Merge pull request #1213 from chrisfilo/fix/cmd_bool

added support for boolean flags in nipype_cmd

Author: satra

nipype/utils/nipype_cmd.py

@@ -2,7 +2,7 @@
 import argparse
 import inspect
 import sys
-from nipype.interfaces.base import Interface, InputMultiPath
+from nipype.interfaces.base import Interface, InputMultiPath, traits
 from nipype.utils.misc import str2bool
 
 def listClasses(module=None):
@@ -24,6 +24,9 @@ def add_options(parser=None, module=None, function=None):
         for name, spec in sorted(interface.inputs.traits(transient=None).items()):
             desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:]
             args = {}
+            
+            if spec.is_trait_type(traits.Bool):
+                args["action"] = 'store_true'
 
             if hasattr(spec, "mandatory") and spec.mandatory:
                 if spec.is_trait_type(InputMultiPath):
@@ -43,16 +46,17 @@ def run_instance(interface, options):
         for input_name, _ in interface.inputs.items():
             if getattr(options, input_name) != None:
                 value = getattr(options, input_name)
-                #traits cannot cast from string to float or int
-                try:
-                    value = float(value)
-                except:
-                    pass
-                #try to cast string input to boolean
-                try:
-                    value = str2bool(value)
-                except:
-                    pass
+                if not isinstance(value, bool):
+                    #traits cannot cast from string to float or int
+                    try:
+                        value = float(value)
+                    except:
+                        pass
+                    #try to cast string input to boolean
+                    try:
+                        value = str2bool(value)
+                    except:
+                        pass
                 try:
                     setattr(interface.inputs, input_name,
                             value)

nipype/utils/tests/test_cmd.py

@@ -88,7 +88,7 @@ def test_run_4d_realign_without_arguments(self):
         self.assertEqual(stderr.getvalue(),
 """usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h]
                                                        [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]]
-                                                       [--ignore_exception IGNORE_EXCEPTION]
+                                                       [--ignore_exception]
                                                        [--loops [LOOPS [LOOPS ...]]]
                                                        [--slice_order SLICE_ORDER]
                                                        [--speedup [SPEEDUP [SPEEDUP ...]]]
@@ -113,4 +113,4 @@ def test_run_4d_realign_help(self):
         self.assertTrue("Run FmriRealign4d" in stdout.getvalue())
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()