def viz_mean_excitability(sid, rid):
regpos, w, obsmask, surfaces, contacts = read_structural_data(sid, rid)
vlines, vmeshes, vcontacts = viz_structure(regpos, w, surfaces, contacts)
# Load results
nreg = regpos.shape[0]
res = io.parse_csv([
f"run/solo/INC/vep/id{sid:03d}/output/r{rid:02d}_all/chain_{chain}.csv"
for chain in [1, 2]
])
cinf = res['c']
# cmean = np.mean(cinf, axis=0)
# pexc = np.mean(cinf > 2.0, axis=0)
scalar = np.percentile(cinf, 50, axis=0)
# Regions
cmap = 'plasma'
# vmin = np.min(scalar)
# vmax = np.max(scalar)
vmin, vmax = -2, 2
vpoints = []
for i in range(nreg):
if not obsmask[i]:
vpoints.append(
vp.Sphere(regpos[i],
r=4,
c=vp.colorMap(scalar[i], cmap, vmin, vmax)))
else:
vpoints.append(
vp.Cube(regpos[i],
side=6,
c=vp.colorMap(scalar[i], cmap, vmin, vmax)))
vbar = vp.Points(regpos, r=0.01).pointColors(scalar,
cmap=cmap,
vmin=vmin,
vmax=vmax)
vbar.addScalarBar(horizontal=True, pos=(0.8, 0.02))
def slider(widget, event):
percentile = widget.GetRepresentation().GetValue()
scalar = np.percentile(cinf, percentile, axis=0)
for i in range(nreg):
vpoints[i].color(vp.colorMap(scalar[i], cmap, vmin, vmax))
vplotter = vp.Plotter(axes=0)
vplotter.addSlider2D(slider,
0.,
100.,
value=50.0,
pos=3,
title="Percentile")
vplotter.show(vpoints, vlines, vmeshes, vcontacts, vbar)
def viz_network_scalar(centres,
scalars,
weights,
obsmask,
surfs,
view='topdown',
size=(1000, 1000),
cmap='viridis',
vmin=None,
vmax=None):
vp.embedWindow(False)
if vmin is None:
vmin = np.min(scalars)
if vmax is None:
vmax = np.max(scalars)
vlines, vmeshes = viz_structure(centres, weights, surfs, w_perc=3)
nreg = centres.shape[0]
# Regions
vpoints = []
for i in range(nreg):
if not obsmask[i]:
vpoints.append(
vp.Sphere(centres[i],
r=4,
c=vp.colorMap(scalars[i], cmap, vmin, vmax)))
else:
vpoints.append(
vp.Cube(centres[i],
side=6,
c=vp.colorMap(scalars[i], cmap, vmin, vmax)))
if view == 'topdown':
args = dict(elevation=0, azimuth=0, roll=0, zoom=1.4)
elif view == 'leftright':
args = dict(elevation=0, azimuth=270, roll=90, zoom=1.4)
elif view == 'rightleft':
args = dict(elevation=0, azimuth=90, roll=270, zoom=1.4)
else:
raise ValueError(f"Unexpected view: {view}")
vplotter = vp.Plotter(axes=0, offscreen=True, size=size)
vplotter.show(vpoints, vlines, vmeshes, N=1, **args)
img = vp.screenshot(None, scale=1, returnNumpy=True)
vp.clear()
vp.closePlotter()
return img
def viz_excitability(sid, rid):
regpos, w, obsmask, surfaces, contacts = read_structural_data(sid, rid)
vlines, vmeshes, vcontacts = viz_structure(regpos, w, surfaces, contacts)
# Load results
nreg = regpos.shape[0]
res = io.parse_csv([
f"run/solo/INC/vep/id{sid:03d}/output/r{rid:02d}_all/chain_{chain}.csv"
for chain in [1, 2]
])
cinf = res['c']
ctr = 2.0
pexc = np.mean(cinf > ctr, axis=0)
# Regions
cmap = 'Reds'
vmin, vmax = 0, 0.15
# vmin, vmax = -2, 0
vpoints = []
for i in range(nreg):
if not obsmask[i]:
vpoints.append(
vp.Sphere(regpos[i],
r=4,
c=vp.colorMap(pexc[i], cmap, vmin, vmax)))
else:
vpoints.append(
