Module vedo.pyplot
Advanced plotting utility functions
Expand source code
import warnings
import numpy as np
import vtk
import vedo
from vedo import addons
from vedo import colors
from vedo import utils
from vedo.mesh import merge, Mesh
from vedo.assembly import Assembly
from vedo import shapes
__doc__ = """
.. image:: https://vedo.embl.es/images/pyplot/fitPolynomial2.png
Advanced plotting utility functions
"""
__all__ = [
"Figure",
"Histogram1D", # uncomment to generate docs
"Histogram2D",
"PlotXY",
"PlotBars",
"plot",
"histogram",
"fit",
"donut",
"violin",
"whisker",
"streamplot",
"matrix",
"DirectedGraph",
]
##########################################################################
class LabelData:
"""Helper internal class to hold label information"""
def __init__(self):
self.text = "dataset"
self.tcolor = "black"
self.marker = "s"
self.mcolor = "black"
##########################################################################
class Figure(Assembly):
"""
Parameters
----------
xlim : list
range of the x-axis as [x0, x1]
ylim : list
range of the y-axis as [y0, y1]
aspect : float, str
the desired aspect ratio of the histogram. Default is 4/3.
Use `aspect="equal"` to force the same units in x and y.
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
axes : dict
an extra dictionary of options for the axes
"""
def __init__(
self,
xlim,
ylim,
aspect=4/3,
padding=(0.05, 0.05, 0.05, 0.05),
**kwargs,
):
self.xlim = np.array(xlim)
self.ylim = np.array(ylim)
self.aspect = aspect
self.padding = padding
if not utils.isSequence(self.padding):
self.padding = [self.padding, self.padding, self.padding, self.padding]
self.force_scaling_types = (
shapes.Glyph,
shapes.Line,
shapes.Rectangle,
shapes.DashedLine,
shapes.Tube,
shapes.Ribbon,
shapes.GeoCircle,
shapes.Arc,
shapes.Grid,
# shapes.Arrows, # todo
# shapes.Arrows2D, # todo
shapes.Brace, # todo
)
options = dict(kwargs)
self.title = options.pop("title", "")
self.xtitle = options.pop("xtitle", " ")
self.ytitle = options.pop("ytitle", " ")
numberOfDivisions = 6
self.legend = None
self.labels = []
self.label = options.pop("label", None)
if self.label:
self.labels = [self.label]
self.axopts = options.pop("axes", {})
if isinstance(self.axopts, (bool, int, float)):
if self.axopts:
self.axopts = {}
if self.axopts or isinstance(self.axopts, dict):
numberOfDivisions = self.axopts.pop("numberOfDivisions", numberOfDivisions)
self.axopts["xtitle"] = self.xtitle
self.axopts["ytitle"] = self.ytitle
if "xyGrid" not in self.axopts: ## modify the default
self.axopts["xyGrid"] = options.pop("grid", False)
if "xyGridTransparent" not in self.axopts: ## modify the default
self.axopts["xyGridTransparent"] = True
if "xTitlePosition" not in self.axopts: ## modify the default
self.axopts["xTitlePosition"] = 0.5
self.axopts["xTitleJustify"] = "top-center"
if "yTitlePosition" not in self.axopts: ## modify the default
self.axopts["yTitlePosition"] = 0.5
self.axopts["yTitleJustify"] = "bottom-center"
if self.label:
if "c" in self.axopts:
self.label.tcolor = self.axopts["c"]
x0, x1 = self.xlim
y0, y1 = self.ylim
dx = x1 - x0
dy = y1 - y0
x0lim, x1lim = (x0 - self.padding[0] * dx, x1 + self.padding[1] * dx)
y0lim, y1lim = (y0 - self.padding[2] * dy, y1 + self.padding[3] * dy)
dy = y1lim - y0lim
self.axes = None
if xlim[0] >= xlim[1] or ylim[0] >= ylim[1]:
vedo.logger.warning(f"Null range for Figure {self.title}... returning an empty Assembly.")
Assembly.__init__(self)
self.yscale = 0
return
if aspect == "equal":
self.aspect = dx / dy # so that yscale becomes 1
self.yscale = dx / dy / self.aspect
y0lim *= self.yscale
y1lim *= self.yscale
self.x0lim = x0lim
self.x1lim = x1lim
self.y0lim = y0lim
self.y1lim = y1lim
self.ztolerance = options.pop("ztolerance", None)
if self.ztolerance is None:
self.ztolerance = dx / 5000
############## create axes
if self.axopts:
axesopts = self.axopts
if self.axopts is True or self.axopts == 1:
axesopts = {}
tp, ts = utils.makeTicks(
y0lim / self.yscale,
y1lim / self.yscale,
numberOfDivisions,
)
labs = []
for i in range(1, len(tp) - 1):
ynew = utils.linInterpolate(tp[i], [0, 1], [y0lim, y1lim])
labs.append([ynew, ts[i]])
if self.title:
axesopts["htitle"] = self.title
axesopts["yValuesAndLabels"] = labs
axesopts["xrange"] = (x0lim, x1lim)
axesopts["yrange"] = (y0lim, y1lim)
axesopts["zrange"] = (0, 0)
axesopts["yUseBounds"] = True
if "c" not in axesopts and "ac" in options:
axesopts["c"] = options["ac"]
self.axes = addons.Axes(**axesopts)
Assembly.__init__(self, [self.axes])
self.name = "Figure"
return
def __add__(self, *obj):
# just to avoid confusion, superseed Assembly.__add__
return self.__iadd__(*obj)
def __iadd__(self, *obj):
if len(obj) == 1 and isinstance(obj[0], Figure):
return self._check_unpack_and_insert(obj[0])
else:
obj = utils.flatten(obj)
return self.insert(*obj)
def _check_unpack_and_insert(self, fig):
if fig.label:
self.labels.append(fig.label)
if abs(self.yscale - fig.yscale) > 0.0001:
colors.printc("ERROR: adding incompatible Figure. Y-scales are different:",
c='r', invert=True)
colors.printc(" first figure:", self.yscale, c='r')
colors.printc(" second figure:", fig.yscale, c='r')
colors.printc("One or more of these parameters can be the cause:", c="r")
if list(self.xlim) != list(fig.xlim):
colors.printc("xlim --------------------------------------------\n",
" first figure:", self.xlim, "\n",
" second figure:", fig.xlim, c='r')
if list(self.ylim) != list(fig.ylim):
colors.printc("ylim --------------------------------------------\n",
" first figure:", self.ylim, "\n",
" second figure:", fig.ylim, c='r')
if list(self.padding) != list(fig.padding):
colors.printc("padding -----------------------------------------\n",
" first figure:", self.padding,
" second figure:", fig.padding, c='r')
if self.aspect != fig.aspect:
colors.printc("aspect ------------------------------------------\n",
" first figure:", self.aspect,
" second figure:", fig.aspect, c='r')
colors.printc("\n*Consider using fig2 = histogram(..., like=fig1)", c="r")
colors.printc(" Or fig += histogram(..., like=fig)\n", c="r")
return self
offset = self.zbounds()[1] + self.ztolerance
for ele in fig.unpack():
if "Axes" in ele.name:
continue
ele.z(offset)
self.insert(ele, rescale=False)
return self
def insert(self, *objs, rescale=True, as3d=True, adjusted=True, cut=True):
"""
Insert objects into a Figure.
The reccomended syntax is to use "+=", which calls `insert()` under the hood.
If a whole Figure is added with "+=", it is unpacked and its objects are added
one by one.
Parameters
----------
rescale : bool
rescale the y axis position while inserting the object.
as3d : bool
if True keep the aspect ratio of the 3d obect, otherwise stretch it in y.
adjusted : bool
adjust the scaling according to the shortest axis
cut : bool
cut off the parts of the object which go beyond the axes frame.
"""
for a in objs:
if a in self.actors:
# should not add twice the same object in plot
continue
if isinstance(a, vedo.Points): # hacky way to identify Points
if a.NCells() == a.NPoints():
poly = a.polydata(False)
if poly.GetNumberOfPolys() == 0 and poly.GetNumberOfLines() == 0:
as3d = False
rescale = True
if isinstance(a, (shapes.Arrow, shapes.Arrow2D)):
# discard input Arrow and substitute it with a brand new one
# (because scaling would fatally distort the shape)
prop = a.GetProperty()
prop.LightingOff()
py = a.base[1]
a.top[1] = (a.top[1] - py) * self.yscale + py
b = shapes.Arrow2D(a.base, a.top, s=a.s, fill=a.fill).z(a.z())
b.SetProperty(prop)
b.y(py * self.yscale)
a = b
# elif isinstance(a, shapes.Rectangle) and a.radius is not None:
# # discard input Rectangle and substitute it with a brand new one
# # (because scaling would fatally distort the shape of the corners)
# py = a.corner1[1]
# rx1,ry1,rz1 = a.corner1
# rx2,ry2,rz2 = a.corner2
# ry2 = (ry2-py) * self.yscale + py
# b = shapes.Rectangle([rx1,0,rz1], [rx2,ry2,rz2], radius=a.radius).z(a.z())
# b.SetProperty(a.GetProperty())
# b.y(py / self.yscale)
# a = b
else:
if rescale:
if not isinstance(a, Figure):
if as3d and not isinstance(a, self.force_scaling_types):
if adjusted:
scl = np.min([1, self.yscale])
else:
scl = self.yscale
a.scale(scl)
else:
a.scale([1, self.yscale, 1])
# shift it in y
a.y(a.y() * self.yscale)
if cut:
try:
bx0, bx1, by0, by1, _, _ = a.GetBounds()
if self.y0lim > by0:
a.cutWithPlane([0, self.y0lim, 0], [ 0, 1, 0])
if self.y1lim < by1:
a.cutWithPlane([0, self.y1lim, 0], [ 0,-1, 0])
if self.x0lim > bx0:
a.cutWithPlane([self.x0lim, 0, 0], [ 1, 0, 0])
if self.x1lim < bx1:
a.cutWithPlane([self.x1lim, 0, 0], [-1, 0, 0])
except:
# print("insert(): cannot cut", [a])
pass
self.AddPart(a)
self.actors.append(a)
return self
def addLabel(self, text, c=None, marker="", mc="black"):
"""
Manually add en entry label to the legend.
Parameters
----------
text : str
text string for the label.
c : str
color of the text
marker : str, Mesh
a marker char or a Mesh object to be used as marker
mc : str, optional
color for the marker
"""
newlabel = LabelData()
newlabel.text = text.replace("\n", " ")
newlabel.tcolor = c
newlabel.marker = marker
newlabel.mcolor = mc
self.labels.append(newlabel)
return self
def addLegend(self,
pos="top-right",
relative=True,
font=None,
s=1,
c=None,
vspace=1.75,
padding=0.1,
radius=0,
alpha=1,
bc='k7',
lw=1,
lc='k4',
z=0,
):
"""
Add existing labels to form a legend box.
Labels have been previously filled with eg: `plot(..., label="text")`
Parameters
----------
pos : str, list
A string or 2D coordinates. The default is "top-right".
relative : bool
control whether `pos` is absolute or relative, e.i. normalized
to the x and y ranges so that x and y in `pos=[x,y]` should be
both in the range [0,1].
This flag is ignored if a string despcriptor is passed.
Default is True.
font : str, int
font name or number
s : float
global size of the legend
c : str
color of the text
vspace : float
vertical spacing of lines
padding : float
padding of the box as a fraction of the text size
radius : float
border radius of the box
alpha : float
opacity of the box. Values below 1 may cause poor rendering
bacause of antialiasing.
Use alpha = 0 to remove the box.
bc : str
box color
lw : int
border line width of the box in pixel units
lc : int
border line color of the box
z : float
set the zorder as z position (useful to avoid overlap)
"""
sx = self.x1lim - self.x0lim
s = s * sx / 55 # so that input can be about 1
ds = 0
texts = []
mks = []
for i, t in enumerate(self.labels):
label = self.labels[i]
t = label.text
if label.tcolor is not None:
c = label.tcolor
tx = vedo.shapes.Text3D(t, s=s, c=c, justify="center-left", font=font)
y0, y1 = tx.ybounds()
ds = max(y1 - y0, ds)
texts.append(tx)
mk = label.marker
if isinstance(mk, vedo.Points):
mk = mk.clone(deep=False).lighting("off")
cm = mk.centerOfMass()
ty0, ty1 = tx.ybounds()
oby0, oby1 = mk.ybounds()
mk.shift(-cm)
mk.origin(cm)
mk.scale((ty1 - ty0) / (oby1 - oby0))
mk.scale([1.1, 1.1, 0.01])
elif mk == "-":
mk = vedo.shapes.Marker(mk, s=s * 2)
mk.color(label.mcolor)
else:
mk = vedo.shapes.Marker(mk, s=s)
mk.color(label.mcolor)
mks.append(mk)
for i, tx in enumerate(texts):
tx.shift(0, -(i + 0) * ds * vspace)
for i, mk in enumerate(mks):
mk.shift(-ds * 1.75, -(i + 0) * ds * vspace, 0)
acts = texts + mks
aleg = Assembly(acts) # .show(axes=1).close()
x0, x1, y0, y1, _, _ = aleg.GetBounds()
if alpha:
dx = x1 - x0
dy = y1 - y0
if not utils.isSequence(padding):
padding = [padding] * 4
padding = min(padding)
padding = min(padding * dx, padding * dy)
if len(self.labels) == 1:
padding *= 4
x0 -= padding
x1 += padding
y0 -= padding
y1 += padding
box = shapes.Rectangle(
[x0, y0], [x1, y1], radius=radius, c=bc, alpha=alpha,
)
box.shift(0, 0, -dy / 100).pickable(False)
if lc:
box.lc(lc).lw(lw)
aleg.AddPart(box)
xlim = self.xlim
ylim = self.ylim
if isinstance(pos, str):
px, py = 0, 0
rx, ry = (xlim[1] + xlim[0]) / 2, (ylim[1] + ylim[0]) / 2
shx, shy = 0, 0
if "top" in pos:
if "cent" in pos:
px, py = rx, ylim[1]
shx, shy = (x0 + x1) / 2, y1
elif "left" in pos:
px, py = xlim[0], ylim[1]
shx, shy = x0, y1
else: # "right"
px, py = xlim[1], ylim[1]
shx, shy = x1, y1
elif "bot" in pos:
if "left" in pos:
px, py = xlim[0], ylim[0]
shx, shy = x0, y0
elif "right" in pos:
px, py = xlim[1], ylim[0]
shx, shy = x1, y0
else: # "cent"
px, py = rx, ylim[0]
shx, shy = (x0 + x1) / 2, y0
elif "cent" in pos:
if "left" in pos:
px, py = xlim[0], ry
shx, shy = x0, (y0 + y1) / 2
elif "right" in pos:
px, py = xlim[1], ry
shx, shy = x1, (y0 + y1) / 2
else:
vedo.logger.error(f"in addLegend(), cannot understand {pos}")
raise RuntimeError
else:
if relative:
rx, ry = pos[0], pos[1]
px = (xlim[1] - xlim[0]) * rx + xlim[0]
py = (ylim[1] - ylim[0]) * ry + ylim[0]
z *= xlim[1] - xlim[0]
else:
px, py = pos[0], pos[1]
shx, shy = x0, y1
aleg.pos(px - shx, py * self.yscale - shy, self.z() + sx / 50 + z)
self.insert(aleg, rescale=False, cut=False)
self.legend = aleg
aleg.name = "Legend"
return self
#########################################################################################
class Histogram1D(Figure):
"""
Creates a `Histogram1D(Figure)` object.
Parameters
----------
weights : list
An array of weights, of the same shape as `data`. Each value in `data`
only contributes its associated weight towards the bin count (instead of 1).
bins : int
number of bins
density : bool
normalize the area to 1 by dividing by the nr of entries and bin size
logscale : bool
use logscale on y-axis
fill : bool
fill bars woth solid color `c`
gap : float
leave a small space btw bars
radius : float
border radius of the top of the histogram bar. Default value is 0.1.
texture : str
url or path to an image to be used as texture for the bin
outline : bool
show outline of the bins
errors : bool
show error bars
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
aspect : float
the desired aspect ratio of the histogram. Default is 4/3.
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
ztolerance : float
a tolerance factor to superimpose objects (along the z-axis).
.. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_1D.png
"""
def __init__(
self,
data,
weights=None,
bins=None,
errors=False,
density=False,
logscale=False,
fill=True,
radius=0.1,
c="olivedrab",
gap=0.02,
alpha=1,
outline=False,
lw=2,
lc="k",
texture="",
marker="",
ms=None,
mc=None,
ma=None,
# Figure and axes options:
like=None,
xlim=None,
ylim=(0, None),
aspect=4/3,
padding=(0., 0., 0., 0.05),
title="",
xtitle=" ",
ytitle=" ",
ac="k",
grid=False,
ztolerance=None,
label="",
**fig_kwargs,
):
if like is not None:
xlim = like.xlim
ylim = like.ylim
aspect = like.aspect
padding = like.padding
if bins is None:
bins = like.bins
if bins is None:
bins = 20
if utils.isSequence(xlim):
# deal with user passing eg [x0, None]
_x0, _x1 = xlim
if _x0 is None:
_x0 = data.min()
if _x1 is None:
_x1 = data.max()
xlim = [_x0, _x1]
# purge NaN from data
validIds = np.all(np.logical_not(np.isnan(data)))
data = np.array(data[validIds]).ravel()
fs, edges = np.histogram(data, bins=bins, weights=weights, range=xlim)
binsize = edges[1] - edges[0]
ntot = data.shape[0]
fig_kwargs["title"] = title
fig_kwargs["xtitle"] = xtitle
fig_kwargs["ytitle"] = ytitle
fig_kwargs["ac"] = ac
fig_kwargs["ztolerance"] = ztolerance
fig_kwargs["grid"] = grid
unscaled_errors = np.sqrt(fs)
if density:
scaled_errors = unscaled_errors / (ntot * binsize)
fs = fs / (ntot * binsize)
if ytitle == " ":
ytitle = f"counts / ( {ntot}~x~{utils.precision(binsize,3)} )"
fig_kwargs["ytitle"] = ytitle
elif logscale:
se_up = np.log10(fs + unscaled_errors / 2 + 1)
se_dw = np.log10(fs - unscaled_errors / 2 + 1)
scaled_errors = np.c_[se_up, se_dw]
fs = np.log10(fs + 1)
if ytitle == " ":
ytitle = "log_10 (counts+1)"
fig_kwargs["ytitle"] = ytitle
x0, x1 = np.min(edges), np.max(edges)
y0, y1 = ylim[0], np.max(fs)
_errors = []
if errors:
if density:
y1 += max(scaled_errors) / 2
_errors = scaled_errors
elif logscale:
y1 = max(scaled_errors[:, 0])
_errors = scaled_errors
else:
y1 += max(unscaled_errors) / 2
_errors = unscaled_errors
if like is None:
ylim = list(ylim)
if xlim is None:
xlim = [x0, x1]
if ylim[1] is None:
ylim[1] = y1
if ylim[0] != 0:
ylim[0] = y0
self.entries = ntot
self.frequencies = fs
self.errors = _errors
self.edges = edges
self.centers = (edges[0:-1] + edges[1:]) / 2
self.mean = data.mean()
self.std = data.std()
self.bins = edges # internally used by "like"
############################### stats legend as htitle
addstats = False
if not title:
if "axes" not in fig_kwargs:
addstats = True
axesopts = dict()
fig_kwargs["axes"] = axesopts
elif fig_kwargs["axes"] is False:
pass
else:
axesopts = fig_kwargs["axes"]
if "htitle" not in axesopts:
addstats = True
if addstats:
htitle = f"Entries:~~{int(self.entries)} "
htitle += f"Mean:~~{utils.precision(self.mean, 4)} "
htitle += f"STD:~~{utils.precision(self.std, 4)} "
axesopts["htitle"] = htitle
axesopts["hTitleJustify"] = "bottom-left"
axesopts["hTitleSize"] = 0.016
axesopts["hTitleOffset"] = [-0.49, 0.01, 0]
if mc is None:
mc = lc
if ma is None:
ma = alpha
if label:
nlab = LabelData()
nlab.text = label
nlab.tcolor = ac
nlab.marker = marker
nlab.mcolor = mc
if not marker:
nlab.marker = "s"
nlab.mcolor = c
fig_kwargs["label"] = nlab
############################################### Figure init
Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs)
if not self.yscale:
return None
if utils.isSequence(bins):
myedges = np.array(bins)
bins = len(bins) - 1
else:
myedges = edges
bin_centers = []
for i in range(bins):
x = (myedges[i] + myedges[i + 1]) / 2
bin_centers.append([x, fs[i], 0])
rs = []
maxheigth = 0
if not fill and not outline and not errors and not marker:
outline = True # otherwise it's empty..
if fill: #####################
if outline:
gap = 0
for i in range(bins):
F = fs[i]
if not F:
continue
p0 = (myedges[i] + gap * binsize, 0, 0)
p1 = (myedges[i + 1] - gap * binsize, F, 0)
if radius:
if gap:
rds = np.array([0, 0, radius, radius])
else:
rd1 = 0 if i < bins - 1 and fs[i + 1] >= F else radius / 2
rd2 = 0 if i > 0 and fs[i - 1] >= F else radius / 2
rds = np.array([0, 0, rd1, rd2])
p1_yscaled = [p1[0], p1[1]*self.yscale, 0]
r = shapes.Rectangle(p0, p1_yscaled, radius=rds*binsize, res=6)
r.scale([1, 1/self.yscale, 1])
r.radius = None # so it doesnt get recreated and rescaled by insert()
else:
r = shapes.Rectangle(p0, p1)
if texture:
r.texture(texture)
c = "w"
# if texture: # causes Segmentation fault vtk9.0.3
# if i>0 and rs[i-1].GetTexture(): # reuse the same texture obj
# r.texture(rs[i-1].GetTexture())
# else:
# r.texture(texture)
# c = 'w'
r.PickableOff()
maxheigth = max(maxheigth, p1[1])
if c in colors.cmaps_names:
col = colors.colorMap((p0[0]+p1[0])/2, c, myedges[0], myedges[-1])
else:
col = c
r.color(col).alpha(alpha).lighting("off")
r.z(self.ztolerance)
rs.append(r)
if outline: #####################
lns = [[myedges[0], 0, 0]]
for i in range(bins):
lns.append([myedges[i], fs[i], 0])
lns.append([myedges[i + 1], fs[i], 0])
maxheigth = max(maxheigth, fs[i])
lns.append([myedges[-1], 0, 0])
outl = shapes.Line(lns, c=lc, alpha=alpha, lw=lw)
outl.z(self.ztolerance * 2)
rs.append(outl)
if errors: #####################
for i in range(bins):
x = self.centers[i]
f = fs[i]
if not f:
continue
err = _errors[i]
if utils.isSequence(err):
el = shapes.Line([x, err[0], 0], [x, err[1], 0], c=lc, alpha=alpha, lw=lw)
else:
el = shapes.Line([x, f-err/2, 0], [x, f+err/2, 0], c=lc, alpha=alpha, lw=lw)
el.z(self.ztolerance*3)
rs.append(el)
if marker: #####################
# remove empty bins (we dont want a marker there)
bin_centers = np.array(bin_centers)
bin_centers = bin_centers[bin_centers[:, 1] > 0]
if utils.isSequence(ms): ### variable point size
mk = shapes.Marker(marker, s=1)
mk.scale([1, 1 / self.yscale, 1])
msv = np.zeros_like(bin_centers)
msv[:, 0] = ms
marked = shapes.Glyph(
bin_centers,
glyphObj=mk,
c=mc,
orientationArray=msv,
scaleByVectorSize=True,
)
else: ### fixed point size
if ms is None:
ms = (xlim[1] - xlim[0]) / 100.0
else:
ms = (xlim[1] - xlim[0]) / 100.0 * ms
if utils.isSequence(mc):
mk = shapes.Marker(marker, s=ms)
mk.scale([1, 1 / self.yscale, 1])
msv = np.zeros_like(bin_centers)
msv[:, 0] = 1
marked = shapes.Glyph(
bin_centers,
glyphObj=mk,
c=mc,
orientationArray=msv,
scaleByVectorSize=True,
)
else:
mk = shapes.Marker(marker, s=ms)
mk.scale([1, 1 / self.yscale, 1])
marked = shapes.Glyph(bin_centers, glyphObj=mk, c=mc)
marked.alpha(ma)
marked.z(self.ztolerance * 4)
rs.append(marked)
self.insert(*rs, as3d=False)
self.name = "Histogram1D"
#########################################################################################
class Histogram2D(Figure):
"""
Input data formats `[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]`
are both valid.
