STYLE: Made PEP8-compliant \ENH: Finished mri_ls_LDA testing

Author: dmwelch

nipype/interfaces/freesurfer/model.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""The freesurfer module provides basic functions for interfacing with freesurfer tools.
+"""The freesurfer module provides basic functions for interfacing with
+ freesurfer tools.
 
  Change directory to provide relative paths for doctests
  >>> import os
@@ -769,22 +770,36 @@ def _gen_filename(self, name):
  return self._list_outputs()[name]
  return None
 
+
 class MS_LDAInputSpec(FSTraitedSpec):
- lda_labels = traits.List(traits.Int(), argstr='-lda %s', mandatory=True, minlen=2, maxlen=2, sep=' ', position=1,
+ lda_labels = traits.List(traits.Int(), argstr='-lda %s', mandatory=True,
+ minlen=2, maxlen=2, sep=' ', position=1,
  desc='pair of class labels to optimize')
- weight_file = traits.File(argstr='-weight %s', mandatory=True, position=2, desc='filename for the LDA weights (input or output)')
- output_synth = traits.File(exists=False, argstr='-synth %s', mandatory=True, position=3, desc='filename for the synthesized output volume')
- label_file = traits.File(exists=True, argstr='-label %s', position=4, desc='filename of the label volume')
- mask_file = traits.File(exists=True, argstr='-mask %s', position=5, desc='filename of the brain mask volume')
- shift = traits.Int(argstr='-shift %d', position=6, desc='shift all values equal to the given value to zero')
- conform = traits.Bool(argstr='-conform', position=7, desc='Conform the input volumes (brain mask typically already conformed)')
- use_weights = traits.Bool(argstr='-W', position=8, desc='Use the weights from a previously generated weight file')
- images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, copyfile=False, desc='list of input FLASH images' )
+ weight_file = traits.File(argstr='-weight %s', mandatory=True,
+ position=2,
+ desc='filename for the LDA weights (input or output)')
+ output_synth = traits.File(exists=False, argstr='-synth %s',
+ mandatory=True, position=3,
+ desc='filename for the synthesized output volume')
+ label_file = traits.File(exists=True, argstr='-label %s', position=4,
+ desc='filename of the label volume')
+ mask_file = traits.File(exists=True, argstr='-mask %s', position=5,
+ desc='filename of the brain mask volume')
+ shift = traits.Int(argstr='-shift %d', position=6,
+ desc='shift all values equal to the given value to zero')
+ conform = traits.Bool(argstr='-conform', position=7,
+ desc='Conform the input volumes (brain mask typically already conformed)')
+ use_weights = traits.Bool(argstr='-W', position=8,
+ desc='Use the weights from a previously generated weight file')
+ images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
+ copyfile=False, desc='list of input FLASH images')
+
 
 class MS_LDAOutputSpec(TraitedSpec):
  weight_file = File(exists=True, desc='')
  vol_synth_file = File(exists=True, desc='')
 
+
 class MS_LDA(FSCommand):
  """Perform LDA reduction on the intensity space of an arbitrary # of FLASH images
 
@@ -821,7 +836,8 @@ def _format_arg(self, name, spec, value):
  if name is 'use_weights':
  if self.inputs.use_weights is True:
  self._verify_weights_file_exists()
- else: return ''
+ else:
+ return ''
  # TODO: Fix bug when boolean values are set explicitly to false
  return super(MS_LDA, self)._format_arg(name, spec, value)