Merge pull request #471 from chrisfilo/fix/ants

ANTS: Removed unnecessary copyfiles and added output_image option.

Author: chrisgorgo

nipype/interfaces/ants/resampling.py

@@ -103,12 +103,14 @@ def _list_outputs(self):
 class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=True,
                             desc='image dimension (2 or 3)', position=1)
-    input_image = File(argstr='%s', mandatory=True, copyfile=True,
+    input_image = File(argstr='%s', mandatory=True,
                         desc=('image to apply transformation to (generally a '
-                              'coregistered functional)') )
-    out_postfix = traits.Str('_wimt', argstr='%s', usedefault=True,
-                             desc=('Postfix that is prepended to all output '
-                                   'files (default = _wimt)'))
+                              'coregistered functional)'), position=2)
+    output_image = File(genfile=True, usedefault=True, hash_files=False, argstr='%s', 
+                        desc=('name of the output warped image'), position = 3, xor=['out_postfix'])
+    out_postfix = File("_wimt", usedefault=True, hash_files=False, 
+                        desc=('Postfix that is prepended to all output '
+                                   'files (default = _wimt)'), xor=['output_image'])
     reference_image = File(argstr='-R %s', xor=['tightest_box'],
                        desc='reference image space that you wish to warp INTO')
     tightest_box = traits.Bool(argstr='--tightest-bounding-box',
@@ -123,13 +125,16 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
                               desc='Use nearest neighbor interpolation')
     use_bspline = traits.Bool(argstr='--use-Bspline',
                               desc='Use 3rd order B-Spline interpolation')
-    transformation_series = InputMultiPath(File(exists=True, copyfile=False), argstr='%s',
+    transformation_series = InputMultiPath(File(exists=True), argstr='%s',
                              desc='transformation file(s) to be applied',
-                             mandatory=True, copyfile=False)
+                             mandatory=True)
     invert_affine = traits.List(traits.Int,
-                    desc=('List of Affine transformations to invert. '
+                    desc=('List of Affine transformations to invert.'
                           'E.g.: [1,4,5] inverts the 1st, 4th, and 5th Affines '
-                          'found in transformation_series'))
+                          'found in transformation_series. Note that indexing '
+                          'starts with 1 and does not include warp fields. Affine '
+                          'transformations are distinguished '
+                          'from warp fields by the word "affine" included in their filenames.'))
 
 class WarpImageMultiTransformOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc='Warped image')
@@ -161,16 +166,19 @@ class WarpImageMultiTransform(ANTSCommand):
     _cmd = 'WarpImageMultiTransform'
     input_spec = WarpImageMultiTransformInputSpec
     output_spec = WarpImageMultiTransformOutputSpec
+    
+    def _gen_filename(self, name):
+        if name == 'out_file':
+            _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
+            return ''.join((name, self.inputs.out_postfix, ext))
+        return None
 
     def _format_arg(self, opt, spec, val):
-        if opt == 'out_postfix':
-            _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-            return name + val + ext
         if opt == 'transformation_series':
             series = []
             affine_counter = 0
             for transformation in val:
-                if 'Affine' in transformation and \
+                if "affine" in transformation.lower() and \
                     isdefined(self.inputs.invert_affine):
                     affine_counter += 1
                     if affine_counter in self.inputs.invert_affine:
@@ -181,11 +189,10 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-        outputs['output_image'] = os.path.join(os.getcwd(),
-                                             ''.join((name,
-                                                      self.inputs.out_postfix,
-                                                      ext)))
+        if isdefined(self.inputs.output_image):
+            outputs['output_image'] = os.path.abspath(self.inputs.output_image)
+        else:
+            outputs['output_image'] = os.path.abspath(self._gen_filename('output_image'))
         return outputs