From 5d3f6ee3e35d8c0d63d5710d2519cfec85b93b13 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Jan 2025 13:11:03 +0000
Subject: [PATCH] New extrapolation test for applywarp
---
unit_tests/fugue/applywarp/feedsRun | 73 +++++++++++++---------
unit_tests/fugue/applywarp/roi_out.nii.gz | 3 +
unit_tests/fugue/applywarp/roi_ref.nii.gz | 3 +
unit_tests/fugue/applywarp/roi_warp.nii.gz | 3 +
4 files changed, 53 insertions(+), 29 deletions(-)
create mode 100644 unit_tests/fugue/applywarp/roi_out.nii.gz
create mode 100644 unit_tests/fugue/applywarp/roi_ref.nii.gz
create mode 100644 unit_tests/fugue/applywarp/roi_warp.nii.gz
diff --git a/unit_tests/fugue/applywarp/feedsRun b/unit_tests/fugue/applywarp/feedsRun
index f990735..ce3e00b 100755
--- a/unit_tests/fugue/applywarp/feedsRun
+++ b/unit_tests/fugue/applywarp/feedsRun
@@ -3,26 +3,32 @@
import os
import shlex
import sys
+import os.path as op
import subprocess as sp
import numpy as np
import nibabel as nib
-from fsl.data.image import Image
+from pathlib import Path
+from fsl.data.image import Image, addExt
import fsl.transform.affine as affine
+from fsl.wrappers import applywarp, LOAD
+from pyfeeds import evalImage
-def applywarp(src, ref):
- cmd = f'applywarp --in={src} --ref={ref} --usesqform --out=out'
- sp.run(shlex.split(cmd), check=True)
- return Image('out')
+SCRIPT_DIR = Path(op.abspath(op.dirname(__file__)))
-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/warpfns!8 (commit 65329a37d0830d4453381579408c3bbfa5a3bed6)
+#
+# Make sure that regions outside of the FOV
+# in the input image are extrapolated correctly
+def test_applywarp_normal_usage():
+ src = Path(os.environ['FSLDIR']) / 'data' / 'standard' / 'MNI152_T1_2mm'
+ ref = SCRIPT_DIR / 'roi_ref'
+ warp = SCRIPT_DIR / 'roi_warp'
+ expect = addExt(SCRIPT_DIR / 'roi_out')
+ applywarp(src, ref, 'roi_got', warp=warp)
+ assert np.isclose(evalImage(expect, addExt('roi_got')), 0)
+
# fsl/fugue!6
#
@@ -37,6 +43,14 @@ def make_image(fname, data, sform, sform_code, qform, qform_code):
# diagonal
def test_applywarp_uses_sqform_correctly():
+ 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
+
srcdata = np.zeros((20, 20, 20))
refdata = np.zeros((20, 20, 20))
@@ -52,32 +66,33 @@ def test_applywarp_uses_sqform_correctly():
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))
+ src = make_image('src', srcdata, srcaff, 2, eye, 1)
+ ref = make_image('ref', refdata, refaff, 2, eye, 1)
+ applywarp('src', 'ref', 'out', usesqform=True)
+ assert np.isclose(evalImage(addExt('out'), addExt('ref')), 0)
# 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))
+ src = make_image('src', srcdata, srcaff, 2, eye, 0)
+ ref = make_image('ref', refdata, refaff, 2, eye, 0)
+ applywarp('src', 'ref', 'out', usesqform=True)
+ assert np.isclose(evalImage(addExt('out'), addExt('ref')), 0)
# 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))
+ src = make_image('src', srcdata, eye, 0, srcaff, 2)
+ ref = make_image('ref', refdata, eye, 0, refaff, 2)
+ applywarp('src', 'ref', 'out', usesqform=True)
+ assert np.isclose(evalImage(addExt('out'), addExt('ref')), 0)
# 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))
+ src = make_image('src', srcdata, eye, 0, srcaff, 0)
+ ref = make_image('ref', refdata, eye, 0, refaff, 0)
+ applywarp('src', 'ref', 'out', usesqform=True)
+ assert not np.isclose(evalImage(addExt('out'), addExt('ref')), 0)
+ assert np.isclose(evalImage(addExt('out'), addExt('src')), 0)
if __name__ == '__main__':
os.chdir(sys.argv[1])
+ test_applywarp_normal_usage()
test_applywarp_uses_sqform_correctly()
diff --git a/unit_tests/fugue/applywarp/roi_out.nii.gz b/unit_tests/fugue/applywarp/roi_out.nii.gz
new file mode 100644
index 0000000..8b3e8e9
--- /dev/null
+++ b/unit_tests/fugue/applywarp/roi_out.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:74535c5db3c9fb980b32a58770c49d8d05e8a48b410fdde761bb3b6209c074eb
+size 4280
diff --git a/unit_tests/fugue/applywarp/roi_ref.nii.gz b/unit_tests/fugue/applywarp/roi_ref.nii.gz
new file mode 100644
index 0000000..432a2a1
--- /dev/null
+++ b/unit_tests/fugue/applywarp/roi_ref.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:995186689c7be8b19629f0cfb4e1e8cb9dcfb4d516f37027c9b0b436d4217ed4
+size 11625
diff --git a/unit_tests/fugue/applywarp/roi_warp.nii.gz b/unit_tests/fugue/applywarp/roi_warp.nii.gz
new file mode 100644
index 0000000..3e0275c
--- /dev/null
+++ b/unit_tests/fugue/applywarp/roi_warp.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4b293f7b02753de9bb6ce0404cb1c8b00d628952b2306e81153ec714e48b0306
+size 33852
--
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