def bench_csdeconv(center=(50, 40, 40), width=12):
img, gtab, labels_img = read_stanford_labels()
data = img.get_data()
labels = labels_img.get_data()
shape = labels.shape
mask = np.in1d(labels, [1, 2])
mask.shape = shape
a, b, c = center
hw = width // 2
idx = (slice(a - hw, a + hw), slice(b - hw, b + hw), slice(c - hw, c + hw))
data_small = data[idx].copy()
mask_small = mask[idx].copy()
voxels = mask_small.sum()
cmd = "model.fit(data_small, mask_small)"
print("== Benchmarking CSD fit on %d voxels ==" % voxels)
msg = "SH order - %d, gradient directons - %d :: %g sec"
# Basic case
sh_order = 8
model = ConstrainedSphericalDeconvModel(gtab, None, sh_order=sh_order)
time = npt.measure(cmd)
print(msg % (sh_order, num_grad(gtab), time))
# Smaller data set
data_small = data_small[..., :75].copy()
gtab = GradientTable(gtab.gradients[:75])
model = ConstrainedSphericalDeconvModel(gtab, None, sh_order=sh_order)
time = npt.measure(cmd)
print(msg % (sh_order, num_grad(gtab), time))
# Super resolution
sh_order = 12
model = ConstrainedSphericalDeconvModel(gtab, None, sh_order=sh_order)
time = npt.measure(cmd)
print(msg % (sh_order, num_grad(gtab), time))
for getting directions from a diffusion data set. 2) A method for identifying different tissue types within the data set. 3) A set of seeds from which to begin tracking. This example shows how to combine the 3 parts described above to create a tractography reconstruction from a diffusion data set. """ """ To begin, let's load an example HARDI data set from Stanford. If you have not already downloaded this data set, the first time you run this example you will need to be connected to the internet and this dataset will be downloaded to your computer. """ from dipy.data import read_stanford_labels hardi_img, gtab, labels_img = read_stanford_labels() data = hardi_img.get_data() labels = labels_img.get_data() affine = hardi_img.affine """ This dataset provides a label map in which all white matter tissues are labeled either 1 or 2. Lets create a white matter mask to restrict tracking to the white matter. """ white_matter = (labels == 1) | (labels == 2) """ 1. The first thing we need to begin fiber tracking is a way of getting directions from this diffusion data set. In order to do that, we can fit the
def test_contour_from_roi():
# Render volume
renderer = window.renderer()
data = np.zeros((50, 50, 50))
data[20:30, 25, 25] = 1.
data[25, 20:30, 25] = 1.
affine = np.eye(4)
surface = actor.contour_from_roi(data, affine,
color=np.array([1, 0, 1]),
opacity=.5)
renderer.add(surface)
renderer.reset_camera()
renderer.reset_clipping_range()
# window.show(renderer)
# Test binarization
renderer2 = window.renderer()
data2 = np.zeros((50, 50, 50))
data2[20:30, 25, 25] = 1.
data2[35:40, 25, 25] = 1.
affine = np.eye(4)
surface2 = actor.contour_from_roi(data2, affine,
color=np.array([0, 1, 1]),
opacity=.5)
renderer2.add(surface2)
renderer2.reset_camera()
renderer2.reset_clipping_range()
# window.show(renderer2)
arr = window.snapshot(renderer, 'test_surface.png', offscreen=True)
arr2 = window.snapshot(renderer2, 'test_surface2.png', offscreen=True)
report = window.analyze_snapshot(arr, find_objects=True)
report2 = window.analyze_snapshot(arr2, find_objects=True)
npt.assert_equal(report.objects, 1)
npt.assert_equal(report2.objects, 2)
# test on real streamlines using tracking example
from dipy.data import read_stanford_labels
from dipy.reconst.shm import CsaOdfModel
from dipy.data import default_sphere
from dipy.direction import peaks_from_model
from dipy.tracking.local import ThresholdTissueClassifier
from dipy.tracking import utils
from dipy.tracking.local import LocalTracking
from dipy.viz.colormap import line_colors
hardi_img, gtab, labels_img = read_stanford_labels()
data = hardi_img.get_data()
labels = labels_img.get_data()
affine = hardi_img.get_affine()
white_matter = (labels == 1) | (labels == 2)
csa_model = CsaOdfModel(gtab, sh_order=6)
csa_peaks = peaks_from_model(csa_model, data, default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=white_matter)
classifier = ThresholdTissueClassifier(csa_peaks.gfa, .25)
seed_mask = labels == 2
seeds = utils.seeds_from_mask(seed_mask, density=[1, 1, 1], affine=affine)
# Initialization of LocalTracking.
# The computation happens in the next step.
streamlines = LocalTracking(csa_peaks, classifier, seeds, affine,
step_size=2)
# Compute streamlines and store as a list.
streamlines = list(streamlines)
# Prepare the display objects.
streamlines_actor = actor.line(streamlines, line_colors(streamlines))
seedroi_actor = actor.contour_from_roi(seed_mask, affine, [0, 1, 1], 0.5)
# Create the 3d display.
r = window.ren()
r2 = window.ren()
r.add(streamlines_actor)
arr3 = window.snapshot(r, 'test_surface3.png', offscreen=True)
report3 = window.analyze_snapshot(arr3, find_objects=True)
r2.add(streamlines_actor)
r2.add(seedroi_actor)
arr4 = window.snapshot(r2, 'test_surface4.png', offscreen=True)
report4 = window.analyze_snapshot(arr4, find_objects=True)
# assert that the seed ROI rendering is not far
# away from the streamlines (affine error)
npt.assert_equal(report3.objects, report4.objects)
import numpy as np
from dipy.data import (read_stanford_labels, default_sphere,
read_stanford_pve_maps)
from dipy.direction import DeterministicMaximumDirectionGetter
from dipy.io.trackvis import save_trk
from dipy.reconst.csdeconv import (ConstrainedSphericalDeconvModel,
auto_response)
from dipy.tracking.local import LocalTracking
from dipy.tracking import utils
from dipy.viz import fvtk
from dipy.viz.colormap import line_colors
ren = fvtk.ren()
hardi_img, gtab, labels_img = read_stanford_labels()
_, _, img_pve_wm = read_stanford_pve_maps()
data = hardi_img.get_data()
labels = labels_img.get_data()
affine = hardi_img.affine
white_matter = img_pve_wm.get_data()
seed_mask = np.logical_and(labels == 2, white_matter == 1)
seeds = utils.seeds_from_mask(seed_mask, density=2, affine=affine)
response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd_model.fit(data, mask=white_matter)
dg = DeterministicMaximumDirectionGetter.from_shcoeff(csd_fit.shm_coeff,