From 03a67a96f68e06b0f862a20f0a32e5e95eea10c4 Mon Sep 17 00:00:00 2001 From: salma1601 Date: Sun, 17 Dec 2017 13:42:50 +0100 Subject: [PATCH 1/4] add verbosity options --- nipype/interfaces/afni/preprocess.py | 6 ++++++ nipype/interfaces/afni/tests/test_auto_Allineate.py | 4 ++++ nipype/interfaces/afni/tests/test_auto_Copy.py | 2 ++ nipype/interfaces/afni/tests/test_auto_TCat.py | 2 ++ nipype/interfaces/afni/tests/test_auto_TStat.py | 2 ++ nipype/interfaces/afni/utils.py | 9 +++++++++ 6 files changed, 25 insertions(+) diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index c96616273d..7c3b3359f4 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/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.') + verb = 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): diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index b8b79df004..0fd29f1479 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/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', ), + verb=dict(argstr='-verb', + ), warp_type=dict(argstr='-warp %s', ), warpfreeze=dict(argstr='-warpfreeze', diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 0917a0628e..273cb9bbb6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/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, ), + verb=dict(argstr='-verb', + ), ) inputs = Copy.input_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 597ead13cb..b28f983fa7 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/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, ), + verb=dict(argstr='-verb', + ), ) inputs = TCat.input_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 2315d81512..f2a0bc561b 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -33,6 +33,8 @@ def test_TStat_inputs(): terminal_output=dict(deprecated='1.0.0', nohash=True, ), + verbose=dict(argstr='-verb %s', + ), ) inputs = TStat.input_spec() diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 3e03adda92..0a71ea340a 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -751,6 +751,9 @@ class CopyInputSpec(AFNICommandInputSpec): argstr='%s', position=-1, name_source='in_file') + verb = 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) + verb = traits.Bool( + desc='Print out some verbose output as the program', + argstr='-verb') class TCat(AFNICommand): From a9099ed219d8aa9171f527db6bcdb553bf6a4c6e Mon Sep 17 00:00:00 2001 From: salma1601 Date: Sun, 17 Dec 2017 13:47:29 +0100 Subject: [PATCH 2/4] update MaskTool test --- nipype/interfaces/afni/tests/test_auto_MaskTool.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 775b34adab..eeaef55562 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/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() From 6e487b76968b0b177c7efd7a8c3c3945c22d51db Mon Sep 17 00:00:00 2001 From: salma1601 Date: Sun, 17 Dec 2017 13:47:52 +0100 Subject: [PATCH 3/4] update Tstat test --- nipype/interfaces/afni/tests/test_auto_TStat.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index f2a0bc561b..2315d81512 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -33,8 +33,6 @@ def test_TStat_inputs(): terminal_output=dict(deprecated='1.0.0', nohash=True, ), - verbose=dict(argstr='-verb %s', - ), ) inputs = TStat.input_spec() From 6829757e45360fec94c0d7aefe80f02d8f2c444a Mon Sep 17 00:00:00 2001 From: salma1601 Date: Mon, 18 Dec 2017 16:56:17 +0100 Subject: [PATCH 4/4] rather use verbose than verb --- nipype/interfaces/afni/preprocess.py | 4 ++-- nipype/interfaces/afni/tests/test_auto_Allineate.py | 2 +- nipype/interfaces/afni/tests/test_auto_Copy.py | 2 +- nipype/interfaces/afni/tests/test_auto_TCat.py | 2 +- nipype/interfaces/afni/utils.py | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 7c3b3359f4..5d90591953 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -438,12 +438,12 @@ class AllineateInputSpec(AFNICommandInputSpec): traits.Enum(*_dirs), argstr='-nwarp_fixdep%s', desc='To fix non-linear warp dependency along directions.') - verb = traits.Bool( + verbose = traits.Bool( argstr='-verb', desc='Print out verbose progress reports.') quiet = traits.Bool( argstr='-quiet', - desc='Don\'t print out verbose progress reports.') + desc="Don't print out verbose progress reports.") class AllineateOutputSpec(TraitedSpec): diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 0fd29f1479..73ecc66414 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -120,7 +120,7 @@ def test_Allineate_inputs(): ), usetemp=dict(argstr='-usetemp', ), - verb=dict(argstr='-verb', + verbose=dict(argstr='-verb', ), warp_type=dict(argstr='-warp %s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 273cb9bbb6..43fa537eb4 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -30,7 +30,7 @@ def test_Copy_inputs(): terminal_output=dict(deprecated='1.0.0', nohash=True, ), - verb=dict(argstr='-verb', + verbose=dict(argstr='-verb', ), ) inputs = Copy.input_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index b28f983fa7..f74a122828 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -32,7 +32,7 @@ def test_TCat_inputs(): terminal_output=dict(deprecated='1.0.0', nohash=True, ), - verb=dict(argstr='-verb', + verbose=dict(argstr='-verb', ), ) inputs = TCat.input_spec() diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 0a71ea340a..bce63c61e0 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -751,7 +751,7 @@ class CopyInputSpec(AFNICommandInputSpec): argstr='%s', position=-1, name_source='in_file') - verb = traits.Bool( + verbose = traits.Bool( desc='print progress reports', argstr='-verb') @@ -1991,7 +1991,7 @@ class TCatInputSpec(AFNICommandInputSpec): 'dataset mean back in. Option -rlt++ adds overall mean of all ' 'dataset timeseries back in.', position=1) - verb = traits.Bool( + verbose = traits.Bool( desc='Print out some verbose output as the program', argstr='-verb')