Test that applywarp --usesqform adheres to FSL sform/qform usage conventions.

This test will fail until fugue!6 (merged) is merged

unit_tests/fugue/applywarp/feedsRun

+#!/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()