Use keyword `like=...` if you want to use the same format of a previously
created Figure (useful when superimposing Figures) to make sure
they are compatible and comparable. If they are not compatible
you will receive an error message.
Parameters
----------
bins : list
binning as (nx, ny)
weights : list
array of weights to assign to each entry
cmap : str, lookuptable
color map name or look up table
alpha : float
opacity of the histogram
gap : float
separation between adjacent bins as a fraction for their size
scalarbar : bool
add a scalarbar to right of the histogram
like : Figure
grab and use the same format of the given Figure (for superimposing)
xlim : list
[x0, x1] range of interest. If left to None will automatically
choose the minimum or the maximum of the data range.
Data outside the range are completely ignored.
ylim : list
[y0, y1] range of interest. If left to None will automatically
choose the minimum or the maximum of the data range.
Data outside the range are completely ignored.
aspect : float
the desired aspect ratio of the figure.
title : str
title of the plot to appear on top.
If left blank some statistics will be shown.
xtitle : str
x axis title
ytitle : str
y axis title
ztitle : str
title for the scalar bar
ac : str
axes color, additional keyword for Axes can also be added
using e.g. `axes=dict(xyGrid=True)`
.. hint:: examples/pyplot/histo_2d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_2D.png
"""
def __init__(
self,
xvalues,
yvalues=None,
bins=25,
weights=None,
cmap="cividis",
alpha=1,
gap=0,
scalarbar=True,
# Figure and axes options:
like=None,
xlim=None,
ylim=(None, None),
zlim=(None, None),
aspect=1,
title="",
xtitle=" ",
ytitle=" ",
ztitle="",
ac="k",
**fig_kwargs,
):
if yvalues is None:
# assume [(x1,y1), (x2,y2) ...] format
yvalues = xvalues[:, 1]
xvalues = xvalues[:, 0]
padding = [0, 0, 0, 0]
if like is not None:
xlim = like.xlim
ylim = like.ylim
aspect = like.aspect
padding = like.padding
if bins is None:
bins = like.bins
if bins is None:
bins = 20
if isinstance(bins, int):
bins = (bins, bins)
if utils.isSequence(xlim):
# deal with user passing eg [x0, None]
_x0, _x1 = xlim
if _x0 is None:
_x0 = xvalues.min()
if _x1 is None:
_x1 = xvalues.max()
xlim = [_x0, _x1]
if utils.isSequence(ylim):
# deal with user passing eg [x0, None]
_y0, _y1 = ylim
if _y0 is None:
_y0 = yvalues.min()
if _y1 is None:
_y1 = yvalues.max()
ylim = [_y0, _y1]
H, xedges, yedges = np.histogram2d(
xvalues, yvalues, weights=weights, bins=bins, range=(xlim, ylim),
)
xlim = np.min(xedges), np.max(xedges)
ylim = np.min(yedges), np.max(yedges)
dx, dy = xlim[1] - xlim[0], ylim[1] - ylim[0]
fig_kwargs["title"] = title
fig_kwargs["xtitle"] = xtitle
fig_kwargs["ytitle"] = ytitle
fig_kwargs["ac"] = ac
self.entries = len(xvalues)
self.frequencies = H
self.edges = (xedges, yedges)
self.mean = (xvalues.mean(), yvalues.mean())
self.std = (xvalues.std(), yvalues.std())
self.bins = bins # internally used by "like"
############################### stats legend as htitle
addstats = False
if not title:
if "axes" not in fig_kwargs:
addstats = True
axesopts = dict()
fig_kwargs["axes"] = axesopts
elif fig_kwargs["axes"] is False:
pass
else:
axesopts = fig_kwargs["axes"]
if "htitle" not in fig_kwargs["axes"]:
addstats = True
if addstats:
htitle = f"Entries:~~{int(self.entries)} "
htitle += f"Mean:~~{utils.precision(self.mean, 3)} "
htitle += f"STD:~~{utils.precision(self.std, 3)} "
axesopts["htitle"] = htitle
axesopts["hTitleJustify"] = "bottom-left"
axesopts["hTitleSize"] = 0.0175
axesopts["hTitleOffset"] = [-0.49, 0.01, 0]
############################################### Figure init
Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs)
if not self.yscale:
return None
##################### the grid
acts = []
g = shapes.Grid(
pos=[(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, 0],
s=(dx, dy),
res=bins[:2],
)
g.alpha(alpha).lw(0).wireframe(False).flat().lighting("off")
g.cmap(cmap, np.ravel(H.T), on="cells", vmin=zlim[0], vmax=zlim[1])
if gap:
g.shrink(abs(1 - gap))
if scalarbar:
sc = g.addScalarBar3D(ztitle, c=ac).scalarbar
sc.scale([self.yscale, 1, 1]) ## prescale trick
sbnds = sc.xbounds()
sc.x(self.x1lim + (sbnds[1] - sbnds[0]) * 0.75)
acts.append(sc)
acts.append(g)
self.insert(*acts, as3d=False)
self.name = "Histogram2D"
#########################################################################################
class PlotBars(Figure):
"""
Creates a `PlotBars(Figure)` object.
Input must be in format `[counts, labels, colors, edges]`.
Either or both `edges` and `colors` are optional and can be omitted.
Use keyword `like=...` if you want to use the same format of a previously
created Figure (useful when superimposing Figures) to make sure
they are compatible and comparable. If they are not compatible
you will receive an error message.
Parameters
----------
errors : bool
show error bars
logscale : bool
use logscale on y-axis
fill : bool
fill bars woth solid color `c`
gap : float
leave a small space btw bars
radius : float
border radius of the top of the histogram bar. Default value is 0.1.
texture : str
url or path to an image to be used as texture for the bin
outline : bool
show outline of the bins
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
ac : str
axes color
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
aspect : float
the desired aspect ratio of the figure. Default is 4/3.
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
.. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_1D.png
"""
def __init__(
self,
data,
errors=False,
logscale=False,
fill=True,
gap=0.02,
radius=0.05,
c="olivedrab",
alpha=1,
texture="",
outline=False,
lw=2,
lc="k",
# Figure and axes options:
like=None,
xlim=(None, None),
ylim=(0, None),
aspect=4/3,
padding=(0.025, 0.025, 0, 0.05),
#
title="",
xtitle=" ",
ytitle=" ",
ac="k",
grid=False,
ztolerance=None,
**fig_kwargs,
):
ndata = len(data)
if ndata == 4:
counts, xlabs, cols, edges = data
elif ndata == 3:
counts, xlabs, cols = data
edges = np.array(range(len(counts) + 1)) + 0.5
elif ndata == 2:
counts, xlabs = data
edges = np.array(range(len(counts) + 1)) + 0.5
cols = [c] * len(counts)
else:
m = "barplot error: data must be given as [counts, labels, colors, edges] not\n"
vedo.logger.error(m + f" {data}\n bin edges and colors are optional.")
raise RuntimeError()
# sanity checks
assert len(counts) == len(xlabs)
assert len(counts) == len(cols)
assert len(counts) == len(edges) - 1
counts = np.asarray(counts)
edges = np.asarray(edges)
if logscale:
counts = np.log10(counts + 1)
if ytitle == " ":
ytitle = "log_10 (counts+1)"
if like is not None:
xlim = like.xlim
ylim = like.ylim
aspect = like.aspect
padding = like.padding
if utils.isSequence(xlim):
# deal with user passing eg [x0, None]
_x0, _x1 = xlim
if _x0 is None:
_x0 = np.min(edges)
if _x1 is None:
_x1 = np.max(edges)
xlim = [_x0, _x1]
x0, x1 = np.min(edges), np.max(edges)
y0, y1 = ylim[0], np.max(counts)
if like is None:
ylim = list(ylim)
if xlim is None:
xlim = [x0, x1]
if ylim[1] is None:
ylim[1] = y1
if ylim[0] != 0:
ylim[0] = y0
fig_kwargs["title"] = title
fig_kwargs["xtitle"] = xtitle
fig_kwargs["ytitle"] = ytitle
fig_kwargs["ac"] = ac
fig_kwargs["ztolerance"] = ztolerance
fig_kwargs["grid"] = grid
centers = (edges[0:-1] + edges[1:]) / 2
binsizes = (centers - edges[0:-1]) * 2
if "axes" not in fig_kwargs:
fig_kwargs["axes"] = dict()
_xlabs = []
for center, xlb in zip(centers, xlabs):
_xlabs.append([center, str(xlb)])
fig_kwargs["axes"]["xValuesAndLabels"] = _xlabs
############################################### Figure
self.statslegend = ""
self.edges = edges
self.centers = centers
self.bins = edges # internal used by "like"
Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs)
if not self.yscale:
return None
rs = []
maxheigth = 0
if fill: #####################
if outline:
gap = 0
for i in range(len(centers)):
binsize = binsizes[i]
p0 = (edges[i] + gap * binsize, 0, 0)
p1 = (edges[i + 1] - gap * binsize, counts[i], 0)
if radius:
rds = np.array([0, 0, radius, radius])
p1_yscaled = [p1[0], p1[1]*self.yscale, 0]
r = shapes.Rectangle(p0, p1_yscaled, radius=rds*binsize, res=6)
r.scale([1, 1/self.yscale, 1])
r.radius = None # so it doesnt get recreated and rescaled by insert()
else:
r = shapes.Rectangle(p0, p1)
if texture:
r.texture(texture)
c = "w"
r.PickableOff()
maxheigth = max(maxheigth, p1[1])
if c in colors.cmaps_names:
col = colors.colorMap((p0[0] + p1[0]) / 2, c, edges[0], edges[-1])
else:
col = cols[i]
r.color(col).alpha(alpha).lighting("off")
r.name = f"bar_{i}"
r.z(self.ztolerance)
rs.append(r)
elif outline: #####################
lns = [[edges[0], 0, 0]]
for i in range(len(centers)):
lns.append([edges[i], counts[i], 0])
lns.append([edges[i + 1], counts[i], 0])
maxheigth = max(maxheigth, counts[i])
lns.append([edges[-1], 0, 0])
outl = shapes.Line(lns, c=lc, alpha=alpha, lw=lw).z(self.ztolerance)
outl.name = f"bar_outline_{i}"
rs.append(outl)
if errors: #####################
for x, f in centers:
err = np.sqrt(f)
el = shapes.Line([x, f-err/2, 0], [x, f+err/2, 0], c=lc, alpha=alpha, lw=lw)
el.z(self.ztolerance * 2)
rs.append(el)
self.insert(*rs, as3d=False)
self.name = "PlotBars"
#########################################################################################
class PlotXY(Figure):
"""
Creates a `PlotXY(Figure)` object.
Parameters
----------
xerrors : bool
show error bars associated to each point in x
yerrors : bool
show error bars associated to each point in y
lw : int
width of the line connecting points in pixel units.
Set it to 0 to remove the line.
lc : str
line color
la : float
line "alpha", opacity of the line
dashed : bool
draw a dashed line instead of a continous line
splined : bool
spline the line joining the point as a countinous curve
elw : int
width of error bar lines in units of pixels
ec : color
color of error bar, by default the same as marker color
errorBand : bool
represent errors on y as a filled error band.
Use ``ec`` keyword to modify its color.
marker : str, int
use a marker for the data points
ms : float
marker size
mc : color
color of the marker
ma : float
opacity of the marker
xlim : list
set limits to the range for the x variable
ylim : list
set limits to the range for the y variable
aspect : float, str
Desired aspect ratio.
Use `aspect="equal"` to force the same units in x and y.
Scaling factor is saved in Figure.yscale.
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
title : str
title to appear on the top of the frame, like a header.
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
ac : str
axes color
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
ztolerance : float
a tolerance factor to superimpose objects (along the z-axis).
Example:
.. code-block:: python
import numpy as np
from vedo.pyplot import plot
x = np.arange(0, np.pi, 0.1)
fig = plot(x, np.sin(2*x), 'r0-', aspect='equal')
fig+= plot(x, np.cos(2*x), 'blue4 o-', like=fig)
fig.show()
.. image:: https://user-images.githubusercontent.com/32848391/74363882-c3638300-4dcb-11ea-8a78-eb492ad9711f.png
.. hint::
examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py
.. image:: https://vedo.embl.es/images/pyplot/plot_pip.png
"""
def __init__(
self,
#
data,
xerrors=None,
yerrors=None,
#
lw=2,
lc="k",
la=1,
dashed=False,
splined=False,
#
elw=2, # error line width
ec=None, # error line or band color
errorBand=False, # errors in x are ignored
#
marker="",
ms=None,
mc=None,
ma=None,
# Figure and axes options:
like=None,
xlim=None,
ylim=(None, None),
aspect=4/3,
padding=0.05,
#
title="",
xtitle=" ",
ytitle=" ",
ac="k",
grid=True,
ztolerance=None,
label="",
**fig_kwargs,
):
line = False
if lw > 0:
line = True
if marker == "" and not line and not splined:
marker = "o"
if like is not None:
xlim = like.xlim
ylim = like.ylim
aspect = like.aspect
padding = like.padding
if utils.isSequence(xlim):
# deal with user passing eg [x0, None]
_x0, _x1 = xlim
if _x0 is None:
_x0 = data.min()
if _x1 is None:
_x1 = data.max()
xlim = [_x0, _x1]
# purge NaN from data
validIds = np.all(np.logical_not(np.isnan(data)))
data = np.array(data[validIds])[0]
fig_kwargs["title"] = title
fig_kwargs["xtitle"] = xtitle
fig_kwargs["ytitle"] = ytitle
fig_kwargs["ac"] = ac
fig_kwargs["ztolerance"] = ztolerance
fig_kwargs["grid"] = grid
x0, y0 = np.min(data, axis=0)
x1, y1 = np.max(data, axis=0)
if xerrors is not None and not errorBand:
x0 = min(data[:, 0] - xerrors)
x1 = max(data[:, 0] + xerrors)
if yerrors is not None:
y0 = min(data[:, 1] - yerrors)
y1 = max(data[:, 1] + yerrors)
if like is None:
if xlim is None:
xlim = (None, None)
xlim = list(xlim)
if xlim[0] is None:
xlim[0] = x0
if xlim[1] is None:
xlim[1] = x1
ylim = list(ylim)
if ylim[0] is None:
ylim[0] = y0
if ylim[1] is None:
ylim[1] = y1
self.entries = len(data)
self.mean = data.mean()
self.std = data.std()
######### the PlotXY marker
if mc is None:
mc = lc
if ma is None:
ma = la
if label:
nlab = LabelData()
nlab.text = label
nlab.tcolor = ac
nlab.marker = marker
if line and marker == "":
nlab.marker = "-"
nlab.mcolor = mc
fig_kwargs["label"] = nlab
############################################### Figure init
Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs)
if not self.yscale:
return None
acts = []
######### the PlotXY Line or Spline
if dashed:
l = shapes.DashedLine(data, c=lc, alpha=la, lw=lw)
acts.append(l)
elif splined:
l = shapes.KSpline(data).lw(lw).c(lc).alpha(la)
acts.append(l)
elif line:
l = shapes.Line(data, c=lc, alpha=la).lw(lw)
acts.append(l)
if marker:
pts = np.c_[data, np.zeros(len(data))]
if utils.isSequence(ms):
### variable point size
mk = shapes.Marker(marker, s=1)
mk.scale([1, 1 / self.yscale, 1])
msv = np.zeros_like(pts)
msv[:, 0] = ms
marked = shapes.Glyph(
pts, glyphObj=mk, c=mc, orientationArray=msv, scaleByVectorSize=True
)
else:
### fixed point size
if ms is None:
ms = (xlim[1] - xlim[0]) / 100.0
if utils.isSequence(mc):
fig_kwargs["marker_color"] = None # for labels
mk = shapes.Marker(marker, s=ms)
mk.scale([1, 1 / self.yscale, 1])
msv = np.zeros_like(pts)
msv[:, 0] = 1
marked = shapes.Glyph(
pts,
glyphObj=mk,
c=mc,
orientationArray=msv,
scaleByVectorSize=True,
)
else:
mk = shapes.Marker(marker, s=ms)
mk.scale([1, 1 / self.yscale, 1])
marked = shapes.Glyph(pts, glyphObj=mk, c=mc)
marked.name = "Marker"
marked.alpha(ma)
marked.z(3 * self.ztolerance)
acts.append(marked)
######### the PlotXY marker errors
if ec is None:
if mc is None:
ec = lc
else:
ec = mc
ztol = self.ztolerance
if errorBand:
yerrors = np.abs(yerrors)
du = np.array(data)
dd = np.array(data)
du[:, 1] += yerrors
dd[:, 1] -= yerrors
if splined:
res = len(data) * 20
band1 = shapes.KSpline(du, res=res)
band2 = shapes.KSpline(dd, res=res)
band = shapes.Ribbon(band1, band2, res=(res, 2))
else:
dd = list(reversed(dd.tolist()))
band = shapes.Line(du.tolist() + dd, closed=True)
band.triangulate().lw(0)
if ec is None:
band.c(lc)
else:
band.c(ec)
band.lighting("off").alpha(la).z(ztol)
acts.append(band)
else:
## xerrors
if xerrors is not None:
if len(xerrors) == len(data):
errs = []
for i, val in enumerate(data):
xval, yval = val
xerr = xerrors[i] / 2
el = shapes.Line((xval-xerr, yval, ztol), (xval+xerr, yval, ztol))
el.lw(elw)
errs.append(el)
mxerrs = merge(errs).c(ec).lw(lw).alpha(ma).z(2 * ztol)
acts.append(mxerrs)
else:
vedo.logger.error("in PlotXY(xerrors=...): mismatch in array length")
## yerrors
if yerrors is not None:
if len(yerrors) == len(data):
errs = []
for i, val in enumerate(data):
xval, yval = val
yerr = yerrors[i]
el = shapes.Line((xval, yval-yerr, ztol), (xval, yval+yerr, ztol))
el.lw(elw)
errs.append(el)
myerrs = merge(errs).c(ec).lw(lw).alpha(ma).z(2 * ztol)
acts.append(myerrs)
else:
vedo.logger.error("in PlotXY(yerrors=...): mismatch in array length")
self.insert(*acts, as3d=False)
self.name = "PlotXY"
def plot(*args, **kwargs):
"""
Draw a 2D line plot, or scatter plot, of variable x vs variable y.
Input format can be either `[allx], [allx, ally] or [(x1,y1), (x2,y2), ...]`
Use `like=...` if you want to use the same format of a previously
created Figure (useful when superimposing Figures) to make sure
they are compatible and comparable. If they are not compatible
you will receive an error message.
Parameters
----------
xerrors : bool
show error bars associated to each point in x
yerrors : bool
show error bars associated to each point in y
lw : int
width of the line connecting points in pixel units.
Set it to 0 to remove the line.
lc : str
line color
la : float
line "alpha", opacity of the line
dashed : bool
draw a dashed line instead of a continous line
splined : bool
spline the line joining the point as a countinous curve
elw : int
width of error bar lines in units of pixels
ec : color
color of error bar, by default the same as marker color
errorBand : bool
represent errors on y as a filled error band.
Use ``ec`` keyword to modify its color.
marker : str, int
use a marker for the data points
ms : float
marker size
mc : color
color of the marker
ma : float
opacity of the marker
xlim : list
set limits to the range for the x variable
ylim : list
set limits to the range for the y variable
aspect : float
Desired aspect ratio.
If None, it is automatically calculated to get a reasonable aspect ratio.
Scaling factor is saved in Figure.yscale
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
title : str
title to appear on the top of the frame, like a header.
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
ac : str
axes color
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
ztolerance : float
a tolerance factor to superimpose objects (along the z-axis).
Example:
.. code-block:: python
from vedo.pyplot import plot
import numpy as np
x = np.linspace(0, 6.28, num=50)
plot(np.sin(x), 'r').plot(np.cos(x), 'bo-').show()
.. image:: https://user-images.githubusercontent.com/32848391/74363882-c3638300-4dcb-11ea-8a78-eb492ad9711f.png
.. hint::
examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py
.. image:: https://vedo.embl.es/images/pyplot/plot_pip.png
-------------------------------------------------------------------------
.. note:: mode="bar"
Creates a `PlotBars(Figure)` object.
Input must be in format `[counts, labels, colors, edges]`.
Either or both `edges` and `colors` are optional and can be omitted.
Parameters
----------
errors : bool
show error bars
logscale : bool
use logscale on y-axis
fill : bool
fill bars woth solid color `c`
gap : float
leave a small space btw bars
radius : float
border radius of the top of the histogram bar. Default value is 0.1.
texture : str
url or path to an image to be used as texture for the bin
outline : bool
show outline of the bins
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
ac : str
axes color
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
aspect : float
the desired aspect ratio of the figure. Default is 4/3.
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
.. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_1D.png
----------------------------------------------------------------------
.. note:: 2D functions
If input is an external function or a formula, draw the surface
representing the function `f(x,y)`.
Parameters
----------
x : float
x range of values
y : float
y range of values
zlimits : float
limit the z range of the independent variable
zlevels : int
will draw the specified number of z-levels contour lines
showNan : bool
show where the function does not exist as red points
bins : list
number of bins in x and y
.. hint:: plot_fxy.py
.. image:: https://vedo.embl.es/images/pyplot/plot_fxy.png
--------------------------------------------------------------------
.. note:: mode="complex"
If ``mode='complex'`` draw the real value of the function and color map the imaginary part.
Parameters
----------
cmap : str
diverging color map (white means imag(z)=0)
lw : float
line with of the binning
bins : list
binning in x and y
.. hint:: examples/pyplot/plot_fxy.py
..image:: https://user-images.githubusercontent.com/32848391/73392962-1709a300-42db-11ea-9278-30c9d6e5eeaa.png
--------------------------------------------------------------------
.. note:: mode="polar"
If ``mode='polar'`` input arrays are interpreted as a list of polar angles and radii.
Build a polar (radar) plot by joining the set of points in polar coordinates.
Parameters
----------
title : str
plot title
tsize : float
title size
bins : int
number of bins in phi
r1 : float
inner radius
r2 : float
outer radius
lsize : float
label size
c : color
color of the line
ac : color
color of the frame and labels
alpha : float
opacity of the frame
ps : int
point size in pixels, if ps=0 no point is drawn
lw : int
line width in pixels, if lw=0 no line is drawn
deg : bool
input array is in degrees
vmax : float
normalize radius to this maximum value
fill : bool
fill convex area with solid color
splined : bool
interpolate the set of input points
showDisc : bool
draw the outer ring axis
nrays : int
draw this number of axis rays (continuous and dashed)
showLines : bool
draw lines to the origin
showAngles : bool
draw angle values
.. hint:: examples/pyplot/histo_polar.py
.. image:: https://user-images.githubusercontent.com/32848391/64992590-7fc82400-d8d4-11e9-9c10-795f4756a73f.png
--------------------------------------------------------------------
.. note:: mode="spheric"
If ``mode='spheric'`` input must be an external function rho(theta, phi).
A surface is created in spherical coordinates.
Return an ``Figure(Assembly)`` of 2 objects: the unit
sphere (in wireframe representation) and the surface `rho(theta, phi)`.
