Editing few options on the interface FillLesions

Author: byvernault

nipype/interfaces/niftyseg/lesions.py

@@ -45,48 +45,47 @@ class FillLesionsInputSpec(CommandLineInputSpec):
 
     # Optional arguments
     desc = "Dilate the mask <int> times (in voxels, by default 0)"
-    in_dilation = traits.Int(desc=desc, argstr='-dil %d', mandatory=False)
+    in_dilation = traits.Int(desc=desc, argstr='-dil %d')
 
     desc = 'Percentage of minimum number of voxels between patches <float> \
 (by default 0.5).'
-    match = traits.Float(desc=desc, argstr='-match %f', mandatory=False)
+    match = traits.Float(desc=desc, argstr='-match %f')
 
     desc = 'Minimum percentage of valid voxels in target patch <float> \
 (by default 0).'
-    search = traits.Float(desc=desc, argstr='-search %f', mandatory=False)
+    search = traits.Float(desc=desc, argstr='-search %f')
 
     desc = 'Smoothing by <float> (in minimal 6-neighbourhood voxels \
 (by default 0.1)).'
-    smooth = traits.Float(desc=desc, argstr='-smo %f', mandatory=False)
+    smooth = traits.Float(desc=desc, argstr='-smo %f')
 
     desc = 'Search regions size respect biggest patch size (by default 4).'
-    size = traits.Int(desc=desc, argstr='-size %d', mandatory=False)
+    size = traits.Int(desc=desc, argstr='-size %d')
 
     desc = 'Patch cardinality weighting factor (by default 2).'
-    cwf = traits.Float(desc=desc, argstr='-cwf %f', mandatory=False)
+    cwf = traits.Float(desc=desc, argstr='-cwf %f')
 
     desc = 'Give a binary mask with the valid search areas.'
-    bin_mask = File(desc=desc, argstr='-mask %s', mandatory=False)
+    bin_mask = File(desc=desc, argstr='-mask %s')
 
     desc = "Guizard et al. (FIN 2015) method, it doesn't include the \
 multiresolution/hierarchical inpainting part, this part needs to be done \
 with some external software such as reg_tools and reg_resample from NiftyReg. \
 By default it uses the method presented in Prados et al. (Neuroimage 2016)."
-    other = traits.Bool(desc=desc, argstr='-other', mandatory=False)
+    other = traits.Bool(desc=desc, argstr='-other')
+
+    use_2d = traits.Bool(desc='Uses 2D patches in the Z axis, by default 3D.',
+                         argstr='-2D')
 
     debug = traits.Bool(desc='Save all intermidium files (by default OFF).',
-                        argstr='-debug', mandatory=False)
+                        argstr='-debug')
 
     desc = 'Set output <datatype> (char, short, int, uchar, ushort, uint, \
 float, double).'
-    out_datatype = traits.String(desc=desc, argstr='-odt %s', mandatory=False)
+    out_datatype = traits.String(desc=desc, argstr='-odt %s')
 
     verbose = traits.Bool(desc='Verbose (by default OFF).',
-                          argstr='-v', mandatory=False)
-
-    # Set the number of omp thread to use
-    omp_core = traits.Int(desc='Number of openmp thread to use. Default: 4',
-                          argstr='-omp %d')
+                          argstr='-v')
 
 
 class FillLesionsOutputSpec(TraitedSpec):

nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py

@@ -7,13 +7,10 @@ def test_FillLesions_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
     bin_mask=dict(argstr='-mask %s',
-    mandatory=False,
     ),
     cwf=dict(argstr='-cwf %f',
-    mandatory=False,
     ),
     debug=dict(argstr='-debug',
-    mandatory=False,
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -22,7 +19,6 @@ def test_FillLesions_inputs():
     usedefault=True,
     ),
     in_dilation=dict(argstr='-dil %d',
-    mandatory=False,
     ),
     in_file=dict(argstr='-i %s',
     mandatory=True,
@@ -33,34 +29,27 @@ def test_FillLesions_inputs():
     position=2,
     ),
     match=dict(argstr='-match %f',
-    mandatory=False,
-    ),
-    omp_core=dict(argstr='-omp %d',
     ),
     other=dict(argstr='-other',
-    mandatory=False,
     ),
     out_datatype=dict(argstr='-odt %s',
-    mandatory=False,
     ),
     out_file=dict(argstr='-o %s',
     name_source=['in_file'],
     name_template='%s_lesions_filled.nii.gz',
     position=3,
     ),
     search=dict(argstr='-search %f',
-    mandatory=False,
     ),
     size=dict(argstr='-size %d',
-    mandatory=False,
     ),
     smooth=dict(argstr='-smo %f',
-    mandatory=False,
     ),
     terminal_output=dict(nohash=True,
     ),
+    use_2d=dict(argstr='-2D',
+    ),
     verbose=dict(argstr='-v',
-    mandatory=False,
     ),
     )
     inputs = FillLesions.input_spec()