From 506e534a193911cda468564f2ff729c4a293133c Mon Sep 17 00:00:00 2001
From: Christoph Arthofer <christoph.arthofer@ndcn.ox.ac.uk>
Date: Tue, 3 Aug 2021 11:58:55 +0100
Subject: [PATCH] ENH: Added wrapper for epi_reg
---
fsl/wrappers/__init__.py | 1 +
fsl/wrappers/epi_reg.py | 41 ++++++++++++++++++++++++++++
tests/test_wrappers/test_wrappers.py | 8 ++++++
3 files changed, 50 insertions(+)
mode change 100644 => 100755 fsl/wrappers/__init__.py
create mode 100755 fsl/wrappers/epi_reg.py
mode change 100644 => 100755 tests/test_wrappers/test_wrappers.py
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
old mode 100644
new mode 100755
index 19292be71..7848a07b7
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -110,4 +110,5 @@ from .misc import (fslreorient2std, # noqa
slicer,
cluster,
gps)
+from .epi_reg import epi_reg
from . import tbss # noqa
diff --git a/fsl/wrappers/epi_reg.py b/fsl/wrappers/epi_reg.py
new file mode 100755
index 000000000..fe955689a
--- /dev/null
+++ b/fsl/wrappers/epi_reg.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+#
+# epi_reg.py - Wrapper for the epi_reg command.
+#
+# Author:
+#
+"""This module provides the :func:`epi_reg` function, a wrapper for the FSL
+`epi_reg <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg>`_ command.
+"""
+
+import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
+
+@wutils.fileOrImage('epi', 't1', 't1brain', 'fmap', 'fmapmag', 'fmapmagbrain', 'gdc', 'wmseg', 'weight', outprefix='out')
+@wutils.fslwrapper
+def epi_reg(epi, t1, t1brain, out='epi_reg', **kwargs):
+ """Wrapper for the ``epi_reg`` command.
+
+ :arg epi: Input EPI image
+ :arg t1: Input wholehead T1 image
+ :arg t1brain: Input brain extracted T1 image
+ :arg out: Output name
+ """
+ asrt.assertIsNifti(epi)
+ asrt.assertIsNifti(t1)
+ asrt.assertIsNifti(t1brain)
+
+ valmap = {
+ 'nofmapreg' : wutils.SHOW_IF_TRUE,
+ 'noclean' : wutils.SHOW_IF_TRUE,
+ 'v' : wutils.SHOW_IF_TRUE,
+ }
+
+ cmd = ['epi_reg', '--epi='+epi, '--t1='+t1, '--t1brain='+t1brain, '--out='+out]
+
+ cmd += wutils.applyArgStyle('--=',
+ valmap=valmap,
+ singlechar_args=True,
+ **kwargs)
+
+ return cmd
diff --git a/tests/test_wrappers/test_wrappers.py b/tests/test_wrappers/test_wrappers.py
old mode 100644
new mode 100755
index 2c8b9b1aa..5eaea8177
--- a/tests/test_wrappers/test_wrappers.py
+++ b/tests/test_wrappers/test_wrappers.py
@@ -93,6 +93,14 @@ def test_flirt():
assert checkResult(result.stdout[0], *expected)
+def test_epi_reg():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('epi_reg',)) as fsldir:
+ epi_reg = op.join(fsldir, 'bin', 'epi_reg')
+ result = fw.epi_reg('epi', 't1', 't1brain', 'out')
+ expected = epi_reg + ' --epi=epi --t1=t1 --t1brain=t1brain --out=out'
+ assert result.stdout[0] == expected
+
+
def test_applyxfm():
with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('flirt',)) as fsldir:
flirt = op.join(fsldir, 'bin', 'flirt')
--
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