Merge remote-tracking branch 'upstream/master' into enh-mrtrix3

Author: matteomancini

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/tests/test_auto_Unifize.py

@@ -6,6 +6,8 @@
 def test_Unifize_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    cl_frac=dict(argstr='-clfrac %f',
+    ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
@@ -31,14 +33,19 @@ def test_Unifize_inputs():
     ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
+    name_template='%s_unifized',
     ),
     outputtype=dict(),
+    quiet=dict(argstr='-quiet',
+    ),
     rbt=dict(argstr='-rbt %f %f %f',
     ),
     scale_file=dict(argstr='-ssave %s',
     ),
     t2=dict(argstr='-T2',
     ),
+    t2_up=dict(argstr='-T2up %f',
+    ),
     terminal_output=dict(deprecated='1.0.0',
     nohash=True,
     ),

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):
@@ -2291,6 +2300,7 @@ class UnifizeInputSpec(AFNICommandInputSpec):
         exists=True,
         copyfile=False)
     out_file = File(
+        name_template='%s_unifized',
         desc='output image file name',
         argstr='-prefix %s',
         name_source='in_file')
@@ -2337,6 +2347,22 @@ class UnifizeInputSpec(AFNICommandInputSpec):
              'b = bottom percentile of normalizing data range, [default=70.0]\n'
              'r = top percentile of normalizing data range, [default=80.0]\n',
         argstr='-rbt %f %f %f')
+    t2_up = traits.Float(
+        desc='Option for AFNI experts only.'
+             'Set the upper percentile point used for T2-T1 inversion. '
+             'Allowed to be anything between 90 and 100 (inclusive), with '
+             'default to 98.5  (for no good reason).',
+        argstr='-T2up %f')
+    cl_frac = traits.Float(
+        desc='Option for AFNI experts only.'
+             'Set the automask \'clip level fraction\'. Must be between '
+             '0.1 and 0.9. A small fraction means to make the initial '
+             'threshold for clipping (a la 3dClipLevel) smaller, which '
+             'will tend to make the mask larger.  [default=0.1]',
+        argstr='-clfrac %f')
+    quiet = traits.Bool(
+        desc='Don\'t print the progress messages.',
+        argstr='-quiet')
 
 
 class UnifizeOutputSpec(TraitedSpec):