Parameters
----------
rfunc : function
handle to a user defined function `rho(theta, phi)`.
normalize : bool
scale surface to fit inside the unit sphere
res : int
grid resolution of the unit sphere
scalarbar : bool
add a 3D scalarbar to the plot for radius
c : color
color of the unit sphere
alpha : float
opacity of the unit sphere
cmap : str
color map for the surface
.. hint:: examples/pyplot/plot_spheric.py
.. image:: https://vedo.embl.es/images/pyplot/plot_spheric.png
"""
mode = kwargs.pop("mode", "")
if "spher" in mode:
return _plotSpheric(args[0], **kwargs)
if "bar" in mode:
return PlotBars(args[0], **kwargs)
if isinstance(args[0], str) or "function" in str(type(args[0])):
if "complex" in mode:
return _plotFz(args[0], **kwargs)
return _plotFxy(args[0], **kwargs)
# grab the matplotlib-like options
optidx = None
for i, a in enumerate(args):
if i > 0 and isinstance(a, str):
optidx = i
break
if optidx:
opts = args[optidx].replace(" ", "")
if "--" in opts:
opts = opts.replace("--", "")
kwargs["dashed"] = True
elif "-" in opts:
opts = opts.replace("-", "")
else:
kwargs["lw"] = 0
symbs = ['.','o','O', '0', 'p','*','h','D','d','v','^','>','<','s', 'x', 'a']
allcols = list(colors.colors.keys()) + list(colors.color_nicks.keys())
for cc in allcols:
if cc == "o":
continue
if cc in opts:
opts = opts.replace(cc, "")
kwargs["lc"] = cc
kwargs["mc"] = cc
break
for ss in symbs:
if ss in opts:
opts = opts.replace(ss, "", 1)
kwargs["marker"] = ss
break
opts.replace(" ", "")
if opts:
vedo.logger.error(f"in plot(), could not understand option(s): {opts}")
if optidx == 1 or optidx is None:
if utils.isSequence(args[0][0]):
# print('case 1', 'plot([(x,y),..])')
data = np.array(args[0])
x = np.array(data[:, 0])
y = np.array(data[:, 1])
elif len(args) == 1 or optidx == 1:
# print('case 2', 'plot(x)')
x = np.linspace(0, len(args[0]), num=len(args[0]))
y = np.array(args[0])
elif utils.isSequence(args[1]):
# print('case 3', 'plot(allx,ally)')
x = np.array(args[0])
y = np.array(args[1])
elif utils.isSequence(args[0]) and utils.isSequence(args[0][0]):
# print('case 4', 'plot([allx,ally])')
x = np.array(args[0][0])
y = np.array(args[0][1])
elif optidx == 2:
# print('case 5', 'plot(x,y)')
x = np.array(args[0])
y = np.array(args[1])
else:
vedo.logger.error(f"plot(): Could not understand input arguments {args}")
return None
if "polar" in mode:
return _plotPolar(np.c_[x, y], **kwargs)
return PlotXY(np.c_[x, y], **kwargs)
def histogram(*args, **kwargs):
"""
Histogramming for 1D and 2D data arrays.
This is meant as a convenience function that creates the appropriate object
based on the shape of the provided input data.
Use keyword `like=...` if you want to use the same format of a previously
created Figure (useful when superimposing Figures) to make sure
they are compatible and comparable. If they are not compatible
you will receive an error message.
-------------------------------------------------------------------------
.. note:: default mode, for 1D arrays
Creates a `Histogram1D(Figure)` object.
Parameters
----------
weights : list
An array of weights, of the same shape as `data`. Each value in `data`
only contributes its associated weight towards the bin count (instead of 1).
bins : int
number of bins
vrange : list
restrict the range of the histogram
density : bool
normalize the area to 1 by dividing by the nr of entries and bin size
logscale : bool
use logscale on y-axis
fill : bool
fill bars woth solid color `c`
gap : float
leave a small space btw bars
radius : float
border radius of the top of the histogram bar. Default value is 0.1.
texture : str
url or path to an image to be used as texture for the bin
outline : bool
show outline of the bins
errors : bool
show error bars
xtitle : str
title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")`
ytitle : str
title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")`
padding : float, list
keep a padding space from the axes (as a fraction of the axis size).
This can be a list of four numbers.
aspect : float
the desired aspect ratio of the histogram. Default is 4/3.
grid : bool
show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)`
ztolerance : float
a tolerance factor to superimpose objects (along the z-axis).
.. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_1D.png
-------------------------------------------------------------------------
.. note:: default mode, for 2D arrays
Input data formats `[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]`
are both valid.
Parameters
----------
bins : list
binning as (nx, ny)
weights : list
array of weights to assign to each entry
cmap : str, lookuptable
color map name or look up table
alpha : float
opacity of the histogram
gap : float
separation between adjacent bins as a fraction for their size
scalarbar : bool
add a scalarbar to right of the histogram
like : Figure
grab and use the same format of the given Figure (for superimposing)
xlim : list
[x0, x1] range of interest. If left to None will automatically
choose the minimum or the maximum of the data range.
Data outside the range are completely ignored.
ylim : list
[y0, y1] range of interest. If left to None will automatically
choose the minimum or the maximum of the data range.
Data outside the range are completely ignored.
aspect : float
the desired aspect ratio of the figure.
title : str
title of the plot to appear on top.
If left blank some statistics will be shown.
xtitle : str
x axis title
ytitle : str
y axis title
ztitle : str
title for the scalar bar
ac : str
axes color, additional keyword for Axes can also be added
using e.g. `axes=dict(xyGrid=True)`
.. hint:: examples/pyplot/histo_2d.py
.. image:: https://vedo.embl.es/images/pyplot/histo_2D.png
-------------------------------------------------------------------------
.. note:: mode="hexbin"
If ``mode='hexbin'``, build a hexagonal histogram from a list of x and y values.
Parameters
----------
xtitle : str
x axis title
bins : int
nr of bins for the smaller range in x or y
vrange : list
range in x and y in format `[(xmin,xmax), (ymin,ymax)]`
norm : float
sets a scaling factor for the z axis (frequency axis)
fill : bool
draw solid hexagons
cmap : str
color map name for elevation
.. hint:: examples/pyplot/histo_hexagonal.py
.. image:: https://vedo.embl.es/images/pyplot/histo_hexagonal.png
-------------------------------------------------------------------------
.. note:: mode="polar"
If ``mode='polar'`` assume input is polar coordinate system (rho, theta):
Parameters
----------
weights : list
Array of weights, of the same shape as the input.
Each value only contributes its associated weight towards the bin count (instead of 1).
title : str
histogram title
tsize : float
title size
bins : int
number of bins in phi
r1 : float
inner radius
r2 : float
outer radius
phigap : float
gap angle btw 2 radial bars, in degrees
rgap : float
gap factor along radius of numeric angle labels
lpos : float
label gap factor along radius
lsize : float
label size
c : color
color of the histogram bars, can be a list of length `bins`
bc : color
color of the frame and labels
alpha : float
opacity of the frame
cmap : str
color map name
deg : bool
input array is in degrees
vmin : float
minimum value of the radial axis
vmax : float
maximum value of the radial axis
labels : list
list of labels, must be of length `bins`
showDisc : bool
show the outer ring axis
nrays : int
draw this number of axis rays (continuous and dashed)
showLines : bool
show lines to the origin
showAngles : bool
show angular values
showErrors : bool
show error bars
.. hint:: examples/pyplot/histo_polar.py
.. image:: https://vedo.embl.es/images/pyplot/histo_polar.png
-------------------------------------------------------------------------
.. note:: mode="spheric"
If ``mode='spheric'``, build a histogram from list of theta and phi values.
Parameters
----------
rmax : float
maximum radial elevation of bin
res : int
sphere resolution
cmap : str
color map name
lw : int
line width of the bin edges
scalarbar : bool
add a scalarbar to plot
.. hint:: examples/pyplot/histo_spheric.py
.. image:: https://vedo.embl.es/images/pyplot/histo_spheric.png
"""
mode = kwargs.pop("mode", "")
if len(args) == 2: # x, y
if "spher" in mode:
return _histogramSpheric(args[0], args[1], **kwargs)
if "hex" in mode:
return _histogramHexBin(args[0], args[1], **kwargs)
return Histogram2D(args[0], args[1], **kwargs)
elif len(args) == 1:
if isinstance(args[0], vedo.Volume):
data = args[0].pointdata[0]
elif isinstance(args[0], vedo.Points):
pd0 = args[0].pointdata[0]
if pd0:
data = pd0.ravel()
else:
data = args[0].celldata[0].ravel()
else:
data = np.array(args[0])
if "spher" in mode:
return _histogramSpheric(args[0][:, 0], args[0][:, 1], **kwargs)
if len(data.shape) == 1:
if "polar" in mode:
return _histogramPolar(data, **kwargs)
return Histogram1D(data, **kwargs)
else:
if "hex" in mode:
return _histogramHexBin(args[0][:, 0], args[0][:, 1], **kwargs)
return Histogram2D(args[0], **kwargs)
print("histogram(): Could not understand input", args[0])
return None
def fit(
points,
deg=1,
niter=0,
nstd=3,
xerrors=None,
yerrors=None,
vrange=None,
res=250,
lw=3,
c='red4',
):
"""
Polynomial fitting with parameter error and error bands calculation.
Returns a ``vedo.shapes.Line`` object.
Errors bars in both x and y are supported.
Additional information about the fitting output can be accessed with:
``fit = fitPolynomial(pts)``
- *fit.coefficients* will contain the coefficients of the polynomial fit
- *fit.coefficientErrors*, errors on the fitting coefficients
- *fit.MonteCarloCoefficients*, fitting coefficient set from MC generation
- *fit.covarianceMatrix*, covariance matrix as a numpy array
- *fit.reducedChi2*, reduced chi-square of the fitting
- *fit.ndof*, number of degrees of freedom
- *fit.dataSigma*, mean data dispersion from the central fit assuming Chi2=1
- *fit.errorLines*, a ``vedo.shapes.Line`` object for the upper and lower error band
- *fit.errorBand*, the ``vedo.mesh.Mesh`` object representing the error band
Errors on x and y can be specified. If left to `None` an estimate is made from
the statistical spread of the dataset itself. Errors are always assumed gaussian.
Parameters
----------
deg : int
degree of the polynomial to be fitted
niter : int
number of monte-carlo iterations to compute error bands.
If set to 0, return the simple least-squares fit with naive error estimation
on coefficients only. A reasonable non-zero value to set is about 500, in
this case *errorLines*, *errorBand* and the other class attributes are filled
nstd : float
nr. of standard deviation to use for error calculation
xerrors : list
array of the same length of points with the errors on x
yerrors : list
array of the same length of points with the errors on y
vrange : list
specify the domain range of the fitting line
(only affects visualization, but can be used to extrapolate the fit
outside the data range)
res : int
resolution of the output fitted line and error lines
.. hint:: examples/pyplot/fitPolynomial1.py
.. image:: https://vedo.embl.es/images/pyplot/fitPolynomial1.png
"""
if isinstance(points, vedo.pointcloud.Points):
points = points.points()
points = np.asarray(points)
if len(points) == 2: # assume user is passing [x,y]
points = np.c_[points[0], points[1]]
x = points[:, 0]
y = points[:, 1] # ignore z
n = len(x)
ndof = n - deg - 1
if vrange is not None:
x0, x1 = vrange
else:
x0, x1 = np.min(x), np.max(x)
if xerrors is not None:
x0 -= xerrors[0] / 2
x1 += xerrors[-1] / 2
tol = (x1 - x0) / 10000
xr = np.linspace(x0, x1, res)
# project x errs on y
if xerrors is not None:
xerrors = np.asarray(xerrors)
if yerrors is not None:
yerrors = np.asarray(yerrors)
w = 1.0 / yerrors
coeffs = np.polyfit(x, y, deg, w=w, rcond=None)
else:
coeffs = np.polyfit(x, y, deg, rcond=None)
# update yerrors, 1 bootstrap iteration is enough
p1d = np.poly1d(coeffs)
der = (p1d(x + tol) - p1d(x)) / tol
yerrors = np.sqrt(yerrors * yerrors + np.power(der * xerrors, 2))
if yerrors is not None:
yerrors = np.asarray(yerrors)
w = 1.0 / yerrors
coeffs, V = np.polyfit(x, y, deg, w=w, rcond=None, cov=True)
else:
w = 1
coeffs, V = np.polyfit(x, y, deg, rcond=None, cov=True)
p1d = np.poly1d(coeffs)
theor = p1d(xr)
fitl = shapes.Line(xr, theor, lw=lw, c=c).z(tol * 2)
fitl.coefficients = coeffs
fitl.covarianceMatrix = V
residuals2_sum = np.sum(np.power(p1d(x) - y, 2)) / ndof
sigma = np.sqrt(residuals2_sum)
fitl.reducedChi2 = np.sum(np.power((p1d(x) - y) * w, 2)) / ndof
fitl.ndof = ndof
fitl.dataSigma = sigma # worked out from data using chi2=1 hypo
fitl.name = "LinePolynomialFit"
if not niter:
fitl.coefficientErrors = np.sqrt(np.diag(V))
return fitl ################################
if yerrors is not None:
sigma = yerrors
else:
w = None
fitl.reducedChi2 = 1
Theors, all_coeffs = [], []
for i in range(niter):
noise = np.random.randn(n) * sigma
coeffs = np.polyfit(x, y + noise, deg, w=w, rcond=None)
all_coeffs.append(coeffs)
P1d = np.poly1d(coeffs)
Theor = P1d(xr)
Theors.append(Theor)
all_coeffs = np.array(all_coeffs)
fitl.MonteCarloCoefficients = all_coeffs
stds = np.std(Theors, axis=0)
fitl.coefficientErrors = np.std(all_coeffs, axis=0)
# check distributions on the fly
# for i in range(deg+1):
# histogram(all_coeffs[:,i],title='par'+str(i)).show(new=1)
# histogram(all_coeffs[:,0], all_coeffs[:,1],
# xtitle='param0', ytitle='param1',scalarbar=1).show(new=1)
# histogram(all_coeffs[:,1], all_coeffs[:,2],
# xtitle='param1', ytitle='param2').show(new=1)
# histogram(all_coeffs[:,0], all_coeffs[:,2],
# xtitle='param0', ytitle='param2').show(new=1)
error_lines = []
for i in [nstd, -nstd]:
el = shapes.Line(xr, theor + stds * i, lw=1, alpha=0.2, c="k").z(tol)
error_lines.append(el)
el.name = "ErrorLine for sigma=" + str(i)
fitl.errorLines = error_lines
l1 = error_lines[0].points().tolist()
cband = l1 + list(reversed(error_lines[1].points().tolist())) + [l1[0]]
fitl.errorBand = shapes.Line(cband).triangulate().lw(0).c("k", 0.15)
fitl.errorBand.name = "PolynomialFitErrorBand"
return fitl
def _plotFxy(
z,
xlim=(0, 3),
ylim=(0, 3),
zlim=(None, None),
showNan=True,
zlevels=10,
c=None,
bc="aqua",
alpha=1,
texture="",
bins=(100, 100),
axes=True,
):
if c is not None:
texture = None # disable
ps = vtk.vtkPlaneSource()
ps.SetResolution(bins[0], bins[1])
ps.SetNormal([0, 0, 1])
ps.Update()
poly = ps.GetOutput()
dx = xlim[1] - xlim[0]
dy = ylim[1] - ylim[0]
todel, nans = [], []
for i in range(poly.GetNumberOfPoints()):
px, py, _ = poly.GetPoint(i)
xv = (px + 0.5) * dx + xlim[0]
yv = (py + 0.5) * dy + ylim[0]
try:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
zv = z(xv, yv)
if np.isnan(zv) or np.isinf(zv) or np.iscomplex(zv):
zv = 0
todel.append(i)
nans.append([xv, yv, 0])
except:
zv = 0
todel.append(i)
nans.append([xv, yv, 0])
poly.GetPoints().SetPoint(i, [xv, yv, zv])
if todel:
cellIds = vtk.vtkIdList()
poly.BuildLinks()
for i in todel:
poly.GetPointCells(i, cellIds)
for j in range(cellIds.GetNumberOfIds()):
poly.DeleteCell(cellIds.GetId(j)) # flag cell
poly.RemoveDeletedCells()
cl = vtk.vtkCleanPolyData()
cl.SetInputData(poly)
cl.Update()
poly = cl.GetOutput()
if not poly.GetNumberOfPoints():
vedo.logger.error("function is not real in the domain")
return None
if zlim[0]:
tmpact1 = Mesh(poly)
a = tmpact1.cutWithPlane((0, 0, zlim[0]), (0, 0, 1))
poly = a.polydata()
if zlim[1]:
tmpact2 = Mesh(poly)
a = tmpact2.cutWithPlane((0, 0, zlim[1]), (0, 0, -1))
poly = a.polydata()
cmap = ""
if c in colors.cmaps_names:
cmap = c
c = None
bc = None
mesh = Mesh(poly, c, alpha).computeNormals().lighting("plastic")
if cmap:
mesh.addElevationScalars().cmap(cmap)
if bc:
mesh.bc(bc)
if texture:
mesh.texture(texture)
acts = [mesh]
if zlevels:
elevation = vtk.vtkElevationFilter()
elevation.SetInputData(poly)
bounds = poly.GetBounds()
elevation.SetLowPoint(0, 0, bounds[4])
elevation.SetHighPoint(0, 0, bounds[5])
elevation.Update()
bcf = vtk.vtkBandedPolyDataContourFilter()
bcf.SetInputData(elevation.GetOutput())
bcf.SetScalarModeToValue()
bcf.GenerateContourEdgesOn()
bcf.GenerateValues(zlevels, elevation.GetScalarRange())
bcf.Update()
zpoly = bcf.GetContourEdgesOutput()
zbandsact = Mesh(zpoly, "k", alpha).lw(1).lighting("off")
zbandsact.mapper().SetResolveCoincidentTopologyToPolygonOffset()
acts.append(zbandsact)
if showNan and todel:
bb = mesh.GetBounds()
if bb[4] <= 0 and bb[5] >= 0:
zm = 0.0
else:
zm = (bb[4] + bb[5]) / 2
nans = np.array(nans) + [0, 0, zm]
nansact = shapes.Points(nans, r=2, c="red5", alpha=alpha)
nansact.GetProperty().RenderPointsAsSpheresOff()
acts.append(nansact)
if isinstance(axes, dict):
axs = addons.Axes(mesh, **axes)
acts.append(axs)
elif axes:
axs = addons.Axes(mesh)
acts.append(axs)
assem = Assembly(acts)
assem.name = "plotFxy"
return assem
def _plotFz(
z,
x=(-1, 1),
y=(-1, 1),
zlimits=(None, None),
cmap="PiYG",
alpha=1,
lw=0.1,
bins=(75, 75),
axes=True,
):
ps = vtk.vtkPlaneSource()
ps.SetResolution(bins[0], bins[1])
ps.SetNormal([0, 0, 1])
ps.Update()
poly = ps.GetOutput()
dx = x[1] - x[0]
dy = y[1] - y[0]
arrImg = []
for i in range(poly.GetNumberOfPoints()):
px, py, _ = poly.GetPoint(i)
xv = (px + 0.5) * dx + x[0]
yv = (py + 0.5) * dy + y[0]
try:
zv = z(np.complex(xv), np.complex(yv))
except:
zv = 0
poly.GetPoints().SetPoint(i, [xv, yv, np.real(zv)])
arrImg.append(np.imag(zv))
mesh = Mesh(poly, alpha).lighting("plastic")
v = max(abs(np.min(arrImg)), abs(np.max(arrImg)))
mesh.cmap(cmap, arrImg, vmin=-v, vmax=v)
mesh.computeNormals().lw(lw)
if zlimits[0]:
mesh.cutWithPlane((0, 0, zlimits[0]), (0, 0, 1))
if zlimits[1]:
mesh.cutWithPlane((0, 0, zlimits[1]), (0, 0, -1))
acts = [mesh]
if axes:
axs = addons.Axes(mesh, ztitle="Real part")
acts.append(axs)
asse = Assembly(acts)
asse.name = "plotFz"
if isinstance(z, str):
asse.name += " " + z
return asse
def _plotPolar(
rphi,
title="",
tsize=0.1,
lsize=0.05,
r1=0,
r2=1,
c="blue",
bc="k",
alpha=1,
ps=5,
lw=3,
deg=False,
vmax=None,
fill=False,
splined=False,
showDisc=True,
nrays=8,
showLines=True,
showAngles=True,
):
if len(rphi) == 2:
rphi = np.stack((rphi[0], rphi[1]), axis=1)
rphi = np.array(rphi, dtype=float)
thetas = rphi[:, 0]
radii = rphi[:, 1]
k = 180 / np.pi
if deg:
thetas = np.array(thetas, dtype=float) / k
vals = []
for v in thetas: # normalize range
t = np.arctan2(np.sin(v), np.cos(v))
if t < 0:
t += 2 * np.pi
vals.append(t)
thetas = np.array(vals, dtype=float)
if vmax is None:
vmax = np.max(radii)
angles = []
points = []
for t, r in zip(thetas, radii):
r = r / vmax * r2 + r1
ct, st = np.cos(t), np.sin(t)
points.append([r * ct, r * st, 0])
p0 = points[0]
points.append(p0)
r2e = r1 + r2
lines = None
if splined:
lines = shapes.KSpline(points, closed=True)
lines.c(c).lw(lw).alpha(alpha)
elif lw:
lines = shapes.Line(points)
lines.c(c).lw(lw).alpha(alpha)
points.pop()
ptsact = None
if ps:
ptsact = shapes.Points(points, r=ps, c=c, alpha=alpha)
filling = None
if fill and lw:
faces = []
coords = [[0, 0, 0]] + lines.points().tolist()
for i in range(1, lines.N()):
faces.append([0, i, i + 1])
filling = Mesh([coords, faces]).c(c).alpha(alpha)
back = None
back2 = None
if showDisc:
back = shapes.Disc(r1=r2e, r2=r2e * 1.01, c=bc, res=(1, 360))
back.z(-0.01).lighting("off").alpha(alpha)
back2 = shapes.Disc(r1=r2e / 2, r2=r2e / 2 * 1.005, c=bc, res=(1, 360))
back2.z(-0.01).lighting("off").alpha(alpha)
ti = None
if title:
ti = shapes.Text3D(title, (0, 0, 0), s=tsize, depth=0, justify="top-center")
ti.pos(0, -r2e * 1.15, 0.01)
rays = []
if showDisc:
rgap = 0.05
for t in np.linspace(0, 2 * np.pi, num=nrays, endpoint=False):
ct, st = np.cos(t), np.sin(t)
if showLines:
l = shapes.Line((0, 0, -0.01), (r2e * ct * 1.03, r2e * st * 1.03, -0.01))
rays.append(l)
ct2, st2 = np.cos(t + np.pi / nrays), np.sin(t + np.pi / nrays)
