basename`. (defaults is '' )
change_ext : bool
Flag to change the filename extension to the FSL output type.
(default True)
Returns
-------
fname : str
New filename based on given parameters.
"""
if basename == '':
msg = 'Unable to generate filename for command %s. ' % self.cmd
msg += 'basename is not set!'
raise ValueError(msg)
if cwd is None:
cwd = os.getcwd()
if ext is None:
ext = Info.output_type_to_ext(self.inputs.output_type)
if change_ext:
if suffix:
suffix = ''.join((suffix, ext))
else:
suffix = ext
if suffix is None:
suffix = ''
fname = fname_presuffix(basename, suffix=suffix,
use_ext=False, newpath=cwd)
return fname
def _list_outputs(self):
"""Create a Bunch which contains all possible files generated
by running the interface. Some files are always generated, others
depending on which ``inputs`` options are set.
Returns
-------
outputs : Bunch object
Bunch object containing all possible files generated by
interface object.
If None, file was not generated
Else, contains path, filename of generated outputfile
"""
outputs = self._outputs().get()
ext = Info.output_type_to_ext(self.inputs.output_type)
outbase = 'vol*'
if isdefined(self.inputs.out_base_name):
outbase = '%s*' % self.inputs.out_base_name
outputs['out_files'] = sorted(glob(os.path.join(os.getcwd(),
outbase + ext)))
return outputs
def _list_outputs(self):
"""Create a Bunch which contains all possible files generated
by running the interface. Some files are always generated, others
depending on which ``inputs`` options are set.
Returns
-------
outputs : Bunch object
Bunch object containing all possible files generated by
interface object.
If None, file was not generated
Else, contains path, filename of generated outputfile
"""
outputs = self._outputs().get()
ext = Info.output_type_to_ext(self.inputs.output_type)
outbase = 'vol*'
if isdefined(self.inputs.out_base_name):
outbase = '%s*' % self.inputs.out_base_name
outputs['out_files'] = sorted(glob(os.path.join(os.getcwd(),
outbase + ext)))
return outputs
def _list_fsl_split_outputs(self):
""" Method to list the fsl split interface outputs
Returns
-------
outputs: dict
all the interface outputs
"""
from glob import glob
from nipype.interfaces.fsl.base import Info
from nipype.interfaces.base import isdefined
# Get the nipype outputs
outputs = self._outputs().get()
# Modify the path outputs
ext = Info.output_type_to_ext(self.inputs.output_type)
outbase = 'vol*'
if isdefined(self.inputs.out_base_name):
outbase = '%s*' % self.inputs.out_base_name
outputs['out_files'] = sorted(glob(
os.path.join(self.inputs.output_directory, outbase + ext)))
return outputs
