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Afni verbosity #2345

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Merged
merged 4 commits into from
Jan 5, 2018
Merged

Afni verbosity #2345

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03a67a9
add verbosity options
salma1601 Dec 17, 2017
a9099ed
update MaskTool test
salma1601 Dec 17, 2017
6e487b7
update Tstat test
salma1601 Dec 17, 2017
6829757
rather use verbose than verb
salma1601 Dec 18, 2017
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6 changes: 6 additions & 0 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
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4 changes: 4 additions & 0 deletions nipype/interfaces/afni/tests/test_auto_Allineate.py
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Expand Up @@ -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',
Expand All @@ -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',
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2 changes: 2 additions & 0 deletions nipype/interfaces/afni/tests/test_auto_Copy.py
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Expand Up @@ -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()

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2 changes: 2 additions & 0 deletions nipype/interfaces/afni/tests/test_auto_MaskTool.py
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Expand Up @@ -49,6 +49,8 @@ def test_MaskTool_inputs():
),
union=dict(argstr='-union',
),
verbose=dict(argstr='-verb %s',
),
)
inputs = MaskTool.input_spec()

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2 changes: 2 additions & 0 deletions nipype/interfaces/afni/tests/test_auto_TCat.py
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Expand Up @@ -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()

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9 changes: 9 additions & 0 deletions nipype/interfaces/afni/utils.py
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Expand Up @@ -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):
Expand Down Expand Up @@ -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(
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Note that you have verbose in Copy. If it's okay to mix-and-match (i.e., there are some interfaces that already have verbose), I'd prefer that you use verbose for all new additions. If this would be the first interface with verbose, I'd say switch it to verb for consistency.

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Sorry I am not sure to follow. I added verbose to Allineate, Copy, MaskTool andTcat. These interfaces had no verbosity parameter before. I didn't touch the other ones which had already a verb or a verbose parameter as you told me.

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Sorry, I think I wrote this just as you made those changes. I wasn't sure if you were going to keep it at verb, but the changes you made look good. You can safely ignore that last message. (Also this one.)

desc='specify verbosity level, for 0 to 3',
argstr='-verb %s')


class MaskToolOutputSpec(TraitedSpec):
Expand Down Expand Up @@ -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):
Expand Down