def test_gui(self):
pp = Pointset(3)
pp.append(0, 0, 0)
pp.append(0, 1, 0)
pp.append(1, 2, 0)
pp.append(0, 2, 1)
# Create all solids
vv.solidBox((0, 0, 0))
sphere = vv.solidSphere((3, 0, 0))
cone = vv.solidCone((6, 0, 0))
# a cone with 4 faces is a pyramid
pyramid = vv.solidCone((9, 0, 0), N=4)
vv.solidCylinder((0, 3, 0), (1, 1, 2))
ring = vv.solidRing((3, 3, 0))
vv.solidTeapot((6, 3, 0))
vv.solidLine(pp+Point(9, 3, 0), radius=0.2)
# Make the ring green
ring.faceColor = 'g'
# Make the sphere dull
sphere.specular = 0
sphere.diffuse = 0.4
# Show lines in yellow pyramid
pyramid.faceColor = 'r'
pyramid.edgeShading = 'plain'
# Colormap example
N = cone._vertices.shape[0]
cone.SetValues(np.linspace(0, 1, N))
cone.colormap = vv.CM_JET
def __init__(self, kinData, axes, name, label, fs, parent = None):
self.name = name
self.label = label
self.labelOffset = Sensor.labelOffsets['midsagittal']
self.axes = axes
self.fs = fs
self.vMags = None
baseVector = vv.Point(0,0,1)
self.quats = [vv.Quaternion(kinData[i,3],kinData[i,4],kinData[i,5],kinData[i,6]) for i in xrange(kinData.shape[0])]
self.positions = np.array(kinData[:,0:3])
self.orientations = [tuple(self.quats[i].rotate_point(baseVector)) for i in xrange(kinData.shape[0])]
self.cone = vv.solidCone(translation = tuple(self.positions[0]),scaling = (1.5,1.5,1.5),direction = self.orientations[0],axesAdjust = False, axes = self.axes)
self.text = vv.Text(self.axes, self.label, self.positions[0,0]+self.labelOffset[0], self.positions[0,1]+self.labelOffset[1], self.positions[0,2]+self.labelOffset[2])
self.color = Sensor.colorDict[Sensor.colorOrder[Sensor.numSensors]]
self.cone.faceColor = self.color
self.intervalPoints = vv.Pointset(self.positions)
Sensor.numSensors+=1
verticesPerFace=4)
#
if translation is not None:
m.translation = translation
if scaling is not None:
m.scaling = scaling
if direction is not None:
m.direction = direction
if rotation is not None:
m.rotation = rotation
# Set flat shading?
if N < 8 or M < 8:
m.faceShading = 'flat'
# Adjust axes
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.cameraType = '3d'
axes.SetLimits()
# Done
axes.Draw()
return m
if __name__ == '__main__':
m = vv.solidCone(N=12)
m.SetTexture(vv.imread('astronaut.png'))
"""
import numpy as np
import visvis as vv
from visvis import Point, Pointset
vv.figure()
a = vv.gca()
# Define points for the line
pp = Pointset(3)
pp.append(0,0,0); pp.append(0,1,0); pp.append(1,2,0); pp.append(0,2,1)
# Create all solids
box = vv.solidBox((0,0,0))
sphere = vv.solidSphere((3,0,0))
cone = vv.solidCone((6,0,0))
pyramid = vv.solidCone((9,0,0), N=4) # a cone with 4 faces is a pyramid
cylinder = vv.solidCylinder((0,3,0),(1,1,2))
ring = vv.solidRing((3,3,0))
teapot = vv.solidTeapot((6,3,0))
line = vv.solidLine(pp+Point(9,3,0), radius = 0.2)
# Let's put a face on that cylinder
# This works because 2D texture coordinates are automatically generated for
# the sphere, cone, cylinder and ring.
im = vv.imread('astronaut.png')
cylinder.SetTexture(im)
# Make the ring green
ring.faceColor = 'g'
def view(mol, viewer='native'):
'''Render the molecule
The mayavi backend doesn't work under python 3. The native backend uses
visvis to render the molecule. This is very slow.
It's better to use the molecular viewer.
Args:
mol (molecule.Molecule): The molecule instance to render
viewer: The backend to use. Valid choices are 'native', 'maya'
and, 'avogadro' (default: native).
