Improved input options description.

Author: chrisgorgo

nipype/utils/nipype_cmd.py

@@ -19,18 +19,21 @@ def add_options(parser=None, module=None, function=None):
     if parser and module and function:
         __import__(module)
         interface = getattr(sys.modules[module],function)()
-
-        for k,v in interface.inputs.items():
-            if hasattr(v, "mandatory") and v.mandatory:
-                parser.add_argument(k, help=v.desc)
+        
+        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:]
+            if hasattr(spec, "mandatory") and spec.mandatory:
+                parser.add_argument(name, help=desc)
             else:
-                parser.add_argument("--%s"%k, dest=k,
-                                help=v.desc)
+                parser.add_argument("--%s"%name, dest=name,
+                                    help=desc)
     return parser, interface
 
 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)

nipype/utils/tests/test_cmd.py

@@ -120,31 +120,40 @@ def test_run_4d_realign_help(self):
 Run FmriRealign4d
 
 positional arguments:
-  in_file               File to realign
-  tr                    TR in seconds
+  in_file               (a list of items which are an existing file name) File
+                        to realign
+  tr                    (a float) TR in seconds
 
 optional arguments:
   -h, --help            show this help message and exit
   --between_loops BETWEEN_LOOPS
-                        loops used to realign different runs
+                        (a list of items which are an integer, nipype default
+                        value: [5]) loops used to realign different runs
   --ignore_exception IGNORE_EXCEPTION
-                        Print an error message instead of throwing an
-                        exception in case the interface fails to run
-  --loops LOOPS         loops within each run
+                        (a boolean, nipype default value: False) Print an
+                        error message instead of throwing an exception in case
+                        the interface fails to run
+  --loops LOOPS         (a list of items which are an integer, nipype default
+                        value: [5]) loops within each run
   --slice_order SLICE_ORDER
-                        0 based slice order. This would be equivalent to
+                        (a list of items which are an integer) 0 based slice
+                        order. This would be equivalent to
                         enteringnp.argsort(spm_slice_order) for this field.
                         This effectsinterleaved acquisition. This field will
                         be deprecated infuture Nipy releases and be replaced
-                        by actual sliceacquisition times.
-  --speedup SPEEDUP     successive image sub-sampling factors for acceleration
-  --start START         time offset into TR to align slices to
+                        by actual sliceacquisition times. requires:
+                        time_interp
+  --speedup SPEEDUP     (a list of items which are an integer, nipype default
+                        value: [5]) successive image sub-sampling factors for
+                        acceleration
+  --start START         (a float, nipype default value: 0.0) time offset into
+                        TR to align slices to
   --time_interp TIME_INTERP
-                        Assume smooth changes across time e.g., fmri series.
-                        If you don't want slice timing correction set this to
-                        undefined
+                        (True) Assume smooth changes across time e.g., fmri
+                        series. If you don't want slice timing correction set
+                        this to undefined requires: slice_order
   --tr_slices TR_SLICES
-                        TR slices
+                        (a float) TR slices requires: time_interp
 """)