From 3be2b416a4072cdb5ff10c467702d85bd142de5b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 8 Jul 2019 15:04:46 +0100
Subject: [PATCH] TEST: More flirt.py unit tests, tests for fnirt.py
---
tests/test_transform/test_flirt.py | 67 ++++++++++++---
tests/test_transform/test_fnirt.py | 128 +++++++++++++++++++++++++++++
2 files changed, 185 insertions(+), 10 deletions(-)
create mode 100644 tests/test_transform/test_fnirt.py
diff --git a/tests/test_transform/test_flirt.py b/tests/test_transform/test_flirt.py
index c301fc75c..d2dd68e29 100644
--- a/tests/test_transform/test_flirt.py
+++ b/tests/test_transform/test_flirt.py
@@ -5,16 +5,20 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+import itertools as it
import os.path as op
import numpy as np
-import fsl.data.image as fslimage
-import fsl.transform as transform
-import fsl.utils.tempdir as tempdir
+import fsl.data.image as fslimage
+import fsl.transform.flirt as flirt
+import fsl.transform.affine as affine
+import fsl.utils.tempdir as tempdir
from .test_affine import readlines
+from .. import make_random_image
+
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -22,17 +26,60 @@ datadir = op.join(op.dirname(__file__), 'testdata')
def test_read_write():
with tempdir.tempdir():
aff = np.random.random((4, 4))
- transform.writeFlirt(aff, 'aff.mat')
- got = transform.readFlirt('aff.mat')
+ flirt.writeFlirt(aff, 'aff.mat')
+ got = flirt.readFlirt('aff.mat')
assert np.all(np.isclose(aff, got))
def test_fromFlirt():
- pass
+
+ src = affine.compose(np.random.randint( 1, 5, 3),
+ np.random.randint(-20, 20, 3),
+ np.random.random(3) - 0.5)
+ ref = affine.compose(np.random.randint( 1, 5, 3),
+ np.random.randint(-20, 20, 3),
+ np.random.random(3) - 0.5)
+
+ src = fslimage.Image(make_random_image(xform=src))
+ ref = fslimage.Image(make_random_image(xform=ref))
+ flirtmat = affine.concat(ref.getAffine('world', 'fsl'),
+ src.getAffine('fsl', 'world'))
+
+
+ spaces = it.permutations(('voxel', 'fsl', 'world'), 2)
+
+ for from_, to in spaces:
+ got = flirt.fromFlirt(flirtmat, src, ref, from_, to)
+ exp = affine.concat(ref.getAffine('fsl', to),
+ flirtmat,
+ src.getAffine(from_, 'fsl'))
+
+ assert np.all(np.isclose(got, exp))
def test_toFlirt():
- pass
+
+ src = affine.compose(np.random.randint( 1, 5, 3),
+ np.random.randint(-20, 20, 3),
+ np.random.random(3) - 0.5)
+ ref = affine.compose(np.random.randint( 1, 5, 3),
+ np.random.randint(-20, 20, 3),
+ np.random.random(3) - 0.5)
+
+ src = fslimage.Image(make_random_image(xform=src))
+ ref = fslimage.Image(make_random_image(xform=ref))
+ flirtmat = affine.concat(ref.getAffine('world', 'fsl'),
+ src.getAffine('fsl', 'world'))
+
+
+ spaces = it.permutations(('voxel', 'fsl', 'world'), 2)
+
+ for from_, to in spaces:
+ xform = affine.concat(ref.getAffine('world', to),
+ src.getAffine(from_, 'world'))
+ got = flirt.toFlirt(xform, src, ref, from_, to)
+
+ assert np.all(np.isclose(got, flirtmat))
def test_flirtMatrixToSform():
@@ -53,7 +100,7 @@ def test_flirtMatrixToSform():
srcImg = fslimage.Image(np.zeros(srcShape), xform=srcXform)
refImg = fslimage.Image(np.zeros(refShape), xform=refXform)
- result = transform.flirtMatrixToSform(flirtMat, srcImg, refImg)
+ result = flirt.flirtMatrixToSform(flirtMat, srcImg, refImg)
assert np.all(np.isclose(result, expected))
@@ -78,8 +125,8 @@ def test_sformToFlirtMatrix():
srcImg2.voxToWorldMat = srcXformOvr
- result1 = transform.sformToFlirtMatrix(srcImg1, refImg, srcXformOvr)
- result2 = transform.sformToFlirtMatrix(srcImg2, refImg)
+ result1 = flirt.sformToFlirtMatrix(srcImg1, refImg, srcXformOvr)
+ result2 = flirt.sformToFlirtMatrix(srcImg2, refImg)
assert np.all(np.isclose(result1, expected))
assert np.all(np.isclose(result2, expected))
diff --git a/tests/test_transform/test_fnirt.py b/tests/test_transform/test_fnirt.py
new file mode 100644
index 000000000..323d93e43
--- /dev/null
+++ b/tests/test_transform/test_fnirt.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+#
+# test_fnirt.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os.path as op
+import itertools as it
+
+import numpy as np
+
+import pytest
+
+import fsl.data.image as fslimage
+import fsl.transform.affine as affine
+import fsl.transform.nonlinear as nonlinear
+import fsl.transform.fnirt as fnirt
+
+from .test_nonlinear import _random_affine_field
+
+
+datadir = op.join(op.dirname(__file__), 'testdata', 'nonlinear')
+
+
+def test_readFnirt():
+
+ src = op.join(datadir, 'src')
+ ref = op.join(datadir, 'ref')
+ coef = op.join(datadir, 'coefficientfield')
+ disp = op.join(datadir, 'displacementfield')
+
+ src = fslimage.Image(src)
+ ref = fslimage.Image(ref)
+ coef = fnirt.readFnirt(coef, src, ref)
+ disp = fnirt.readFnirt(disp, src, ref)
+
+ with pytest.raises(ValueError):
+ fnirt.readFnirt(src, src, ref)
+
+ assert isinstance(coef, nonlinear.CoefficientField)
+ assert isinstance(disp, nonlinear.DisplacementField)
+
+ assert coef.src.sameSpace(src)
+ assert coef.ref.sameSpace(ref)
+ assert disp.src.sameSpace(src)
+ assert disp.ref.sameSpace(ref)
+ assert coef.srcSpace == 'fsl'
+ assert coef.refSpace == 'fsl'
+ assert disp.srcSpace == 'fsl'
+ assert disp.refSpace == 'fsl'
+
+
+def test_toFnirt():
+
+ def check(got, exp):
+ tol = dict(atol=1e-5, rtol=1e-5)
+ assert np.all(np.isclose(got.data, exp.data, **tol))
+ assert got.src.sameSpace(exp.src)
+ assert got.ref.sameSpace(exp.ref)
+ assert got.srcSpace == 'fsl'
+ assert got.refSpace == 'fsl'
+
+ basefield, xform = _random_affine_field()
+ src = basefield.src
+ ref = basefield.ref
+
+ spaces = it.permutations(('voxel', 'fsl', 'world'), 2)
+
+ for from_, to in spaces:
+ field = nonlinear.convertDisplacementSpace(basefield, from_, to)
+ got = fnirt.toFnirt(field)
+ check(got, basefield)
+
+ src = fslimage.Image(op.join(datadir, 'src'))
+ ref = fslimage.Image(op.join(datadir, 'ref'))
+ coef = fnirt.readFnirt(op.join(datadir, 'coefficientfield'), src, ref)
+ disp = fnirt.readFnirt(op.join(datadir, 'displacementfield'), src, ref)
+ got = fnirt.toFnirt(coef)
+ check(got, disp)
+
+
+def test_fromFnirt():
+
+ basefield, basexform = _random_affine_field()
+ src = basefield.src
+ ref = basefield.ref
+ spaces = list(it.permutations(('voxel', 'fsl', 'world'), 2))
+
+ for from_, to in spaces:
+
+ got = fnirt.fromFnirt(basefield, from_, to)
+
+ assert got.srcSpace == to
+ assert got.refSpace == from_
+
+ coords = [np.random.randint(0, basefield.shape[0], 5),
+ np.random.randint(0, basefield.shape[1], 5),
+ np.random.randint(0, basefield.shape[2], 5)]
+ coords = np.array(coords).T
+
+ coords = affine.transform(coords, ref.getAffine('voxel', from_))
+
+ aff = affine.concat(src.getAffine('fsl', to),
+ basexform,
+ ref.getAffine(from_, 'fsl'))
+
+ got = got.transform(coords)
+ exp = affine.transform(coords, aff)
+
+ enan = np.isnan(exp)
+ gnan = np.isnan(got)
+
+ assert np.all(np.isclose(enan, gnan))
+ assert np.all(np.isclose(exp[~enan], got[~gnan]))
+
+ # Converting from a FNIRT coefficient field
+ src = fslimage.Image(op.join(datadir, 'src'))
+ ref = fslimage.Image(op.join(datadir, 'ref'))
+ coef = fnirt.readFnirt(op.join(datadir, 'coefficientfield'), src, ref)
+ disp = fnirt.readFnirt(op.join(datadir, 'displacementfield'), src, ref)
+
+ for from_, to in spaces:
+
+ cnv = fnirt.fromFnirt(coef, from_, to)
+ exp = nonlinear.convertDisplacementSpace(disp, from_, to)
+ tol = dict(atol=1e-5, rtol=1e-5)
+ assert np.all(np.isclose(cnv.data, exp.data, **tol))
--
GitLab