dcmstack create directory if does not exist. pep8 fixes

Author: oesteban

nipype/interfaces/dcmstack.py

@@ -9,8 +9,10 @@
 """
 
 from __future__ import absolute_import
-import os, string
-from os import path
+import os
+import string
+import errno
+from os import path as op
 from glob import glob
 from nipype.interfaces.base import (TraitedSpec,
  DynamicTraitedSpec,
@@ -33,6 +35,7 @@
 except ImportError:
  have_dcmstack = False
 
+
 def sanitize_path_comp(path_comp):
  result = []
  for char in path_comp:
@@ -78,9 +81,18 @@ def _get_out_path(self, meta, idx=None):
 
  out_path = os.getcwd()
  if isdefined(self.inputs.out_path):
- out_path = path.abspath(self.inputs.out_path)
- return path.join(out_path, out_fn)
+ out_path = op.abspath(self.inputs.out_path)
+
+ # now, mkdir -p $out_path
+ try:
+ op.makedirs(out_path)
+ except OSError as exc: # Python >2.5
+ if exc.errno == errno.EEXIST and op.isdir(out_path):
+ pass
+ else:
+ raise
 
+ return op.join(out_path, out_fn)
 
 
 class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
@@ -100,6 +112,7 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
 class DcmStackOutputSpec(TraitedSpec):
  out_file = File(exists=True)
 
+
 class DcmStack(NiftiGeneratorBase):
  '''Create one Nifti file from a set of DICOM files. Can optionally embed
  meta data.
@@ -119,8 +132,8 @@ class DcmStack(NiftiGeneratorBase):
 
  def _get_filelist(self, trait_input):
  if isinstance(trait_input, six.string_types):
- if path.isdir(trait_input):
- return glob(path.join(trait_input, '*.dcm'))
+ if op.isdir(trait_input):
+ return glob(op.join(trait_input, '*.dcm'))
  else:
  return glob(trait_input)
 
@@ -155,9 +168,11 @@ def _list_outputs(self):
  outputs["out_file"] = self.out_path
  return outputs
 
+
 class GroupAndStackOutputSpec(TraitedSpec):
  out_list = traits.List(desc="List of output nifti files")
 
+
 class GroupAndStack(DcmStack):
  '''Create (potentially) multiple Nifti files for a set of DICOM files.
  '''
@@ -185,6 +200,7 @@ def _list_outputs(self):
  outputs["out_list"] = self.out_list
  return outputs
 
+
 class LookupMetaInputSpec(TraitedSpec):
  in_file = File(mandatory=True,
  exists=True,
@@ -197,6 +213,7 @@ class LookupMetaInputSpec(TraitedSpec):
  "lookup and the values specify the output names")
  )
 
+
 class LookupMeta(BaseInterface):
  '''Lookup meta data values from a Nifti with embeded meta data.
 
@@ -253,6 +270,7 @@ def _list_outputs(self):
  outputs.update(self.result)
  return outputs
 
+
 class CopyMetaInputSpec(TraitedSpec):
  src_file = File(mandatory=True, exists=True)
  dest_file = File(mandatory=True, exists=True)
@@ -262,9 +280,11 @@ class CopyMetaInputSpec(TraitedSpec):
  exclude_classes = traits.List(desc="List of meta data "
  "classifications to exclude")
 
+
 class CopyMetaOutputSpec(TraitedSpec):
  dest_file = File(exists=True)
 
+
 class CopyMeta(BaseInterface):
  '''Copy meta data from one Nifti file to another. Useful for preserving
  meta data after some processing steps.'''
@@ -296,8 +316,8 @@ def _run_interface(self, runtime):
  dest.meta_ext.slice_dim = src.meta_ext.slice_dim
  dest.meta_ext.shape = src.meta_ext.shape
 
- self.out_path = path.join(os.getcwd(),
- path.basename(self.inputs.dest_file))
+ self.out_path = op.join(os.getcwd(),
+ op.basename(self.inputs.dest_file))
  dest.to_filename(self.out_path)
 
  return runtime
@@ -307,6 +327,7 @@ def _list_outputs(self):
  outputs['dest_file'] = self.out_path
  return outputs
 
+
 class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
  in_files = traits.List(mandatory=True,
  desc="List of Nifti files to merge")
@@ -318,16 +339,19 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
  "specified, the last singular or "
  "non-existant dimension is used.")
 
+
 class MergeNiftiOutputSpec(TraitedSpec):
  out_file = File(exists=True, desc="Merged Nifti file")
 
+
 def make_key_func(meta_keys, index=None):
  def key_func(src_nii):
  result = [src_nii.get_meta(key, index) for key in meta_keys]
  return result
 
  return key_func
 
+
 class MergeNifti(NiftiGeneratorBase):
  '''Merge multiple Nifti files into one. Merges together meta data
  extensions as well.'''
@@ -361,18 +385,23 @@ def _list_outputs(self):
  outputs['out_file'] = self.out_path
  return outputs
 
+
 class SplitNiftiInputSpec(NiftiGeneratorBaseInputSpec):
  in_file = File(exists=True, mandatory=True, desc="Nifti file to split")
  split_dim = traits.Int(desc="Dimension to split along. If not "
  "specified, the last dimension is used.")
 
+
 class SplitNiftiOutputSpec(TraitedSpec):
  out_list = traits.List(File(exists=True),
  desc="Split Nifti files")
 
+
 class SplitNifti(NiftiGeneratorBase):
- '''Split one Nifti file into many along the specified dimension. Each
- result has an updated meta data extension as well.'''
+ '''
+ Split one Nifti file into many along the specified dimension. Each
+ result has an updated meta data extension as well.
+ '''
  input_spec = SplitNiftiInputSpec
  output_spec = SplitNiftiOutputSpec