fix trait all_rois and tests

Author: salma1601

nipype/interfaces/afni/tests/test_auto_CenterMass.py

@@ -0,0 +1,58 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import CenterMass
+
+
+def test_CenterMass_inputs():
+    input_map = dict(all_rois=dict(argstr='-all_rois',
+    ),
+    args=dict(argstr='%s',
+    ),
+    automask=dict(argstr='-automask',
+    ),
+    cm_file=dict(argstr='> %s',
+    descr='File to write center of mass to',
+    keep_extension=False,
+    name_source='in_file',
+    name_template='%s_cm.out',
+    position=-1,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    copyfile=True,
+    mandatory=True,
+    position=-2,
+    ),
+    local_ijk=dict(argstr='-local_ijk',
+    ),
+    mask_file=dict(argstr='-mask %s',
+    ),
+    roi_vals=dict(argstr='-roi_vals %s',
+    ),
+    set_cm=dict(argstr='-set %f %f %f',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = CenterMass.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_CenterMass_outputs():
+    output_map = dict(cm=dict(),
+    cm_file=dict(),
+    out_file=dict(),
+    )
+    outputs = CenterMass.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/afni/utils.py

@@ -656,7 +656,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
          name_template='%s_cm.out',
          keep_extension=False,
          descr="File to write center of mass to",
-         argstr=" > %s",
+         argstr="> %s",
          position=-1)
     mask_file = File(
         desc='Only voxels with nonzero values in the provided mask will be '
@@ -681,7 +681,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
              'v1, v2, etc. This option is handy for getting ROI centers of '
              'mass.',
         argstr='-roi_vals %s')
-    automask = traits.Bool(
+    all_rois = traits.Bool(
         desc='Don\'t bother listing the values of ROIs you want: The program '
              'will find all of them and produce a full list',
         argstr='-all_rois')
@@ -693,8 +693,10 @@ class CenterMassOutputSpec(TraitedSpec):
         desc='output file')
     cm_file = File(
         desc='file with the center of mass coordinates')
-    cm = traits.Tuple(
-        traits.Float(), traits.Float(), traits.Float(),
+    cm = traits.Either(
+        traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
+        traits.List(traits.Tuple(traits.Float(), traits.Float(),
+                                 traits.Float())),
         desc='center of mass')
 
 
@@ -716,10 +718,10 @@ class CenterMass(AFNICommandBase):
     >>> from nipype.interfaces import afni
     >>> cm = afni.CenterMass()
     >>> cm.inputs.in_file = 'structural.nii'
-    >>> cm.inputs.out_file = 'cm.txt'
-    >>> cm.inputs.set_cm = (0, 0, 0)
+    >>> cm.inputs.cm_file = 'cm.txt'
+    >>> cm.inputs.roi_vals = [2, 10]
     >>> cm.cmdline  # doctest: +ALLOW_UNICODE
-    '3dcm -set 0 0 0 structural.nii > cm.txt'
+    '3dCM -roi_vals 2 10 structural.nii > cm.txt'
     >>> res = 3dcm.run()  # doctest: +SKIP
     """
 
@@ -732,7 +734,10 @@ def _list_outputs(self):
         outputs['out_file'] = os.path.abspath(self.inputs.in_file)
         outputs['cm_file'] = os.path.abspath(self.inputs.cm_file)
         sout = np.loadtxt(outputs['cm_file'])  # pylint: disable=E1101
-        outputs['cm'] = tuple(sout)
+        if len(sout) > 1:
+            outputs['cm'] = [tuple(s) for s in sout]
+        else:
+            outputs['cm'] = tuple(sout)
         return outputs