From 63f2f13347153c41c2749b54307af05e3e3d5f74 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 7 Dec 2023 16:50:57 +0000
Subject: [PATCH] Basic unit test for vecreg
---
unit_tests/fdt/vecreg/feedsInputs | 1 +
unit_tests/fdt/vecreg/feedsRun | 65 +++++++++++++++++++++++++++++++
2 files changed, 66 insertions(+)
create mode 100644 unit_tests/fdt/vecreg/feedsInputs
create mode 100755 unit_tests/fdt/vecreg/feedsRun
diff --git a/unit_tests/fdt/vecreg/feedsInputs b/unit_tests/fdt/vecreg/feedsInputs
new file mode 100644
index 0000000..33b70e2
--- /dev/null
+++ b/unit_tests/fdt/vecreg/feedsInputs
@@ -0,0 +1 @@
+fsl_course_data/fdt2
diff --git a/unit_tests/fdt/vecreg/feedsRun b/unit_tests/fdt/vecreg/feedsRun
new file mode 100755
index 0000000..773f06c
--- /dev/null
+++ b/unit_tests/fdt/vecreg/feedsRun
@@ -0,0 +1,65 @@
+#!/usr/bin/env fslpython
+
+import os
+import sys
+
+sys.path.append('/home/paulmc/Projects/fslpy/')
+
+from pathlib import Path
+
+import numpy as np
+
+from fsl.data.image import Image
+from fsl.wrappers import vecreg, concatxfm, invxfm, convertwarp
+
+from pyfeeds.evaluate import cmpVectorArrays
+
+
+def main():
+ fsldir = Path(os.environ['FSLDIR'])
+ outdir = Path(sys.argv[1])
+ indir = Path(sys.argv[2])/'fsl_course_data'/'fdt2'
+ dyads = indir/'diffusion.bedpostX'/'dyads1.nii.gz'
+ std = fsldir/'data'/'standard'/'MNI152_T1_2mm.nii.gz'
+ str2std = indir/'diffusion.bedpostX'/'xfms'/'str2standard.mat'
+ diff2str = indir/'structural'/'xfms'/'diff2str.mat'
+ diff2std_warp = indir/'structural'/'xfms'/'diff2standard_warp.nii.gz'
+
+ # Create diff2std/std2diff affines
+ std2diff = outdir/'std2diff.mat'
+ diff2std = outdir/'diff2std.mat'
+ concatxfm(diff2str, str2std, diff2std)
+ invxfm(diff2std, std2diff)
+
+ # create a copy of the diff2std warp
+ # which does not encode the diff2std
+ # affine
+ diff2std_warp_no_premat = outdir/'diff2std_no_pm_warp.nii.gz'
+ convertwarp(diff2std_warp_no_premat, std,
+ warp1=diff2std_warp,
+ premat=std2diff,
+ relout=True)
+
+ # Transform dyads with the full diff2std
+ # warp (which encodes the diff->standard
+ # affine transform) - this will be used
+ # as a benchmark
+ dyads_std = outdir/'dyads1_std.nii.gz'
+ vecreg(dyads, dyads_std, std, warpfield=diff2std_warp)
+
+ # Transform dyads with the raw diff2std
+ # warp, and specify the diff2std affine
+ # as premat. The result should match
+ # that from the first vecreg call above.
+ dyads_std_with_premat = outdir/'dyads1_std_with_premat.nii.gz'
+ vecreg(dyads, dyads_std_with_premat, std,
+ warpfield=diff2std_warp_no_premat,
+ premat=diff2std)
+
+ dyads1 = Image(dyads_std).data
+ dyads2 = Image(dyads_std_with_premat).data
+ assert np.isclose(cmpVectorArrays(dyads1, dyads2), 0)
+
+
+if __name__ == '__main__':
+ main()
--
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