vp.Cube(regpos[i],
side=6,
c=vp.colorMap(pexc[i], cmap, vmin, vmax)))
vbar = vp.Points(regpos, r=0.01).pointColors(pexc,
cmap=cmap,
vmin=vmin,
vmax=vmax)
vbar.addScalarBar(horizontal=True, pos=(0.8, 0.02))
def cslider(widget, event):
ctr = widget.GetRepresentation().GetValue()
pexc = np.mean(cinf > ctr, axis=0)
for i in range(nreg):
vpoints[i].color(vp.colorMap(pexc[i], cmap, vmin, vmax))
vplotter = vp.Plotter(axes=0)
vplotter.addSlider2D(cslider, -3.0, 3.0, value=2.0, pos=3, title="c")
vplotter.show(vpoints, vlines, vmeshes, vcontacts, vbar)
def viz_seizure(sid, rid):
regpos, w, obsmask, surfaces, contacts = read_structural_data(sid, rid)
vlines, vmeshes, vcontacts = viz_structure(regpos, w, surfaces, contacts)
# Load results
nreg = regpos.shape[0]
res = io.parse_csv([
f"run/solo/INC/vep/id{sid:03d}/output/r{rid:02d}_all/chain_{chain}.csv"
for chain in [1, 2]
])
tinf = res['t']
t = 0.0
psz = np.mean(tinf < t, axis=0)
# Regions
cmap = 'bwr'
vmin, vmax = 0, 1
vpoints = []
for i in range(nreg):
if not obsmask[i]:
vpoints.append(
vp.Sphere(regpos[i],
r=4,
c=vp.colorMap(psz[i], cmap, vmin, vmax)))
else:
vpoints.append(
vp.Cube(regpos[i],
side=6,
c=vp.colorMap(psz[i], cmap, vmin, vmax)))
vbar = vp.Points(regpos, r=0.01).pointColors(psz,
cmap=cmap,
vmin=vmin,
vmax=vmax)
vbar.addScalarBar(horizontal=True, pos=(0.8, 0.02))
def tslider(widget, event):
t = widget.GetRepresentation().GetValue()
psz = np.mean(tinf < t, axis=0)
for i in range(nreg):
vpoints[i].color(vp.colorMap(psz[i], cmap, vmin, vmax))
vplotter = vp.Plotter(axes=0)
vplotter.addSlider2D(tslider, 0, 90.0, value=0.0, pos=3, title="t")
vplotter.show(vpoints, vlines, vmeshes, vcontacts, vbar)
def viz_structure(regpos, w, surfaces, contacts):
# Connections
wmax = np.max(w)
vlines = []
for reg1, reg2 in zip(*np.where(w > np.percentile(w.flat, 97))):
vlines.append(
vp.Line(regpos[reg1],
regpos[reg2],
c='k',
lw=15 * w[reg1, reg2] / wmax))
# Brain surfaces
vmeshes = [
vp.Mesh([verts, triangs], 'grey', alpha=0.05)
for verts, triangs in surfaces
]
# Electrodes
ncontacts = contacts.shape[0]
vcontacts = []
for i in range(ncontacts):
vcontacts.append(vp.Sphere(contacts[i], r=0.8, c='green'))
return vlines, vmeshes, vcontacts
def _buttonfunc(self):
if self.timerId is not None:
self.plotter.timerCallback("destroy", self.timerId)
if not self.isplaying:
self.timerId = self.plotter.timerCallback("create", dt=100)
self.button.switch()
self.isplaying = not self.isplaying
def handle_timer(self, event):
#####################################################################
### Animate your stuff here ###
#####################################################################
#print(event) # info about what was clicked and more
#print(self.plotter.actors) # to access object from the internal list
earth.rotateZ(1) # rotate the Earth by 1deg
moon.color(self.counter) # change color to the Moon
txt2d.text("Moon color is:").color(self.counter).background(self.counter,0.1)
txt2d.text(vedo.getColorName(self.counter), "top-center")
