def get_axes(world):
axes = Axes(
world,
xtitle='y: North (m)', # swap axis to plot correctly
ytitle='x: East (m)',
ztitle='z: TVD (m)',
xTitleJustify='bottom-right',
yTitleJustify='top-right',
zTitleJustify='top-right',
xyGrid2=True,
xyGrid=False,
zxGrid=True,
yzGrid2=True,
zxGridTransparent=True,
yzGrid2Transparent=True,
yzGrid=False,
xLabelRotation=-1,
yLabelRotation=1,
zLabelRotation=1,
)
for a in axes.unpack(): # unpack the Assembly to access its elements
if 'title' in a.name or 'NumericLabel' in a.name:
a.mirror('y')
if 'yNumericLabel' in a.name:
a.scale(0.8)
return axes
def onkeypress(
self,
evt): ###################################### MORPH & GENERATE
if evt.keyPressed == 'm': ##--------- morph mesh1 based on the existing arrows
if len(self.arrow_starts) != len(self.arrow_stops):
printc("You must select your end point first!", c='y')
return
output = [self.mesh1.clone().c('grey4'), self.mesh2, self.msg2]
warped_plane = self.plane1.clone().pickable(False)
warped_plane.warp(self.arrow_starts,
self.arrow_stops,
mode=self.mode)
output.append(warped_plane +
Axes(warped_plane, xyGrid=0, textScale=0.6))
mw = self.mesh1.clone().applyTransform(
warped_plane.transform).c('red4')
output.append(mw)
T_inv = warped_plane.transform.GetInverse()
a = Points(self.arrow_starts,
r=10).applyTransform(warped_plane.transform)
b = Points(self.arrow_stops,
r=10).applyTransform(warped_plane.transform)
self.dottedln = Lines(
a, b, res=self.n).applyTransform(T_inv).pointSize(5)
output.append(self.dottedln)
self.msg1.text(self.instructions)
self.msg2.text("Morphed output:")
self.plotter.clear(at=1).addRendererFrame().add(output, at=1)
elif evt.keyPressed == 'g': ##------- generate intermediate shapes
if not self.dottedln:
return
intermediates = []
allpts = self.dottedln.points()
allpts = allpts.reshape(len(self.arrow_starts), self.n + 1, 3)
for i in range(self.n + 1):
pi = allpts[:, i, :]
m_nterp = self.mesh1.clone().warp(self.arrow_starts,
pi,
mode=self.mode).c('b3').lw(1)
intermediates.append(m_nterp)
self.msg2.text("Morphed output + Interpolation:")
self.plotter.add(intermediates, at=1)
self.dottedln = None
elif evt.keyPressed == 'c': ##------- clear all
self.arrow_starts = []
self.arrow_stops = []
self.toggle = False
self.dottedln = None
self.msg1.text(self.instructions)
self.msg2.text("[output will show here]")
self.plotter.clear(at=0).clear(at=1).addRendererFrame()
self.plotter.add([self.plane1, self.msg1, self.mesh1, self.mesh2],
at=0)
self.plotter.add([self.plane2, self.msg2], at=1)
def start(
self): ################################################ show stuff
paxes = Axes(self.plane1, xyGrid=0, textScale=0.6)
self.plotter.show(self.plane1,
paxes,
self.msg1,
self.mesh1,
self.mesh2,
at=0)
self.plotter.show(self.plane2, self.msg2, at=1, mode='image')
if len(self.arrow_starts):
self.draw(True)
self.draw(False)
self.msg1.text(self.instructions)
self.plotter.show(interactive=True, zoom=1.3).close()
"""Customizing Axes.