lm = shapes.DashedLine(
(0, 0, -0.01), (r2e * ct2, r2e * st2, -0.01), spacing=0.25
)
rays.append(lm)
elif showAngles: # just the ticks
l = shapes.Line(
(r2e * ct * 0.98, r2e * st * 0.98, -0.01),
(r2e * ct * 1.03, r2e * st * 1.03, -0.01),
)
if showAngles:
if 0 <= t < np.pi / 2:
ju = "bottom-left"
elif t == np.pi / 2:
ju = "bottom-center"
elif np.pi / 2 < t <= np.pi:
ju = "bottom-right"
elif np.pi < t < np.pi * 3 / 2:
ju = "top-right"
elif t == np.pi * 3 / 2:
ju = "top-center"
else:
ju = "top-left"
a = shapes.Text3D(int(t * k), pos=(0, 0, 0), s=lsize, depth=0, justify=ju)
a.pos(r2e * ct * (1 + rgap), r2e * st * (1 + rgap), -0.01)
angles.append(a)
mrg = merge(back, back2, angles, rays, ti)
if mrg:
mrg.color(bc).alpha(alpha).lighting("off")
rh = Assembly([lines, ptsact, filling] + [mrg])
rh.base = np.array([0, 0, 0], dtype=float)
rh.top = np.array([0, 0, 1], dtype=float)
rh.name = "plotPolar"
return rh
def _plotSpheric(rfunc, normalize=True, res=33, scalarbar=True, c="grey", alpha=0.05, cmap="jet"):
sg = shapes.Sphere(res=res, quads=True)
sg.alpha(alpha).c(c).wireframe()
cgpts = sg.points()
r, theta, phi = utils.cart2spher(*cgpts.T)
newr, inans = [], []
for i in range(len(r)):
try:
ri = rfunc(theta[i], phi[i])
if np.isnan(ri):
inans.append(i)
newr.append(1)
else:
newr.append(ri)
except:
inans.append(i)
newr.append(1)
newr = np.array(newr, dtype=float)
if normalize:
newr = newr / np.max(newr)
newr[inans] = 1
nanpts = []
if inans:
redpts = utils.spher2cart(newr[inans], theta[inans], phi[inans])
nanpts.append(shapes.Points(redpts, r=4, c="r"))
pts = utils.spher2cart(newr, theta, phi)
ssurf = sg.clone().points(pts)
if inans:
ssurf.deleteCellsByPointIndex(inans)
ssurf.alpha(1).wireframe(0).lw(0.1)
ssurf.cmap(cmap, newr)
ssurf.computeNormals()
if scalarbar:
xm = np.max([np.max(pts[0]), 1])
ym = np.max([np.abs(np.max(pts[1])), 1])
ssurf.mapper().SetScalarRange(np.min(newr), np.max(newr))
sb3d = ssurf.addScalarBar3D(s=(xm * 0.07, ym), c="k").scalarbar
sb3d.rotateX(90).pos(xm * 1.1, 0, -0.5)
else:
sb3d = None
sg.pickable(False)
asse = Assembly([ssurf, sg] + nanpts + [sb3d])
asse.name = "plotSpheric"
return asse
def _histogramHexBin(
xvalues,
yvalues,
bins=12,
norm=1,
fill=True,
c=None,
cmap="terrain_r",
alpha=1,
):
xmin, xmax = np.min(xvalues), np.max(xvalues)
ymin, ymax = np.min(yvalues), np.max(yvalues)
dx, dy = xmax - xmin, ymax - ymin
if utils.isSequence(bins):
n, m = bins
else:
if xmax - xmin < ymax - ymin:
n = bins
m = np.rint(dy / dx * n / 1.2 + 0.5).astype(int)
else:
m = bins
n = np.rint(dx / dy * m * 1.2 + 0.5).astype(int)
src = vtk.vtkPointSource()
src.SetNumberOfPoints(len(xvalues))
src.Update()
pointsPolydata = src.GetOutput()
values = np.stack((xvalues, yvalues), axis=1)
zs = [[0.0]] * len(values)
values = np.append(values, zs, axis=1)
pointsPolydata.GetPoints().SetData(utils.numpy2vtk(values, dtype=float))
cloud = Mesh(pointsPolydata)
col = None
if c is not None:
col = colors.getColor(c)
hexs, binmax = [], 0
ki, kj = 1.33, 1.12
r = 0.47 / n * 1.2 * dx
for i in range(n + 3):
for j in range(m + 2):
cyl = vtk.vtkCylinderSource()
cyl.SetResolution(6)
cyl.CappingOn()
cyl.SetRadius(0.5)
cyl.SetHeight(0.1)
cyl.Update()
t = vtk.vtkTransform()
if not i % 2:
p = (i / ki, j / kj, 0)
else:
p = (i / ki, j / kj + 0.45, 0)
q = (p[0] / n * 1.2 * dx + xmin, p[1] / m * dy + ymin, 0)
ids = cloud.closestPoint(q, radius=r, returnCellId=True)
ne = len(ids)
if fill:
t.Translate(p[0], p[1], ne / 2)
t.Scale(1, 1, ne * 10)
else:
t.Translate(p[0], p[1], ne)
t.RotateX(90) # put it along Z
tf = vtk.vtkTransformPolyDataFilter()
tf.SetInputData(cyl.GetOutput())
tf.SetTransform(t)
tf.Update()
if c is None:
col = i
h = Mesh(tf.GetOutput(), c=col, alpha=alpha).flat()
h.lighting("plastic")
h.PickableOff()
hexs.append(h)
if ne > binmax:
binmax = ne
if cmap is not None:
for h in hexs:
z = h.GetBounds()[5]
col = colors.colorMap(z, cmap, 0, binmax)
h.color(col)
asse = Assembly(hexs)
asse.SetScale(1.2 / n * dx, 1 / m * dy, norm / binmax * (dx + dy) / 4)
asse.SetPosition(xmin, ymin, 0)
asse.base = np.array([0, 0, 0], dtype=float)
asse.top = np.array([0, 0, 1], dtype=float)
asse.name = "histogramHexBin"
return asse
def _histogramPolar(
values,
weights=None,
title="",
tsize=0.1,
bins=16,
r1=0.25,
r2=1,
phigap=0.5,
rgap=0.05,
lpos=1,
lsize=0.04,
c='grey',
bc="k",
alpha=1,
cmap=None,
deg=False,
vmin=None,
vmax=None,
labels=(),
showDisc=True,
nrays=8,
showLines=True,
showAngles=True,
showErrors=False,
):
k = 180 / np.pi
if deg:
values = np.array(values, dtype=float) / k
else:
values = np.array(values, dtype=float)
vals = []
for v in values: # normalize range
t = np.arctan2(np.sin(v), np.cos(v))
if t < 0:
t += 2 * np.pi
vals.append(t + 0.00001)
histodata, edges = np.histogram(
vals, weights=weights, bins=bins, range=(0, 2 * np.pi)
)
thetas = []
for i in range(bins):
thetas.append((edges[i] + edges[i + 1]) / 2)
if vmin is None:
vmin = np.min(histodata)
if vmax is None:
vmax = np.max(histodata)
errors = np.sqrt(histodata)
r2e = r1 + r2
if showErrors:
r2e += np.max(errors) / vmax * 1.5
back = None
if showDisc:
back = shapes.Disc(r1=r2e, r2=r2e * 1.01, c=bc, res=(1, 360))
back.z(-0.01)
slices = []
lines = []
angles = []
errbars = []
for i, t in enumerate(thetas):
r = histodata[i] / vmax * r2
d = shapes.Disc((0, 0, 0), r1, r1 + r, res=(1, 360))
delta = np.pi / bins - np.pi / 2 - phigap / k
d.cutWithPlane(normal=(np.cos(t + delta), np.sin(t + delta), 0))
d.cutWithPlane(normal=(np.cos(t - delta), np.sin(t - delta), 0))
if cmap is not None:
cslice = colors.colorMap(histodata[i], cmap, vmin, vmax)
d.color(cslice)
else:
if c is None:
d.color(i)
elif utils.isSequence(c) and len(c) == bins:
d.color(c[i])
else:
d.color(c)
d.alpha(alpha).lighting("off")
slices.append(d)
ct, st = np.cos(t), np.sin(t)
if showErrors:
showLines = False
err = np.sqrt(histodata[i]) / vmax * r2
errl = shapes.Line(
((r1 + r - err) * ct, (r1 + r - err) * st, 0.01),
((r1 + r + err) * ct, (r1 + r + err) * st, 0.01),
)
errl.alpha(alpha).lw(3).color(bc)
errbars.append(errl)
labs = []
rays = []
if showDisc:
outerdisc = shapes.Disc(r1=r2e, r2=r2e * 1.01, c=bc, res=(1, 360))
outerdisc.z(-0.01)
innerdisc = shapes.Disc(r1=r2e / 2, r2=r2e / 2 * 1.005, c=bc, res=(1, 360))
innerdisc.z(-0.01)
rays.append(outerdisc)
rays.append(innerdisc)
rgap = 0.05
for t in np.linspace(0, 2 * np.pi, num=nrays, endpoint=False):
ct, st = np.cos(t), np.sin(t)
if showLines:
l = shapes.Line((0, 0, -0.01), (r2e * ct * 1.03, r2e * st * 1.03, -0.01))
rays.append(l)
ct2, st2 = np.cos(t + np.pi / nrays), np.sin(t + np.pi / nrays)
lm = shapes.DashedLine(
(0, 0, -0.01), (r2e * ct2, r2e * st2, -0.01), spacing=0.25
)
rays.append(lm)
elif showAngles: # just the ticks
l = shapes.Line(
(r2e * ct * 0.98, r2e * st * 0.98, -0.01),
(r2e * ct * 1.03, r2e * st * 1.03, -0.01),
)
if showAngles:
if 0 <= t < np.pi / 2:
ju = "bottom-left"
elif t == np.pi / 2:
ju = "bottom-center"
elif np.pi / 2 < t <= np.pi:
ju = "bottom-right"
elif np.pi < t < np.pi * 3 / 2:
ju = "top-right"
elif t == np.pi * 3 / 2:
ju = "top-center"
else:
ju = "top-left"
a = shapes.Text3D(int(t * k), pos=(0, 0, 0), s=lsize, depth=0, justify=ju)
a.pos(r2e * ct * (1 + rgap), r2e * st * (1 + rgap), -0.01)
angles.append(a)
ti = None
if title:
ti = shapes.Text3D(title, (0, 0, 0), s=tsize, depth=0, justify="top-center")
ti.pos(0, -r2e * 1.15, 0.01)
for i, t in enumerate(thetas):
if i < len(labels):
lab = shapes.Text3D(
labels[i], (0, 0, 0), s=lsize, depth=0, justify="center" # font="VTK",
)
lab.pos(
r2e * np.cos(t) * (1 + rgap) * lpos / 2,
r2e * np.sin(t) * (1 + rgap) * lpos / 2,
0.01,
)
labs.append(lab)
mrg = merge(lines, angles, rays, ti, labs)
if mrg:
mrg.color(bc).lighting("off")
acts = slices + errbars + [mrg]
asse = Assembly(acts)
asse.frequencies = histodata
asse.bins = edges
asse.name = "histogramPolar"
return asse
def _histogramSpheric(
thetavalues, phivalues, rmax=1.2, res=8, cmap="rainbow", scalarbar=True,
):
x, y, z = utils.spher2cart(np.ones_like(thetavalues) * 1.1, thetavalues, phivalues)
ptsvals = np.c_[x, y, z]
sg = shapes.Sphere(res=res, quads=True).shrink(0.999).computeNormals().lw(0.1)
sgfaces = sg.faces()
sgpts = sg.points()
# sgpts = np.vstack((sgpts, [0,0,0]))
# idx = sgpts.shape[0]-1
# newfaces = []
# for fc in sgfaces:
# f1,f2,f3,f4 = fc
# newfaces.append([idx,f1,f2, idx])
# newfaces.append([idx,f2,f3, idx])
# newfaces.append([idx,f3,f4, idx])
# newfaces.append([idx,f4,f1, idx])
newsg = sg # Mesh((sgpts, sgfaces)).computeNormals().phong()
newsgpts = newsg.points()
cntrs = sg.cellCenters()
counts = np.zeros(len(cntrs))
for p in ptsvals:
cell = sg.closestPoint(p, returnCellId=True)
counts[cell] += 1
acounts = np.array(counts, dtype=float)
counts *= (rmax - 1) / np.max(counts)
for cell, cn in enumerate(counts):
if not cn:
continue
fs = sgfaces[cell]
pts = sgpts[fs]
_, t1, p1 = utils.cart2spher(pts[:, 0], pts[:, 1], pts[:, 2])
x, y, z = utils.spher2cart(1 + cn, t1, p1)
newsgpts[fs] = np.c_[x, y, z]
newsg.points(newsgpts)
newsg.cmap(cmap, acounts, on="cells")
if scalarbar:
newsg.addScalarBar()
newsg.name = "histogramSpheric"
return newsg
def donut(
fractions,
title="",
tsize=0.3,
r1=1.7,
r2=1,
phigap=0,
lpos=0.8,
lsize=0.15,
c=None,
bc="k",
alpha=1,
labels=(),
showDisc=False,
):
"""
Donut plot or pie chart.
Parameters
----------
title : str
plot title
tsize : float
title size
r1 : float inner radius
r2 : float
outer radius, starting from r1
phigap : float
gap angle btw 2 radial bars, in degrees
lpos : float
label gap factor along radius
lsize : float
label size
c : color
color of the plot slices
bc : color
color of the disc frame
alpha : float
opacity of the disc frame
labels : list
list of labels
showDisc : bool
show the outer ring axis
.. hist:: examples/pyplot/donut.py
.. image:: https://vedo.embl.es/images/pyplot/donut.png
"""
fractions = np.array(fractions, dtype=float)
angles = np.add.accumulate(2 * np.pi * fractions)
angles[-1] = 2 * np.pi
if angles[-2] > 2 * np.pi:
print("Error in donut(): fractions must sum to 1.")
raise RuntimeError
cols = []
for i, th in enumerate(np.linspace(0, 2 * np.pi, 360, endpoint=False)):
for ia, a in enumerate(angles):
if th < a:
cols.append(c[ia])
break
labs = ()
if labels:
angles = np.concatenate([[0], angles])
labs = [""] * 360
for i in range(len(labels)):
a = (angles[i + 1] + angles[i]) / 2
j = int(a / np.pi * 180)
labs[j] = labels[i]
data = np.linspace(0, 2 * np.pi, 360, endpoint=False) + 0.005
dn = _histogramPolar(
data,
title=title,
bins=360,
r1=r1,
r2=r2,
phigap=phigap,
lpos=lpos,
lsize=lsize,
tsize=tsize,
c=cols,
bc=bc,
alpha=alpha,
vmin=0,
vmax=1,
labels=labs,
showDisc=showDisc,
showLines=0,
showAngles=0,
showErrors=0,
)
dn.name = "donut"
return dn
def violin(
values,
bins=10,
vlim=None,
x=0,
width=3,
splined=True,
fill=True,
c="violet",
alpha=1,
outline=True,
centerline=True,
lc="darkorchid",
lw=3,
):
"""
Violin style histogram.
Parameters
----------
bins : int
number of bins
vlim : list
input value limits. Crop values outside range
x : float
x-position of the violin axis
width : float
width factor of the normalized distribution
splined : bool
spline the outline
fill : bool
fill violin with solid color
outline : bool
add the distribution outline
centerline : bool
add the vertical centerline at x
lc : color
line color
.. hint:: examples/pyplot/histo_violin.py
.. image:: https://vedo.embl.es/images/pyplot/histo_violin.png
"""
fs, edges = np.histogram(values, bins=bins, range=vlim)
mine, maxe = np.min(edges), np.max(edges)
fs = fs.astype(float) / len(values) * width
rs = []
if splined:
lnl, lnr = [(0, edges[0], 0)], [(0, edges[0], 0)]
for i in range(bins):
xc = (edges[i] + edges[i + 1]) / 2
yc = fs[i]
lnl.append([-yc, xc, 0])
lnr.append([yc, xc, 0])
lnl.append((0, edges[-1], 0))
lnr.append((0, edges[-1], 0))
spl = shapes.KSpline(lnl).x(x)
spr = shapes.KSpline(lnr).x(x)
spl.color(lc).alpha(alpha).lw(lw)
spr.color(lc).alpha(alpha).lw(lw)
if outline:
rs.append(spl)
rs.append(spr)
if fill:
rb = shapes.Ribbon(spl, spr, c=c, alpha=alpha).lighting("off")
rs.append(rb)
else:
lns1 = [[0, mine, 0]]
for i in range(bins):
lns1.append([fs[i], edges[i], 0])
lns1.append([fs[i], edges[i + 1], 0])
lns1.append([0, maxe, 0])
lns2 = [[0, mine, 0]]
for i in range(bins):
lns2.append([-fs[i], edges[i], 0])
lns2.append([-fs[i], edges[i + 1], 0])
lns2.append([0, maxe, 0])
if outline:
rs.append(shapes.Line(lns1, c=lc, alpha=alpha, lw=lw).x(x))
rs.append(shapes.Line(lns2, c=lc, alpha=alpha, lw=lw).x(x))
if fill:
for i in range(bins):
p0 = (-fs[i], edges[i], 0)
p1 = (fs[i], edges[i + 1], 0)
r = shapes.Rectangle(p0, p1).x(p0[0] + x)
r.color(c).alpha(alpha).lighting("off")
rs.append(r)
if centerline:
cl = shapes.Line([0, mine, 0.01], [0, maxe, 0.01], c=lc, alpha=alpha, lw=2).x(x)
rs.append(cl)
asse = Assembly(rs)
asse.name = "violin"
return asse
def whisker(
data,
s=0.25,
c='k',
lw=2,
bc='blue',
alpha=0.25,
r=5,
jitter=True,
horizontal=False,
):
"""
Generate a "whisker" bar from a 1-dimensional dataset.
Parameters
----------
s : float
size of the box
c : color
color of the lines
lw : float
line width
bc : color
color of the box
alpha : float
transparency of the box
r : float
point radius in pixels (use value 0 to disable)
jitter : bool
add some randomness to points to avoid overlap
horizontal : bool
set horizontal layout
.. hint:: examples/pyplot/whiskers.py
.. image:: https://vedo.embl.es/images/pyplot/whiskers.png
"""
xvals = np.zeros_like(np.array(data))
if jitter:
xjit = np.random.randn(len(xvals)) * s / 9
xjit = np.clip(xjit, -s / 2.1, s / 2.1)
xvals += xjit
dmean = np.mean(data)
dq05 = np.quantile(data, 0.05)
dq25 = np.quantile(data, 0.25)
dq75 = np.quantile(data, 0.75)
dq95 = np.quantile(data, 0.95)
pts = None
if r:
pts = shapes.Points([xvals, data], c=c, r=r)
rec = shapes.Rectangle([-s / 2, dq25], [s / 2, dq75], c=bc, alpha=alpha)
rec.GetProperty().LightingOff()
rl = shapes.Line(
[[-s / 2, dq25], [s / 2, dq25], [s / 2, dq75], [-s / 2, dq75]], closed=True
)
l1 = shapes.Line([0, dq05, 0], [0, dq25, 0], c=c, lw=lw)
l2 = shapes.Line([0, dq75, 0], [0, dq95, 0], c=c, lw=lw)
lm = shapes.Line([-s / 2, dmean], [s / 2, dmean])
lns = merge(l1, l2, lm, rl)
asse = Assembly([lns, rec, pts])
if horizontal:
asse.rotateZ(-90)
asse.name = "Whisker"
asse.info["mean"] = dmean
asse.info["quantile_05"] = dq05
asse.info["quantile_25"] = dq25
asse.info["quantile_75"] = dq75
asse.info["quantile_95"] = dq95
return asse
def streamplot(
X,
Y,
U,
V,
direction="both",
maxPropagation=None,
mode=1,
lw=0.001,
c=None,
probes=(),
):
"""
Generate a streamline plot of a vectorial field (U,V) defined at positions (X,Y).
Returns a ``Mesh`` object.
Parameters
----------
direction : str
either "forward", "backward" or "both"
maxPropagation : float
maximum physical length of the streamline
lw : float
line width in absolute units
mode : int
mode of varying the line width
- 0 - do not vary line width
- 1 - vary line width by first vector component
- 2 - vary line width vector magnitude
- 3 - vary line width by absolute value of first vector component
.. hint:: examples/pyplot/plot_stream.py
.. image:: https://vedo.embl.es/images/pyplot/plot_stream.png
"""
n = len(X)
m = len(Y[0])
if n != m:
print("Limitation in streamplot(): only square grids are allowed.", n, m)
raise RuntimeError()
xmin, xmax = X[0][0], X[-1][-1]
ymin, ymax = Y[0][0], Y[-1][-1]
field = np.sqrt(U * U + V * V)
vol = vedo.Volume(field, dims=(n, n, 1))
uf = np.ravel(U, order="F")
vf = np.ravel(V, order="F")
vects = np.c_[uf, vf, np.zeros_like(uf)]
vol.addPointArray(vects, "vects")
if len(probes) == 0:
probe = shapes.Grid(pos=((n-1)/2,(n-1)/2,0), s=(n-1, n-1), res=(n-1,n-1))
else:
if isinstance(probes, vedo.Points):
probes = probes.points()
else:
probes = np.array(probes, dtype=float)
if len(probes[0]) == 2:
probes = np.c_[probes[:, 0], probes[:, 1], np.zeros(len(probes))]
sv = [(n - 1) / (xmax - xmin), (n - 1) / (ymax - ymin), 1]
probes = probes - [xmin, ymin, 0]
probes = np.multiply(probes, sv)
probe = vedo.Points(probes)
stream = vedo.shapes.StreamLines(
vol,
probe,
tubes={"radius": lw, "mode": mode,},
lw=lw,
maxPropagation=maxPropagation,
direction=direction,
)
if c is not None:
stream.color(c)
else:
stream.addScalarBar()
stream.lighting("off")
stream.scale([1 / (n - 1) * (xmax - xmin), 1 / (n - 1) * (ymax - ymin), 1])
stream.shift(xmin, ymin)
return stream
def matrix(
M,
title='Matrix',
xtitle='',
ytitle='',
xlabels=(),
ylabels=(),
xrotation=0,
cmap='Reds',
vmin=None,
vmax=None,
precision=2,
font='Theemim',
scale=0,
scalarbar=True,
lc='white',
lw=0,
c='black',
alpha=1,
):
"""
Generate a matrix, or a 2D color-coded plot with bin labels.
Returns an ``Assembly`` object.
Parameters
----------
M : list or numpy array
the input array to visualize
title : str
title of the plot
xtitle : str
title of the horizontal colmuns
ytitle : str
title of the vertical rows
xlabels : list
individual string labels for each column. Must be of length m
ylabels : list
individual string labels for each row. Must be of length n
xrotation : float
rotation of the horizontal labels
cmap : str
color map name
vmin : float
minimum value of the colormap range
vmax : float
maximum value of the colormap range
precision : int
number of digits for the matrix entries or bins
font : str
font name
scale : float
size of the numeric entries or bin values
scalarbar : bool
add a scalar bar to the right of the plot
lc : str
color of the line separating the bins
lw : float
Width of the line separating the bins
c : str
text color
alpha : float
plot transparency
.. hint:: examples/pyplot/np_matrix.py
.. image:: https://vedo.embl.es/images/pyplot/np_matrix.png
"""
M = np.asarray(M)
n, m = M.shape
gr = shapes.Grid(res=(m, n), s=(m / (m + n) * 2, n / (m + n) * 2), c=c, alpha=alpha)
gr.wireframe(False).lc(lc).lw(lw)
matr = np.flip(np.flip(M), axis=1).ravel(order="C")
gr.cmap(cmap, matr, on="cells", vmin=vmin, vmax=vmax)
sbar = None
if scalarbar:
gr.addScalarBar3D(titleFont=font, labelFont=font)
sbar = gr.scalarbar
labs = None
if scale != 0:
labs = gr.labels(
cells=True,
scale=scale / max(m, n),
precision=precision,
font=font,
justify="center",
c=c,
)
labs.z(0.001)
t = None
if title:
if title == "Matrix":
title += " " + str(n) + "x" + str(m)
t = shapes.Text3D(title, font=font, s=0.04, justify="bottom-center", c=c)
t.shift(0, n / (m + n) * 1.05)
xlabs = None
if len(xlabels) == m:
xlabs = []
jus = "top-center"
if xrotation > 44:
jus = "right-center"
for i in range(m):
xl = shapes.Text3D(xlabels[i], font=font, s=0.02, justify=jus, c=c).rotateZ(
xrotation
)
xl.shift((2 * i - m + 1) / (m + n), -n / (m + n) * 1.05)
xlabs.append(xl)
ylabs = None
if len(ylabels) == n:
ylabels = list(reversed(ylabels))
ylabs = []
for i in range(n):
yl = shapes.Text3D(
ylabels[i], font=font, s=0.02, justify="right-center", c=c
)
yl.shift(-m / (m + n) * 1.05, (2 * i - n + 1) / (m + n))
ylabs.append(yl)
xt = None
if xtitle:
xt = shapes.Text3D(xtitle, font=font, s=0.035, justify="top-center", c=c)
xt.shift(0, -n / (m + n) * 1.05)
if xlabs is not None:
y0, y1 = xlabs[0].ybounds()
xt.shift(0, -(y1 - y0) - 0.55 / (m + n))
yt = None
if ytitle:
yt = shapes.Text3D(
ytitle, font=font, s=0.035, justify="bottom-center", c=c
).rotateZ(90)
yt.shift(-m / (m + n) * 1.05, 0)
if ylabs is not None:
x0, x1 = ylabs[0].xbounds()
yt.shift(-(x1 - x0) - 0.55 / (m + n), 0)
asse = Assembly(gr, sbar, labs, t, xt, yt, xlabs, ylabs)
asse.name = "Matrix"
return asse
def CornerPlot(points, pos=1, s=0.2, title="", c="b", bg="k", lines=True, dots=True):
"""
Return a ``vtkXYPlotActor`` that is a plot of `x` versus `y`,
where `points` is a list of `(x,y)` points.
Assign position following this convention:
- 1, topleft,
- 2, topright,
- 3, bottomleft,
- 4, bottomright.
