Merge branch 'master' into 'master'

ENH: Added wrapper for epi_reg

See merge request fsl/fslpy!306

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

fsl/wrappers/epi_reg.py

+#!/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

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')