Merge branch 'evan-patch-fmap' into 'master'

ENH: wrapper and test for fsl_prepare_fieldmap

See merge request fsl/fslpy!265

fsl/wrappers/__init__.py

@@ -101,7 +101,8 @@ from .fslmaths     import (fslmaths,)       # noqa
 from .fslstats     import (fslstats,)       # noqa
 from .fugue        import (fugue,           # noqa
                            prelude,
-                           sigloss)
+                           sigloss,
+                           fsl_prepare_fieldmap)
 from .melodic      import (melodic,         # noqa
                            fsl_regfilt)
 from .misc         import (fslreorient2std, # noqa

fsl/wrappers/fugue.py

@@ -83,3 +83,19 @@ def prelude(**kwargs):
                                              **kwargs)
 
     return cmd
+
+@wutils.fileOrImage('phase_image', 'magnitude_image', 'out_image')
+@wutils.fslwrapper
+def fsl_prepare_fieldmap(phase_image, magnitude_image, out_image, deltaTE, scanner=None, **kwargs):
+    """Wrapper for the ``fsl_prepare_fieldmap`` command. <scanner> defaults to 'SIEMENS'"""
+    if scanner is None:
+        scanner = 'SIEMENS'
+    
+    valmap = {
+        'nocheck' : wutils.SHOW_IF_TRUE,
+    }
+    
+    cmd = ['fsl_prepare_fieldmap', scanner, phase_image, magnitude_image, out_image, str(deltaTE)]
+    cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+
+    return cmd

tests/test_wrappers/test_wrappers.py

@@ -385,3 +385,14 @@ def test_tbss():
         assert fw.tbss.non_FA('alt')[0]     == ' '.join([exes['non_FA'], 'alt'])
         assert fw.tbss.fill('stat', 0.4, 'mean_fa', 'output', n=True).stdout[0] == \
             ' '.join([exes['fill'], 'stat', '0.4', 'mean_fa', 'output', '-n'])
+
+def test_fsl_prepare_fieldmap():
+    with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fsl_prepare_fieldmap',)) as fsldir:
+        fpf = op.join(fsldir, 'bin', 'fsl_prepare_fieldmap')
+        result   = fw.fsl_prepare_fieldmap(phase_image='ph', 
+                                                 magnitude_image='mag', 
+                                                 out_image='out', 
+                                                 deltaTE=2.46, 
+                                                 nocheck=True)
+        expected = (fpf, ('SIEMENS', 'ph', 'mag', 'out', '2.46', '--nocheck'))
+        assert checkResult(result.stdout[0], *expected)