txt2d.text("..press q to quit", "bottom-right")
self.plotter.render()
self.counter += 1
viewer = Viewer(axes=1, dt=150).initialize()
earth = vedo.Earth()
moon = vedo.Sphere(r=0.1).x(1.5).color('k7')
txt2d = vedo.CornerAnnotation().font("Kanopus")
viewer.show(earth, moon, txt2d, viewup='z')
def make_video(sid, rid, video_file):
regpos, w, obsmask, surfaces, contacts = read_structural_data(sid, rid)
vlines, vmeshes, vcontacts = viz_structure(regpos, w, surfaces, contacts)
# Load results
res = io.parse_csv([
f"run/solo/INC/vep/id{sid:03d}/output/r{rid:02d}_all/chain_{chain}.csv"
for chain in [1, 2]
])
tinf = res['t']
t = 0.0
psz = np.mean(tinf < t, axis=0)
nreg = regpos.shape[0]
# Regions
cmap = 'bwr'
vpoints = []
for i in range(nreg):
if not obsmask[i]:
vpoints.append(
vp.Sphere(regpos[i], r=4, c=vp.colorMap(psz[i], cmap, 0, 1)))
else:
vpoints.append(
vp.Cube(regpos[i], side=6, c=vp.colorMap(psz[i], cmap, 0, 1)))
vbar = vp.Points(regpos, r=0.01).pointColors(psz,
cmap=cmap,
vmin=0,
vmax=1)
vbar.addScalarBar(horizontal=True, pos=(0.8, 0.02))
vtext = vp.Text2D(f"t = {t:4.1f} s", pos=0, s=2, c='black')
center = np.mean(regpos, axis=0)
dist = 2.5 * (np.max(regpos[:, 1]) - np.min(regpos[:, 1]))
# Video -------------------------------------------------------
vplotter = vp.Plotter(axes=0,
interactive=0,
offscreen=True,
size=(1800, 1800))
nframes = 3000
vplotter += vpoints
vplotter += vlines
vplotter += vmeshes
video = vp.Video(name=video_file, duration=90)
ratios = np.array([30, 3, 5, 30, 5, 3, 30, 10])
frames = (nframes * ratios / np.sum(ratios)).astype(int)
# Run and pause
animate(vplotter,
video,
frames[0],
vpoints,
tinf,
pos=center + dist * np.r_[0, 0, 1],
foc=center,
viewup=(0, 1, 1),
prange=(0, 45),
time=lambda p: p)
animate(vplotter,
video,
frames[1],
vpoints,
tinf,
pos=center + dist * np.r_[0, 0, 1],
foc=center,
viewup=(0, 1, 1),
time=45.)
## Fly around
pos = lambda angle: center + dist * np.array(
[0, -np.sin(angle), np.cos(angle)])
animate(vplotter,
video,
frames[2],
vpoints,
tinf,
pos=pos,
foc=center,
viewup=(0, 1, 1),
prange=(0, np.pi / 2),
time=45.,
endpoint=False)
pos = lambda angle: center + dist * np.array(
[-np.sin(angle), -np.cos(angle), 0])
animate(vplotter,
video,
frames[3],
vpoints,
tinf,
pos=pos,
foc=center,
viewup=(0, 0, 1),
prange=(0, 2 * np.pi),
time=45.)
pos = lambda angle: center + dist * np.array(
[0, -np.sin(angle), np.cos(angle)])
animate(vplotter,
video,
frames[4],
vpoints,
tinf,
pos=pos,
foc=center,
viewup=(0, 1, 1),
prange=(np.pi / 2, 0),
time=45.,
startpoint=False)
# Pause + run + pause
animate(vplotter,
video,
frames[5],
vpoints,
tinf,
pos=center + dist * np.r_[0, 0, 1],
foc=center,
viewup=(0, 1, 1),
time=45.)
animate(vplotter,
video,
frames[6],
vpoints,
tinf,
pos=center + dist * np.r_[0, 0, 1],
foc=center,
viewup=(0, 1, 1),
prange=(45, 90),
time=lambda p: p)
animate(vplotter,
video,
frames[7],
vpoints,
tinf,
pos=center + dist * np.r_[0, 0, 1],
foc=center,
viewup=(0, 1, 1),
time=90.)
video.close()