Merge branch 'master' into 'master'

ENH: wrapper for `fslorient` tool

See merge request fsl/fslpy!315

fsl/wrappers/__init__.py

@@ -110,6 +110,7 @@ from fsl.wrappers.fugue        import (fugue,
 from fsl.wrappers.melodic      import (melodic,
                                        fsl_regfilt)
 from fsl.wrappers.misc         import (fslreorient2std,
+                                       fslorient,
                                        fslroi,
                                        slicer,
                                        cluster,

fsl/wrappers/misc.py

@@ -29,6 +29,34 @@ def fslreorient2std(input, output=None):
     return cmd
 
 
+@wutils.fileOrImage('input')
+@wutils.fslwrapper
+def fslorient(input, **kwargs):
+    """Wrapper for the ``fslorient`` tool."""
+
+    asrt.assertIsNifti(input)
+
+    valmap = {
+        'getorient'                : wutils.SHOW_IF_TRUE,
+        'getsform'                 : wutils.SHOW_IF_TRUE,
+        'getqform'                 : wutils.SHOW_IF_TRUE,
+        'getsformcode'             : wutils.SHOW_IF_TRUE,
+        'getqformcode'             : wutils.SHOW_IF_TRUE,
+        'copysform2qform'          : wutils.SHOW_IF_TRUE,
+        'copyqform2sform'          : wutils.SHOW_IF_TRUE,
+        'deleteorient'             : wutils.SHOW_IF_TRUE,
+        'forceradiological'        : wutils.SHOW_IF_TRUE,
+        'forceneurological'        : wutils.SHOW_IF_TRUE,
+        'swaporient'               : wutils.SHOW_IF_TRUE,
+    }
+
+    cmd = ['fslorient']
+    cmd += wutils.applyArgStyle('-', valsep=' ', valmap=valmap, **kwargs)
+    cmd += [input]
+
+    return cmd
+
+
 @wutils.fileOrImage('input', 'output')
 @wutils.fslwrapper
 def fslroi(input, output, *args):

tests/test_wrappers/test_wrappers.py

@@ -250,6 +250,21 @@ def test_fsl_regfilt():
         assert checkResult(result.stdout[0], *expected)
 
 
+def test_fslorient():
+    with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslorient',)) as fsldir:
+        fslo    = op.join(fsldir, 'bin', 'fslorient')
+        result   = fw.fslorient('input', setsform=(-2, 0, 0, 90, 0, 2, 0, -126, 0, 0, 2, -72, 0, 0, 0, 1))
+        expected = fslo + ' -setsform -2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1' + ' input'
+        assert result.stdout[0] == expected
+
+        result   = fw.fslorient('input', getorient=True)
+        expected = fslo + ' -getorient' + ' input'
+        assert result.stdout[0] == expected
+
+        result   = fw.fslorient('input', setsformcode=1)
+        expected = fslo + ' -setsformcode 1' + ' input'
+        assert result.stdout[0] == expected
+
 
 def test_fslreorient2std():
     with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslreorient2std',)) as fsldir: