/usr/lib/python2.7/dist-packages/dipy/reconst/tests/test_gqi.py is in python-dipy 0.10.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 | import numpy as np
from dipy.data import get_data, dsi_voxels
from dipy.core.sphere import Sphere
from dipy.core.gradients import gradient_table
from dipy.sims.voxel import SticksAndBall
from dipy.reconst.gqi import GeneralizedQSamplingModel
from dipy.data import get_sphere
from numpy.testing import (assert_equal,
assert_almost_equal,
run_module_suite)
from dipy.reconst.tests.test_dsi import sticks_and_ball_dummies
from dipy.core.subdivide_octahedron import create_unit_sphere
from dipy.core.sphere_stats import angular_similarity
from dipy.reconst.odf import gfa
from dipy.direction.peaks import peak_directions
def test_gqi():
#load symmetric 724 sphere
sphere = get_sphere('symmetric724')
#load icosahedron sphere
sphere2 = create_unit_sphere(5)
btable = np.loadtxt(get_data('dsi515btable'))
bvals = btable[:,0]
bvecs = btable[:,1:]
gtab = gradient_table(bvals, bvecs)
data, golden_directions = SticksAndBall(gtab, d=0.0015,
S0=100, angles=[(0, 0), (90, 0)],
fractions=[50, 50], snr=None)
gq = GeneralizedQSamplingModel(gtab, method='gqi2', sampling_length=1.4)
#symmetric724
gqfit = gq.fit(data)
odf = gqfit.odf(sphere)
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2, 1)
#5 subdivisions
gqfit = gq.fit(data)
odf2 = gqfit.odf(sphere2)
directions, values, indices = peak_directions(odf2, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2, 1)
sb_dummies=sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
odf = gq.fit(data).odf(sphere2)
directions, values, indices = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_mvoxel_gqi():
data, gtab = dsi_voxels()
sphere = get_sphere('symmetric724')
gq = GeneralizedQSamplingModel(gtab, 'standard')
gqfit = gq.fit(data)
all_odfs = gqfit.odf(sphere)
# Check that the first and last voxels each have 2 peaks
odf = all_odfs[0, 0, 0]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
odf = all_odfs[-1, -1, -1]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
if __name__ == "__main__":
run_module_suite()
|