From e3a4f76b782aef94e5d833ff2c0886188ab8e8f9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 25 Jul 2022 18:28:07 +0100
Subject: [PATCH] Test that applywarp --usesqform adheres to FSL sform/qform
usage conventions.
---
unit_tests/fugue/applywarp/feedsRun | 81 +++++++++++++++++++++++++++++
1 file changed, 81 insertions(+)
create mode 100755 unit_tests/fugue/applywarp/feedsRun
diff --git a/unit_tests/fugue/applywarp/feedsRun b/unit_tests/fugue/applywarp/feedsRun
new file mode 100755
index 0000000..73b53bb
--- /dev/null
+++ b/unit_tests/fugue/applywarp/feedsRun
@@ -0,0 +1,81 @@
+#!/usr/bin/env fslpython
+
+
+import shlex
+import subprocess as sp
+import numpy as np
+import nibabel as nib
+from fsl.data.image import Image
+import fsl.transform.affine as affine
+
+
+def applywarp(src, ref):
+ cmd = f'applywarp --in={src} --ref={ref} --usesqform --out=out'
+ sp.run(shlex.split(cmd), check=True)
+ return Image('out')
+
+
+def make_image(fname, data, sform, sform_code, qform, qform_code):
+ hdr = nib.Nifti1Header()
+ hdr.set_sform(sform, sform_code)
+ hdr.set_qform(qform, qform_code)
+ img = Image(data, header=hdr)
+ img.save(fname)
+ return img
+
+# fsl/fugue!6
+#
+# Make sure that applywarp --usesqform
+# will correctly use the sform or qform
+#
+# FSL affine precedence rules are as follows:
+#
+# 1. If sform_code != 0, use sform; else
+# 2. If qform_code != 0, use qform; else
+# 3. Use a scaling matrix with pixdims along the
+# diagonal
+def test_applywarp_uses_sqform_correctly():
+
+ srcdata = np.zeros((20, 20, 20))
+ refdata = np.zeros((20, 20, 20))
+
+ # Data from the two images
+ # aligned via their affines -
+ # src should be resampled so
+ # as to be identical to ref
+ srcdata[ 6: 9, 6: 9, 6: 9] = 1
+ refdata[16:19, 16:19, 16:19] = 1
+
+ eye = np.eye(4)
+ srcaff = affine.scaleOffsetXform(1, [ 5, 5, 5])
+ refaff = affine.scaleOffsetXform(1, [-5, -5, -5])
+
+ # aligned via sform
+ src = make_image('src', srcdata, srcaff, 2, eye, 1)
+ ref = make_image('ref', refdata, refaff, 2, eye, 1)
+ result = applywarp('src', 'ref')
+ assert np.all(np.isclose(result.data, ref.data))
+
+ # aligned via sform again
+ src = make_image('src', srcdata, srcaff, 2, eye, 0)
+ ref = make_image('ref', refdata, refaff, 2, eye, 0)
+ result = applywarp('src', 'ref')
+ assert np.all(np.isclose(result.data, ref.data))
+
+ # aligned via qform
+ src = make_image('src', srcdata, eye, 0, srcaff, 2)
+ ref = make_image('ref', refdata, eye, 0, refaff, 2)
+ result = applywarp('src', 'ref')
+ assert np.all(np.isclose(result.data, ref.data))
+
+ # not aligned - should result in a scaling
+ # matrix being used (an identify matrix here)
+ src = make_image('src', srcdata, eye, 0, srcaff, 0)
+ ref = make_image('ref', refdata, eye, 0, refaff, 0)
+ result = applywarp('src', 'ref')
+ assert not np.all(np.isclose(result.data, ref.data))
+ assert np.all(np.isclose(result.data, src.data))
+
+
+if __name__ == '__main__':
+ test_applywarp_uses_sqform_correctly()
--
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