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FIX: Restore AFNICommand._get_fname, required by some interfaces #3071

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Merged
merged 1 commit into from
Oct 8, 2019
Merged

FIX: Restore AFNICommand._get_fname, required by some interfaces #3071

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51 changes: 50 additions & 1 deletion nipype/interfaces/afni/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from distutils import spawn

from ... import logging, LooseVersion
from ...utils.filemanip import split_filename
from ...utils.filemanip import split_filename, fname_presuffix
from ..base import (CommandLine, traits, CommandLineInputSpec, isdefined, File,
TraitedSpec, PackageInfo)
from ...external.due import BibTeX
Expand Down Expand Up @@ -237,6 +237,55 @@ def _list_outputs(self):
outputs[name] = outputs[name] + "+orig.BRIK"
return outputs

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 not 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.outputtype)
if change_ext:
suffix = ''.join((suffix, ext)) if suffix else ext

if suffix is None:
suffix = ''
fname = fname_presuffix(
basename, suffix=suffix, use_ext=False, newpath=cwd)
return fname


def no_afni():
"""Check whether AFNI is not available."""
Expand Down
52 changes: 0 additions & 52 deletions nipype/interfaces/afni/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -309,58 +309,6 @@ def _list_outputs(self):
return outputs


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.

"""
from nipype.utils.filemanip import fname_presuffix

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.outputtype)
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


class RemlfitInputSpec(AFNICommandInputSpec):
# mandatory files
in_files = InputMultiPath(
Expand Down