Merge branch 'master' into fix/AreaWeighedP2PDistance

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -6,6 +6,7 @@ Next release
 * FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
        fix bug in area weighted distance, and added optimizations
        (https://github.com/nipy/nipype/pull/1016)
+* FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
 * ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
 * ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
 * ENH: Improve JSON interfaces: default settings when reading and consistent output creation

nipype/algorithms/metrics.py

@@ -572,7 +572,7 @@ def _run_interface(self, runtime):
         nb.Nifti1Image(errmap.astype(np.float32), nii_ref.get_affine(),
                        hdr).to_filename(self._out_file)
 
-        return runtime 
+        return runtime
 
     def _list_outputs(self):
         outputs = self.output_spec().get()

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -23,7 +23,8 @@ def test_ErrorMap_inputs():
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 def test_ErrorMap_outputs():
-    output_map = dict(out_map=dict(),
+    output_map = dict(distance=dict(),
+    out_map=dict(),
     )
     outputs = ErrorMap.output_spec()
 

nipype/algorithms/tests/test_errormap.py

@@ -32,7 +32,7 @@ def test_errormap():
 	errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz')
 	errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz')
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 1.125 
+	yield assert_equal, result.outputs.distance, 1.125
 
 	# Square metric
 	errmap.inputs.metric = 'sqeuclidean'
@@ -42,9 +42,9 @@ def test_errormap():
 	# Linear metric
 	errmap.inputs.metric = 'euclidean'
 	result = errmap.run()
-	yield assert_equal, result.outputs.distance, 0.875 
+	yield assert_equal, result.outputs.distance, 0.875
 
-	# Masked 
+	# Masked
 	errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz')
 	result = errmap.run()
 	yield assert_equal, result.outputs.distance, 1.0

nipype/interfaces/ants/registration.py

@@ -395,7 +395,7 @@ class Registration(ANTSCommand):
     >>> outputs = reg4._list_outputs()
     >>> print outputs #doctest: +ELLIPSIS
     {'reverse_invert_flags': [], 'inverse_composite_transform': ['.../nipype/testing/data/output_InverseComposite.h5'], 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': <undefined>, 'forward_invert_flags': [], 'reverse_transforms': [], 'composite_transform': ['.../nipype/testing/data/output_Composite.h5'], 'forward_transforms': []}
-    
+
     >>> # Test collapse transforms flag
     >>> reg4b = copy.deepcopy(reg4)
     >>> reg4b.inputs.write_composite_transform = False

nipype/interfaces/camino/dti.py

@@ -549,7 +549,11 @@ class Track(CommandLine):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['tracked'] = os.path.abspath(self._gen_outfilename())
+        if isdefined(self.inputs.out_file):
+            out_file_path = os.path.abspath(self.inputs.out_file)
+        else:
+            out_file_path = os.path.abspath(self._gen_outfilename())
+        outputs['tracked'] = out_file_path
         return outputs
 
     def _gen_filename(self, name):