def test_points(interactive=False):
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
points_actor = actor.point(points, colors)
renderer = window.Renderer()
renderer.add(points_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr, colors=colors)
npt.assert_equal(report.objects, 3)
def test_points(interactive=False):
points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
points_actor = actor.point(points, colors)
renderer = window.Renderer()
renderer.add(points_actor)
renderer.reset_camera()
renderer.reset_clipping_range()
if interactive:
window.show(renderer, reset_camera=False)
npt.assert_equal(renderer.GetActors().GetNumberOfItems(), 1)
arr = window.snapshot(renderer)
report = window.analyze_snapshot(arr,
colors=colors)
npt.assert_equal(report.objects, 3)
# Extract feature of every streamline.
centers = np.asarray(list(map(feature.extract, streamlines)))
# Color each center of mass according to the cluster they belong to.
colormap = colormap.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
# Visualization
scene = window.Scene()
scene.clear()
scene.SetBackground(0, 0, 0)
scene.add(actor.streamtube(streamlines, window.colors.white, opacity=0.05))
scene.add(actor.point(centers[:, 0, :], colormap_full, point_radius=0.2))
window.record(scene,
n_frames=1,
out_path='center_of_mass_feature.png',
size=(600, 600))
if interactive:
window.show(scene)
"""
.. figure:: center_of_mass_feature.png
:align: center
Showing the center of mass of each streamline and colored according to
the QuickBundles results.
.. _clustering-examples-MidpointFeature:
phi = test[:, 2]
# Gradient Table formation for the heck of it
gtab_b3000 = gradient_table(b3000_bvals, b3000_bvecs)
# Generate a Hemisphere figure plot
hsph_initial = HemiSphere(theta=theta, phi=phi)
# Enables/disables interactive visualization
interactive = True
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(
actor.point(hsph_initial.vertices, window.colors.red, point_radius=0.05))
if interactive:
window.show(ren)
print('The Points should be looking good visually !')
print('Lets form the much needed sphere')
sphere_grad = Sphere(xyz=np.vstack((hsph_initial.vertices,
-hsph_initial.vertices)))
window.rm_all(ren)
ren.add(
actor.point(sphere_grad.vertices, actor.colors.green, point_radius=0.05))
if interactive:
hsph_updated, potential = disperse_charges(hsph_initial, 5000)
"""
In ``hsph_updated`` we have the updated ``HemiSphere`` with the points nicely
distributed on the hemisphere. Let's visualize them.
"""
from dipy.viz import window, actor
# Enables/disables interactive visualization
interactive = False
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(
actor.point(hsph_initial.vertices, window.colors.red, point_radius=0.05))
ren.add(
actor.point(hsph_updated.vertices, window.colors.green, point_radius=0.05))
print('Saving illustration as initial_vs_updated.png')
window.record(ren, out_path='initial_vs_updated.png', size=(300, 300))
if interactive:
window.show(ren)
"""
.. figure:: initial_vs_updated.png
:align: center
Example of electrostatic repulsion of red points which become green points.
We can also create a sphere from the hemisphere and show it in the following way.
"""
# Extract feature of every streamline.
centers = np.asarray(list(map(feature.extract, streamlines)))
# Color each center of mass according to the cluster they belong to.
colormap = actor.create_colormap(np.arange(len(clusters)))
colormap_full = np.ones((len(streamlines), 3))
for cluster, color in zip(clusters, colormap):
colormap_full[cluster.indices] = color
# Visualization
ren = window.Renderer()
window.clear(ren)
ren.SetBackground(0, 0, 0)
ren.add(actor.streamtube(streamlines, window.colors.white, opacity=0.05))
ren.add(actor.point(centers[:, 0, :], colormap_full, point_radius=0.2))
window.record(ren, n_frames=1, out_path='center_of_mass_feature.png', size=(600, 600))
if interactive:
window.show(ren)
"""
.. figure:: center_of_mass_feature.png
:align: center
Showing the center of mass of each streamline and colored according to
the QuickBundles results.
