Merge pull request #1352 from BRAINSia/FixMRIsConvert

FIX: Fixes the 'out_file' and out_datatype inputs for MRIsConvert.

Author: hjmjohnson

nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py

@@ -30,11 +30,12 @@ def test_MRIsConvert_inputs():
     ),
     origname=dict(argstr='-o %s',
     ),
-    out_datatype=dict(mandatory=True,
+    out_datatype=dict(xor=['out_file'],
     ),
-    out_file=dict(argstr='./%s',
+    out_file=dict(argstr='%s',
     genfile=True,
     position=-1,
+    xor=['out_datatype'],
     ),
     parcstats_file=dict(argstr='--parcstats %s',
     ),

nipype/interfaces/freesurfer/utils.py

@@ -814,10 +814,12 @@ class MRIsConvertInputSpec(FSTraitedSpec):
     origname = traits.String(argstr="-o %s", desc="read orig positions")
 
     in_file = File(exists=True, mandatory=True, position=-2, argstr='%s', desc='File to read/convert')
-    out_file = File(argstr='./%s', position=-1, genfile=True, desc='output filename or True to generate one')
-    # Not really sure why the ./ is necessary but the module fails without it
+    out_file = File(argstr='%s', position=-1, genfile=True,
+                    xor=['out_datatype'], mandatory=True,
+                    desc='output filename or True to generate one')
 
-    out_datatype = traits.Enum("ico", "tri", "stl", "vtk", "gii", "mgh", "mgz", mandatory=True,
+    out_datatype = traits.Enum("ico", "tri", "stl", "vtk", "gii", "mgh", "mgz",
+                               xor=['out_file'], mandatory=True,
                                desc="These file formats are supported:  ASCII:       .asc"
                                "ICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume': .mgh, .mgz")
 
@@ -846,19 +848,26 @@ class MRIsConvert(FSCommand):
     input_spec = MRIsConvertInputSpec
     output_spec = MRIsConvertOutputSpec
 
+    def _format_arg(self, name, spec, value):
+        if name == "out_file" and not os.path.isabs(value):
+            value = os.path.abspath(value)
+        return super(MRIsConvert, self)._format_arg(name, spec, value)
+    
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["converted"] = os.path.abspath(self._gen_outfilename())
         return outputs
 
     def _gen_filename(self, name):
         if name is 'out_file':
-            return self._gen_outfilename()
+            return os.path.abspath(self._gen_outfilename())
         else:
             return None
 
     def _gen_outfilename(self):
-        if isdefined(self.inputs.annot_file):
+        if isdefined(self.inputs.out_file):
+            return self.inputs.out_file
+        elif isdefined(self.inputs.annot_file):
             _, name, ext = split_filename(self.inputs.annot_file)
         elif isdefined(self.inputs.parcstats_file):
             _, name, ext = split_filename(self.inputs.parcstats_file)