def analyse_track(
scene,
points_file,
add_surface_to_points=True,
spline_points=100,
fit_degree=3,
spline_smoothing=0.05,
point_radius=30,
spline_radius=10,
verbose=True,
):
"""
Given a file of points, fit a spline function, and add to a brainrender
scene.
:param scene: brainrender scene object
:param points_file:
:param bool add_surface_to_points: Add the closest part of the brain
surface to the list of points
:param spline_points: How many points define the spline
:param fit_degree: spline fit degree
:param spline_smoothing: spline fit smoothing
:param point_radius: size of the points in the brainrender scene
:param spline_radius: size of the rendered spline in the brainrender
scene
:param bool verbose: Whether to print the progress
:return:
scene: brainrender scene with the surface point added.
spline: vedo spline object
"""
points = pd.read_hdf(points_file)
scene.add_cells(
points,
color_by_region=True,
res=12,
radius=point_radius,
verbose=False,
)
points = np.array(points)
if add_surface_to_points:
scene, points = add_surface_point_to_points(scene,
points,
point_radius,
verbose=verbose)
far_point = np.expand_dims(points[-1], axis=0)
scene.add_vtkactor(Spheres(far_point, r=point_radius).color("n"))
spline = (Spline(
points,
smooth=spline_smoothing,
degree=fit_degree,
res=spline_points,
).pointSize(spline_radius).color("n"))
return scene, spline
"""Customizing axes style
(40+ control parameters!)
Title font: """
from vedo import Box, Lines, Points, Spline, show, settings
settings.defaultFont = 'Theemim'
# an invisible box:
world = Box(pos=(2.7, 0, 0), size=(12, 10, 8), alpha=0)
# a dummy spline with its shadow on the xy plane
pts = Points([(-2, -3.2, -1.5), (3, -1.2, -2), (7, 3, 4)], r=12)
spl = Spline(pts,
res=50).addShadow(z=-4) # make spline and add its shadow at z=-4
lns = Lines(spl, spl.shadow) # join spline points with its own shadow
# make a dictionary of axes options
axes_opts = dict(
xtitle=
'My variable \Omega^\lowerxi_lm in units of \mum^3', # latex-style syntax
ytitle='This is my highly\ncustomized y-axis',
ztitle=
'z in units of Å', # many unicode chars are supported (type: vedo -r fonts)
yValuesAndLabels=[(-3.2, 'Mark^a_-3.2'), (-1.2, 'Carmen^b_-1.2'),
(3, 'John^c_3')],
textScale=1.3, # make all text 30% bigger
numberOfDivisions=5, # approximate number of divisions on longest axis
axesLineWidth=2,
gridLineWidth=1,
zxGrid2=True, # show zx plane on opposite side of the bounding box
yzGrid2=True, # show yz plane on opposite side of the bounding box
"""Mesh a line contour with quads of variable resolution"""
from vedo import Spline, Grid, show
import numpy as np
shape = Spline(
[
[0.0, 0.0],
[1.0, 0.0],
[1.1, 4.0],
[1.0, 1.5],
[0.2, 5.0],
[-1., 3.0],
[0.4, 2.7],
[-1., 2.4],
],
closed=True,
).color('red4').lineWidth(5)
xcoords = np.arange(-2.0, 2.5, 0.075)
ycoords = np.arange(-0.5, 5.5, 0.075)
xcoords += np.cos(xcoords + 0.6) * 0.75 # make quads shrink and stretch
ycoords += np.sin(ycoords + 0.5) * 0.75 # to refine mesh resolution
grd = Grid(sx=xcoords, sy=ycoords) # create a gridded plane
msh = shape.tomesh(grid=grd, quads=True)
show(shape, msh, __doc__, axes=1)
"""Customizing axes style
(40+ control parameters!)
Title font: """
from vedo import Box, Lines, Points, Spline, show, settings
settings.defaultFont = 'Theemim'
# an invisible box:
world = Box(pos=(2.7, 0, 0), size=(12, 10, 8), alpha=0)
# a dummy spline with its shadow on the xy plane
pts = Points([(-2, -3.2, -1.5), (3, -1.2, -2), (7, 3, 4)], r=12)
spl = Spline(pts, res=50).addShadow(
plane='z', point=-4) # make spline and add its shadow at z=-4
lns = Lines(spl, spl.shadow) # join spline points with its own shadow
# make a dictionary of axes options
axes_opts = dict(
xtitle=
'My variable \Omega^\lowerxi_lm in units of \mum^3', # latex-style syntax
ytitle='This is my highly\ncustomized y-axis',
ztitle=
'z in units of Å', # many unicode chars are supported (type: vedo -r fonts)
yValuesAndLabels=[(-3.2, 'Mark^a_-3.2'), (-1.2, 'Carmen^b_-1.2'),
(3, 'John^c_3')],
textScale=1.3, # make all text 30% bigger
numberOfDivisions=5, # approximate number of divisions on longest axis
axesLineWidth=2,
gridLineWidth=1,
zxGrid2=True, # show zx plane on opposite side of the bounding box
yzGrid2=True, # show yz plane on opposite side of the bounding box