"""
if len(points) == 2: # passing [allx, ally]
points = np.stack((points[0], points[1]), axis=1)
c = colors.getColor(c) # allow different codings
array_x = vtk.vtkFloatArray()
array_y = vtk.vtkFloatArray()
array_x.SetNumberOfTuples(len(points))
array_y.SetNumberOfTuples(len(points))
for i, p in enumerate(points):
array_x.InsertValue(i, p[0])
array_y.InsertValue(i, p[1])
field = vtk.vtkFieldData()
field.AddArray(array_x)
field.AddArray(array_y)
data = vtk.vtkDataObject()
data.SetFieldData(field)
xyplot = vtk.vtkXYPlotActor()
xyplot.AddDataObjectInput(data)
xyplot.SetDataObjectXComponent(0, 0)
xyplot.SetDataObjectYComponent(0, 1)
xyplot.SetXValuesToValue()
xyplot.SetAdjustXLabels(0)
xyplot.SetAdjustYLabels(0)
xyplot.SetNumberOfXLabels(3)
xyplot.GetProperty().SetPointSize(5)
xyplot.GetProperty().SetLineWidth(2)
xyplot.GetProperty().SetColor(colors.getColor(bg))
xyplot.SetPlotColor(0, c[0], c[1], c[2])
xyplot.SetXTitle(title)
xyplot.SetYTitle("")
xyplot.ExchangeAxesOff()
xyplot.SetPlotPoints(dots)
if not lines:
xyplot.PlotLinesOff()
if isinstance(pos, str):
spos = 2
if "top" in pos:
if "left" in pos:
spos = 1
elif "right" in pos:
spos = 2
elif "bottom" in pos:
if "left" in pos:
spos = 3
elif "right" in pos:
spos = 4
pos = spos
if pos == 1:
xyplot.GetPositionCoordinate().SetValue(0.0, 0.8, 0)
elif pos == 2:
xyplot.GetPositionCoordinate().SetValue(0.76, 0.8, 0)
elif pos == 3:
xyplot.GetPositionCoordinate().SetValue(0.0, 0.0, 0)
elif pos == 4:
xyplot.GetPositionCoordinate().SetValue(0.76, 0.0, 0)
else:
xyplot.GetPositionCoordinate().SetValue(pos[0], pos[1], 0)
xyplot.GetPosition2Coordinate().SetValue(s, s, 0)
return xyplot
def CornerHistogram(
values,
bins=20,
vrange=None,
minbin=0,
logscale=False,
title="",
c="g",
bg="k",
alpha=1,
pos="bottom-left",
s=0.175,
lines=True,
dots=False,
nmax=None,
):
"""
Build a histogram from a list of values in n bins.
The resulting object is a 2D actor.
Use ``vrange`` to restrict the range of the histogram.
Use ``nmax`` to limit the sampling to this max nr of entries
Use `pos` to assign its position:
- 1, topleft,
- 2, topright,
- 3, bottomleft,
- 4, bottomright,
- (x, y), as fraction of the rendering window
"""
if hasattr(values, "inputdata"):
values = utils.vtk2numpy(values.inputdata().GetPointData().GetScalars())
n = values.shape[0]
if nmax and nmax < n:
# subsample:
idxs = np.linspace(0, n, num=int(nmax), endpoint=False).astype(int)
values = values[idxs]
fs, edges = np.histogram(values, bins=bins, range=vrange)
if minbin:
fs = fs[minbin:-1]
if logscale:
fs = np.log10(fs + 1)
pts = []
for i in range(len(fs)):
pts.append([(edges[i] + edges[i + 1]) / 2, fs[i]])
cplot = CornerPlot(pts, pos, s, title, c, bg, lines, dots)
cplot.SetNumberOfYLabels(2)
cplot.SetNumberOfXLabels(3)
tprop = vtk.vtkTextProperty()
tprop.SetColor(colors.getColor(bg))
tprop.SetFontFamily(vtk.VTK_FONT_FILE)
tprop.SetFontFile(utils.getFontPath(vedo.settings.defaultFont))
tprop.SetOpacity(alpha)
cplot.SetAxisTitleTextProperty(tprop)
cplot.GetProperty().SetOpacity(alpha)
cplot.GetXAxisActor2D().SetLabelTextProperty(tprop)
cplot.GetXAxisActor2D().SetTitleTextProperty(tprop)
cplot.GetXAxisActor2D().SetFontFactor(0.55)
cplot.GetYAxisActor2D().SetLabelFactor(0.0)
cplot.GetYAxisActor2D().LabelVisibilityOff()
return cplot
class DirectedGraph(Assembly, vedo.base.BaseActor):
"""
A graph consists of a collection of nodes (without postional information)
and a collection of edges connecting pairs of nodes.
The task is to determine the node positions only based on their connections.
This class is derived from class ``Assembly``, and it assembles 4 Mesh objects
representing the graph, the node labels, edge labels and edge arrows.
Parameters
----------
c : color
Color of the Graph
n : int
number of the initial set of nodes
layout : int, str
layout in ['2d', 'fast2d', 'clustering2d', 'circular',
'circular3d', 'cone', 'force', 'tree']
Each of these layouts has diferent available options.
---------------------------------------------------------------
.. note:: Options for layouts '2d', 'fast2d' and 'clustering2d'
Parameters
----------
seed : int
seed of the random number generator used to jitter point positions
restDistance : float
manually set the resting distance
maxNumberOfIterations : int
the maximum number of iterations to be used
zrange : list
expand 2d graph along z axis.
---------------------------------------------------------------
.. note:: Options for layouts 'circular', and 'circular3d':
Parameters
----------
radius : float
set the radius of the circles
height : float
set the vertical (local z) distance between the circles
zrange : float
expand 2d graph along z axis
---------------------------------------------------------------
.. note:: Options for layout 'cone'
Parameters
----------
compactness : float
ratio between the average width of a cone in the tree,
and the height of the cone.
compression : bool
put children closer together, possibly allowing sub-trees to overlap.
This is useful if the tree is actually the spanning tree of a graph.
spacing : float
space between layers of the tree
---------------------------------------------------------------
.. note:: Options for layout 'force'
Parameters
----------
seed : int
seed the random number generator used to jitter point positions
bounds : list
set the region in space in which to place the final graph
maxNumberOfIterations : int
the maximum number of iterations to be used
threeDimensional : bool
allow optimization in the 3rd dimension too
randomInitialPoints : bool
use random positions within the graph bounds as initial points
.. hint:: examples/pyplot/lineage_graph.py, graph_network.py
.. image:: https://vedo.embl.es/images/pyplot/graph_network.png
"""
def __init__(self, **kargs):
vedo.base.BaseActor.__init__(self)
self.nodes = []
self.edges = []
self._nodeLabels = [] # holds strings
self._edgeLabels = []
self.edgeOrientations = []
self.edgeGlyphPosition = 0.6
self.zrange = 0.0
self.rotX = 0
self.rotY = 0
self.rotZ = 0
self.arrowScale = 0.15
self.nodeLabelScale = None
self.nodeLabelJustify = "bottom-left"
self.edgeLabelScale = None
self.mdg = vtk.vtkMutableDirectedGraph()
n = kargs.pop("n", 0)
for _ in range(n):
self.addNode()
self._c = kargs.pop("c", (0.3, 0.3, 0.3))
self.gl = vtk.vtkGraphLayout()
self.font = kargs.pop("font", "")
s = kargs.pop("layout", "2d")
if isinstance(s, int):
ss = [
"2d",
"fast2d",
"clustering2d",
"circular",
"circular3d",
"cone",
"force",
"tree",
]
s = ss[s]
self.layout = s
if "2d" in s:
if "clustering" in s:
self.strategy = vtk.vtkClustering2DLayoutStrategy()
elif "fast" in s:
self.strategy = vtk.vtkFast2DLayoutStrategy()
else:
self.strategy = vtk.vtkSimple2DLayoutStrategy()
self.rotX = 180
opt = kargs.pop("restDistance", None)
if opt is not None:
self.strategy.SetRestDistance(opt)
opt = kargs.pop("seed", None)
if opt is not None:
self.strategy.SetRandomSeed(opt)
opt = kargs.pop("maxNumberOfIterations", None)
if opt is not None:
self.strategy.SetMaxNumberOfIterations(opt)
self.zrange = kargs.pop("zrange", 0)
elif "circ" in s:
if "3d" in s:
self.strategy = vtk.vtkSimple3DCirclesStrategy()
self.strategy.SetDirection(0, 0, -1)
self.strategy.SetAutoHeight(True)
self.strategy.SetMethod(1)
self.rotX = -90
opt = kargs.pop("radius", None) # float
if opt is not None:
self.strategy.SetMethod(0)
self.strategy.SetRadius(opt) # float
opt = kargs.pop("height", None)
if opt is not None:
self.strategy.SetAutoHeight(False)
self.strategy.SetHeight(opt) # float
else:
self.strategy = vtk.vtkCircularLayoutStrategy()
self.zrange = kargs.pop("zrange", 0)
elif "cone" in s:
self.strategy = vtk.vtkConeLayoutStrategy()
self.rotX = 180
opt = kargs.pop("compactness", None)
if opt is not None:
self.strategy.SetCompactness(opt)
opt = kargs.pop("compression", None)
if opt is not None:
self.strategy.SetCompression(opt)
opt = kargs.pop("spacing", None)
if opt is not None:
self.strategy.SetSpacing(opt)
elif "force" in s:
self.strategy = vtk.vtkForceDirectedLayoutStrategy()
opt = kargs.pop("seed", None)
if opt is not None:
self.strategy.SetRandomSeed(opt)
opt = kargs.pop("bounds", None)
if opt is not None:
self.strategy.SetAutomaticBoundsComputation(False)
self.strategy.SetGraphBounds(opt) # list
opt = kargs.pop("maxNumberOfIterations", None)
if opt is not None:
self.strategy.SetMaxNumberOfIterations(opt) # int
opt = kargs.pop("threeDimensional", True)
if opt is not None:
self.strategy.SetThreeDimensionalLayout(opt) # bool
opt = kargs.pop("randomInitialPoints", None)
if opt is not None:
self.strategy.SetRandomInitialPoints(opt) # bool
elif "tree" in s:
self.strategy = vtk.vtkSpanTreeLayoutStrategy()
self.rotX = 180
else:
vedo.logger.error(f"Cannot understand layout {s}. Available layouts:")
vedo.logger.error(
"[2d,fast2d,clustering2d,circular,circular3d,cone,force,tree]"
)
raise RuntimeError()
self.gl.SetLayoutStrategy(self.strategy)
if len(kargs):
vedo.logger.error(f"Cannot understand options: {kargs}")
def addNode(self, label="id"):
"""Add a new node to the ``Graph``."""
v = self.mdg.AddVertex() # vtk calls it vertex..
self.nodes.append(v)
if label == "id":
label = int(v)
self._nodeLabels.append(str(label))
return v
def addEdge(self, v1, v2, label=""):
"""Add a new edge between to nodes.
An extra node is created automatically if needed."""
nv = len(self.nodes)
if v1 >= nv:
for _ in range(nv, v1 + 1):
self.addNode()
nv = len(self.nodes)
if v2 >= nv:
for _ in range(nv, v2 + 1):
self.addNode()
e = self.mdg.AddEdge(v1, v2)
self.edges.append(e)
self._edgeLabels.append(str(label))
return e
def addChild(self, v, nodeLabel="id", edgeLabel=""):
"""Add a new edge to a new node as its child.
The extra node is created automatically if needed."""
nv = len(self.nodes)
if v >= nv:
for _ in range(nv, v + 1):
self.addNode()
child = self.mdg.AddChild(v)
self.edges.append((v, child))
self.nodes.append(child)
if nodeLabel == "id":
nodeLabel = int(child)
self._nodeLabels.append(str(nodeLabel))
self._edgeLabels.append(str(edgeLabel))
return child
def build(self):
"""
Build the ``DirectedGraph(Assembly)``.
Accessory objects are also created for labels and arrows.
"""
self.gl.SetZRange(self.zrange)
self.gl.SetInputData(self.mdg)
self.gl.Update()
graphToPolyData = vtk.vtkGraphToPolyData()
graphToPolyData.EdgeGlyphOutputOn()
graphToPolyData.SetEdgeGlyphPosition(self.edgeGlyphPosition)
graphToPolyData.SetInputData(self.gl.GetOutput())
graphToPolyData.Update()
dgraph = Mesh(graphToPolyData.GetOutput(0))
# dgraph.clean() # WRONG!!! dont uncomment
dgraph.flat().color(self._c).lw(2)
dgraph.name = "DirectedGraph"
diagsz = self.diagonalSize() / 1.42
if not diagsz:
return None
dgraph.SetScale(1 / diagsz)
if self.rotX:
dgraph.rotateX(self.rotX)
if self.rotY:
dgraph.rotateY(self.rotY)
if self.rotZ:
dgraph.rotateZ(self.rotZ)
vecs = graphToPolyData.GetOutput(1).GetPointData().GetVectors()
self.edgeOrientations = utils.vtk2numpy(vecs)
# Use Glyph3D to repeat the glyph on all edges.
arrows = None
if self.arrowScale:
arrowSource = vtk.vtkGlyphSource2D()
arrowSource.SetGlyphTypeToEdgeArrow()
arrowSource.SetScale(self.arrowScale)
arrowSource.Update()
arrowGlyph = vtk.vtkGlyph3D()
arrowGlyph.SetInputData(0, graphToPolyData.GetOutput(1))
arrowGlyph.SetInputData(1, arrowSource.GetOutput())
arrowGlyph.Update()
arrows = Mesh(arrowGlyph.GetOutput())
arrows.SetScale(1 / diagsz)
arrows.lighting("off").color(self._c)
if self.rotX:
arrows.rotateX(self.rotX)
if self.rotY:
arrows.rotateY(self.rotY)
if self.rotZ:
arrows.rotateZ(self.rotZ)
arrows.name = "DirectedGraphArrows"
nodeLabels = dgraph.labels(
self._nodeLabels,
scale=self.nodeLabelScale,
precision=0,
font=self.font,
justify=self.nodeLabelJustify,
)
nodeLabels.color(self._c).pickable(True)
nodeLabels.name = "DirectedGraphNodeLabels"
edgeLabels = dgraph.labels(
self._edgeLabels,
cells=True,
scale=self.edgeLabelScale,
precision=0,
font=self.font,
)
edgeLabels.color(self._c).pickable(True)
edgeLabels.name = "DirectedGraphEdgeLabels"
Assembly.__init__(self, [dgraph, nodeLabels, edgeLabels, arrows])
self.name = "DirectedGraphAssembly"
return selfFunctions
def donut(fractions, title='', tsize=0.3, r1=1.7, r2=1, phigap=0, lpos=0.8, lsize=0.15, c=None, bc='k', alpha=1, labels=(), showDisc=False)-
Donut plot or pie chart.
Parameters
title:str- plot title
tsize:float- title size
r1:float inner radiusr2:float- outer radius, starting from r1
phigap:float- gap angle btw 2 radial bars, in degrees
lpos:float- label gap factor along radius
lsize:float- label size
c:color- color of the plot slices
bc:color- color of the disc frame
alpha:float- opacity of the disc frame
labels:list- list of labels
showDisc:bool- show the outer ring axis
Hist: examples/pyplot/donut.py
Expand source code
def donut( fractions, title="", tsize=0.3, r1=1.7, r2=1, phigap=0, lpos=0.8, lsize=0.15, c=None, bc="k", alpha=1, labels=(), showDisc=False, ): """ Donut plot or pie chart. Parameters ---------- title : str plot title tsize : float title size r1 : float inner radius r2 : float outer radius, starting from r1 phigap : float gap angle btw 2 radial bars, in degrees lpos : float label gap factor along radius lsize : float label size c : color color of the plot slices bc : color color of the disc frame alpha : float opacity of the disc frame labels : list list of labels showDisc : bool show the outer ring axis .. hist:: examples/pyplot/donut.py .. image:: https://vedo.embl.es/images/pyplot/donut.png """ fractions = np.array(fractions, dtype=float) angles = np.add.accumulate(2 * np.pi * fractions) angles[-1] = 2 * np.pi if angles[-2] > 2 * np.pi: print("Error in donut(): fractions must sum to 1.") raise RuntimeError cols = [] for i, th in enumerate(np.linspace(0, 2 * np.pi, 360, endpoint=False)): for ia, a in enumerate(angles): if th < a: cols.append(c[ia]) break labs = () if labels: angles = np.concatenate([[0], angles]) labs = [""] * 360 for i in range(len(labels)): a = (angles[i + 1] + angles[i]) / 2 j = int(a / np.pi * 180) labs[j] = labels[i] data = np.linspace(0, 2 * np.pi, 360, endpoint=False) + 0.005 dn = _histogramPolar( data, title=title, bins=360, r1=r1, r2=r2, phigap=phigap, lpos=lpos, lsize=lsize, tsize=tsize, c=cols, bc=bc, alpha=alpha, vmin=0, vmax=1, labels=labs, showDisc=showDisc, showLines=0, showAngles=0, showErrors=0, ) dn.name = "donut" return dn def fit(points, deg=1, niter=0, nstd=3, xerrors=None, yerrors=None, vrange=None, res=250, lw=3, c='red4')-
Polynomial fitting with parameter error and error bands calculation.
Returns a
Lineobject.Errors bars in both x and y are supported.
Additional information about the fitting output can be accessed with:
fit = fitPolynomial(pts)- fit.coefficients will contain the coefficients of the polynomial fit
- fit.coefficientErrors, errors on the fitting coefficients
- fit.MonteCarloCoefficients, fitting coefficient set from MC generation
- fit.covarianceMatrix, covariance matrix as a numpy array
- fit.reducedChi2, reduced chi-square of the fitting
- fit.ndof, number of degrees of freedom
-
fit.dataSigma, mean data dispersion from the central fit assuming Chi2=1
-
fit.errorLines, a
Lineobject for the upper and lower error band - fit.errorBand, the
Meshobject representing the error band
Errors on x and y can be specified. If left to
Nonean estimate is made from the statistical spread of the dataset itself. Errors are always assumed gaussian.Parameters
deg:int- degree of the polynomial to be fitted
niter:int- number of monte-carlo iterations to compute error bands. If set to 0, return the simple least-squares fit with naive error estimation on coefficients only. A reasonable non-zero value to set is about 500, in this case errorLines, errorBand and the other class attributes are filled
nstd:float- nr. of standard deviation to use for error calculation
xerrors:list- array of the same length of points with the errors on x
yerrors:list- array of the same length of points with the errors on y
vrange:list- specify the domain range of the fitting line (only affects visualization, but can be used to extrapolate the fit outside the data range)
res:int- resolution of the output fitted line and error lines
Hint: examples/pyplot/fitPolynomial1.py
Expand source code
def fit( points, deg=1, niter=0, nstd=3, xerrors=None, yerrors=None, vrange=None, res=250, lw=3, c='red4', ): """ Polynomial fitting with parameter error and error bands calculation. Returns a ``vedo.shapes.Line`` object. Errors bars in both x and y are supported. Additional information about the fitting output can be accessed with: ``fit = fitPolynomial(pts)`` - *fit.coefficients* will contain the coefficients of the polynomial fit - *fit.coefficientErrors*, errors on the fitting coefficients - *fit.MonteCarloCoefficients*, fitting coefficient set from MC generation - *fit.covarianceMatrix*, covariance matrix as a numpy array - *fit.reducedChi2*, reduced chi-square of the fitting - *fit.ndof*, number of degrees of freedom - *fit.dataSigma*, mean data dispersion from the central fit assuming Chi2=1 - *fit.errorLines*, a ``vedo.shapes.Line`` object for the upper and lower error band - *fit.errorBand*, the ``vedo.mesh.Mesh`` object representing the error band Errors on x and y can be specified. If left to `None` an estimate is made from the statistical spread of the dataset itself. Errors are always assumed gaussian. Parameters ---------- deg : int degree of the polynomial to be fitted niter : int number of monte-carlo iterations to compute error bands. If set to 0, return the simple least-squares fit with naive error estimation on coefficients only. A reasonable non-zero value to set is about 500, in this case *errorLines*, *errorBand* and the other class attributes are filled nstd : float nr. of standard deviation to use for error calculation xerrors : list array of the same length of points with the errors on x yerrors : list array of the same length of points with the errors on y vrange : list specify the domain range of the fitting line (only affects visualization, but can be used to extrapolate the fit outside the data range) res : int resolution of the output fitted line and error lines .. hint:: examples/pyplot/fitPolynomial1.py .. image:: https://vedo.embl.es/images/pyplot/fitPolynomial1.png """ if isinstance(points, vedo.pointcloud.Points): points = points.points() points = np.asarray(points) if len(points) == 2: # assume user is passing [x,y] points = np.c_[points[0], points[1]] x = points[:, 0] y = points[:, 1] # ignore z n = len(x) ndof = n - deg - 1 if vrange is not None: x0, x1 = vrange else: x0, x1 = np.min(x), np.max(x) if xerrors is not None: x0 -= xerrors[0] / 2 x1 += xerrors[-1] / 2 tol = (x1 - x0) / 10000 xr = np.linspace(x0, x1, res) # project x errs on y if xerrors is not None: xerrors = np.asarray(xerrors) if yerrors is not None: yerrors = np.asarray(yerrors) w = 1.0 / yerrors coeffs = np.polyfit(x, y, deg, w=w, rcond=None) else: coeffs = np.polyfit(x, y, deg, rcond=None) # update yerrors, 1 bootstrap iteration is enough p1d = np.poly1d(coeffs) der = (p1d(x + tol) - p1d(x)) / tol yerrors = np.sqrt(yerrors * yerrors + np.power(der * xerrors, 2)) if yerrors is not None: yerrors = np.asarray(yerrors) w = 1.0 / yerrors coeffs, V = np.polyfit(x, y, deg, w=w, rcond=None, cov=True) else: w = 1 coeffs, V = np.polyfit(x, y, deg, rcond=None, cov=True) p1d = np.poly1d(coeffs) theor = p1d(xr) fitl = shapes.Line(xr, theor, lw=lw, c=c).z(tol * 2) fitl.coefficients = coeffs fitl.covarianceMatrix = V residuals2_sum = np.sum(np.power(p1d(x) - y, 2)) / ndof sigma = np.sqrt(residuals2_sum) fitl.reducedChi2 = np.sum(np.power((p1d(x) - y) * w, 2)) / ndof fitl.ndof = ndof fitl.dataSigma = sigma # worked out from data using chi2=1 hypo fitl.name = "LinePolynomialFit" if not niter: fitl.coefficientErrors = np.sqrt(np.diag(V)) return fitl ################################ if yerrors is not None: sigma = yerrors else: w = None fitl.reducedChi2 = 1 Theors, all_coeffs = [], [] for i in range(niter): noise = np.random.randn(n) * sigma coeffs = np.polyfit(x, y + noise, deg, w=w, rcond=None) all_coeffs.append(coeffs) P1d = np.poly1d(coeffs) Theor = P1d(xr) Theors.append(Theor) all_coeffs = np.array(all_coeffs) fitl.MonteCarloCoefficients = all_coeffs stds = np.std(Theors, axis=0) fitl.coefficientErrors = np.std(all_coeffs, axis=0) # check distributions on the fly # for i in range(deg+1): # histogram(all_coeffs[:,i],title='par'+str(i)).show(new=1) # histogram(all_coeffs[:,0], all_coeffs[:,1], # xtitle='param0', ytitle='param1',scalarbar=1).show(new=1) # histogram(all_coeffs[:,1], all_coeffs[:,2], # xtitle='param1', ytitle='param2').show(new=1) # histogram(all_coeffs[:,0], all_coeffs[:,2], # xtitle='param0', ytitle='param2').show(new=1) error_lines = [] for i in [nstd, -nstd]: el = shapes.Line(xr, theor + stds * i, lw=1, alpha=0.2, c="k").z(tol) error_lines.append(el) el.name = "ErrorLine for sigma=" + str(i) fitl.errorLines = error_lines l1 = error_lines[0].points().tolist() cband = l1 + list(reversed(error_lines[1].points().tolist())) + [l1[0]] fitl.errorBand = shapes.Line(cband).triangulate().lw(0).c("k", 0.15) fitl.errorBand.name = "PolynomialFitErrorBand" return fitl def histogram(*args, **kwargs)-
Histogramming for 1D and 2D data arrays.
