From c24578f75291e6beb8a3a464c277e132296b6ef1 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Thu, 23 Jul 2020 11:36:19 +0100
Subject: [PATCH] ENH: add wrapper for gps
---
fsl/wrappers/__init__.py | 3 ++-
fsl/wrappers/misc.py | 19 +++++++++++++++++++
tests/test_wrappers/test_wrappers.py | 10 +++++++++-
3 files changed, 30 insertions(+), 2 deletions(-)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 87f410cb9..25f5ff9f1 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -107,4 +107,5 @@ from .melodic import (melodic, # noqa
from .misc import (fslreorient2std, # noqa
fslroi,
slicer,
- cluster)
+ cluster,
+ gps)
diff --git a/fsl/wrappers/misc.py b/fsl/wrappers/misc.py
index 9c2188828..925081483 100644
--- a/fsl/wrappers/misc.py
+++ b/fsl/wrappers/misc.py
@@ -85,3 +85,22 @@ def cluster(input, thresh, **kwargs):
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
+
+@wutils.fileOrArray('out', 'init')
+@wutils.fslwrapper
+def gps(out, ndir, **kwargs):
+ """Wrapper of the ``gps`` command
+
+ Usage example to get 128 gradient orientations on the whole sphere::
+
+ from fsl.wrappers import gps, LOAD
+ bvecs = gps(LOAD, 128, optws=True)['out']
+ """
+ valmap = {name: wutils.SHOW_IF_TRUE for name in [
+ 'optws', 'report', 'verbose'
+ ]}
+
+ cmd = ['gps', f'--ndir={ndir}', f'--out={out}']
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+
+ return cmd
diff --git a/tests/test_wrappers/test_wrappers.py b/tests/test_wrappers/test_wrappers.py
index 695bedfb3..a75cf2734 100644
--- a/tests/test_wrappers/test_wrappers.py
+++ b/tests/test_wrappers/test_wrappers.py
@@ -336,7 +336,6 @@ def test_fast():
assert result.stdout[0] == ' '.join(expected)
-
def test_fsl_anat():
with asrt.disabled(), \
run.dryrun(), \
@@ -349,3 +348,12 @@ def test_fsl_anat():
'-s', '25']
assert result.stdout[0] == ' '.join(expected)
+
+
+def test_gps():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('gps',)) as fsldir:
+ gps = op.join(fsldir, 'bin', 'gps')
+ result = fw.gps('bvecs', 128, optws=True, ranseed=123)
+ expected = (gps + ' --ndir=128 --out=bvecs',
+ ('--optws', '--ranseed=123'))
+ assert checkResult(result.stdout[0], *expected)
--
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