Dcm2nii and related tests

Author: mick-d

nipype/interfaces/dcm2nii.py

@@ -21,7 +21,7 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
                                   copyfile=False, mandatory=True)
     anonymize = traits.Bool(True, argstr='-a', usedefault=True, position=0)
     config_file = File(exists=True, argstr="-b %s", genfile=True, position=1)
-    collapse_folders = traits.Bool(True, argstr='-c', usedefault=True, position=2)    
+    collapse_folders = traits.Bool(True, argstr='-c', usedefault=True, position=2)
     date_in_filename = traits.Bool(True, argstr='-d', usedefault=True, position=3)
     events_in_filename = traits.Bool(True, argstr='-e', usedefault=True, position=4)
     source_in_filename = traits.Bool(False, argstr='-f', usedefault=True, position=5)
@@ -56,7 +56,7 @@ class Dcm2nii(CommandLine):
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
     >>> converter.cmdline #doctest: +ELLIPSIS
-    'dcm2nii -g y -n y -i n -o . -b config.ini functional_1.dcm'
+    'dcm2nii -a y -b config.ini -c y -d y -e y -f n -g y -i n -n y -o . -p y -v y -x n functional_1.dcm'
     >>> converter.run() # doctest: +SKIP
     """
 
@@ -69,7 +69,7 @@ def _format_arg(self, opt, spec, val):
         if opt in ['anonymize', 'collapse_folders', 'date_in_filename', 'events_in_filename',
                    'source_in_filename','gzip_output', 'id_in_filename','nii_output',
                    'protocol_in_filename','reorient','spm_analyze','convert_all_pars',
-                   'reorient_and_crop']:          
+                   'reorient_and_crop']:
             spec = deepcopy(spec)
             if val:
                 spec.argstr += ' y'

nipype/interfaces/tests/test_auto_Dcm2nii.py

@@ -4,50 +4,77 @@
 
 def test_Dcm2nii_inputs():
     input_map = dict(anonymize=dict(argstr='-a',
-    position=2,
+    position=0,
+    usedefault=True,
     ),
     args=dict(argstr='%s',
-    position=9,
+    position=15,
+    ),
+    collapse_folders=dict(argstr='-c',
+    position=2,
+    usedefault=True,
     ),
     config_file=dict(argstr='-b %s',
     genfile=True,
-    position=7,
+    position=1,
     ),
     convert_all_pars=dict(argstr='-v',
-    position=8,
+    position=13,
+    usedefault=True,
+    ),
+    date_in_filename=dict(argstr='-d',
+    position=3,
+    usedefault=True,
     ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    events_in_filename=dict(argstr='-e',
+    position=4,
+    usedefault=True,
+    ),
     gzip_output=dict(argstr='-g',
-    position=0,
+    position=6,
     usedefault=True,
     ),
     id_in_filename=dict(argstr='-i',
-    position=3,
+    position=7,
     usedefault=True,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
     nii_output=dict(argstr='-n',
-    position=1,
+    position=8,
     usedefault=True,
     ),
     output_dir=dict(argstr='-o %s',
     genfile=True,
-    position=6,
+    position=9,
+    ),
+    protocol_in_filename=dict(argstr='-p',
+    position=10,
+    usedefault=True,
     ),
     reorient=dict(argstr='-r',
-    position=4,
+    position=11,
     ),
     reorient_and_crop=dict(argstr='-x',
+    position=14,
+    usedefault=True,
+    ),
+    source_in_filename=dict(argstr='-f',
     position=5,
+    usedefault=True,
     ),
     source_names=dict(argstr='%s',
     copyfile=False,
     mandatory=True,
-    position=10,
+    position=16,
+    ),
+    spm_analyze=dict(argstr='-s',
+    position=12,
+    xor=['nii_output'],
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,