Fix/vol2surf

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/base.py

@@ -1349,9 +1349,9 @@ def _terminal_output_update(self):
     def set_default_terminal_output(cls, output_type):
         """Set the default terminal output for CommandLine Interfaces.
 
-        This method is used to set default terminal output for 
-        CommandLine Interfaces.  However, setting this will not 
-        update the output type for any existing instances.  For these, 
+        This method is used to set default terminal output for
+        CommandLine Interfaces.  However, setting this will not
+        update the output type for any existing instances.  For these,
         assign the <instance>.inputs.terminal_output.
         """
 

nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py

@@ -91,7 +91,7 @@ def test_SampleToSurface_inputs():
     ),
     subject_id=dict(),
     subjects_dir=dict(),
-    surf_reg=dict(argstr='--surfreg',
+    surf_reg=dict(argstr='--surfreg %s',
     requires=['target_subject'],
     ),
     surface=dict(argstr='--surf %s',

nipype/interfaces/freesurfer/utils.py

@@ -89,8 +89,8 @@ class SampleToSurfaceInputSpec(FSTraitedSpec):
     subject_id = traits.String(desc="subject id")
     target_subject = traits.String(argstr="--trgsubject %s",
                      desc="sample to surface of different subject than source")
-    surf_reg = traits.Bool(argstr="--surfreg", requires=["target_subject"],
-                           desc="use surface registration to target subject")
+    surf_reg = traits.String(argstr="--surfreg %s", requires=["target_subject"],
+                           desc="registration surface to target subject (default sphere.reg)")
     ico_order = traits.Int(argstr="--icoorder %d", requires=["target_subject"],
                            desc="icosahedron order when target_subject is 'ico'")
 
@@ -1276,4 +1276,4 @@ def _gen_outfilename(self):
             return os.path.abspath(self.inputs.out_file)
         else:
             _, name, ext = split_filename(self.inputs.in_file)
-            return os.path.abspath(name + '_smoothed' + ext)
+            return os.path.abspath(name + '_smoothed' + ext)

nipype/utils/nipype_cmd.py

@@ -19,7 +19,7 @@ def add_options(parser=None, module=None, function=None):
     if parser and module and function:
         __import__(module)
         interface = getattr(sys.modules[module],function)()
-        
+
         inputs = interface.input_spec()
         for name, spec in sorted(interface.inputs.traits(transient=None).items()):
             desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:]
@@ -33,7 +33,7 @@ def add_options(parser=None, module=None, function=None):
 def run_instance(interface, options):
     if interface:
         print "setting function inputs"
-            
+
         for input_name, _ in interface.inputs.items():
             if getattr(options, input_name) != None:
                 value = getattr(options, input_name)
@@ -48,23 +48,23 @@ def run_instance(interface, options):
                             value)
                 except ValueError, e:
                     print "Error when setting the value of %s: '%s'"%(input_name, str(e))
-                    
+
         print interface.inputs
         res = interface.run()
-        print res.outputs    
+        print res.outputs
 
 
 def main(argv):
-    
+
     if len(argv) == 2 and not argv[1].startswith("-"):
         listClasses(argv[1])
         sys.exit(0)
-    
+
     parser = argparse.ArgumentParser(description='Nipype interface runner', prog=argv[0])
     parser.add_argument("module", type=str, help="Module name")
     parser.add_argument("interface", type=str, help="Interface name")
     parsed = parser.parse_args(args=argv[1:3])
-    
+
     _, prog = os.path.split(argv[0])
     interface_parser = argparse.ArgumentParser(description="Run %s"%parsed.interface, prog=" ".join([prog] + argv[1:3]))
     interface_parser, interface  = add_options(interface_parser, parsed.module, parsed.interface)

nipype/utils/tests/test_cmd.py

@@ -22,24 +22,24 @@ def test_main_returns_2_on_empty(self):
         with self.assertRaises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
                 nipype_cmd.main(['nipype_cmd'])
-        
+
         exit_exception = cm.exception
         self.assertEqual(exit_exception.code, 2)
-        
-        self.assertEqual(stderr.getvalue(), 
+
+        self.assertEqual(stderr.getvalue(),
 """usage: nipype_cmd [-h] module interface
 nipype_cmd: error: too few arguments
 """)
         self.assertEqual(stdout.getvalue(), '')
-        
+
     def test_main_returns_0_on_help(self):
         with self.assertRaises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
                 nipype_cmd.main(['nipype_cmd', '-h'])
-        
+
         exit_exception = cm.exception
         self.assertEqual(exit_exception.code, 0)
-        
+
         self.assertEqual(stderr.getvalue(), '')
         self.assertEqual(stdout.getvalue(),
 """usage: nipype_cmd [-h] module interface
@@ -53,15 +53,15 @@ def test_main_returns_0_on_help(self):
 optional arguments:
   -h, --help  show this help message and exit
 """)
-    
+
     def test_list_nipy_interfacesp(self):
         with self.assertRaises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
                 nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy'])
-        
+
         exit_exception = cm.exception
         self.assertEqual(exit_exception.code, 0)
-        
+
         self.assertEqual(stderr.getvalue(), '')
         self.assertEqual(stdout.getvalue(),
 """Available Interfaces:
@@ -77,10 +77,10 @@ def test_run_4d_realign_without_arguments(self):
         with self.assertRaises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
                 nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d'])
-        
+
         exit_exception = cm.exception
         self.assertEqual(exit_exception.code, 2)
-        
+
         self.assertEqual(stderr.getvalue(),
 """usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h]
                                                        [--between_loops BETWEEN_LOOPS]
@@ -95,15 +95,15 @@ def test_run_4d_realign_without_arguments(self):
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """)
         self.assertEqual(stdout.getvalue(), '')
-        
+
     def test_run_4d_realign_help(self):
         with self.assertRaises(SystemExit) as cm:
             with capture_sys_output() as (stdout, stderr):
                 nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d', '-h'])
-        
+
         exit_exception = cm.exception
         self.assertEqual(exit_exception.code, 0)
-        
+
         self.assertEqual(stderr.getvalue(), '')
         self.assertTrue("Run FmriRealign4d" in stdout.getvalue())