This is meant as a convenience function that creates the appropriate object based on the shape of the provided input data.
Use keyword
like=...if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message.
Note: default mode, for 1D arrays
Creates a
Histogram1D(Figure)object.Parameters
weights:list- An array of weights, of the same shape as
data. Each value indataonly contributes its associated weight towards the bin count (instead of 1). bins:int- number of bins
vrange:list- restrict the range of the histogram
density:bool- normalize the area to 1 by dividing by the nr of entries and bin size
logscale:bool- use logscale on y-axis
fill:bool- fill bars woth solid color
c gap:float- leave a small space btw bars
radius:float- border radius of the top of the histogram bar. Default value is 0.1.
texture:str- url or path to an image to be used as texture for the bin
outline:bool- show outline of the bins
errors:bool- show error bars
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
aspect:float- the desired aspect ratio of the histogram. Default is 4/3.
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True) ztolerance:float- a tolerance factor to superimpose objects (along the z-axis).
Hint: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
Note: default mode, for 2D arrays
Input data formats
[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]are both valid.Parameters
bins:list- binning as (nx, ny)
weights:list- array of weights to assign to each entry
cmap:str, lookuptable- color map name or look up table
alpha:float- opacity of the histogram
gap:float- separation between adjacent bins as a fraction for their size
scalarbar:bool- add a scalarbar to right of the histogram
like:Figure- grab and use the same format of the given Figure (for superimposing)
xlim:list- [x0, x1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored.
ylim:list- [y0, y1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored.
aspect:float- the desired aspect ratio of the figure.
title:str- title of the plot to appear on top. If left blank some statistics will be shown.
xtitle:str- x axis title
ytitle:str- y axis title
ztitle:str- title for the scalar bar
ac:str- axes color, additional keyword for Axes can also be added
using e.g.
axes=dict(xyGrid=True)
Hint: examples/pyplot/histo_2d.py
Note: mode="hexbin"
If
mode='hexbin', build a hexagonal histogram from a list of x and y values.Parameters
xtitle:str- x axis title
bins:int- nr of bins for the smaller range in x or y
vrange:list- range in x and y in format
[(xmin,xmax), (ymin,ymax)] norm:float- sets a scaling factor for the z axis (frequency axis)
fill:bool- draw solid hexagons
cmap:str- color map name for elevation
Hint: examples/pyplot/histo_hexagonal.py
Note: mode="polar"
If
mode='polar'assume input is polar coordinate system (rho, theta):Parameters
weights:list- Array of weights, of the same shape as the input. Each value only contributes its associated weight towards the bin count (instead of 1).
title:str- histogram title
tsize:float- title size
bins:int- number of bins in phi
r1:float- inner radius
r2:float- outer radius
phigap:float- gap angle btw 2 radial bars, in degrees
rgap:float- gap factor along radius of numeric angle labels
lpos:float- label gap factor along radius
lsize:float- label size
c:color- color of the histogram bars, can be a list of length
bins bc:color- color of the frame and labels
alpha:float- opacity of the frame
cmap:str- color map name
deg:bool- input array is in degrees
vmin:float- minimum value of the radial axis
vmax:float- maximum value of the radial axis
labels:list- list of labels, must be of length
bins showDisc:bool- show the outer ring axis
nrays:int- draw this number of axis rays (continuous and dashed)
showLines:bool- show lines to the origin
showAngles:bool- show angular values
showErrors:bool- show error bars
Hint: examples/pyplot/histo_polar.py
Note: mode="spheric"
If
mode='spheric', build a histogram from list of theta and phi values.Parameters
rmax:float- maximum radial elevation of bin
res:int- sphere resolution
cmap:str- color map name
lw:int- line width of the bin edges
scalarbar:bool- add a scalarbar to plot
Hint: examples/pyplot/histo_spheric.py
Expand source code
def histogram(*args, **kwargs): """ Histogramming for 1D and 2D data arrays. This is meant as a convenience function that creates the appropriate object based on the shape of the provided input data. Use keyword `like=...` if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message. ------------------------------------------------------------------------- .. note:: default mode, for 1D arrays Creates a `Histogram1D(Figure)` object. Parameters ---------- weights : list An array of weights, of the same shape as `data`. Each value in `data` only contributes its associated weight towards the bin count (instead of 1). bins : int number of bins vrange : list restrict the range of the histogram density : bool normalize the area to 1 by dividing by the nr of entries and bin size logscale : bool use logscale on y-axis fill : bool fill bars woth solid color `c` gap : float leave a small space btw bars radius : float border radius of the top of the histogram bar. Default value is 0.1. texture : str url or path to an image to be used as texture for the bin outline : bool show outline of the bins errors : bool show error bars xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. aspect : float the desired aspect ratio of the histogram. Default is 4/3. grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` ztolerance : float a tolerance factor to superimpose objects (along the z-axis). .. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py .. image:: https://vedo.embl.es/images/pyplot/histo_1D.png ------------------------------------------------------------------------- .. note:: default mode, for 2D arrays Input data formats `[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]` are both valid. Parameters ---------- bins : list binning as (nx, ny) weights : list array of weights to assign to each entry cmap : str, lookuptable color map name or look up table alpha : float opacity of the histogram gap : float separation between adjacent bins as a fraction for their size scalarbar : bool add a scalarbar to right of the histogram like : Figure grab and use the same format of the given Figure (for superimposing) xlim : list [x0, x1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored. ylim : list [y0, y1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored. aspect : float the desired aspect ratio of the figure. title : str title of the plot to appear on top. If left blank some statistics will be shown. xtitle : str x axis title ytitle : str y axis title ztitle : str title for the scalar bar ac : str axes color, additional keyword for Axes can also be added using e.g. `axes=dict(xyGrid=True)` .. hint:: examples/pyplot/histo_2d.py .. image:: https://vedo.embl.es/images/pyplot/histo_2D.png ------------------------------------------------------------------------- .. note:: mode="hexbin" If ``mode='hexbin'``, build a hexagonal histogram from a list of x and y values. Parameters ---------- xtitle : str x axis title bins : int nr of bins for the smaller range in x or y vrange : list range in x and y in format `[(xmin,xmax), (ymin,ymax)]` norm : float sets a scaling factor for the z axis (frequency axis) fill : bool draw solid hexagons cmap : str color map name for elevation .. hint:: examples/pyplot/histo_hexagonal.py .. image:: https://vedo.embl.es/images/pyplot/histo_hexagonal.png ------------------------------------------------------------------------- .. note:: mode="polar" If ``mode='polar'`` assume input is polar coordinate system (rho, theta): Parameters ---------- weights : list Array of weights, of the same shape as the input. Each value only contributes its associated weight towards the bin count (instead of 1). title : str histogram title tsize : float title size bins : int number of bins in phi r1 : float inner radius r2 : float outer radius phigap : float gap angle btw 2 radial bars, in degrees rgap : float gap factor along radius of numeric angle labels lpos : float label gap factor along radius lsize : float label size c : color color of the histogram bars, can be a list of length `bins` bc : color color of the frame and labels alpha : float opacity of the frame cmap : str color map name deg : bool input array is in degrees vmin : float minimum value of the radial axis vmax : float maximum value of the radial axis labels : list list of labels, must be of length `bins` showDisc : bool show the outer ring axis nrays : int draw this number of axis rays (continuous and dashed) showLines : bool show lines to the origin showAngles : bool show angular values showErrors : bool show error bars .. hint:: examples/pyplot/histo_polar.py .. image:: https://vedo.embl.es/images/pyplot/histo_polar.png ------------------------------------------------------------------------- .. note:: mode="spheric" If ``mode='spheric'``, build a histogram from list of theta and phi values. Parameters ---------- rmax : float maximum radial elevation of bin res : int sphere resolution cmap : str color map name lw : int line width of the bin edges scalarbar : bool add a scalarbar to plot .. hint:: examples/pyplot/histo_spheric.py .. image:: https://vedo.embl.es/images/pyplot/histo_spheric.png """ mode = kwargs.pop("mode", "") if len(args) == 2: # x, y if "spher" in mode: return _histogramSpheric(args[0], args[1], **kwargs) if "hex" in mode: return _histogramHexBin(args[0], args[1], **kwargs) return Histogram2D(args[0], args[1], **kwargs) elif len(args) == 1: if isinstance(args[0], vedo.Volume): data = args[0].pointdata[0] elif isinstance(args[0], vedo.Points): pd0 = args[0].pointdata[0] if pd0: data = pd0.ravel() else: data = args[0].celldata[0].ravel() else: data = np.array(args[0]) if "spher" in mode: return _histogramSpheric(args[0][:, 0], args[0][:, 1], **kwargs) if len(data.shape) == 1: if "polar" in mode: return _histogramPolar(data, **kwargs) return Histogram1D(data, **kwargs) else: if "hex" in mode: return _histogramHexBin(args[0][:, 0], args[0][:, 1], **kwargs) return Histogram2D(args[0], **kwargs) print("histogram(): Could not understand input", args[0]) return None def matrix(M, title='Matrix', xtitle='', ytitle='', xlabels=(), ylabels=(), xrotation=0, cmap='Reds', vmin=None, vmax=None, precision=2, font='Theemim', scale=0, scalarbar=True, lc='white', lw=0, c='black', alpha=1)-
Generate a matrix, or a 2D color-coded plot with bin labels.
Returns an
Assemblyobject.Parameters
M:listornumpy array- the input array to visualize
title:str- title of the plot
xtitle:str- title of the horizontal colmuns
ytitle:str- title of the vertical rows
xlabels:list- individual string labels for each column. Must be of length m
ylabels:list- individual string labels for each row. Must be of length n
xrotation:float- rotation of the horizontal labels
cmap:str- color map name
vmin:float- minimum value of the colormap range
vmax:float- maximum value of the colormap range
precision:int- number of digits for the matrix entries or bins
font:str- font name
scale:float- size of the numeric entries or bin values
scalarbar:bool- add a scalar bar to the right of the plot
lc:str- color of the line separating the bins
lw:float- Width of the line separating the bins
c:str- text color
alpha:float- plot transparency
Hint: examples/pyplot/np_matrix.py
Expand source code
def matrix( M, title='Matrix', xtitle='', ytitle='', xlabels=(), ylabels=(), xrotation=0, cmap='Reds', vmin=None, vmax=None, precision=2, font='Theemim', scale=0, scalarbar=True, lc='white', lw=0, c='black', alpha=1, ): """ Generate a matrix, or a 2D color-coded plot with bin labels. Returns an ``Assembly`` object. Parameters ---------- M : list or numpy array the input array to visualize title : str title of the plot xtitle : str title of the horizontal colmuns ytitle : str title of the vertical rows xlabels : list individual string labels for each column. Must be of length m ylabels : list individual string labels for each row. Must be of length n xrotation : float rotation of the horizontal labels cmap : str color map name vmin : float minimum value of the colormap range vmax : float maximum value of the colormap range precision : int number of digits for the matrix entries or bins font : str font name scale : float size of the numeric entries or bin values scalarbar : bool add a scalar bar to the right of the plot lc : str color of the line separating the bins lw : float Width of the line separating the bins c : str text color alpha : float plot transparency .. hint:: examples/pyplot/np_matrix.py .. image:: https://vedo.embl.es/images/pyplot/np_matrix.png """ M = np.asarray(M) n, m = M.shape gr = shapes.Grid(res=(m, n), s=(m / (m + n) * 2, n / (m + n) * 2), c=c, alpha=alpha) gr.wireframe(False).lc(lc).lw(lw) matr = np.flip(np.flip(M), axis=1).ravel(order="C") gr.cmap(cmap, matr, on="cells", vmin=vmin, vmax=vmax) sbar = None if scalarbar: gr.addScalarBar3D(titleFont=font, labelFont=font) sbar = gr.scalarbar labs = None if scale != 0: labs = gr.labels( cells=True, scale=scale / max(m, n), precision=precision, font=font, justify="center", c=c, ) labs.z(0.001) t = None if title: if title == "Matrix": title += " " + str(n) + "x" + str(m) t = shapes.Text3D(title, font=font, s=0.04, justify="bottom-center", c=c) t.shift(0, n / (m + n) * 1.05) xlabs = None if len(xlabels) == m: xlabs = [] jus = "top-center" if xrotation > 44: jus = "right-center" for i in range(m): xl = shapes.Text3D(xlabels[i], font=font, s=0.02, justify=jus, c=c).rotateZ( xrotation ) xl.shift((2 * i - m + 1) / (m + n), -n / (m + n) * 1.05) xlabs.append(xl) ylabs = None if len(ylabels) == n: ylabels = list(reversed(ylabels)) ylabs = [] for i in range(n): yl = shapes.Text3D( ylabels[i], font=font, s=0.02, justify="right-center", c=c ) yl.shift(-m / (m + n) * 1.05, (2 * i - n + 1) / (m + n)) ylabs.append(yl) xt = None if xtitle: xt = shapes.Text3D(xtitle, font=font, s=0.035, justify="top-center", c=c) xt.shift(0, -n / (m + n) * 1.05) if xlabs is not None: y0, y1 = xlabs[0].ybounds() xt.shift(0, -(y1 - y0) - 0.55 / (m + n)) yt = None if ytitle: yt = shapes.Text3D( ytitle, font=font, s=0.035, justify="bottom-center", c=c ).rotateZ(90) yt.shift(-m / (m + n) * 1.05, 0) if ylabs is not None: x0, x1 = ylabs[0].xbounds() yt.shift(-(x1 - x0) - 0.55 / (m + n), 0) asse = Assembly(gr, sbar, labs, t, xt, yt, xlabs, ylabs) asse.name = "Matrix" return asse def plot(*args, **kwargs)-
Draw a 2D line plot, or scatter plot, of variable x vs variable y. Input format can be either
[allx], [allx, ally] or [(x1,y1), (x2,y2), …]Use
like=...if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message.Parameters
xerrors:bool- show error bars associated to each point in x
yerrors:bool- show error bars associated to each point in y
lw:int- width of the line connecting points in pixel units. Set it to 0 to remove the line.
lc:str- line color
la:float- line "alpha", opacity of the line
dashed:bool- draw a dashed line instead of a continous line
splined:bool- spline the line joining the point as a countinous curve
elw:int- width of error bar lines in units of pixels
ec:color- color of error bar, by default the same as marker color
errorBand:bool- represent errors on y as a filled error band.
Use
eckeyword to modify its color. marker:str, int- use a marker for the data points
ms:float- marker size
mc:color- color of the marker
ma:float- opacity of the marker
xlim:list- set limits to the range for the x variable
ylim:list- set limits to the range for the y variable
aspect:float- Desired aspect ratio. If None, it is automatically calculated to get a reasonable aspect ratio. Scaling factor is saved in Figure.yscale
padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
title:str- title to appear on the top of the frame, like a header.
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") ac:str- axes color
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True) ztolerance:float- a tolerance factor to superimpose objects (along the z-axis).
Example
.. code-block:: python
from vedo.pyplot import plot import numpy as np x = np.linspace(0, 6.28, num=50) plot(np.sin(x), 'r').plot(np.cos(x), 'bo-').show()
Hint
examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py
Note: mode="bar"
Creates a
PlotBars(Figure)object.Input must be in format
[counts, labels, colors, edges]. Either or bothedgesandcolorsare optional and can be omitted.Parameters
errors:bool- show error bars
logscale:bool- use logscale on y-axis
fill:bool- fill bars woth solid color
c gap:float- leave a small space btw bars
radius:float- border radius of the top of the histogram bar. Default value is 0.1.
texture:str- url or path to an image to be used as texture for the bin
outline:bool- show outline of the bins
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") ac:str- axes color
padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
aspect:float- the desired aspect ratio of the figure. Default is 4/3.
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True)
Hint: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
Note: 2D functions
If input is an external function or a formula, draw the surface representing the function
f(x,y).Parameters
x:float- x range of values
y:float- y range of values
zlimits:float- limit the z range of the independent variable
zlevels:int- will draw the specified number of z-levels contour lines
showNan:bool- show where the function does not exist as red points
bins:list- number of bins in x and y
Hint: plot_fxy.py
Note: mode="complex"
If
mode='complex'draw the real value of the function and color map the imaginary part.Parameters
cmap:str- diverging color map (white means imag(z)=0)
lw:float- line with of the binning
bins:list- binning in x and y
Hint: examples/pyplot/plot_fxy.py
Note: mode="polar"
If
mode='polar'input arrays are interpreted as a list of polar angles and radii. Build a polar (radar) plot by joining the set of points in polar coordinates.Parameters
title:str- plot title
tsize:float- title size
bins:int- number of bins in phi
r1:float- inner radius
r2:float- outer radius
lsize:float- label size
c:color- color of the line
ac:color- color of the frame and labels
alpha:float- opacity of the frame
ps:int- point size in pixels, if ps=0 no point is drawn
lw:int- line width in pixels, if lw=0 no line is drawn
deg:bool- input array is in degrees
vmax:float- normalize radius to this maximum value
fill:bool- fill convex area with solid color
splined:bool- interpolate the set of input points
showDisc:bool- draw the outer ring axis
nrays:int- draw this number of axis rays (continuous and dashed)
showLines:bool- draw lines to the origin
showAngles:bool- draw angle values
Hint: examples/pyplot/histo_polar.py
Note: mode="spheric"
If
mode='spheric'input must be an external function rho(theta, phi). A surface is created in spherical coordinates.Return an
Figure(Assembly)of 2 objects: the unit sphere (in wireframe representation) and the surfacerho(theta, phi).Parameters
rfunc:function- handle to a user defined function
rho(theta, phi). normalize:bool- scale surface to fit inside the unit sphere
res:int- grid resolution of the unit sphere
scalarbar:bool- add a 3D scalarbar to the plot for radius
c:color- color of the unit sphere
alpha:float- opacity of the unit sphere
cmap:str- color map for the surface
Hint: examples/pyplot/plot_spheric.py
Expand source code
def plot(*args, **kwargs): """ Draw a 2D line plot, or scatter plot, of variable x vs variable y. Input format can be either `[allx], [allx, ally] or [(x1,y1), (x2,y2), ...]` Use `like=...` if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message. Parameters ---------- xerrors : bool show error bars associated to each point in x yerrors : bool show error bars associated to each point in y lw : int width of the line connecting points in pixel units. Set it to 0 to remove the line. lc : str line color la : float line "alpha", opacity of the line dashed : bool draw a dashed line instead of a continous line splined : bool spline the line joining the point as a countinous curve elw : int width of error bar lines in units of pixels ec : color color of error bar, by default the same as marker color errorBand : bool represent errors on y as a filled error band. Use ``ec`` keyword to modify its color. marker : str, int use a marker for the data points ms : float marker size mc : color color of the marker ma : float opacity of the marker xlim : list set limits to the range for the x variable ylim : list set limits to the range for the y variable aspect : float Desired aspect ratio. If None, it is automatically calculated to get a reasonable aspect ratio. Scaling factor is saved in Figure.yscale padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. title : str title to appear on the top of the frame, like a header. xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` ac : str axes color grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` ztolerance : float a tolerance factor to superimpose objects (along the z-axis). Example: .. code-block:: python from vedo.pyplot import plot import numpy as np x = np.linspace(0, 6.28, num=50) plot(np.sin(x), 'r').plot(np.cos(x), 'bo-').show() .. image:: https://user-images.githubusercontent.com/32848391/74363882-c3638300-4dcb-11ea-8a78-eb492ad9711f.png .. hint:: examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py .. image:: https://vedo.embl.es/images/pyplot/plot_pip.png ------------------------------------------------------------------------- .. note:: mode="bar" Creates a `PlotBars(Figure)` object. Input must be in format `[counts, labels, colors, edges]`. Either or both `edges` and `colors` are optional and can be omitted. Parameters ---------- errors : bool show error bars logscale : bool use logscale on y-axis fill : bool fill bars woth solid color `c` gap : float leave a small space btw bars radius : float border radius of the top of the histogram bar. Default value is 0.1. texture : str url or path to an image to be used as texture for the bin outline : bool show outline of the bins xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` ac : str axes color padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. aspect : float the desired aspect ratio of the figure. Default is 4/3. grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` .. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py .. image:: https://vedo.embl.es/images/pyplot/histo_1D.png ---------------------------------------------------------------------- .. note:: 2D functions If input is an external function or a formula, draw the surface representing the function `f(x,y)`. Parameters ---------- x : float x range of values y : float y range of values zlimits : float limit the z range of the independent variable zlevels : int will draw the specified number of z-levels contour lines showNan : bool show where the function does not exist as red points bins : list number of bins in x and y .. hint:: plot_fxy.py .. image:: https://vedo.embl.es/images/pyplot/plot_fxy.png -------------------------------------------------------------------- .. note:: mode="complex" If ``mode='complex'`` draw the real value of the function and color map the imaginary part. Parameters ---------- cmap : str diverging color map (white means imag(z)=0) lw : float line with of the binning bins : list binning in x and y .. hint:: examples/pyplot/plot_fxy.py ..image:: https://user-images.githubusercontent.com/32848391/73392962-1709a300-42db-11ea-9278-30c9d6e5eeaa.png -------------------------------------------------------------------- .. note:: mode="polar" If ``mode='polar'`` input arrays are interpreted as a list of polar angles and radii. Build a polar (radar) plot by joining the set of points in polar coordinates. Parameters ---------- title : str plot title tsize : float title size bins : int number of bins in phi r1 : float inner radius r2 : float outer radius lsize : float label size c : color color of the line ac : color color of the frame and labels alpha : float opacity of the frame ps : int point size in pixels, if ps=0 no point is drawn lw : int line width in pixels, if lw=0 no line is drawn deg : bool input array is in degrees vmax : float normalize radius to this maximum value fill : bool fill convex area with solid color splined : bool interpolate the set of input points showDisc : bool draw the outer ring axis nrays : int draw this number of axis rays (continuous and dashed) showLines : bool draw lines to the origin showAngles : bool draw angle values .. hint:: examples/pyplot/histo_polar.py .. image:: https://user-images.githubusercontent.com/32848391/64992590-7fc82400-d8d4-11e9-9c10-795f4756a73f.png -------------------------------------------------------------------- .. note:: mode="spheric" If ``mode='spheric'`` input must be an external function rho(theta, phi). A surface is created in spherical coordinates. Return an ``Figure(Assembly)`` of 2 objects: the unit sphere (in wireframe representation) and the surface `rho(theta, phi)`. Parameters ---------- rfunc : function handle to a user defined function `rho(theta, phi)`. normalize : bool scale surface to fit inside the unit sphere res : int grid resolution of the unit sphere scalarbar : bool add a 3D scalarbar to the plot for radius c : color color of the unit sphere alpha : float opacity of the unit sphere cmap : str color map for the surface .. hint:: examples/pyplot/plot_spheric.py .. image:: https://vedo.embl.es/images/pyplot/plot_spheric.png """ mode = kwargs.pop("mode", "") if "spher" in mode: return _plotSpheric(args[0], **kwargs) if "bar" in mode: return PlotBars(args[0], **kwargs) if isinstance(args[0], str) or "function" in str(type(args[0])): if "complex" in mode: return _plotFz(args[0], **kwargs) return _plotFxy(args[0], **kwargs) # grab the matplotlib-like options optidx = None for i, a in enumerate(args): if i > 0 and isinstance(a, str): optidx = i break if optidx: opts = args[optidx].replace(" ", "") if "--" in opts: opts = opts.replace("--", "") kwargs["dashed"] = True elif "-" in opts: opts = opts.replace("-", "") else: kwargs["lw"] = 0 symbs = ['.','o','O', '0', 'p','*','h','D','d','v','^','>','<','s', 'x', 'a'] allcols = list(colors.colors.keys()) + list(colors.color_nicks.keys()) for cc in allcols: if cc == "o": continue if cc in opts: opts = opts.replace(cc, "") kwargs["lc"] = cc kwargs["mc"] = cc break for ss in symbs: if ss in opts: opts = opts.replace(ss, "", 1) kwargs["marker"] = ss break opts.replace(" ", "") if opts: vedo.logger.error(f"in plot(), could not understand option(s): {opts}") if optidx == 1 or optidx is None: if utils.isSequence(args[0][0]): # print('case 1', 'plot([(x,y),..])') data = np.array(args[0]) x = np.array(data[:, 0]) y = np.array(data[:, 1]) elif len(args) == 1 or optidx == 1: # print('case 2', 'plot(x)') x = np.linspace(0, len(args[0]), num=len(args[0])) y = np.array(args[0]) elif utils.isSequence(args[1]): # print('case 3', 'plot(allx,ally)') x = np.array(args[0]) y = np.array(args[1]) elif utils.isSequence(args[0]) and utils.isSequence(args[0][0]): # print('case 4', 'plot([allx,ally])') x = np.array(args[0][0]) y = np.array(args[0][1]) elif optidx == 2: # print('case 5', 'plot(x,y)') x = np.array(args[0]) y = np.array(args[1]) else: vedo.logger.error(f"plot(): Could not understand input arguments {args}") return None if "polar" in mode: return _plotPolar(np.c_[x, y], **kwargs) return PlotXY(np.c_[x, y], **kwargs) def streamplot(X, Y, U, V, direction='both', maxPropagation=None, mode=1, lw=0.001, c=None, probes=())-
Generate a streamline plot of a vectorial field (U,V) defined at positions (X,Y). Returns a
Meshobject.Parameters
direction:str- either "forward", "backward" or "both"
maxPropagation:float- maximum physical length of the streamline
lw:float- line width in absolute units
mode:int-
mode of varying the line width
- 0 - do not vary line width
- 1 - vary line width by first vector component
- 2 - vary line width vector magnitude
- 3 - vary line width by absolute value of first vector component
Hint: examples/pyplot/plot_stream.py
Expand source code
def streamplot( X, Y, U, V, direction="both", maxPropagation=None, mode=1, lw=0.001, c=None, probes=(), ): """ Generate a streamline plot of a vectorial field (U,V) defined at positions (X,Y). Returns a ``Mesh`` object. Parameters ---------- direction : str either "forward", "backward" or "both" maxPropagation : float maximum physical length of the streamline lw : float line width in absolute units mode : int mode of varying the line width - 0 - do not vary line width - 1 - vary line width by first vector component - 2 - vary line width vector magnitude - 3 - vary line width by absolute value of first vector component .. hint:: examples/pyplot/plot_stream.py .. image:: https://vedo.embl.es/images/pyplot/plot_stream.png """ n = len(X) m = len(Y[0]) if n != m: print("Limitation in streamplot(): only square grids are allowed.", n, m) raise RuntimeError() xmin, xmax = X[0][0], X[-1][-1] ymin, ymax = Y[0][0], Y[-1][-1] field = np.sqrt(U * U + V * V) vol = vedo.Volume(field, dims=(n, n, 1)) uf = np.ravel(U, order="F") vf = np.ravel(V, order="F") vects = np.c_[uf, vf, np.zeros_like(uf)] vol.addPointArray(vects, "vects") if len(probes) == 0: probe = shapes.Grid(pos=((n-1)/2,(n-1)/2,0), s=(n-1, n-1), res=(n-1,n-1)) else: if isinstance(probes, vedo.Points): probes = probes.points() else: probes = np.array(probes, dtype=float) if len(probes[0]) == 2: probes = np.c_[probes[:, 0], probes[:, 1], np.zeros(len(probes))] sv = [(n - 1) / (xmax - xmin), (n - 1) / (ymax - ymin), 1] probes = probes - [xmin, ymin, 0] probes = np.multiply(probes, sv) probe = vedo.Points(probes) stream = vedo.shapes.StreamLines( vol, probe, tubes={"radius": lw, "mode": mode,}, lw=lw, maxPropagation=maxPropagation, direction=direction, ) if c is not None: stream.color(c) else: stream.addScalarBar() stream.lighting("off") stream.scale([1 / (n - 1) * (xmax - xmin), 1 / (n - 1) * (ymax - ymin), 1]) stream.shift(xmin, ymin) return stream def violin(values, bins=10, vlim=None, x=0, width=3, splined=True, fill=True, c='violet', alpha=1, outline=True, centerline=True, lc='darkorchid', lw=3)-
Violin style histogram.
