Merge pull request #504 from bpinsard/bug/afni

fixing wrong output directory in afni base gen_filename

Author: chrisgorgo

nipype/interfaces/afni/base.py

@@ -216,9 +216,10 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
         else:
-            return super(AFNICommand, self)._gen_filename(name)
+            return os.path.join(os.getcwd(),
+                                super(AFNICommand, self)._gen_filename(name))
 
     def _overload_extension(self, value):
         path, base, _ = split_filename(value)
@@ -231,7 +232,8 @@ def _list_outputs(self):
             outputs = self.output_spec().get()
             for name in out_names:
                 out = self._gen_filename(name)
-                outputs[name] = os.path.abspath(out)
+                if isdefined(out):
+                    outputs[name] = os.path.abspath(out)
             return outputs
 
 

nipype/interfaces/afni/preprocess.py

@@ -12,7 +12,7 @@
 import os
 from .base import AFNIBaseCommandInputSpec, AFNIBaseCommand
 from ..base import (Directory, CommandLineInputSpec, CommandLine, TraitedSpec,
-                    traits, isdefined, File, InputMultiPath)
+                    traits, isdefined, File, InputMultiPath, Undefined)
 from ...utils.filemanip import (load_json, save_json, split_filename)
 from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.afni.base import AFNICommand, AFNICommandInputSpec,\
@@ -280,7 +280,7 @@ class ResampleInputSpec(AFNICommandInputSpec):
                              argstr='-orient %s')
 
 
-class Resample(AFNIBaseCommand):
+class Resample(AFNICommand):
     """Resample or reorient an image using AFNI 3dresample command
 
     For complete details, see the `3dresample Documentation.
@@ -534,7 +534,7 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
         elif name == "brain_file" and isdefined(self.inputs.apply_suffix):
             suffix = ''
             prefix = ''
@@ -543,7 +543,7 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
         elif name == "apply_mask" and isdefined(self.inputs.apply_suffix):
             suffix = ''
             prefix = ''
@@ -552,9 +552,10 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
-        else:
-            return super(AFNICommand, self)._gen_filename(name)
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
+        elif hasattr(self.inputs,name) and isdefined(getattr(self.inputs,name)):
+            return super(Automask, self)._gen_filename(name)
+        return Undefined
 
     def _list_outputs(self):
         outputs = super(Automask, self)._list_outputs()