Merge pull request #2345 from salma1601/afni_verbosity

Afni verbosity

Author: mgxd

nipype/interfaces/afni/preprocess.py

@@ -438,6 +438,12 @@ class AllineateInputSpec(AFNICommandInputSpec):
         traits.Enum(*_dirs),
         argstr='-nwarp_fixdep%s',
         desc='To fix non-linear warp dependency along directions.')
+    verbose = traits.Bool(
+        argstr='-verb',
+        desc='Print out verbose progress reports.')
+    quiet = traits.Bool(
+        argstr='-quiet',
+        desc="Don't print out verbose progress reports.")
 
 
 class AllineateOutputSpec(TraitedSpec):

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -95,6 +95,8 @@ def test_Allineate_inputs():
     outputtype=dict(),
     overwrite=dict(argstr='-overwrite',
     ),
+    quiet=dict(argstr='-quiet',
+    ),
     reference=dict(argstr='-base %s',
     ),
     replacebase=dict(argstr='-replacebase',
@@ -118,6 +120,8 @@ def test_Allineate_inputs():
     ),
     usetemp=dict(argstr='-usetemp',
     ),
+    verbose=dict(argstr='-verb',
+    ),
     warp_type=dict(argstr='-warp %s',
     ),
     warpfreeze=dict(argstr='-warpfreeze',

nipype/interfaces/afni/tests/test_auto_Copy.py

@@ -30,6 +30,8 @@ def test_Copy_inputs():
     terminal_output=dict(deprecated='1.0.0',
     nohash=True,
     ),
+    verbose=dict(argstr='-verb',
+    ),
     )
     inputs = Copy.input_spec()
 

nipype/interfaces/afni/tests/test_auto_MaskTool.py

@@ -49,6 +49,8 @@ def test_MaskTool_inputs():
     ),
     union=dict(argstr='-union',
     ),
+    verbose=dict(argstr='-verb %s',
+    ),
     )
     inputs = MaskTool.input_spec()
 

nipype/interfaces/afni/tests/test_auto_TCat.py

@@ -32,6 +32,8 @@ def test_TCat_inputs():
     terminal_output=dict(deprecated='1.0.0',
     nohash=True,
     ),
+    verbose=dict(argstr='-verb',
+    ),
     )
     inputs = TCat.input_spec()
 

nipype/interfaces/afni/utils.py

@@ -751,6 +751,9 @@ class CopyInputSpec(AFNICommandInputSpec):
         argstr='%s',
         position=-1,
         name_source='in_file')
+    verbose = traits.Bool(
+        desc='print progress reports',
+        argstr='-verb')
 
 
 class Copy(AFNICommand):
@@ -1377,6 +1380,9 @@ class MaskToolInputSpec(AFNICommandInputSpec):
              'or using the labels in {R,L,A,P,I,S}.',
         argstr='-fill_dirs %s',
         requires=['fill_holes'])
+    verbose = traits.Int(
+        desc='specify verbosity level, for 0 to 3',
+        argstr='-verb %s')
 
 
 class MaskToolOutputSpec(TraitedSpec):
@@ -1985,6 +1991,9 @@ class TCatInputSpec(AFNICommandInputSpec):
              'dataset mean back in. Option -rlt++ adds overall mean of all '
              'dataset timeseries back in.',
         position=1)
+    verbose = traits.Bool(
+        desc='Print out some verbose output as the program',
+        argstr='-verb')
 
 
 class TCat(AFNICommand):