From d7f2541f0b448224a69d81934280c1f28d3b7e36 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 7 Sep 2022 16:24:34 +0100
Subject: [PATCH] TEST: unit test for fslcomplex
---
unit_tests/avwutils/fslcomplex/feedsRun | 126 ++++++++++++++++++++++++
1 file changed, 126 insertions(+)
create mode 100755 unit_tests/avwutils/fslcomplex/feedsRun
diff --git a/unit_tests/avwutils/fslcomplex/feedsRun b/unit_tests/avwutils/fslcomplex/feedsRun
new file mode 100755
index 0000000..0350948
--- /dev/null
+++ b/unit_tests/avwutils/fslcomplex/feedsRun
@@ -0,0 +1,126 @@
+#!/usr/bin/env python
+"""Test that fslcomplex produces correct outputs. Specifically tests that the
+output files have orientation info that matches that of the input files.
+"""
+
+import numpy as np
+import nibabel as nib
+import subprocess as sp
+import os.path as op
+import shlex
+import sys
+import traceback
+
+from fsl.utils.tempdir import tempdir
+from fsl.data.image import addExt
+
+
+def sprun(cmd):
+ print(f'RUN {cmd}')
+ sp.run(shlex.split(cmd), check=True)
+
+
+def imtest(path):
+ try:
+ addExt(path)
+ return True
+ except Exception:
+ return False
+
+
+# radio=[True|False] -> whether or not
+# to add a flip on the affine X axis
+def create_test_input_data(radio):
+
+ real = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+ imag = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
+ comp = real + imag * 1j
+ abso = np.abs(comp)
+ phase = np.arctan2(comp.imag, comp.real)
+ comp4d = np.concatenate((comp.reshape(10, 10, 10, 1),
+ comp.reshape(10, 10, 10, 1)), 3)
+
+ affine = np.diag([3, 3, 3, 0])
+ affine[:3, 3] = [10, 20, 30]
+
+ if radio:
+ affine[0, 0] *= -1
+
+ real = nib.Nifti1Image(real, affine)
+ imag = nib.Nifti1Image(imag, affine)
+ comp = nib.Nifti1Image(comp, affine)
+ comp4d = nib.Nifti1Image(comp4d, affine)
+ abso = nib.Nifti1Image(abso, affine)
+ phase = nib.Nifti1Image(phase, affine)
+
+ real .set_qform(*real .get_sform(coded=True))
+ imag .set_qform(*comp .get_sform(coded=True))
+ comp .set_qform(*comp .get_sform(coded=True))
+ comp4d.set_qform(*comp4d.get_sform(coded=True))
+ abso .set_qform(*abso .get_sform(coded=True))
+ phase .set_qform(*phase .get_sform(coded=True))
+
+ real .to_filename('real_in.nii.gz')
+ imag .to_filename('imag_in.nii.gz')
+ comp .to_filename('complex_in.nii.gz')
+ comp4d.to_filename('complex4d_in.nii.gz')
+ abso .to_filename('abs_in.nii.gz')
+ phase .to_filename('phase_in.nii.gz')
+
+
+def compare_images(file1, file2):
+ img1 = nib.load(addExt(file1))
+ img2 = nib.load(addExt(file2))
+ data1 = np.asanyarray(img1.dataobj)
+ data2 = np.asanyarray(img2.dataobj)
+ assert img1.header['sform_code'] == img2.header['sform_code']
+ assert img1.header['qform_code'] == img2.header['qform_code']
+ assert np.all(np.isclose(img1.get_sform(), img2.get_sform()))
+ assert np.all(np.isclose(img1.get_qform(), img2.get_qform()))
+ assert np.all(np.isclose(img1.header['pixdim'], img2.header['pixdim']))
+ assert np.all(np.isclose(data1, data2))
+
+
+def test_fslcomplex_call(args, infiles, outfiles, radio):
+ with tempdir():
+ create_test_input_data(radio)
+ sprun(f'fslcomplex {args} {infiles} {outfiles}')
+ for outfile in outfiles.split(' '):
+
+ if not imtest(outfile):
+ continue
+
+ prefix = outfile.split('_')[0]
+ infile = f'{prefix}_in'
+
+ print(f'Comparing {outfile} against {infile}')
+
+ compare_images(infile, outfile)
+
+
+if __name__ == '__main__':
+ tests = [
+ ('-realabs', 'complex_in', 'abs_out'),
+ ('-realphase', 'complex_in', 'phase_out'),
+ ('-realpolar', 'complex_in', 'abs_out phase_out'),
+ ('-realcartesian', 'complex_in', 'real_out imag_out'),
+ ('-complex', 'real_in imag_in', 'complex_out'),
+ ('-complexpolar', 'abs_in phase_in', 'complex_out'),
+ ('-copyonly', 'complex_in', 'complex_out'),
+ ('-complexsplit', 'complex4d_in', 'complex_out 0 0'),
+ ('-complexsplit', 'complex4d_in', 'complex_out 1 1'),
+ ('-complexmerge', 'complex_in complex_in', 'complex4d_out'),
+ ]
+
+ result = 0
+ for radio in [True, False]:
+ for args, infiles, outfiles in tests:
+ try:
+ test_fslcomplex_call(args, infiles, outfiles, radio)
+ print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] PASSED')
+ except Exception as e:
+ print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] FAILED')
+ traceback.print_exc()
+ result = 1
+
+ sys.exit(result)
--
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