Merge branch 'enh/fslmaths' into 'master'

Enh/fslmaths

See merge request fsl/fslpy!304

AUTHOR

@@ -4,4 +4,5 @@ Matthew Webster <matthew.webster@ndcn.ox.ac.uk>
 Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
 Martin Craig <martin.craig@eng.ox.ac.uk>
 Taylor Hanayik <taylor.hanayik@ndcn.ox.ac.uk>
-Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
\ No newline at end of file
+Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
+Christoph Arthofer <christoph.arthofer@ndcn.oxc.ac.uk>
\ No newline at end of file

CHANGELOG.rst

@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.6.4 (Tuesday 3rd August 2021)
+-------------------------------
+
+
+Added
+^^^^^
+
+
+* New :meth:`.fslmaths.kernel` and :meth:`.fslmaths.fmeanu` options on the
+  :class:`.fslmaths` wrapper (!304).
+
 
 3.6.3 (Wednesday 28th July 2021)
 --------------------------------

fsl/wrappers/fslmaths.py

@@ -163,6 +163,16 @@ class fslmaths(object):
         self.__args.extend(("-bptf", hp_sigma, lp_sigma))
         return self
 
+    def kernel(self, kernel='3D'):
+        """2D or (default) 3D kernel"""
+        self.__args.extend(("-kernel", kernel))
+        return self
+
+    def fmeanu(self):
+        """Mean filtering, kernel weighted, un-normalised (gives edge effects)"""
+        self.__args.append("-fmeanu")
+        return self
+
     def run(self, output=None):
         """Save output of operations to image. Set ``output`` to a filename to have
         the result saved to file, or omit ``output`` entirely to have the

tests/test_wrappers/test_wrappers.py

@@ -291,14 +291,15 @@ def test_fslmaths():
             .fillh().ero().dilM().dilF().add('addim').sub('subim') \
             .mul('mulim').div('divim').mas('masim').rem('remim')   \
             .thr('thrim').uthr('uthrim').inm('inmim').bptf(1, 10) \
-            .smooth(sigma=6).run('output')
+            .smooth(sigma=6).kernel('3D').fmeanu().run('output')
 
         expected = [cmd, 'input',
                     '-abs', '-bin', '-binv', '-recip', '-Tmean', '-Tstd',
                     '-Tmin', '-Tmax', '-fillh', '-ero', '-dilM', '-dilF',
                     '-add addim', '-sub subim', '-mul mulim', '-div divim',
                     '-mas masim', '-rem remim', '-thr thrim', '-uthr uthrim',
-                    '-inm inmim', '-bptf 1 10', '-s 6', 'output']
+                    '-inm inmim', '-bptf 1 10', '-s 6', '-kernel 3D', '-fmeanu',
+                    'output']
         expected = ' '.join(expected)
 
         assert result.stdout[0] == expected