Rturns:
None
'''
# mayavi
if viewer == 'maya':
from mayavi import mlab
for atom in mol.atoms:
pts = mlab.points3d(atom.r[0], atom.r[1], atom.r[2],
scale_factor=0.75,
scale_mode='none',
resolution=20,
color=atom.color())
for i, j in mol.bonds():
mlab.plot3d([mol.atoms[i].r[0], mol.atoms[j].r[0]],
[mol.atoms[i].r[1], mol.atoms[j].r[1]],
[mol.atoms[i].r[2], mol.atoms[j].r[2]],
tube_radius=0.1,
tube_sides=20)
mlab.show()
# avogadro
if viewer == 'avogadro':
from subprocess import call
write_xyz(mol, 'avogadro.xyz')
call(['avogadro', 'avogadro.xyz'])
call(['rm', 'avogadro.xyz'])
# visvis
if viewer == 'native':
import visvis as vv
for atom in mol.atoms:
x, y, z = atom.r
at = vv.solidSphere((x, y, z), atom.radius()*0.25)
at.faceColor = atom.color()
for bond in mol.bonds():
pp = vv.Pointset(3)
pp.append(bond.atoms[0].r)
pp.append(bond.atoms[1].r)
vv.solidLine(pp, radius=0.15, N=16)
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([4, 3, 3])
x = vv.solidLine(pp, radius=0.05)
x.faceColor = 'r'
conex = vv.solidCone([4, 3, 3], scaling=[0.1, 0.1, 0.1], direction=[1, 0, 0])
conex.faceColor = 'r'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 4, 3])
y = vv.solidLine(pp, radius=0.05)
y.faceColor = 'g'
coney = vv.solidCone([3, 4, 3], scaling=[0.1, 0.1, 0.1], direction=[0, 1, 0])
coney.faceColor = 'g'
pp = vv.Pointset(3)
pp.append([3, 3, 3])
pp.append([3, 3, 4])
z = vv.solidLine(pp, radius=0.05)
z.faceColor = 'b'
conez = vv.solidCone([3, 3, 4], scaling=[0.1, 0.1, 0.1], direction=[0, 0, 1])
conez.faceColor = 'b'
# Set axes settings
axes = vv.gca()
axes.SetLimits(rangeX=(-5, 5), rangeY=(-5, 5), rangeZ=(-5, 5))
vv.axis('off')
app = vv.use()
app.Run()
def plot_reference_sphere(theta=0,
phi=0,
isometric=True,
ax=None,
azimuth=None,
elevation=None,
degrees=True,
labels=True,
light_ambient=.6,
zoom=1.4,
arrow_color=(.25, .95, .8),
close_figure=False):
if azimuth is None:
azimuth = DEFAULT_AZIMUTH
if elevation is None:
elevation = DEFAULT_ELEVATION
import visvis as vv
if ax is None:
app = vv.use()
fig = vv.figure()
ax = vv.subplot(111)
else:
app = None
fig = ax.GetFigure()
ax.axis.visible = 0
ax.axis.xLabel = 'x'
ax.axis.yLabel = 'y'
ax.axis.zLabel = 'z'
# coordinate system
length = 1.4
cyl_diameter = .05
for i in range(3):
direction = np.zeros((3, ))
direction[i] = 1
cyl = vv.solidCylinder(translation=(0, 0, 0),
scaling=(cyl_diameter, cyl_diameter, length),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = (.75, .75, .75)
translation = np.zeros((3, ))
translation[i] = length
cone = vv.solidCone(translation=tuple(translation),
scaling=(.1, .1, .2),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cone.faceColor = (.75, .75, .75)
# example direction
length = 1
shrink = .825
direction = sph2cart(1, theta, phi, degrees=degrees).ravel()
cyl = vv.solidCylinder(translation=(0, 0, 0),
scaling=(.05, .05, shrink * length),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = arrow_color
translation = direction * shrink
cone = vv.solidCone(translation=tuple(translation),
scaling=(.1, .1, .2),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cone.faceColor = arrow_color
# indicate unit sphere
sphere = vv.solidSphere((0, 0, 0), N=100, M=100)
sphere.faceColor = (.5, .5, .5, .25)
# some lines on sphere indicating main axes
phi = np.linspace(0, 2 * np.pi, 100)
theta = np.ones_like(phi) * np.pi / 2.
