Merge pull request #1093 from oesteban/bug/FixDCMStackOutpath

A new solution to DCMStack output folder

Author: oesteban

CHANGES

@@ -1,7 +1,8 @@
 Next release
 ============
 
-* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089)
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
 * ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets.
 * ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions
        in EPI seqs. (https://github.com/nipy/nipype/pull/1019)

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:
@@ -48,8 +51,7 @@ class NiftiGeneratorBaseInputSpec(TraitedSpec):
                             "meta data to create the output filename(s)")
     out_ext = traits.Str('.nii.gz', usedefault=True,
                          desc="Determines output file type")
-    use_cwd = traits.Bool(True, usedefault=True,
-                          desc='use interface\'s current working directory')
+    out_path = Directory(desc='output path, current working directory if not set')
 
 
 class NiftiGeneratorBase(BaseInterface):
@@ -77,10 +79,20 @@ def _get_out_path(self, meta, idx=None):
         out_fn = (out_fmt % meta) + self.inputs.out_ext
         out_fn = sanitize_path_comp(out_fn)
 
-        if self.inputs.use_cwd:
-            return path.join(os.getcwd(), out_fn)
-        else:
-            return path.abspath(out_fn)
+        out_path = os.getcwd()
+        if isdefined(self.inputs.out_path):
+            out_path = op.abspath(self.inputs.out_path)
+
+            # now, mkdir -p $out_path
+            try:
+                os.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.
 
@@ -233,13 +250,13 @@ def _outputs(self):
             outputs.add_trait(out_name, traits.Any)
             undefined_traits[out_name] = Undefined
         outputs.trait_set(trait_change_notify=False, **undefined_traits)
-        #Not sure why this is needed
+        # Not sure why this is needed
         for out_name in self._meta_keys.values():
             _ = getattr(outputs, out_name)
         return outputs
 
     def _run_interface(self, runtime):
-        #If the 'meta_keys' input is a list, covert it to a dict
+        # If the 'meta_keys' input is a list, covert it to a dict
         self._make_name_map()
         nw = NiftiWrapper.from_filename(self.inputs.in_file)
         self.result = {}
@@ -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
 

nipype/interfaces/tests/test_auto_DcmStack.py

@@ -13,8 +13,7 @@ def test_DcmStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
-    use_cwd=dict(usedefault=True,
-    ),
+    out_path=dict(),
     )
     inputs = DcmStack.input_spec()
 

nipype/interfaces/tests/test_auto_GroupAndStack.py

@@ -13,8 +13,7 @@ def test_GroupAndStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
-    use_cwd=dict(usedefault=True,
-    ),
+    out_path=dict(),
     )
     inputs = GroupAndStack.input_spec()
 

nipype/interfaces/tests/test_auto_MergeNifti.py

@@ -9,9 +9,8 @@ def test_MergeNifti_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     sort_order=dict(),
-    use_cwd=dict(usedefault=True,
-    ),
     )
     inputs = MergeNifti.input_spec()
 

nipype/interfaces/tests/test_auto_SplitNifti.py

@@ -8,9 +8,8 @@ def test_SplitNifti_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     split_dim=dict(),
-    use_cwd=dict(usedefault=True,
-    ),
     )
     inputs = SplitNifti.input_spec()