.. _clustering-examples-MidpointFeature:
Midpoint Feature
================
import numpy as np
from dipy.core.sphere import disperse_charges, Sphere, HemiSphere
from dipy.viz import window, actor
n_pts = 64
theta = np.pi * np.random.rand(n_pts)
phi = 2 * np.pi * np.random.rand(n_pts)
hsph_initial = HemiSphere(theta=theta, phi=phi)
hsph_updated, potential = disperse_charges(hsph_initial, 5000)
# Enables/disables interactive visualization
interactive = True
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(
actor.point(hsph_initial.vertices, window.colors.red, point_radius=0.05))
ren.add(
actor.point(hsph_updated.vertices, window.colors.green, point_radius=0.05))
print('Saving illustration as initial_vs_updated.png')
window.record(ren, out_path='initial_vs_updated.png', size=(300, 300))
if interactive:
window.show(ren)
# print grad3.shape
# vertices = grad3*gradients
vertices = gradients
if omit > 0:
vertices = vertices[omit:, :]
if entry['hemi']:
vertices = np.vstack([vertices, -vertices])
return vertices[omit:, :]
print(sphere_dic.keys())
# vertices = get_vertex_set('create5')
# vertices = get_vertex_set('siem64')
# vertices = get_vertex_set('dsi102')
vertices = get_vertex_set('fy362')
gradients = get_vertex_set('siem64')
gradients = gradients[:gradients.shape[0] / 2]
print(gradients.shape)
from dipy.viz import window, actor
sph = -np.sinc(np.dot(gradients[1], vertices.T))
ren = window.Renderer()
# sph = np.arange(vertices.shape[0])
print(sph.shape)
cols = window.colors(sph, 'jet')
ren.add(actor.point(vertices, cols, point_radius=.1, theta=10, phi=10))
window.show(ren)
def show_seeds(seeds):
renderer = window.Renderer()
points = actor.point(seeds, colors=np.random.rand(*seeds.shape))
renderer.add(points)
window.show(renderer)
bvec_path = r'D:\Users\Vishwesh\PycharmProjects\shore_mapmri\ms_bvecs_b0.bvec'
bval_path = r'D:\Users\Vishwesh\PycharmProjects\shore_mapmri\ms_bvals_b0.bval'
bvals, bvecs = read_bvals_bvecs(bval_path, bvec_path)
print("Debug Here")
# Calculate Spherical Coordinates
b3000_bvecs = bvecs[0:100,:]
test = cart2sphA(b3000_bvecs)
theta = test[:,1]
phi = test[:,2]
# Generate a Hemisphere figure plot
hsph_initial = HemiSphere(theta=theta, phi=phi)
# Enables/disables interactive visualization
interactive = True
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(actor.point(hsph_initial.vertices, window.colors.red, point_radius=0.05))
if interactive:
window.show(ren)
hsph_updated, potential = disperse_charges(hsph_initial, 5000)
"""
In ``hsph_updated`` we have the updated ``HemiSphere`` with the points nicely
distributed on the hemisphere. Let's visualize them.
"""
from dipy.viz import window, actor
# Enables/disables interactive visualization
interactive = False
ren = window.Renderer()
ren.SetBackground(1, 1, 1)
ren.add(actor.point(hsph_initial.vertices, window.colors.red, point_radius=0.05))
ren.add(actor.point(hsph_updated.vertices, window.colors.green, point_radius=0.05))
print('Saving illustration as initial_vs_updated.png')
window.record(ren, out_path='initial_vs_updated.png', size=(300, 300))
if interactive:
window.show(ren)
"""
.. figure:: initial_vs_updated.png
:align: center
Example of electrostatic repulsion of red points which become green points.
We can also create a sphere from the hemisphere and show it in the following way.
"""
def show_seeds(seeds):
renderer = window.Renderer()
points = actor.point(seeds, colors=np.random.rand(*seeds.shape))
renderer.add(points)
window.show(renderer)