r = np.ones_like(phi)
xyz = sph2cart(r, theta, phi, degrees=False)
vv.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
lw=1,
lc=(.5, .5, .5),
ls="-",
mc='b',
axesAdjust=False,
axes=ax)
theta = np.linspace(-np.pi, np.pi, 100)
phi = np.ones_like(theta) * 0
r = np.ones_like(phi)
xyz = sph2cart(r, theta, phi, degrees=False)
vv.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
lw=1,
lc=(.5, .5, .5),
ls="-",
mc='b',
axesAdjust=False,
axes=ax)
theta = np.linspace(-np.pi, np.pi, 100)
phi = np.ones_like(theta) * np.pi / 2.
r = np.ones_like(phi)
xyz = sph2cart(r, theta, phi, degrees=False)
vv.plot(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
lw=1,
lc=(.5, .5, .5),
ls="-",
mc='b',
axesAdjust=False,
axes=ax)
# add pitch and roll axes
aa = np.deg2rad(np.linspace(45, 315, 100) - 90)
r = .25 + .025
d = 1.25 + .05
color = (.25, .25, .25)
# pitch rotation (in x/z plane, i.e. around y-axis)
xx = r * np.cos(aa)
zz = r * np.sin(aa)
yy = d * np.ones_like(xx)
vv.plot(xx, yy, zz, lw=5, lc=color, ls="-", axesAdjust=False, axes=ax)
translation = (xx[0], yy[0], zz[0])
direction = (xx[0] - xx[1], yy[0] - yy[1], zz[0] - zz[1])
cone = vv.solidCone(translation=translation,
scaling=(.05, .05, .1),
direction=direction,
axesAdjust=False,
axes=ax)
cone.faceColor = color
if labels:
vv.Text(ax, 'Pitch', x=0, y=1.25 * d, z=.25, fontSize=28, color=color)
# roll rotation (in y/z plane, i.e. around x-axis)
yy = r * np.cos(aa)
zz = r * np.sin(aa)
xx = d * np.ones_like(xx)
vv.plot(xx, yy, zz, lw=5, lc=color, ls="-", axesAdjust=False, axes=ax)
translation = (xx[-1], yy[-1], zz[-1])
direction = (xx[-1] - xx[-2], yy[-1] - yy[-2], zz[-1] - zz[-2])
cone = vv.solidCone(translation=translation,
scaling=(.05, .05, .1),
direction=direction,
axesAdjust=False,
axes=ax)
cone.faceColor = color
if labels:
vv.Text(ax, 'Roll', x=1.25 * d, y=-.8, z=0, fontSize=28, color=color)
# set camera view
zoom_ = vv.view()['zoom']
if isometric:
vv.view(dict(azimuth=90 + ISO_AZIMUTH, elevation=ISO_ELEVATION),
zoom=zoom * zoom_,
axes=ax)
else:
vv.view(dict(azimuth=90 + azimuth, elevation=elevation),
zoom=zoom * zoom_,
_axes=ax)
ax.light0.ambient = light_ambient
ax.light0.specular = .5
fig.DrawNow()
if app is not None:
app.ProcessEvents()
img = vv.screenshot(None, ob=ax, sf=2, bg=None, format=None)
if close_figure:
vv.close(fig)
fig = None
return fig, img
def plot_mouse_head(show_now=False,
size=(500, 500),
ax=None,
theta=0,
phi=0,
pitch=None,
roll=None,
isometric=True,
azimuth=None,
elevation=None,
zoom=1.5,
gravity_axes=True,
head_axes=True,
close_figure=False,
color_mouse=(.5, .5, .5),
color_head_axes=(.25, .95, .8),
color_gravity_axes=(.75, .75, .75),
backend='visvis',
light_ambient=.6,
light_specular=.5,
arrow_kw=dict(length_cone=.1,
radius_cone=.05,
radius_shaft=.025)):
if azimuth is None:
azimuth = DEFAULT_AZIMUTH
if elevation is None:
elevation = DEFAULT_ELEVATION
t = np.arange(0, 1 * np.pi - 2 * np.pi / 10, np.pi / 10)
r = 2 + np.cos(t)
n = 20
if backend in ['mayavi', 'mlab']:
from mayavi import mlab
from tvtk.tools import visual
fig = mlab.figure(bgcolor=(1, 1, 1), size=size)
