From fa4582178be2cc04fbd302184068633b8768957d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 14 Jul 2019 14:33:18 +0100
Subject: [PATCH] TEST: Test convertx5 script
---
tests/test_scripts/test_fsl_convert_x5.py | 70 ++++++++++++++++++++++-
1 file changed, 68 insertions(+), 2 deletions(-)
diff --git a/tests/test_scripts/test_fsl_convert_x5.py b/tests/test_scripts/test_fsl_convert_x5.py
index 1fbe308e2..686668404 100644
--- a/tests/test_scripts/test_fsl_convert_x5.py
+++ b/tests/test_scripts/test_fsl_convert_x5.py
@@ -1,17 +1,21 @@
#!/usr/bin/env python
+import os.path as op
+
import numpy as np
import fsl.utils.tempdir as tempdir
import fsl.transform.affine as affine
import fsl.transform.flirt as flirt
+import fsl.transform.fnirt as fnirt
import fsl.transform.x5 as x5
import fsl.data.image as fslimage
import fsl.scripts.fsl_convert_x5 as fsl_convert_x5
+
def random_image():
vx, vy, vz = np.random.randint(10, 50, 3)
dx, dy, dz = np.random.randint( 1, 10, 3)
@@ -50,8 +54,70 @@ def test_convert_flirt():
assert src.sameSpace(gotsrc)
assert ref.sameSpace(gotref)
- fsl_convert_x5.main('flirt -s src -r ref src2ref.x5 '
- 'src2ref_copy.mat'.split())
+ fsl_convert_x5.main('flirt src2ref.x5 src2ref_copy.mat'.split())
gotxform = flirt.readFlirt('src2ref_copy.mat')
assert np.all(np.isclose(gotxform, xform))
+
+
+def test_convert_fnirt_displacement_field():
+
+ 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():
+
+ # nii -> x5
+ fsl_convert_x5.main('fnirt -s {} -r {} {} disp.x5'.format(
+ srcfile, reffile, dffile).split())
+
+ # x5 -> nii
+ fsl_convert_x5.main('fnirt disp.x5 disp.nii.gz'.split())
+
+ src = fslimage.Image(srcfile)
+ ref = fslimage.Image(reffile)
+ df = fnirt.readFnirt(dffile, src, ref)
+ dfnii = fnirt.readFnirt('disp.nii.gz', src, ref)
+
+ assert dfnii.src.sameSpace(src)
+ assert dfnii.ref.sameSpace(ref)
+ assert dfnii.srcSpace == df.srcSpace
+ assert dfnii.refSpace == df.refSpace
+ assert dfnii.displacementType == df.displacementType
+ assert np.all(np.isclose(dfnii.data, df.data))
+
+
+def test_convert_fnirt_coefficient_field():
+
+ datadir = op.join(op.dirname(__file__), '..',
+ 'test_transform', 'testdata', 'nonlinear')
+ srcfile = op.join(datadir, 'src.nii.gz')
+ reffile = op.join(datadir, 'ref.nii.gz')
+ cffile = op.join(datadir, 'coefficientfield.nii.gz')
+
+ with tempdir.tempdir():
+
+ # nii -> x5
+ fsl_convert_x5.main('fnirt -s {} -r {} {} coef.x5'.format(
+ srcfile, reffile, cffile).split())
+
+ # x5 -> nii
+ fsl_convert_x5.main('fnirt coef.x5 coef.nii.gz'.split())
+
+ src = fslimage.Image(srcfile)
+ ref = fslimage.Image(reffile)
+ cf = fnirt.readFnirt(cffile, src, ref)
+ cfnii = fnirt.readFnirt('coef.nii.gz', src, ref)
+
+ assert cfnii.src.sameSpace(src)
+ assert cfnii.ref.sameSpace(ref)
+ assert cfnii.srcSpace == cf.srcSpace
+ assert cfnii.refSpace == cf.refSpace
+ assert cfnii.knotSpacing == cf.knotSpacing
+
+ assert np.all(np.isclose(cfnii.fieldToRefMat, cf.fieldToRefMat))
+ assert np.all(np.isclose(cfnii.srcToRefMat, cf.srcToRefMat))
+ assert np.all(np.isclose(cfnii.data, cf.data))
--
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