Cartesian planes can be displaced
from their lower-range default position"""
from vedo import Sphere, Axes, precision, show
sph = Sphere().scale([4, 3, 2]).shift(5, 6, 7).c('green2', 0.1)
axs = Axes(
sph, # build axes for object sph
xtitle="x axis",
ytitle="y axis",
ztitle="z axis",
htitle='An ellipsoid at ' + precision(sph.centerOfMass(), 2),
hTitleFont=1,
hTitleColor='red3',
zxGrid=True,
xyFrameLine=2,
yzFrameLine=2,
zxFrameLine=2,
xyFrameColor='red3',
yzFrameColor='green3',
zxFrameColor='blue3',
xyShift=0.2, # move xy plane 20% along z
yzShift=0.2, # move yz plane 20% along x
zxShift=0.2, # move zx plane 20% along y
)
show(sph, axs, __doc__)
import numpy as np
from vedo import dataurl, Volume, Axes, show
from vedo.pyplot import histogram, plot
cmap = 'nipy_spectral'
alpha = np.array([0, 0, 0.05, 0.2, 0.8, 1])
vol = Volume(dataurl + "embryo.slc")
vol.cmap(cmap).alpha(alpha).addScalarBar3D(c='w')
xvals = np.linspace(*vol.scalarRange(), len(alpha))
p = histogram(vol, logscale=True, c=cmap, bc='white')
p += plot(xvals, alpha * p.ybounds()[1], '--ow').z(1)
show(
[(vol, Axes(vol, c='w'), f"Original Volume\ncolor map: {cmap}"),
(p, "Voxel scalar histogram\nand opacity transfer function")],
N=2,
sharecam=False,
bg=(82, 87, 110),
)
sin(state[2]) * cosa + M2 * L2 * state[3] * state[3] * sina -
(M1 + M2) * G * sin(state[0])) / den1
dydx[2] = state[3]
den2 = (L2 / L1) * den1
dydx[3] = (-M2 * L2 * state[3] * state[3] * sina * cosa +
(M1 + M2) * G * sin(state[0]) * cosa -
(M1 + M2) * L1 * state[1] * state[1] * sina -
(M1 + M2) * G * sin(state[2])) / den2
return dydx
t = np.arange(0.0, 10.0, dt)
state = np.radians([th1, w1, th2, w2])
y = integrate.odeint(derivs, state, t)
P1 = np.dstack([L1 * sin(y[:, 0]), -L1 * cos(y[:, 0])]).squeeze()
P2 = P1 + np.dstack([L2 * sin(y[:, 2]), -L2 * cos(y[:, 2])]).squeeze()
ax = Axes(xrange=(-2, 2), yrange=(-2, 1), htitle=__doc__)
pb = ProgressBar(0, len(t), c="b")
for i in pb.range():
j = max(i - 5, 0)
k = max(i - 10, 0)
l1 = Line([[0, 0], P1[i], P2[i]]).lw(7).c("blue2")
l2 = Line([[0, 0], P1[j], P2[j]]).lw(6).c("blue2", 0.3)
l3 = Line([[0, 0], P1[k], P2[k]]).lw(5).c("blue2", 0.1)
pt = Points([P1[i], P2[i], P1[j], P2[j], P1[k], P2[k]],
r=8).c("blue2", 0.2)
show(l1, l2, l3, pt, ax, interactive=False, size=(900, 700), zoom=1.4)
pb.print()
ws.append(w)
# print(i, 'whisker:\n', w.info)
# build some theoretical expectation to be shown as a grey band
x = np.linspace(-1, 9, 100)
y = x / 5 + 0.2 * np.sin(x)
ye = y**2 / 5 + 0.1 # error on y
line = Line(np.c_[x, y])
band = Ribbon(np.c_[x, y - ye], np.c_[x, y + ye]).c('black', 0.1)
# build braces to inndicate stats significance and dosage
bra1 = Brace([0, 3], [2, 3], comment='*~*', s=0.7, style='[')
bra2 = Brace([4, -1], [8, -1], comment='dose > 3~\mug/kg', s=0.7)
# build custom axes
axes = Axes(
xrange=[-1, 9],
yrange=[-3, 5],
htitle='\beta_c -expression: change in time',
xtitle=' ',
ytitle='Level of \beta_c protein in \muM/l',
xValuesAndLabels=[
(0, 'Experiment^A\nat t=1h'),
(4, 'Experiment^B\nat t=2h'),
(8, 'Experiment^C\nat t=4h'),
],
xLabelSize=0.02,
)
show(ws, bra1, bra2, line, band, __doc__, axes, zoom=1.1)