fig.scene.parallel_projection = True
# head
c = -3
[X, Y, Z] = cylinder(r, n=n)
head = mlab.mesh(X, Y, c + Z * 6, color=(.5, .5, .5))
# nose
[x, y, z] = sphere(20)
nose = mlab.mesh(x * 1.5, y * 1.5, c + z * 1.5 + 6, color=(.5, .5, .5))
# EARS
color = (.5, .5, .5)
hsE1 = mlab.mesh((x * 1.0) - 2.427, (y * 1.8) - 1.763,
c + (z * 0.4) + 0,
color=color)
hsE2 = mlab.mesh((x * 1.0) + 2.427, (y * 1.8) - 1.763,
c + (z * 0.4) + 0,
color=color)
# EYES
[x, y, z] = sphere(10)
color = (.9, .9, .9)
hsEYE1 = mlab.mesh((x * .8) - 1.2, (y * .8) - 1.6,
c + (z * .8) + 3.5,
color=color)
hsEYE2 = mlab.mesh((x * .8) + 1.2, (y * .8) - 1.6,
c + (z * .8) + 3.5,
color=color)
# pupils
hsPUP1 = mlab.mesh((x * .3) - 1.476, (y * .3) - 1.98,
c + (z * .3) + 4.147,
color=(0.1, 0.1, 0.1))
hsPUP2 = mlab.mesh((x * .3) + 1.476, (y * .3) - 1.98,
c + (z * .3) + 4.147,
color=(0.1, 0.1, 0.1))
# whiskers
Px = np.array([-1.154, -1.214, -1.154, +1.154, +1.214, +1.154])
Py = np.array([-0.375, 0, 0.375, -0.375, 0, 0.375])
Pz = np.ones(np.size(Px)) * 3.882
WL = np.array([[0.5, 2], [0.05, 0.4]]) # whisker length
hsWHISK = []
for W in range(0, len(Px)): # W=0
if Px[W] < 0:
XSIGN = -1
else:
XSIGN = +1
if Py[W] < 0:
YSIGN = -1
elif Py[W] == 0:
YSIGN = 0
else:
YSIGN = +1
x = np.append(Px[W], Px[W] + XSIGN * WL[0, :])
y = np.append(Py[W], Py[W] + YSIGN * WL[1, :])
z = np.append(Pz[W], Pz[W])
tck, u = interpolate.splprep([x, y], k=2)
xi, yi = interpolate.splev(np.linspace(0, 1, 100), tck, der=0)
zi = np.ones(np.size(yi)) * Pz[W]
hsWHISK.append(
mlab.plot3d(xi, yi, zi, color=(0, 0, 0), line_width=2))
# rotate all objects
angle_x = -90
angle_y = 0
angle_z = -90
for actor in [head, nose, hsE1, hsE2, hsEYE1, hsEYE2, hsPUP1, hsPUP2]:
actor.actor.actor.rotate_z(angle_z)
actor.actor.actor.rotate_x(angle_x)
actor.actor.actor.rotate_y(angle_y)
# actor.actor.actor.rotate_y(phi)
# actor.actor.actor.rotate_z(theta)
actor.actor.actor.rotate_x(theta)
actor.actor.actor.rotate_y(phi)
for i in range(0, len(hsWHISK)):
hsWHISK[i].actor.actor.rotate_z(angle_z)
hsWHISK[i].actor.actor.rotate_x(angle_x)
hsWHISK[i].actor.actor.rotate_y(angle_y)
hsWHISK[i].actor.actor.rotate_x(theta)
hsWHISK[i].actor.actor.rotate_y(phi)
if head_axes:
# axes of head-centered coordinate system
visual.set_viewer(fig)
arr1 = Arrow3D(0,
0,
0,
0,
-6,
0,
color=color_head_axes,
**arrow_kw)
for arr in [arr1]: # , arr2, arr3]:
arr.actor.rotate_z(angle_z)
arr.actor.rotate_x(angle_x)
arr.actor.rotate_y(angle_y)
arr.actor.rotate_x(theta)
arr.actor.rotate_y(phi)
if gravity_axes:
# gravitational coordinate system
visual.set_viewer(fig)
arr1 = Arrow3D(0, 0, 0, -6, 0, 0, color=(.8, .8, .8), **arrow_kw)
arr2 = Arrow3D(0, 0, 0, 0, -6, 0, color=(.5, .5, .5), **arrow_kw)
arr3 = Arrow3D(0, 0, 0, 0, 0, 6, color=(.25, .25, .25), **arrow_kw)
for arr in [arr1, arr2, arr3]:
arr.actor.rotate_z(angle_z)
arr.actor.rotate_x(angle_x)
arr.actor.rotate_y(angle_y)
if isometric:
fig.scene.isometric_view()
else:
mlab.view(azimuth=azimuth, elevation=elevation, figure=fig)
fig.scene.camera.zoom(zoom)
if show_now:
mlab.show()
img = mlab.screenshot(figure=fig, mode='rgb', antialiased=False)
