From 2fa377aed966796e1fdeb932ac1a49c0ad215256 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 24 Jul 2019 11:53:33 +0100
Subject: [PATCH] TEST: More basic tests for x5 scripts
---
tests/test_scripts/test_fsl_apply_x5.py | 13 ++++
tests/test_scripts/test_fsl_convert_x5.py | 83 +++++++++++++++++++++++
2 files changed, 96 insertions(+)
diff --git a/tests/test_scripts/test_fsl_apply_x5.py b/tests/test_scripts/test_fsl_apply_x5.py
index 96c2740b1..dbe2bd3a7 100644
--- a/tests/test_scripts/test_fsl_apply_x5.py
+++ b/tests/test_scripts/test_fsl_apply_x5.py
@@ -3,6 +3,8 @@
import numpy as np
+import pytest
+
import fsl.scripts.fsl_apply_x5 as fsl_apply_x5
import fsl.data.image as fslimage
import fsl.utils.image.resample as resample
@@ -31,6 +33,17 @@ def _random_image(aff, shape=None):
return fslimage.Image(data, xform=aff)
+def test_help():
+ def run(args):
+ with pytest.raises(SystemExit) as e:
+ fsl_apply_x5.main(args)
+ assert e.value.code == 0
+
+ run([])
+ run(['-h'])
+
+
+
def test_linear():
with tempdir.tempdir():
diff --git a/tests/test_scripts/test_fsl_convert_x5.py b/tests/test_scripts/test_fsl_convert_x5.py
index 4d54e18f3..e65fd9e46 100644
--- a/tests/test_scripts/test_fsl_convert_x5.py
+++ b/tests/test_scripts/test_fsl_convert_x5.py
@@ -2,6 +2,9 @@
import os.path as op
+import hashlib
+
+import pytest
import numpy as np
@@ -28,6 +31,20 @@ def random_image():
return fslimage.Image(data, xform=aff)
+def test_convert_flirt_help():
+
+ def run(args):
+ with pytest.raises(SystemExit) as e:
+ fsl_convert_x5.main(args)
+ assert e.value.code == 0
+
+ run([])
+ run(['-h'])
+ run(['flirt'])
+ run(['fnirt'])
+ run(['flirt', '-h'])
+ run(['fnirt', '-h'])
+
def test_convert_flirt():
with tempdir.tempdir():
@@ -60,6 +77,42 @@ def test_convert_flirt():
assert np.all(np.isclose(gotxform, xform))
+def test_convert_flirt_sameformat():
+ with tempdir.tempdir():
+ src = random_image()
+ ref = random_image()
+ src.save('src')
+ ref.save('ref')
+
+ xform = affine.compose(
+ np.random.randint(1, 10, 3),
+ np.random.randint(-100, 100, 3),
+ (np.random.random(3) - 0.5) * np.pi)
+
+ np.savetxt('src2ref.mat', xform)
+
+ # test both .mat and .x5
+ fsl_convert_x5.main('flirt -s src -r ref '
+ 'src2ref.mat src2ref.x5'.split())
+
+ # mat -> mat
+ fsl_convert_x5.main('flirt -s src -r ref '
+ 'src2ref.mat copy.mat'.split())
+
+ # x5 -> x5
+ fsl_convert_x5.main('flirt -s src -r ref '
+ 'src2ref.x5 copy.x5'.split())
+
+ with open('src2ref.mat', 'rb') as f: origmat = hashlib.md5(f.read()).digest()
+ with open('copy.mat', 'rb') as f: copymat = hashlib.md5(f.read()).digest()
+ with open('src2ref.x5', 'rb') as f: origx5 = hashlib.md5(f.read()).digest()
+ with open('copy.x5', 'rb') as f: copyx5 = hashlib.md5(f.read()).digest()
+
+ assert origmat == copymat
+ assert origx5 == copyx5
+
+
+
def test_convert_fnirt_deformation_field():
datadir = op.join(op.dirname(__file__), '..',
@@ -124,3 +177,33 @@ def test_convert_fnirt_coefficient_field():
diff = np.abs(dfnii.data - df.data)
tols = {'rtol' : 1e-5, 'atol' : 1e-5}
assert np.all(np.isclose(dfnii.data, df.data, **tols))
+
+
+def test_convert_fnirt_sameformat():
+
+ datadir = op.join(op.dirname(__file__), '..',
+ 'test_transform', 'testdata', 'nonlinear')
+ srcfile = op.join(datadir, 'src.nii.gz')
+ reffile = op.join(datadir, 'ref.nii.gz')
+ dffile = op.join(datadir, 'displacementfield.nii.gz')
+
+ with tempdir.tempdir():
+
+ base = list('fnirt -s {} -r {}'.format(srcfile, reffile).split())
+
+ # test both .mat and .x5
+ fsl_convert_x5.main(base + [dffile, 'src2ref.x5'])
+
+ # nii -> nii
+ fsl_convert_x5.main(base + [dffile, 'copy.nii.gz'])
+
+ # x5 -> x5
+ fsl_convert_x5.main(base + [dffile, 'copy.x5'])
+
+ with open(dffile, 'rb') as f: origdef = hashlib.md5(f.read()).digest()
+ with open('copy.nii.gz', 'rb') as f: copydef = hashlib.md5(f.read()).digest()
+ with open('src2ref.x5', 'rb') as f: origx5 = hashlib.md5(f.read()).digest()
+ with open('copy.x5', 'rb') as f: copyx5 = hashlib.md5(f.read()).digest()
+
+ assert origdef == copydef
+ assert origx5 == copyx5
--
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