Parameters
bins:int- number of bins
vlim:list- input value limits. Crop values outside range
x:float- x-position of the violin axis
width:float- width factor of the normalized distribution
splined:bool- spline the outline
fill:bool- fill violin with solid color
outline:bool- add the distribution outline
centerline:bool- add the vertical centerline at x
lc:color- line color
Hint: examples/pyplot/histo_violin.py
Expand source code
def violin( values, bins=10, vlim=None, x=0, width=3, splined=True, fill=True, c="violet", alpha=1, outline=True, centerline=True, lc="darkorchid", lw=3, ): """ Violin style histogram. Parameters ---------- bins : int number of bins vlim : list input value limits. Crop values outside range x : float x-position of the violin axis width : float width factor of the normalized distribution splined : bool spline the outline fill : bool fill violin with solid color outline : bool add the distribution outline centerline : bool add the vertical centerline at x lc : color line color .. hint:: examples/pyplot/histo_violin.py .. image:: https://vedo.embl.es/images/pyplot/histo_violin.png """ fs, edges = np.histogram(values, bins=bins, range=vlim) mine, maxe = np.min(edges), np.max(edges) fs = fs.astype(float) / len(values) * width rs = [] if splined: lnl, lnr = [(0, edges[0], 0)], [(0, edges[0], 0)] for i in range(bins): xc = (edges[i] + edges[i + 1]) / 2 yc = fs[i] lnl.append([-yc, xc, 0]) lnr.append([yc, xc, 0]) lnl.append((0, edges[-1], 0)) lnr.append((0, edges[-1], 0)) spl = shapes.KSpline(lnl).x(x) spr = shapes.KSpline(lnr).x(x) spl.color(lc).alpha(alpha).lw(lw) spr.color(lc).alpha(alpha).lw(lw) if outline: rs.append(spl) rs.append(spr) if fill: rb = shapes.Ribbon(spl, spr, c=c, alpha=alpha).lighting("off") rs.append(rb) else: lns1 = [[0, mine, 0]] for i in range(bins): lns1.append([fs[i], edges[i], 0]) lns1.append([fs[i], edges[i + 1], 0]) lns1.append([0, maxe, 0]) lns2 = [[0, mine, 0]] for i in range(bins): lns2.append([-fs[i], edges[i], 0]) lns2.append([-fs[i], edges[i + 1], 0]) lns2.append([0, maxe, 0]) if outline: rs.append(shapes.Line(lns1, c=lc, alpha=alpha, lw=lw).x(x)) rs.append(shapes.Line(lns2, c=lc, alpha=alpha, lw=lw).x(x)) if fill: for i in range(bins): p0 = (-fs[i], edges[i], 0) p1 = (fs[i], edges[i + 1], 0) r = shapes.Rectangle(p0, p1).x(p0[0] + x) r.color(c).alpha(alpha).lighting("off") rs.append(r) if centerline: cl = shapes.Line([0, mine, 0.01], [0, maxe, 0.01], c=lc, alpha=alpha, lw=2).x(x) rs.append(cl) asse = Assembly(rs) asse.name = "violin" return asse def whisker(data, s=0.25, c='k', lw=2, bc='blue', alpha=0.25, r=5, jitter=True, horizontal=False)-
Generate a "whisker" bar from a 1-dimensional dataset.
Parameters
s:float- size of the box
c:color- color of the lines
lw:float- line width
bc:color- color of the box
alpha:float- transparency of the box
r:float- point radius in pixels (use value 0 to disable)
jitter:bool- add some randomness to points to avoid overlap
horizontal:bool- set horizontal layout
Hint: examples/pyplot/whiskers.py
Expand source code
def whisker( data, s=0.25, c='k', lw=2, bc='blue', alpha=0.25, r=5, jitter=True, horizontal=False, ): """ Generate a "whisker" bar from a 1-dimensional dataset. Parameters ---------- s : float size of the box c : color color of the lines lw : float line width bc : color color of the box alpha : float transparency of the box r : float point radius in pixels (use value 0 to disable) jitter : bool add some randomness to points to avoid overlap horizontal : bool set horizontal layout .. hint:: examples/pyplot/whiskers.py .. image:: https://vedo.embl.es/images/pyplot/whiskers.png """ xvals = np.zeros_like(np.array(data)) if jitter: xjit = np.random.randn(len(xvals)) * s / 9 xjit = np.clip(xjit, -s / 2.1, s / 2.1) xvals += xjit dmean = np.mean(data) dq05 = np.quantile(data, 0.05) dq25 = np.quantile(data, 0.25) dq75 = np.quantile(data, 0.75) dq95 = np.quantile(data, 0.95) pts = None if r: pts = shapes.Points([xvals, data], c=c, r=r) rec = shapes.Rectangle([-s / 2, dq25], [s / 2, dq75], c=bc, alpha=alpha) rec.GetProperty().LightingOff() rl = shapes.Line( [[-s / 2, dq25], [s / 2, dq25], [s / 2, dq75], [-s / 2, dq75]], closed=True ) l1 = shapes.Line([0, dq05, 0], [0, dq25, 0], c=c, lw=lw) l2 = shapes.Line([0, dq75, 0], [0, dq95, 0], c=c, lw=lw) lm = shapes.Line([-s / 2, dmean], [s / 2, dmean]) lns = merge(l1, l2, lm, rl) asse = Assembly([lns, rec, pts]) if horizontal: asse.rotateZ(-90) asse.name = "Whisker" asse.info["mean"] = dmean asse.info["quantile_05"] = dq05 asse.info["quantile_25"] = dq25 asse.info["quantile_75"] = dq75 asse.info["quantile_95"] = dq95 return asse
Classes
class DirectedGraph (**kargs)-
A graph consists of a collection of nodes (without postional information) and a collection of edges connecting pairs of nodes. The task is to determine the node positions only based on their connections.
This class is derived from class
Assembly, and it assembles 4 Mesh objects representing the graph, the node labels, edge labels and edge arrows.Parameters
c:color- Color of the Graph
n:int- number of the initial set of nodes
layout:int, str-
layout in ['2d', 'fast2d', 'clustering2d', 'circular', 'circular3d', 'cone', 'force', 'tree']
Each of these layouts has diferent available options.
Note: Options for layouts '2d', 'fast2d' and 'clustering2d'
Parameters
seed:int- seed of the random number generator used to jitter point positions
restDistance:float- manually set the resting distance
maxNumberOfIterations:int- the maximum number of iterations to be used
zrange:list- expand 2d graph along z axis.
Note: Options for layouts 'circular', and 'circular3d':
Parameters
radius:float- set the radius of the circles
height:float- set the vertical (local z) distance between the circles
zrange:float- expand 2d graph along z axis
Note: Options for layout 'cone'
Parameters
compactness:float- ratio between the average width of a cone in the tree, and the height of the cone.
compression:bool- put children closer together, possibly allowing sub-trees to overlap. This is useful if the tree is actually the spanning tree of a graph.
spacing:float- space between layers of the tree
Note: Options for layout 'force'
Parameters
seed:int- seed the random number generator used to jitter point positions
bounds:list- set the region in space in which to place the final graph
maxNumberOfIterations:int- the maximum number of iterations to be used
threeDimensional:bool- allow optimization in the 3rd dimension too
randomInitialPoints:bool- use random positions within the graph bounds as initial points
Hint: examples/pyplot/lineage_graph.py, graph_network.py
Expand source code
class DirectedGraph(Assembly, vedo.base.BaseActor): """ A graph consists of a collection of nodes (without postional information) and a collection of edges connecting pairs of nodes. The task is to determine the node positions only based on their connections. This class is derived from class ``Assembly``, and it assembles 4 Mesh objects representing the graph, the node labels, edge labels and edge arrows. Parameters ---------- c : color Color of the Graph n : int number of the initial set of nodes layout : int, str layout in ['2d', 'fast2d', 'clustering2d', 'circular', 'circular3d', 'cone', 'force', 'tree'] Each of these layouts has diferent available options. --------------------------------------------------------------- .. note:: Options for layouts '2d', 'fast2d' and 'clustering2d' Parameters ---------- seed : int seed of the random number generator used to jitter point positions restDistance : float manually set the resting distance maxNumberOfIterations : int the maximum number of iterations to be used zrange : list expand 2d graph along z axis. --------------------------------------------------------------- .. note:: Options for layouts 'circular', and 'circular3d': Parameters ---------- radius : float set the radius of the circles height : float set the vertical (local z) distance between the circles zrange : float expand 2d graph along z axis --------------------------------------------------------------- .. note:: Options for layout 'cone' Parameters ---------- compactness : float ratio between the average width of a cone in the tree, and the height of the cone. compression : bool put children closer together, possibly allowing sub-trees to overlap. This is useful if the tree is actually the spanning tree of a graph. spacing : float space between layers of the tree --------------------------------------------------------------- .. note:: Options for layout 'force' Parameters ---------- seed : int seed the random number generator used to jitter point positions bounds : list set the region in space in which to place the final graph maxNumberOfIterations : int the maximum number of iterations to be used threeDimensional : bool allow optimization in the 3rd dimension too randomInitialPoints : bool use random positions within the graph bounds as initial points .. hint:: examples/pyplot/lineage_graph.py, graph_network.py .. image:: https://vedo.embl.es/images/pyplot/graph_network.png """ def __init__(self, **kargs): vedo.base.BaseActor.__init__(self) self.nodes = [] self.edges = [] self._nodeLabels = [] # holds strings self._edgeLabels = [] self.edgeOrientations = [] self.edgeGlyphPosition = 0.6 self.zrange = 0.0 self.rotX = 0 self.rotY = 0 self.rotZ = 0 self.arrowScale = 0.15 self.nodeLabelScale = None self.nodeLabelJustify = "bottom-left" self.edgeLabelScale = None self.mdg = vtk.vtkMutableDirectedGraph() n = kargs.pop("n", 0) for _ in range(n): self.addNode() self._c = kargs.pop("c", (0.3, 0.3, 0.3)) self.gl = vtk.vtkGraphLayout() self.font = kargs.pop("font", "") s = kargs.pop("layout", "2d") if isinstance(s, int): ss = [ "2d", "fast2d", "clustering2d", "circular", "circular3d", "cone", "force", "tree", ] s = ss[s] self.layout = s if "2d" in s: if "clustering" in s: self.strategy = vtk.vtkClustering2DLayoutStrategy() elif "fast" in s: self.strategy = vtk.vtkFast2DLayoutStrategy() else: self.strategy = vtk.vtkSimple2DLayoutStrategy() self.rotX = 180 opt = kargs.pop("restDistance", None) if opt is not None: self.strategy.SetRestDistance(opt) opt = kargs.pop("seed", None) if opt is not None: self.strategy.SetRandomSeed(opt) opt = kargs.pop("maxNumberOfIterations", None) if opt is not None: self.strategy.SetMaxNumberOfIterations(opt) self.zrange = kargs.pop("zrange", 0) elif "circ" in s: if "3d" in s: self.strategy = vtk.vtkSimple3DCirclesStrategy() self.strategy.SetDirection(0, 0, -1) self.strategy.SetAutoHeight(True) self.strategy.SetMethod(1) self.rotX = -90 opt = kargs.pop("radius", None) # float if opt is not None: self.strategy.SetMethod(0) self.strategy.SetRadius(opt) # float opt = kargs.pop("height", None) if opt is not None: self.strategy.SetAutoHeight(False) self.strategy.SetHeight(opt) # float else: self.strategy = vtk.vtkCircularLayoutStrategy() self.zrange = kargs.pop("zrange", 0) elif "cone" in s: self.strategy = vtk.vtkConeLayoutStrategy() self.rotX = 180 opt = kargs.pop("compactness", None) if opt is not None: self.strategy.SetCompactness(opt) opt = kargs.pop("compression", None) if opt is not None: self.strategy.SetCompression(opt) opt = kargs.pop("spacing", None) if opt is not None: self.strategy.SetSpacing(opt) elif "force" in s: self.strategy = vtk.vtkForceDirectedLayoutStrategy() opt = kargs.pop("seed", None) if opt is not None: self.strategy.SetRandomSeed(opt) opt = kargs.pop("bounds", None) if opt is not None: self.strategy.SetAutomaticBoundsComputation(False) self.strategy.SetGraphBounds(opt) # list opt = kargs.pop("maxNumberOfIterations", None) if opt is not None: self.strategy.SetMaxNumberOfIterations(opt) # int opt = kargs.pop("threeDimensional", True) if opt is not None: self.strategy.SetThreeDimensionalLayout(opt) # bool opt = kargs.pop("randomInitialPoints", None) if opt is not None: self.strategy.SetRandomInitialPoints(opt) # bool elif "tree" in s: self.strategy = vtk.vtkSpanTreeLayoutStrategy() self.rotX = 180 else: vedo.logger.error(f"Cannot understand layout {s}. Available layouts:") vedo.logger.error( "[2d,fast2d,clustering2d,circular,circular3d,cone,force,tree]" ) raise RuntimeError() self.gl.SetLayoutStrategy(self.strategy) if len(kargs): vedo.logger.error(f"Cannot understand options: {kargs}") def addNode(self, label="id"): """Add a new node to the ``Graph``.""" v = self.mdg.AddVertex() # vtk calls it vertex.. self.nodes.append(v) if label == "id": label = int(v) self._nodeLabels.append(str(label)) return v def addEdge(self, v1, v2, label=""): """Add a new edge between to nodes. An extra node is created automatically if needed.""" nv = len(self.nodes) if v1 >= nv: for _ in range(nv, v1 + 1): self.addNode() nv = len(self.nodes) if v2 >= nv: for _ in range(nv, v2 + 1): self.addNode() e = self.mdg.AddEdge(v1, v2) self.edges.append(e) self._edgeLabels.append(str(label)) return e def addChild(self, v, nodeLabel="id", edgeLabel=""): """Add a new edge to a new node as its child. The extra node is created automatically if needed.""" nv = len(self.nodes) if v >= nv: for _ in range(nv, v + 1): self.addNode() child = self.mdg.AddChild(v) self.edges.append((v, child)) self.nodes.append(child) if nodeLabel == "id": nodeLabel = int(child) self._nodeLabels.append(str(nodeLabel)) self._edgeLabels.append(str(edgeLabel)) return child def build(self): """ Build the ``DirectedGraph(Assembly)``. Accessory objects are also created for labels and arrows. """ self.gl.SetZRange(self.zrange) self.gl.SetInputData(self.mdg) self.gl.Update() graphToPolyData = vtk.vtkGraphToPolyData() graphToPolyData.EdgeGlyphOutputOn() graphToPolyData.SetEdgeGlyphPosition(self.edgeGlyphPosition) graphToPolyData.SetInputData(self.gl.GetOutput()) graphToPolyData.Update() dgraph = Mesh(graphToPolyData.GetOutput(0)) # dgraph.clean() # WRONG!!! dont uncomment dgraph.flat().color(self._c).lw(2) dgraph.name = "DirectedGraph" diagsz = self.diagonalSize() / 1.42 if not diagsz: return None dgraph.SetScale(1 / diagsz) if self.rotX: dgraph.rotateX(self.rotX) if self.rotY: dgraph.rotateY(self.rotY) if self.rotZ: dgraph.rotateZ(self.rotZ) vecs = graphToPolyData.GetOutput(1).GetPointData().GetVectors() self.edgeOrientations = utils.vtk2numpy(vecs) # Use Glyph3D to repeat the glyph on all edges. arrows = None if self.arrowScale: arrowSource = vtk.vtkGlyphSource2D() arrowSource.SetGlyphTypeToEdgeArrow() arrowSource.SetScale(self.arrowScale) arrowSource.Update() arrowGlyph = vtk.vtkGlyph3D() arrowGlyph.SetInputData(0, graphToPolyData.GetOutput(1)) arrowGlyph.SetInputData(1, arrowSource.GetOutput()) arrowGlyph.Update() arrows = Mesh(arrowGlyph.GetOutput()) arrows.SetScale(1 / diagsz) arrows.lighting("off").color(self._c) if self.rotX: arrows.rotateX(self.rotX) if self.rotY: arrows.rotateY(self.rotY) if self.rotZ: arrows.rotateZ(self.rotZ) arrows.name = "DirectedGraphArrows" nodeLabels = dgraph.labels( self._nodeLabels, scale=self.nodeLabelScale, precision=0, font=self.font, justify=self.nodeLabelJustify, ) nodeLabels.color(self._c).pickable(True) nodeLabels.name = "DirectedGraphNodeLabels" edgeLabels = dgraph.labels( self._edgeLabels, cells=True, scale=self.edgeLabelScale, precision=0, font=self.font, ) edgeLabels.color(self._c).pickable(True) edgeLabels.name = "DirectedGraphEdgeLabels" Assembly.__init__(self, [dgraph, nodeLabels, edgeLabels, arrows]) self.name = "DirectedGraphAssembly" return selfAncestors
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- BaseActor
- Base3DProp
Methods
def addChild(self, v, nodeLabel='id', edgeLabel='')-
Add a new edge to a new node as its child. The extra node is created automatically if needed.
Expand source code
def addChild(self, v, nodeLabel="id", edgeLabel=""): """Add a new edge to a new node as its child. The extra node is created automatically if needed.""" nv = len(self.nodes) if v >= nv: for _ in range(nv, v + 1): self.addNode() child = self.mdg.AddChild(v) self.edges.append((v, child)) self.nodes.append(child) if nodeLabel == "id": nodeLabel = int(child) self._nodeLabels.append(str(nodeLabel)) self._edgeLabels.append(str(edgeLabel)) return child def addEdge(self, v1, v2, label='')-
Add a new edge between to nodes. An extra node is created automatically if needed.
Expand source code
def addEdge(self, v1, v2, label=""): """Add a new edge between to nodes. An extra node is created automatically if needed.""" nv = len(self.nodes) if v1 >= nv: for _ in range(nv, v1 + 1): self.addNode() nv = len(self.nodes) if v2 >= nv: for _ in range(nv, v2 + 1): self.addNode() e = self.mdg.AddEdge(v1, v2) self.edges.append(e) self._edgeLabels.append(str(label)) return e def addNode(self, label='id')-
Add a new node to the
Graph.Expand source code
def addNode(self, label="id"): """Add a new node to the ``Graph``.""" v = self.mdg.AddVertex() # vtk calls it vertex.. self.nodes.append(v) if label == "id": label = int(v) self._nodeLabels.append(str(label)) return v def build(self)-
Build the
DirectedGraph(Assembly). Accessory objects are also created for labels and arrows.Expand source code
def build(self): """ Build the ``DirectedGraph(Assembly)``. Accessory objects are also created for labels and arrows. """ self.gl.SetZRange(self.zrange) self.gl.SetInputData(self.mdg) self.gl.Update() graphToPolyData = vtk.vtkGraphToPolyData() graphToPolyData.EdgeGlyphOutputOn() graphToPolyData.SetEdgeGlyphPosition(self.edgeGlyphPosition) graphToPolyData.SetInputData(self.gl.GetOutput()) graphToPolyData.Update() dgraph = Mesh(graphToPolyData.GetOutput(0)) # dgraph.clean() # WRONG!!! dont uncomment dgraph.flat().color(self._c).lw(2) dgraph.name = "DirectedGraph" diagsz = self.diagonalSize() / 1.42 if not diagsz: return None dgraph.SetScale(1 / diagsz) if self.rotX: dgraph.rotateX(self.rotX) if self.rotY: dgraph.rotateY(self.rotY) if self.rotZ: dgraph.rotateZ(self.rotZ) vecs = graphToPolyData.GetOutput(1).GetPointData().GetVectors() self.edgeOrientations = utils.vtk2numpy(vecs) # Use Glyph3D to repeat the glyph on all edges. arrows = None if self.arrowScale: arrowSource = vtk.vtkGlyphSource2D() arrowSource.SetGlyphTypeToEdgeArrow() arrowSource.SetScale(self.arrowScale) arrowSource.Update() arrowGlyph = vtk.vtkGlyph3D() arrowGlyph.SetInputData(0, graphToPolyData.GetOutput(1)) arrowGlyph.SetInputData(1, arrowSource.GetOutput()) arrowGlyph.Update() arrows = Mesh(arrowGlyph.GetOutput()) arrows.SetScale(1 / diagsz) arrows.lighting("off").color(self._c) if self.rotX: arrows.rotateX(self.rotX) if self.rotY: arrows.rotateY(self.rotY) if self.rotZ: arrows.rotateZ(self.rotZ) arrows.name = "DirectedGraphArrows" nodeLabels = dgraph.labels( self._nodeLabels, scale=self.nodeLabelScale, precision=0, font=self.font, justify=self.nodeLabelJustify, ) nodeLabels.color(self._c).pickable(True) nodeLabels.name = "DirectedGraphNodeLabels" edgeLabels = dgraph.labels( self._edgeLabels, cells=True, scale=self.edgeLabelScale, precision=0, font=self.font, ) edgeLabels.color(self._c).pickable(True) edgeLabels.name = "DirectedGraphEdgeLabels" Assembly.__init__(self, [dgraph, nodeLabels, edgeLabels, arrows]) self.name = "DirectedGraphAssembly" return self
Inherited members
class Figure (xlim, ylim, aspect=1.3333333333333333, padding=(0.05, 0.05, 0.05, 0.05), **kwargs)-
Parameters
xlim:list- range of the x-axis as [x0, x1]
ylim:list- range of the y-axis as [y0, y1]
aspect:float, str- the desired aspect ratio of the histogram. Default is 4/3.