elif backend in ['visvis']:
import visvis as vv
if ax is None:
app = vv.use()
fig = vv.figure()
ax = vv.subplot(111)
else:
app = None
fig = ax.GetFigure()
ax.bgcolor = (1, 1, 1)
ax.axis.visible = 0
ax.axis.xLabel = 'x'
ax.axis.yLabel = 'y'
ax.axis.zLabel = 'z'
# head
c = -3
[X, Y, Z] = cylinder(r, n=n)
head = vv.surf(c + 6 * Z, X, Y)
head.faceColor = color_mouse
# nose
[x, y, z] = sphere(20)
nose = vv.surf(c + z * 1.5 + 6, x * 1.5, y * 1.5)
nose.faceColor = color_mouse
# ears
color = (.5, .5, .5)
ear1 = vv.surf(c + (z * 0.4) + 0, (x * 1.0) - 2.427,
-1 * ((y * 1.8) - 1.763))
ear1.faceColor = color
ear2 = vv.surf(c + (z * 0.4) + 0, (x * 1.0) + 2.427,
-1 * ((y * 1.8) - 1.763))
ear2.faceColor = color_mouse
# eyes
[x, y, z] = sphere(10)
color = (.9, .9, .9)
eye1 = vv.surf(c + (z * .8) + 3.5, (x * .8) - 1.2,
-1 * ((y * .8) - 1.6))
eye2 = vv.surf(c + (z * .8) + 3.5, (x * .8) + 1.2,
-1 * ((y * .8) - 1.6))
[setattr(eye, 'faceColor', color) for eye in [eye1, eye2]]
# pupils
color = (.1, .1, .1)
pupil1 = vv.surf(c + (z * .3) + 4.147 - .5, (x * .3) - 1.476 - .2,
-1 * ((y * .3) - 1.98))
pupil2 = vv.surf(c + (z * .3) + 4.147 - .5, (x * .3) + 1.476 + .2,
-1 * ((y * .3) - 1.98))
[setattr(pupil, 'faceColor', color) for pupil in [pupil1, pupil2]]
# whiskers
Px = np.array([-1.154, -1.214, -1.154, +1.154, +1.214, +1.154])
Py = np.array([-0.375, 0, 0.375, -0.375, 0, 0.375])
Pz = np.ones(np.size(Px)) * 3.882
WL = np.array([[0.5, 2], [0.05, 0.4]]) # whisker length
whiskers = []
for W in range(0, len(Px)): # W=0
if Px[W] < 0:
XSIGN = -1
else:
XSIGN = +1
if Py[W] < 0:
YSIGN = -1
elif Py[W] == 0:
YSIGN = 0
else:
YSIGN = +1
x = np.append(Px[W], Px[W] + XSIGN * WL[0, :])
y = np.append(Py[W], Py[W] + YSIGN * WL[1, :])
z = np.append(Pz[W], Pz[W])
tck, u = interpolate.splprep([x, y], k=2)
xi, yi = interpolate.splev(np.linspace(0, 1, 100), tck, der=0)
zi = np.ones(np.size(yi)) * Pz[W]
whisker = vv.plot(zi, xi, -1 * yi, lw=2, lc=(0, 0, 0))
whiskers.append(whisker)
if head_axes:
# show vector indicating orientation of head
length = 1
shrink = .825
if pitch is not None and roll is not None:
# convert pitch/roll to spherical coordinates by rotating
# a reference point around cartesian axes; note that x and
# y are swapped in visvis
p0 = np.array([0, 0, 1])
a = np.deg2rad(roll)
Rx = np.array([[1, 0, 0], [0, np.cos(a), -np.sin(a)],
[0, np.sin(a), np.cos(a)]])
b = np.deg2rad(pitch)
Ry = np.array([[np.cos(b), 0, np.sin(b)], [0, 1, 0],
[-np.sin(b), 0, np.cos(b)]])
direction = np.dot(Ry, np.dot(Rx, p0)) * length
else:
direction = sph2cart(length, theta, phi, degrees=True).ravel()
cyl = vv.solidCylinder(translation=(0, 0, .25),
scaling=(.05, .05, shrink * length),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = (.25, .95, .8)
cyl.do_not_rotate = True
cyl.do_not_scale = True
translation = direction * shrink + np.array([0, 0, .25])
cone = vv.solidCone(translation=tuple(translation),
scaling=(.1, .1, .2),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cone.faceColor = (.25, .95, .8)
cone.do_not_rotate = True
cone.do_not_scale = True
if gravity_axes:
