From 75ed633531adf756c22b1b7fae97e789331eda0d Mon Sep 17 00:00:00 2001
From: Evan Edmond <evan.edmond@ndcn.ox.ac.uk>
Date: Mon, 7 Dec 2020 11:32:57 +0000
Subject: [PATCH] ENH: add fslmaths simple smoothing
---
fsl/wrappers/fslmaths.py | 5 +++++
tests/test_wrappers/test_wrappers.py | 5 +++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/fsl/wrappers/fslmaths.py b/fsl/wrappers/fslmaths.py
index 2bfd71291..21decf6f2 100644
--- a/fsl/wrappers/fslmaths.py
+++ b/fsl/wrappers/fslmaths.py
@@ -105,6 +105,11 @@ class fslmaths(object):
self.__args.append("-dilF")
return self
+ def smooth(self, sigma):
+ """Spatial smoothing - mean filtering using a gauss kernel of sigma mm"""
+ self.__args.extend(("-s", sigma))
+ return self
+
def add(self, image):
"""Add input to current image."""
self.__args.extend(("-add", image))
diff --git a/tests/test_wrappers/test_wrappers.py b/tests/test_wrappers/test_wrappers.py
index dbffff1d6..e93d494ea 100644
--- a/tests/test_wrappers/test_wrappers.py
+++ b/tests/test_wrappers/test_wrappers.py
@@ -290,14 +290,15 @@ def test_fslmaths():
.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).run('output')
+ .thr('thrim').uthr('uthrim').inm('inmim').bptf(1, 10) \
+ .smooth(sigma=6).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', 'output']
+ '-inm inmim', '-bptf 1 10', '-s 6', 'output']
expected = ' '.join(expected)
assert result.stdout[0] == expected
--
GitLab