Merge branch 'master' into enh/DipyMultiTensorSimulate

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -1,6 +1,10 @@
 Next release
 ============
 
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089)
+* 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)
 * ENH: Added interface to simulate DWIs using the multi-tensor model
        (https://github.com/nipy/nipype/pull/1085)
 * ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
@@ -52,6 +56,7 @@ Next release
 * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
 * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
 * FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
+* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
 
 Release 0.10.0 (October 10, 2014)
 ============

nipype/interfaces/dcmstack.py

@@ -42,12 +42,15 @@ def sanitize_path_comp(path_comp):
             result.append(char)
     return ''.join(result)
 
+
 class NiftiGeneratorBaseInputSpec(TraitedSpec):
     out_format = traits.Str(desc="String which can be formatted with "
                             "meta data to create the output filename(s)")
-    out_ext = traits.Str('.nii.gz',
-                         usedefault=True,
+    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')
+
 
 class NiftiGeneratorBase(BaseInterface):
     '''Base class for interfaces that produce Nifti files, potentially with
@@ -73,7 +76,12 @@ def _get_out_path(self, meta, idx=None):
             out_fmt = '-'.join(out_fmt)
         out_fn = (out_fmt % meta) + self.inputs.out_ext
         out_fn = sanitize_path_comp(out_fn)
-        return path.join(os.getcwd(), out_fn)
+
+        if self.inputs.use_cwd:
+            return path.join(os.getcwd(), out_fn)
+        else:
+            return path.abspath(out_fn)
+
 
 class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
     dicom_files = traits.Either(InputMultiPath(File(exists=True)),

nipype/interfaces/io.py

@@ -1775,13 +1775,20 @@ def _list_outputs(self):
                         outputs[key].append(list_to_filename(outfiles))
                         if self.inputs.download_files:
                             for f in outfiles:
-                                sftp.get(os.path.join(filledtemplate_dir, f), f)
+                                try:
+                                    sftp.get(os.path.join(filledtemplate_dir, f), f)
+                                except IOError:
+                                    iflogger.info('remote file %s not found' % f)
             if any([val is None for val in outputs[key]]):
                 outputs[key] = []
             if len(outputs[key]) == 0:
                 outputs[key] = None
             elif len(outputs[key]) == 1:
                 outputs[key] = outputs[key][0]
+
+        for k, v in outputs.items():
+            outputs[k] = os.path.join(os.getcwd(), v)
+
         return outputs
 
     def _get_ssh_client(self):
@@ -1944,7 +1951,7 @@ def _list_outputs(self):
         if not isdefined(self.inputs.out_file):
             out_file = op.abspath('datasink.json')
         else:
-            out_file = self.inputs.out_file
+            out_file = op.abspath(self.inputs.out_file)
 
         out_dict = self.inputs.in_dict
 

nipype/interfaces/tests/test_auto_DcmStack.py

@@ -13,6 +13,8 @@ def test_DcmStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    use_cwd=dict(usedefault=True,
+    ),
     )
     inputs = DcmStack.input_spec()
 

nipype/interfaces/tests/test_auto_GroupAndStack.py

@@ -13,6 +13,8 @@ def test_GroupAndStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    use_cwd=dict(usedefault=True,
+    ),
     )
     inputs = GroupAndStack.input_spec()
 

nipype/interfaces/tests/test_auto_MergeNifti.py

@@ -10,6 +10,8 @@ def test_MergeNifti_inputs():
     ),
     out_format=dict(),
     sort_order=dict(),
+    use_cwd=dict(usedefault=True,
+    ),
     )
     inputs = MergeNifti.input_spec()
 

nipype/interfaces/tests/test_auto_SplitNifti.py

@@ -9,6 +9,8 @@ def test_SplitNifti_inputs():
     ),
     out_format=dict(),
     split_dim=dict(),
+    use_cwd=dict(usedefault=True,
+    ),
     )
     inputs = SplitNifti.input_spec()