# show vector indicating (negative) orientation of gravity
length = 1
shrink = .825
color = (.75, .75, .75)
direction = np.array([0, 0, 1])
cyl = vv.solidCylinder(translation=(0, 0, .25),
scaling=(.05, .05, shrink * length),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = color
cyl.do_not_rotate = True
cyl.do_not_scale = True
translation = direction * shrink + np.array([0, 0, .25])
cone = vv.solidCone(translation=tuple(translation),
scaling=(.1, .1, .2),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cone.faceColor = color
cone.do_not_rotate = True
cone.do_not_scale = True
# compute pitch and/or roll if not given
if pitch is None or roll is None:
# we have to find rotations (=angles) between the unit vector
# in spherical coordinates (1, theta, phi) and the planes
# for pitch (y/z) and roll (x/z); note that xyz is already
# normaizeed (norm = 1)
xyz = sph2cart(1, theta, phi, degrees=True).ravel()
if pitch is None:
# pitch (y/z plane with normal vector (1, 0, 0))
pitch = 90 - np.degrees(np.arccos(np.dot(xyz, [1, 0, 0])))
if roll is None:
# roll (x/z plane with normal vector (0, -1, 0))
roll = 90 - np.degrees(np.arccos(np.dot(xyz, [0, -1, 0])))
for obj in ax.wobjects:
if not hasattr(obj, 'do_not_scale'):
rot = vv.Transform_Scale(sx=.25, sy=.25, sz=.25)
obj.transformations.append(rot)
if obj.__class__ != vv.core.axises.CartesianAxis and\
not hasattr(obj, 'do_not_rotate'):
# note that x and y are swapped
rot = vv.Transform_Rotate(pitch, ax=0, ay=1, az=0)
obj.transformations.append(rot)
rot = vv.Transform_Rotate(roll, ax=1, ay=0, az=0)
obj.transformations.append(rot)
zoom = vv.view()['zoom']
if isometric:
vv.view(dict(azimuth=90 + ISO_AZIMUTH, elevation=ISO_ELEVATION),
zoom=4 * zoom,
axes=ax)
else:
vv.view(dict(azimuth=90 + azimuth, elevation=elevation),
zoom=4 * zoom,
axes=ax)
ax.light0.ambient = light_ambient
ax.light0.specular = light_specular
fig.DrawNow()
if app is not None:
app.ProcessEvents()
img = vv.screenshot(None, ob=ax, sf=2, bg=None, format=None)
if close_figure:
vv.close(fig)
fig = None
return fig, img
def plot_density_sphere(xyz_centers,
H,
ax=None,
method='hist',
azimuth=None,
elevation=None,
backend='visvis',
oversample=1,
smoothing=None,
zoom=1.7,
cmap='jet',
scaling='log',
log_offset=-.1,
clim=None,
isometric=False,
light_ambient=.6,
light_specular=.5,
avg_direction=None,
pitch_label=True,
roll_label=True,
pitch_arrow=True,
roll_arrow=True,
arrow_color=(.25, .95, .8),
close_figure=False):
if azimuth is None:
azimuth = DEFAULT_AZIMUTH
if elevation is None:
elevation = DEFAULT_ELEVATION
scaling = scaling.lower()
if scaling.startswith('log'):
H = H / float(H.sum())
v = H > 0
if scaling == 'log':
H[v] = np.log(H[v])
elif scaling == 'log2':
H[v] = np.log2(H[v])
H[~v] = H[v].min() + log_offset
if smoothing is not None and smoothing > 1:
x = np.linspace(-3., 3., smoothing)
xx, yy = np.meshgrid(x, x)
G = np.exp((-xx**2 - yy**2))
H = signal.convolve2d(H, G / G.sum(), mode='same', boundary='wrap')
if backend in ['mpl', 'matplotlib']:
if ax is None:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
