Reverting changes for XfmInvert and XfmAvg which failed when testing with volgenmodel.

Author: carlohamalainen

nipype/interfaces/minc/minc.py

@@ -3254,11 +3254,7 @@ class XfmAvgInputSpec(CommandLineInputSpec):
         desc='output file',
         genfile=True,
         argstr='%s',
-        position=-1,
-        name_source=['input_files'],
-        hash_files=False,
-        name_template='%s_xfmavg.xfm',
-        keep_extension=False)
+        position=-1,)
 
     verbose = traits.Bool(
         desc='Print out log messages. Default: False.',
@@ -3316,13 +3312,29 @@ class XfmAvg(CommandLine):
     output_spec = XfmAvgOutputSpec
     _cmd = 'xfmavg'
 
+    def _gen_filename(self, name):
+        if name == 'output_file':
+            output_file = self.inputs.output_file
+
+            if isdefined(output_file):
+                return os.path.abspath(output_file)
+            else:
+                return aggregate_filename(
+                    self.inputs.input_files, 'xfmavg_output') + '.xfm'
+        else:
+            raise NotImplemented
+
+    def _gen_outfilename(self):
+        return self._gen_filename('output_file')
+
     def _list_outputs(self):
-        outputs = super(XfmAvg, self)._list_outputs()
+        outputs = self.output_spec().get()
+        outputs['output_file'] = os.path.abspath(self._gen_outfilename())
 
-        if os.path.exists(outputs['output_file']):
-            if 'grid' in open(outputs['output_file'], 'r').read():
-                outputs['output_grid'] = re.sub(
-                    '.(nlxfm|xfm)$', '_grid_0.mnc', outputs['output_file'])
+        assert os.path.exists(outputs['output_file'])
+        if 'grid' in open(outputs['output_file'], 'r').read():
+            outputs['output_grid'] = re.sub(
+                '.(nlxfm|xfm)$', '_grid_0.mnc', outputs['output_file'])
 
         return outputs
 
@@ -3339,10 +3351,7 @@ class XfmInvertInputSpec(CommandLineInputSpec):
         desc='output file',
         genfile=True,
         argstr='%s',
-        position=-1,
-        name_source=['input_file'],
-        hash_files=False,
-        name_template='%s_xfminvert.xfm')
+        position=-1,)
 
     verbose = traits.Bool(
         desc='Print out log messages. Default: False.',
@@ -3377,13 +3386,29 @@ class XfmInvert(CommandLine):
     output_spec = XfmInvertOutputSpec
     _cmd = 'xfminvert'
 
+    def _gen_filename(self, name):
+        if name == 'output_file':
+            output_file = self.inputs.output_file
+
+            if isdefined(output_file):
+                return os.path.abspath(output_file)
+            else:
+                return aggregate_filename(
+                    [self.inputs.input_file], 'xfminvert_output') + '.xfm'
+        else:
+            raise NotImplemented
+
+    def _gen_outfilename(self):
+        return self._gen_filename('output_file')
+
     def _list_outputs(self):
-        outputs = super(XfmInvert, self)._list_outputs()
+        outputs = self.output_spec().get()
+        outputs['output_file'] = os.path.abspath(self._gen_outfilename())
 
-        if os.path.exists(outputs['output_file']):
-            if 'grid' in open(outputs['output_file'], 'r').read():
-                outputs['output_grid'] = re.sub(
-                    '.(nlxfm|xfm)$', '_grid_0.mnc', outputs['output_file'])
+        assert os.path.exists(outputs['output_file'])
+        if 'grid' in open(outputs['output_file'], 'r').read():
+            outputs['output_grid'] = re.sub(
+                '.(nlxfm|xfm)$', '_grid_0.mnc', outputs['output_file'])
 
         return outputs