Merge remote-tracking branch 'juhuntenburg/enh/refit'

* juhuntenburg/enh/refit:
  adding tests
  adding further options to 3drefit

Author: chrisgorgo

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -0,0 +1,34 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.metrics import ErrorMap
+
+def test_ErrorMap_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_ref=dict(mandatory=True,
+    ),
+    in_tst=dict(mandatory=True,
+    ),
+    mask=dict(),
+    metric=dict(mandatory=True,
+    usedefault=True,
+    ),
+    out_map=dict(),
+    )
+    inputs = ErrorMap.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ErrorMap_outputs():
+    output_map = dict(distance=dict(),
+    out_map=dict(),
+    )
+    outputs = ErrorMap.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/algorithms/tests/test_auto_Overlap.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import Overlap
+
+def test_Overlap_inputs():
+    input_map = dict(bg_overlap=dict(mandatory=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_volume=dict(),
+    out_file=dict(usedefault=True,
+    ),
+    vol_units=dict(mandatory=True,
+    usedefault=True,
+    ),
+    volume1=dict(mandatory=True,
+    ),
+    volume2=dict(mandatory=True,
+    ),
+    weighting=dict(usedefault=True,
+    ),
+    )
+    inputs = Overlap.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_Overlap_outputs():
+    output_map = dict(dice=dict(),
+    diff_file=dict(),
+    jaccard=dict(),
+    labels=dict(),
+    roi_di=dict(),
+    roi_ji=dict(),
+    roi_voldiff=dict(),
+    volume_difference=dict(),
+    )
+    outputs = Overlap.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/afni/preprocess.py

@@ -170,6 +170,20 @@ class RefitInputSpec(CommandLineInputSpec):
     zorigin = traits.Str(desc='z distance for edge voxel offset',
                          argstr='-zorigin %s')
 
+    xdel = traits.Float(desc='new x voxel dimension in mm',
+                        argstr='-xdel %f')
+
+    ydel = traits.Float(desc='new y voxel dimension in mm',
+                        argstr='-ydel %f')
+
+    zdel = traits.Float(desc='new z voxel dimension in mm',
+                        argstr='-zdel %f')
+
+    space = traits.Enum('TLRC', 'MNI', 'ORIG',
+                        argstr='-space %s',
+                        desc='Associates the dataset with a specific' +
+                         ' template type, e.g. TLRC, MNI, ORIG')
+
 
 class Refit(CommandLine):
     """Changes some of the information inside a 3D dataset's header

nipype/interfaces/afni/tests/test_auto_Refit.py

@@ -18,12 +18,20 @@ def test_Refit_inputs():
     mandatory=True,
     position=-1,
     ),
+    space=dict(argstr='-space %s',
+    ),
     terminal_output=dict(nohash=True,
     ),
+    xdel=dict(argstr='-xdel %f',
+    ),
     xorigin=dict(argstr='-xorigin %s',
     ),
+    ydel=dict(argstr='-ydel %f',
+    ),
     yorigin=dict(argstr='-yorigin %s',
     ),
+    zdel=dict(argstr='-zdel %f',
+    ),
     zorigin=dict(argstr='-zorigin %s',
     ),
     )