from matplotlib.colors import LightSource
ls = LightSource(azdeg=315, altdeg=45)
cm = getattr(plt.cm, cmap)
colors = ls.shade(H, cmap=cm, blend_mode='soft', vert_exag=1)
ax.plot_surface(xyz_centers[:, 0].reshape(H),
xyz_centers[:, 1].reshape(H),
xyz_centers[:, 2].reshape(H),
cstride=1,
rstride=1,
facecolors=colors,
linewidth=0,
antialiased=False,
shade=False)
# add arrows in front of sphere
import mousecam_helpers as helpers
arrow_props = dict(arrowstyle='simple',
mutation_scale=15,
mutation_aspect=None,
linewidth=.5,
facecolor=3 * [.75],
edgecolor=3 * [.1])
length = .6
arr = helpers.Arrow3D((1, 1 + length), (0, 0), (0, 0), **arrow_props)
ax.add_artist(arr)
arr = helpers.Arrow3D((0, 0), (1, 1 + length), (0, 0), **arrow_props)
ax.add_artist(arr)
arr = helpers.Arrow3D((0, 0), (0, 0), (1, 1 + length), **arrow_props)
ax.add_artist(arr)
extents = 3 * [[-.6, .6]]
ax.auto_scale_xyz(*extents)
ax.set_aspect('equal')
ax.axis('off')
ax.view_init(elev=elevation, azim=360 - azimuth)
elif backend in ['mayavi', 'mlab']:
from mayavi import mlab
fig = mlab.figure(bgcolor=(1, 1, 1), size=(1000, 1000))
fig.scene.parallel_projection = True
mlab.mesh(xyz_centers[:, 0].reshape(H.shape),
xyz_centers[:, 1].reshape(H.shape),
xyz_centers[:, 2].reshape(H.shape),
scalars=H,
colormap='jet')
from tvtk.tools import visual
visual.set_viewer(fig)
arrow_kw = dict(color=(.75, .75, .75),
length_cone=.1,
radius_cone=.05,
radius_shaft=.025)
Arrow3D(0, 0, 0, 1.4, 0, 0, **arrow_kw)
Arrow3D(0, 0, 0, 0, 1.4, 0, **arrow_kw)
Arrow3D(0, 0, 0, 0, 0, 1.4, **arrow_kw)
if isometric:
fig.scene.isometric_view()
else:
mlab.view(azimuth=-azimuth, elevation=elevation, figure=fig)
fig.scene.camera.zoom(zoom)
ax = mlab.screenshot(figure=fig, mode='rgb', antialiased=False)
elif backend in ['visvis']:
import visvis as vv
app = vv.use()
fig = vv.figure()
ax = vv.subplot(111)
ax.axis.visible = 0
ax.axis.xLabel = 'x'
ax.axis.yLabel = 'y'
ax.axis.zLabel = 'z'
length = 1.4
for i in range(3):
direction = np.zeros((3, ))
direction[i] = 1
cyl = vv.solidCylinder(translation=(0, 0, 0),
scaling=(.05, .05, length),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = (.75, .75, .75)
translation = np.zeros((3, ))
translation[i] = length
cone = vv.solidCone(translation=tuple(translation),
scaling=(.1, .1, .2),
direction=tuple(direction),
axesAdjust=False,
axes=ax)
cone.faceColor = (.75, .75, .75)
surf = vv.surf(xyz_centers[:, 0].reshape(H.shape),
xyz_centers[:, 1].reshape(H.shape),
xyz_centers[:, 2].reshape(H.shape),
H,
axes=ax)
# set colormap
cmap = cmap.lower()
if cmap.endswith('_r'):
cm = vv.colormaps[cmap[:-2]]
cm = cm[::-1]
else:
cm = vv.colormaps[cmap]
surf.colormap = cm
if clim is not None:
# apply colormap limits
surf.clim = clim
# ax.Draw()
# add labels to indicate pitch and/or roll axes
aa = np.deg2rad(np.linspace(45, 315, 100) - 90)
r = .25 + .05
d = 1.25 + .25
color = (.25, .25, .25)
if pitch_arrow:
# pitch rotation (in x/z plane, i.e. around y-axis)
xx = r * np.cos(aa)
zz = r * np.sin(aa)
yy = d * np.ones_like(xx)
vv.plot(xx,
yy,
zz,
lw=5,
lc=color,
ls="-",
axesAdjust=False,
axes=ax)
translation = (xx[0], yy[0], zz[0])
