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ENH+FIX: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve #2426

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Merged
merged 11 commits into from
Feb 13, 2018
Merged

ENH+FIX: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve #2426

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908e326
ENH: add interface for AFNI 3dTproject
mvdoc Feb 2, 2018
49af623
Fix input argstr
mvdoc Feb 3, 2018
75b66ba
FIX: fix out_file when censor_motion is passed in OneDToolPy
mvdoc Feb 3, 2018
fd1037e
Add auto test for TProject, pepify out_file for OneDTool
mvdoc Feb 3, 2018
d3a7526
Fix doctest
mvdoc Feb 3, 2018
d4658cf
ENH: add -noFDR option to 3dDeconvolve
mvdoc Feb 6, 2018
d40a627
ENH: set correct number of jobs/threads for 3dDeconvolve
mvdoc Feb 6, 2018
9d96f4e
REF: jobs -> num_threads in 3dDeconvolve for consistency
mvdoc Feb 7, 2018
b7ea933
Fixes to 3dTProject args
mvdoc Feb 7, 2018
ae7dc34
Set nohash for num_threads in 3dDeconvolve
mvdoc Feb 7, 2018
3adfd64
Merge branch 'master' into enh/3dtproject
mvdoc Feb 12, 2018
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4 changes: 1 addition & 3 deletions nipype/interfaces/afni/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
'instead of the bucket dataset, if possible.',
argstr='-cbucket %s')
out_file = File(desc='output statistics file', argstr='-bucket %s')
jobs = traits.Int(
num_threads = traits.Int(
desc='run the program with provided number of sub-processes',
argstr='-jobs %d')
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Might want to set this to nohash=True, unless there's reason to think the number of threads affects the output.

fout = traits.Bool(
Expand Down Expand Up @@ -278,8 +278,6 @@ def _parse_inputs(self, skip=None):
self.inputs.num_glt = len(self.inputs.gltsym)
if not isdefined(self.inputs.out_file):
self.inputs.out_file = 'Decon.nii'
if isdefined(self.inputs.jobs):
self.inputs.num_threads = self.inputs.jobs

return super(Deconvolve, self)._parse_inputs(skip)

Expand Down
15 changes: 8 additions & 7 deletions nipype/interfaces/afni/preprocess.py
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Expand Up @@ -2425,7 +2425,8 @@ class TProjectInputSpec(AFNICommandInputSpec):
* This is a file of 1s and 0s, indicating which
time points are to be included (1) and which are
to be excluded (0).""",
argstr="-censor %s")
argstr="-censor %s",
exists=True)
censortr = traits.List(
traits.Str(),
desc="""list of strings that specify time indexes
Expand Down Expand Up @@ -2489,7 +2490,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
ort = File(
desc="""Remove each column in file
++ Each column will have its mean removed.""",
exist=True,
exists=True,
argstr="-ort %s")
polort = traits.Int(
desc="""Remove polynomials up to and including degree pp.
Expand All @@ -2505,15 +2506,15 @@ class TProjectInputSpec(AFNICommandInputSpec):
bandpass = traits.Tuple(
traits.Float, traits.Float,
desc="""Remove all frequencies EXCEPT those in the range""",
argstr='-bandpass %f %f')
argstr='-bandpass %g %g')
stopband = traits.Tuple(
traits.Float, traits.Float,
desc="""Remove all frequencies in the range""",
argstr='-stopband %f %f')
argstr='-stopband %g %g')
TR = traits.Float(
desc="""Use time step dd for the frequency calculations,
rather than the value stored in the dataset header.""",
argstr='-TR %f')
argstr='-TR %g')
mask = File(
exist=True,
desc="""Only operate on voxels nonzero in the mset dataset.
Expand All @@ -2530,7 +2531,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
width (FWHM) of fff millimeters.
++ Spatial blurring (if done) is after the time
series filtering.""",
argstr='-blur %f')
argstr='-blur %g')
norm = traits.Bool(
desc="""Normalize each output time series to have sum of
squares = 1. This is the LAST operation.""",
Expand Down Expand Up @@ -2562,7 +2563,7 @@ class TProject(AFNICommand):
>>> tproject.inputs.automask = True
>>> tproject.inputs.out_file = 'projected.nii.gz'
>>> tproject.cmdline
'3dTproject -input functional.nii -automask -bandpass 0.006670 99999.000000 -polort 3 -prefix projected.nii.gz'
'3dTproject -input functional.nii -automask -bandpass 0.00667 99999 -polort 3 -prefix projected.nii.gz'
>>> res = tproject.run() # doctest: +SKIP

"""
Expand Down
6 changes: 1 addition & 5 deletions nipype/interfaces/afni/tests/test_auto_Deconvolve.py
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Expand Up @@ -49,7 +49,6 @@ def test_Deconvolve_inputs():
sep=' ',
),
input1D=dict(argstr='-input1D %s', ),
jobs=dict(argstr='-jobs %d', ),
legendre=dict(argstr='-legendre', ),
local_times=dict(
argstr='-local_times',
Expand All @@ -70,10 +69,7 @@ def test_Deconvolve_inputs():
argstr='-num_stimts %d',
position=-6,
),
num_threads=dict(
nohash=True,
usedefault=True,
),
num_threads=dict(argstr='-jobs %d', ),
ortvec=dict(argstr='-ortvec %s %s', ),
out_file=dict(argstr='-bucket %s', ),
outputtype=dict(),
Expand Down
13 changes: 5 additions & 8 deletions nipype/interfaces/afni/tests/test_auto_TProject.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@

def test_TProject_inputs():
input_map = dict(
TR=dict(argstr='-TR %f', ),
TR=dict(argstr='-TR %g', ),
args=dict(argstr='%s', ),
automask=dict(
argstr='-automask',
xor=['mask'],
),
bandpass=dict(argstr='-bandpass %f %f', ),
blur=dict(argstr='-blur %f', ),
bandpass=dict(argstr='-bandpass %g %g', ),
blur=dict(argstr='-blur %g', ),
cenmode=dict(argstr='-cenmode %s', ),
censor=dict(argstr='-censor %s', ),
censortr=dict(argstr='-CENSORTR %s', ),
Expand Down Expand Up @@ -42,10 +42,7 @@ def test_TProject_inputs():
nohash=True,
usedefault=True,
),
ort=dict(
argstr='-ort %s',
exist=True,
),
ort=dict(argstr='-ort %s', ),
out_file=dict(
argstr='-prefix %s',
name_source='in_file',
Expand All @@ -54,7 +51,7 @@ def test_TProject_inputs():
),
outputtype=dict(),
polort=dict(argstr='-polort %d', ),
stopband=dict(argstr='-stopband %f %f', ),
stopband=dict(argstr='-stopband %g %g', ),
terminal_output=dict(
deprecated='1.0.0',
nohash=True,
Expand Down