New tests for flirt -applyxfm

unit_tests/flirt/applyxfm/feedsRun

+#!/usr/bin/env fslpython
+#
+# Test basic flirt -applyxfm behaviour
+#
+
+
+import os.path as op
+import os
+import sys
+
+import fsl.data.image as fslimage
+import fsl.utils.run as run
+
+import numpy as np
+
+
+thisdir = op.dirname(op.abspath(__file__))
+
+
+def compare_images(a, b):
+
+    print(f'Comparing images {a} and {b}')
+
+    a     = fslimage.Image(a)
+    b     = fslimage.Image(b)
+    adata = a.data
+    bdata = b.data
+
+    assert a.sameSpace(b)
+    assert np.all(np.isclose(adata, bdata))
+
+
+def test_applyxfm():
+    fsldir     = os.environ['FSLDIR']
+    std2mm     = op.join(fsldir, 'data', 'standard', 'MNI152_T1_2mm.nii.gz')
+    std1mm     = op.join(fsldir, 'data', 'standard', 'MNI152_T1_1mm.nii.gz')
+    std2mm_roi = 'std2mm_roi.nii.gz'
+
+    # use a ROI to reduce storage and test extrapolation behaviour
+    run.runfsl(f'fslroi {std2mm} {std2mm_roi} 40 10 40 10 40 10')
+
+    tests  = [
+        '-applyxfm -usesqform -interp nearestneighbour',
+        '-applyxfm -usesqform -interp trilinear',
+        '-applyxfm -usesqform -interp sinc',
+        '-applyxfm -usesqform -interp spline',
+        '-applyxfm -usesqform -interp spline -setbackground 0',
+    ]
+
+    for test in tests:
+        outfname = '_'.join(test.replace('-', '').split())
+        outfname = f'{outfname}.nii.gz'
+        cmd      = f'flirt -in {std2mm_roi} -ref {std1mm} -out {outfname} {test}'
+
+        run.runfsl(cmd)
+
+        expfname = op.join(thisdir, 'benchmarks', outfname)
+
+        compare_images(outfname, expfname)
+
+
+
+if __name__ == '__main__':
+    if len(sys.argv) > 1:
+        os.chdir(sys.argv[1])
+    test_applyxfm()