direction = (xx[0] - xx[1], yy[0] - yy[1], zz[0] - zz[1])
cone = vv.solidCone(translation=translation,
scaling=(.05, .05, .1),
direction=direction,
axesAdjust=False,
axes=ax)
cone.faceColor = color
if pitch_label:
vv.Text(ax, 'Pitch', x=0, y=.9 * d, z=.5, fontSize=28, color=color)
if roll_arrow:
# roll rotation (in y/z plane, i.e. around x-axis)
yy = r * np.cos(aa[::-1])
zz = r * np.sin(aa[::-1])
xx = d * np.ones_like(xx)
vv.plot(xx,
yy,
zz,
lw=5,
lc=color,
ls="-",
axesAdjust=False,
axes=ax)
translation = (xx[0], yy[0], zz[0])
direction = (xx[0] - xx[1], yy[0] - yy[1], zz[0] - zz[1])
cone = vv.solidCone(translation=translation,
scaling=(.05, .05, .1),
direction=direction,
axesAdjust=False,
axes=ax)
cone.faceColor = color
if roll_label:
vv.Text(ax,
'Roll',
x=1.25 * d,
y=-.8,
z=0,
fontSize=28,
color=color)
if avg_direction is not None:
# indicate direction of avg head orientation
avg_direction = avg_direction / np.sqrt(np.sum(avg_direction**2))
avg_direction *= length
cyl = vv.solidCylinder(translation=(0, 0, 0),
scaling=(.05, .05, length),
direction=tuple(avg_direction),
axesAdjust=False,
axes=ax)
cyl.faceColor = arrow_color
cone = vv.solidCone(translation=tuple(avg_direction),
scaling=(.1, .1, .2),
direction=tuple(avg_direction),
axesAdjust=False,
axes=ax)
cone.faceColor = arrow_color
zoom_ = vv.view()['zoom']
if isometric:
vv.view(dict(azimuth=90 + ISO_AZIMUTH, elevation=ISO_ELEVATION),
zoom=zoom_ * zoom,
axes=ax)
else:
vv.view(dict(azimuth=90 + azimuth, elevation=elevation),
zoom=zoom * zoom_,
axes=ax)
ax.light0.ambient = light_ambient
ax.light0.specular = light_specular
fig.DrawNow()
app.ProcessEvents()
img = vv.screenshot(None, ob=ax, sf=2, bg=None, format=None)
ax = img
if close_figure:
vv.close(fig)
fig = None
return fig, ax
verticesPerFace=4)
#
if translation is not None:
m.translation = translation
if scaling is not None:
m.scaling = scaling
if direction is not None:
m.direction = direction
if rotation is not None:
m.rotation = rotation
# Set flat shading?
if N<8 or M<8:
m.faceShading = 'flat'
# Adjust axes
if axesAdjust:
if axes.daspectAuto is None:
axes.daspectAuto = False
axes.cameraType = '3d'
axes.SetLimits()
# Done
axes.Draw()
return m
if __name__ == '__main__':
m = vv.solidCone(N=12)
m.SetTexture( vv.imread('lena.png') )
"""
import numpy as np
import visvis as vv
from visvis import Point, Pointset
vv.figure()
a = vv.gca()
# Define points for the line
pp = Pointset(3)
pp.append(0,0,0); pp.append(0,1,0); pp.append(1,2,0); pp.append(0,2,1)
# Create all solids
box = vv.solidBox((0,0,0))
sphere = vv.solidSphere((3,0,0))
cone = vv.solidCone((6,0,0))
pyramid = vv.solidCone((9,0,0), N=4) # a cone with 4 faces is a pyramid
cylinder = vv.solidCylinder((0,3,0),(1,1,2))
ring = vv.solidRing((3,3,0))
teapot = vv.solidTeapot((6,3,0))
line = vv.solidLine(pp+Point(9,3,0), radius = 0.2)
# Let's put a face on that cylinder
# This works because 2D texture coordinates are automatically generated for
# the sphere, cone, cylinder and ring.
im = vv.imread('lena.png')
cylinder.SetTexture(im)
# Make the ring green
ring.faceColor = 'g'