Use
aspect="equal"to force the same units in x and y. padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True) axes:dict- an extra dictionary of options for the axes
Expand source code
class Figure(Assembly): """ Parameters ---------- xlim : list range of the x-axis as [x0, x1] ylim : list range of the y-axis as [y0, y1] aspect : float, str the desired aspect ratio of the histogram. Default is 4/3. Use `aspect="equal"` to force the same units in x and y. padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` axes : dict an extra dictionary of options for the axes """ def __init__( self, xlim, ylim, aspect=4/3, padding=(0.05, 0.05, 0.05, 0.05), **kwargs, ): self.xlim = np.array(xlim) self.ylim = np.array(ylim) self.aspect = aspect self.padding = padding if not utils.isSequence(self.padding): self.padding = [self.padding, self.padding, self.padding, self.padding] self.force_scaling_types = ( shapes.Glyph, shapes.Line, shapes.Rectangle, shapes.DashedLine, shapes.Tube, shapes.Ribbon, shapes.GeoCircle, shapes.Arc, shapes.Grid, # shapes.Arrows, # todo # shapes.Arrows2D, # todo shapes.Brace, # todo ) options = dict(kwargs) self.title = options.pop("title", "") self.xtitle = options.pop("xtitle", " ") self.ytitle = options.pop("ytitle", " ") numberOfDivisions = 6 self.legend = None self.labels = [] self.label = options.pop("label", None) if self.label: self.labels = [self.label] self.axopts = options.pop("axes", {}) if isinstance(self.axopts, (bool, int, float)): if self.axopts: self.axopts = {} if self.axopts or isinstance(self.axopts, dict): numberOfDivisions = self.axopts.pop("numberOfDivisions", numberOfDivisions) self.axopts["xtitle"] = self.xtitle self.axopts["ytitle"] = self.ytitle if "xyGrid" not in self.axopts: ## modify the default self.axopts["xyGrid"] = options.pop("grid", False) if "xyGridTransparent" not in self.axopts: ## modify the default self.axopts["xyGridTransparent"] = True if "xTitlePosition" not in self.axopts: ## modify the default self.axopts["xTitlePosition"] = 0.5 self.axopts["xTitleJustify"] = "top-center" if "yTitlePosition" not in self.axopts: ## modify the default self.axopts["yTitlePosition"] = 0.5 self.axopts["yTitleJustify"] = "bottom-center" if self.label: if "c" in self.axopts: self.label.tcolor = self.axopts["c"] x0, x1 = self.xlim y0, y1 = self.ylim dx = x1 - x0 dy = y1 - y0 x0lim, x1lim = (x0 - self.padding[0] * dx, x1 + self.padding[1] * dx) y0lim, y1lim = (y0 - self.padding[2] * dy, y1 + self.padding[3] * dy) dy = y1lim - y0lim self.axes = None if xlim[0] >= xlim[1] or ylim[0] >= ylim[1]: vedo.logger.warning(f"Null range for Figure {self.title}... returning an empty Assembly.") Assembly.__init__(self) self.yscale = 0 return if aspect == "equal": self.aspect = dx / dy # so that yscale becomes 1 self.yscale = dx / dy / self.aspect y0lim *= self.yscale y1lim *= self.yscale self.x0lim = x0lim self.x1lim = x1lim self.y0lim = y0lim self.y1lim = y1lim self.ztolerance = options.pop("ztolerance", None) if self.ztolerance is None: self.ztolerance = dx / 5000 ############## create axes if self.axopts: axesopts = self.axopts if self.axopts is True or self.axopts == 1: axesopts = {} tp, ts = utils.makeTicks( y0lim / self.yscale, y1lim / self.yscale, numberOfDivisions, ) labs = [] for i in range(1, len(tp) - 1): ynew = utils.linInterpolate(tp[i], [0, 1], [y0lim, y1lim]) labs.append([ynew, ts[i]]) if self.title: axesopts["htitle"] = self.title axesopts["yValuesAndLabels"] = labs axesopts["xrange"] = (x0lim, x1lim) axesopts["yrange"] = (y0lim, y1lim) axesopts["zrange"] = (0, 0) axesopts["yUseBounds"] = True if "c" not in axesopts and "ac" in options: axesopts["c"] = options["ac"] self.axes = addons.Axes(**axesopts) Assembly.__init__(self, [self.axes]) self.name = "Figure" return def __add__(self, *obj): # just to avoid confusion, superseed Assembly.__add__ return self.__iadd__(*obj) def __iadd__(self, *obj): if len(obj) == 1 and isinstance(obj[0], Figure): return self._check_unpack_and_insert(obj[0]) else: obj = utils.flatten(obj) return self.insert(*obj) def _check_unpack_and_insert(self, fig): if fig.label: self.labels.append(fig.label) if abs(self.yscale - fig.yscale) > 0.0001: colors.printc("ERROR: adding incompatible Figure. Y-scales are different:", c='r', invert=True) colors.printc(" first figure:", self.yscale, c='r') colors.printc(" second figure:", fig.yscale, c='r') colors.printc("One or more of these parameters can be the cause:", c="r") if list(self.xlim) != list(fig.xlim): colors.printc("xlim --------------------------------------------\n", " first figure:", self.xlim, "\n", " second figure:", fig.xlim, c='r') if list(self.ylim) != list(fig.ylim): colors.printc("ylim --------------------------------------------\n", " first figure:", self.ylim, "\n", " second figure:", fig.ylim, c='r') if list(self.padding) != list(fig.padding): colors.printc("padding -----------------------------------------\n", " first figure:", self.padding, " second figure:", fig.padding, c='r') if self.aspect != fig.aspect: colors.printc("aspect ------------------------------------------\n", " first figure:", self.aspect, " second figure:", fig.aspect, c='r') colors.printc("\n*Consider using fig2 = histogram(..., like=fig1)", c="r") colors.printc(" Or fig += histogram(..., like=fig)\n", c="r") return self offset = self.zbounds()[1] + self.ztolerance for ele in fig.unpack(): if "Axes" in ele.name: continue ele.z(offset) self.insert(ele, rescale=False) return self def insert(self, *objs, rescale=True, as3d=True, adjusted=True, cut=True): """ Insert objects into a Figure. The reccomended syntax is to use "+=", which calls `insert()` under the hood. If a whole Figure is added with "+=", it is unpacked and its objects are added one by one. Parameters ---------- rescale : bool rescale the y axis position while inserting the object. as3d : bool if True keep the aspect ratio of the 3d obect, otherwise stretch it in y. adjusted : bool adjust the scaling according to the shortest axis cut : bool cut off the parts of the object which go beyond the axes frame. """ for a in objs: if a in self.actors: # should not add twice the same object in plot continue if isinstance(a, vedo.Points): # hacky way to identify Points if a.NCells() == a.NPoints(): poly = a.polydata(False) if poly.GetNumberOfPolys() == 0 and poly.GetNumberOfLines() == 0: as3d = False rescale = True if isinstance(a, (shapes.Arrow, shapes.Arrow2D)): # discard input Arrow and substitute it with a brand new one # (because scaling would fatally distort the shape) prop = a.GetProperty() prop.LightingOff() py = a.base[1] a.top[1] = (a.top[1] - py) * self.yscale + py b = shapes.Arrow2D(a.base, a.top, s=a.s, fill=a.fill).z(a.z()) b.SetProperty(prop) b.y(py * self.yscale) a = b # elif isinstance(a, shapes.Rectangle) and a.radius is not None: # # discard input Rectangle and substitute it with a brand new one # # (because scaling would fatally distort the shape of the corners) # py = a.corner1[1] # rx1,ry1,rz1 = a.corner1 # rx2,ry2,rz2 = a.corner2 # ry2 = (ry2-py) * self.yscale + py # b = shapes.Rectangle([rx1,0,rz1], [rx2,ry2,rz2], radius=a.radius).z(a.z()) # b.SetProperty(a.GetProperty()) # b.y(py / self.yscale) # a = b else: if rescale: if not isinstance(a, Figure): if as3d and not isinstance(a, self.force_scaling_types): if adjusted: scl = np.min([1, self.yscale]) else: scl = self.yscale a.scale(scl) else: a.scale([1, self.yscale, 1]) # shift it in y a.y(a.y() * self.yscale) if cut: try: bx0, bx1, by0, by1, _, _ = a.GetBounds() if self.y0lim > by0: a.cutWithPlane([0, self.y0lim, 0], [ 0, 1, 0]) if self.y1lim < by1: a.cutWithPlane([0, self.y1lim, 0], [ 0,-1, 0]) if self.x0lim > bx0: a.cutWithPlane([self.x0lim, 0, 0], [ 1, 0, 0]) if self.x1lim < bx1: a.cutWithPlane([self.x1lim, 0, 0], [-1, 0, 0]) except: # print("insert(): cannot cut", [a]) pass self.AddPart(a) self.actors.append(a) return self def addLabel(self, text, c=None, marker="", mc="black"): """ Manually add en entry label to the legend. Parameters ---------- text : str text string for the label. c : str color of the text marker : str, Mesh a marker char or a Mesh object to be used as marker mc : str, optional color for the marker """ newlabel = LabelData() newlabel.text = text.replace("\n", " ") newlabel.tcolor = c newlabel.marker = marker newlabel.mcolor = mc self.labels.append(newlabel) return self def addLegend(self, pos="top-right", relative=True, font=None, s=1, c=None, vspace=1.75, padding=0.1, radius=0, alpha=1, bc='k7', lw=1, lc='k4', z=0, ): """ Add existing labels to form a legend box. Labels have been previously filled with eg: `plot(..., label="text")` Parameters ---------- pos : str, list A string or 2D coordinates. The default is "top-right". relative : bool control whether `pos` is absolute or relative, e.i. normalized to the x and y ranges so that x and y in `pos=[x,y]` should be both in the range [0,1]. This flag is ignored if a string despcriptor is passed. Default is True. font : str, int font name or number s : float global size of the legend c : str color of the text vspace : float vertical spacing of lines padding : float padding of the box as a fraction of the text size radius : float border radius of the box alpha : float opacity of the box. Values below 1 may cause poor rendering bacause of antialiasing. Use alpha = 0 to remove the box. bc : str box color lw : int border line width of the box in pixel units lc : int border line color of the box z : float set the zorder as z position (useful to avoid overlap) """ sx = self.x1lim - self.x0lim s = s * sx / 55 # so that input can be about 1 ds = 0 texts = [] mks = [] for i, t in enumerate(self.labels): label = self.labels[i] t = label.text if label.tcolor is not None: c = label.tcolor tx = vedo.shapes.Text3D(t, s=s, c=c, justify="center-left", font=font) y0, y1 = tx.ybounds() ds = max(y1 - y0, ds) texts.append(tx) mk = label.marker if isinstance(mk, vedo.Points): mk = mk.clone(deep=False).lighting("off") cm = mk.centerOfMass() ty0, ty1 = tx.ybounds() oby0, oby1 = mk.ybounds() mk.shift(-cm) mk.origin(cm) mk.scale((ty1 - ty0) / (oby1 - oby0)) mk.scale([1.1, 1.1, 0.01]) elif mk == "-": mk = vedo.shapes.Marker(mk, s=s * 2) mk.color(label.mcolor) else: mk = vedo.shapes.Marker(mk, s=s) mk.color(label.mcolor) mks.append(mk) for i, tx in enumerate(texts): tx.shift(0, -(i + 0) * ds * vspace) for i, mk in enumerate(mks): mk.shift(-ds * 1.75, -(i + 0) * ds * vspace, 0) acts = texts + mks aleg = Assembly(acts) # .show(axes=1).close() x0, x1, y0, y1, _, _ = aleg.GetBounds() if alpha: dx = x1 - x0 dy = y1 - y0 if not utils.isSequence(padding): padding = [padding] * 4 padding = min(padding) padding = min(padding * dx, padding * dy) if len(self.labels) == 1: padding *= 4 x0 -= padding x1 += padding y0 -= padding y1 += padding box = shapes.Rectangle( [x0, y0], [x1, y1], radius=radius, c=bc, alpha=alpha, ) box.shift(0, 0, -dy / 100).pickable(False) if lc: box.lc(lc).lw(lw) aleg.AddPart(box) xlim = self.xlim ylim = self.ylim if isinstance(pos, str): px, py = 0, 0 rx, ry = (xlim[1] + xlim[0]) / 2, (ylim[1] + ylim[0]) / 2 shx, shy = 0, 0 if "top" in pos: if "cent" in pos: px, py = rx, ylim[1] shx, shy = (x0 + x1) / 2, y1 elif "left" in pos: px, py = xlim[0], ylim[1] shx, shy = x0, y1 else: # "right" px, py = xlim[1], ylim[1] shx, shy = x1, y1 elif "bot" in pos: if "left" in pos: px, py = xlim[0], ylim[0] shx, shy = x0, y0 elif "right" in pos: px, py = xlim[1], ylim[0] shx, shy = x1, y0 else: # "cent" px, py = rx, ylim[0] shx, shy = (x0 + x1) / 2, y0 elif "cent" in pos: if "left" in pos: px, py = xlim[0], ry shx, shy = x0, (y0 + y1) / 2 elif "right" in pos: px, py = xlim[1], ry shx, shy = x1, (y0 + y1) / 2 else: vedo.logger.error(f"in addLegend(), cannot understand {pos}") raise RuntimeError else: if relative: rx, ry = pos[0], pos[1] px = (xlim[1] - xlim[0]) * rx + xlim[0] py = (ylim[1] - ylim[0]) * ry + ylim[0] z *= xlim[1] - xlim[0] else: px, py = pos[0], pos[1] shx, shy = x0, y1 aleg.pos(px - shx, py * self.yscale - shy, self.z() + sx / 50 + z) self.insert(aleg, rescale=False, cut=False) self.legend = aleg aleg.name = "Legend" return selfAncestors
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- Base3DProp
Subclasses
Methods
def addLabel(self, text, c=None, marker='', mc='black')-
Manually add en entry label to the legend.
Parameters
text:str- text string for the label.
c:str- color of the text
marker:str, Mesh- a marker char or a Mesh object to be used as marker
mc:str, optional- color for the marker
Expand source code
def addLabel(self, text, c=None, marker="", mc="black"): """ Manually add en entry label to the legend. Parameters ---------- text : str text string for the label. c : str color of the text marker : str, Mesh a marker char or a Mesh object to be used as marker mc : str, optional color for the marker """ newlabel = LabelData() newlabel.text = text.replace("\n", " ") newlabel.tcolor = c newlabel.marker = marker newlabel.mcolor = mc self.labels.append(newlabel) return self def addLegend(self, pos='top-right', relative=True, font=None, s=1, c=None, vspace=1.75, padding=0.1, radius=0, alpha=1, bc='k7', lw=1, lc='k4', z=0)-
Add existing labels to form a legend box. Labels have been previously filled with eg:
plot(..., label="text")Parameters
pos:str, list- A string or 2D coordinates. The default is "top-right".
relative:bool- control whether
posis absolute or relative, e.i. normalized to the x and y ranges so that x and y inpos=[x,y]should be both in the range [0,1]. This flag is ignored if a string despcriptor is passed. Default is True. font:str, int- font name or number
s:float- global size of the legend
c:str- color of the text
vspace:float- vertical spacing of lines
padding:float- padding of the box as a fraction of the text size
radius:float- border radius of the box
alpha:float- opacity of the box. Values below 1 may cause poor rendering bacause of antialiasing. Use alpha = 0 to remove the box.
bc:str- box color
lw:int- border line width of the box in pixel units
lc:int- border line color of the box
z:float- set the zorder as z position (useful to avoid overlap)
Expand source code
def addLegend(self, pos="top-right", relative=True, font=None, s=1, c=None, vspace=1.75, padding=0.1, radius=0, alpha=1, bc='k7', lw=1, lc='k4', z=0, ): """ Add existing labels to form a legend box. Labels have been previously filled with eg: `plot(..., label="text")` Parameters ---------- pos : str, list A string or 2D coordinates. The default is "top-right". relative : bool control whether `pos` is absolute or relative, e.i. normalized to the x and y ranges so that x and y in `pos=[x,y]` should be both in the range [0,1]. This flag is ignored if a string despcriptor is passed. Default is True. font : str, int font name or number s : float global size of the legend c : str color of the text vspace : float vertical spacing of lines padding : float padding of the box as a fraction of the text size radius : float border radius of the box alpha : float opacity of the box. Values below 1 may cause poor rendering bacause of antialiasing. Use alpha = 0 to remove the box. bc : str box color lw : int border line width of the box in pixel units lc : int border line color of the box z : float set the zorder as z position (useful to avoid overlap) """ sx = self.x1lim - self.x0lim s = s * sx / 55 # so that input can be about 1 ds = 0 texts = [] mks = [] for i, t in enumerate(self.labels): label = self.labels[i] t = label.text if label.tcolor is not None: c = label.tcolor tx = vedo.shapes.Text3D(t, s=s, c=c, justify="center-left", font=font) y0, y1 = tx.ybounds() ds = max(y1 - y0, ds) texts.append(tx) mk = label.marker if isinstance(mk, vedo.Points): mk = mk.clone(deep=False).lighting("off") cm = mk.centerOfMass() ty0, ty1 = tx.ybounds() oby0, oby1 = mk.ybounds() mk.shift(-cm) mk.origin(cm) mk.scale((ty1 - ty0) / (oby1 - oby0)) mk.scale([1.1, 1.1, 0.01]) elif mk == "-": mk = vedo.shapes.Marker(mk, s=s * 2) mk.color(label.mcolor) else: mk = vedo.shapes.Marker(mk, s=s) mk.color(label.mcolor) mks.append(mk) for i, tx in enumerate(texts): tx.shift(0, -(i + 0) * ds * vspace) for i, mk in enumerate(mks): mk.shift(-ds * 1.75, -(i + 0) * ds * vspace, 0) acts = texts + mks aleg = Assembly(acts) # .show(axes=1).close() x0, x1, y0, y1, _, _ = aleg.GetBounds() if alpha: dx = x1 - x0 dy = y1 - y0 if not utils.isSequence(padding): padding = [padding] * 4 padding = min(padding) padding = min(padding * dx, padding * dy) if len(self.labels) == 1: padding *= 4 x0 -= padding x1 += padding y0 -= padding y1 += padding box = shapes.Rectangle( [x0, y0], [x1, y1], radius=radius, c=bc, alpha=alpha, ) box.shift(0, 0, -dy / 100).pickable(False) if lc: box.lc(lc).lw(lw) aleg.AddPart(box) xlim = self.xlim ylim = self.ylim if isinstance(pos, str): px, py = 0, 0 rx, ry = (xlim[1] + xlim[0]) / 2, (ylim[1] + ylim[0]) / 2 shx, shy = 0, 0 if "top" in pos: if "cent" in pos: px, py = rx, ylim[1] shx, shy = (x0 + x1) / 2, y1 elif "left" in pos: px, py = xlim[0], ylim[1] shx, shy = x0, y1 else: # "right" px, py = xlim[1], ylim[1] shx, shy = x1, y1 elif "bot" in pos: if "left" in pos: px, py = xlim[0], ylim[0] shx, shy = x0, y0 elif "right" in pos: px, py = xlim[1], ylim[0] shx, shy = x1, y0 else: # "cent" px, py = rx, ylim[0] shx, shy = (x0 + x1) / 2, y0 elif "cent" in pos: if "left" in pos: px, py = xlim[0], ry shx, shy = x0, (y0 + y1) / 2 elif "right" in pos: px, py = xlim[1], ry shx, shy = x1, (y0 + y1) / 2 else: vedo.logger.error(f"in addLegend(), cannot understand {pos}") raise RuntimeError else: if relative: rx, ry = pos[0], pos[1] px = (xlim[1] - xlim[0]) * rx + xlim[0] py = (ylim[1] - ylim[0]) * ry + ylim[0] z *= xlim[1] - xlim[0] else: px, py = pos[0], pos[1] shx, shy = x0, y1 aleg.pos(px - shx, py * self.yscale - shy, self.z() + sx / 50 + z) self.insert(aleg, rescale=False, cut=False) self.legend = aleg aleg.name = "Legend" return self def insert(self, *objs, rescale=True, as3d=True, adjusted=True, cut=True)-
Insert objects into a Figure.
The reccomended syntax is to use "+=", which calls
insert()under the hood. If a whole Figure is added with "+=", it is unpacked and its objects are added one by one.Parameters
rescale:bool- rescale the y axis position while inserting the object.
as3d:bool- if True keep the aspect ratio of the 3d obect, otherwise stretch it in y.
adjusted:bool- adjust the scaling according to the shortest axis
cut:bool- cut off the parts of the object which go beyond the axes frame.
Expand source code
def insert(self, *objs, rescale=True, as3d=True, adjusted=True, cut=True): """ Insert objects into a Figure. The reccomended syntax is to use "+=", which calls `insert()` under the hood. If a whole Figure is added with "+=", it is unpacked and its objects are added one by one. Parameters ---------- rescale : bool rescale the y axis position while inserting the object. as3d : bool if True keep the aspect ratio of the 3d obect, otherwise stretch it in y. adjusted : bool adjust the scaling according to the shortest axis cut : bool cut off the parts of the object which go beyond the axes frame. """ for a in objs: if a in self.actors: # should not add twice the same object in plot continue if isinstance(a, vedo.Points): # hacky way to identify Points if a.NCells() == a.NPoints(): poly = a.polydata(False) if poly.GetNumberOfPolys() == 0 and poly.GetNumberOfLines() == 0: as3d = False rescale = True if isinstance(a, (shapes.Arrow, shapes.Arrow2D)): # discard input Arrow and substitute it with a brand new one # (because scaling would fatally distort the shape) prop = a.GetProperty() prop.LightingOff() py = a.base[1] a.top[1] = (a.top[1] - py) * self.yscale + py b = shapes.Arrow2D(a.base, a.top, s=a.s, fill=a.fill).z(a.z()) b.SetProperty(prop) b.y(py * self.yscale) a = b # elif isinstance(a, shapes.Rectangle) and a.radius is not None: # # discard input Rectangle and substitute it with a brand new one # # (because scaling would fatally distort the shape of the corners) # py = a.corner1[1] # rx1,ry1,rz1 = a.corner1 # rx2,ry2,rz2 = a.corner2 # ry2 = (ry2-py) * self.yscale + py # b = shapes.Rectangle([rx1,0,rz1], [rx2,ry2,rz2], radius=a.radius).z(a.z()) # b.SetProperty(a.GetProperty()) # b.y(py / self.yscale) # a = b else: if rescale: if not isinstance(a, Figure): if as3d and not isinstance(a, self.force_scaling_types): if adjusted: scl = np.min([1, self.yscale]) else: scl = self.yscale a.scale(scl) else: a.scale([1, self.yscale, 1]) # shift it in y a.y(a.y() * self.yscale) if cut: try: bx0, bx1, by0, by1, _, _ = a.GetBounds() if self.y0lim > by0: a.cutWithPlane([0, self.y0lim, 0], [ 0, 1, 0]) if self.y1lim < by1: a.cutWithPlane([0, self.y1lim, 0], [ 0,-1, 0]) if self.x0lim > bx0: a.cutWithPlane([self.x0lim, 0, 0], [ 1, 0, 0]) if self.x1lim < bx1: a.cutWithPlane([self.x1lim, 0, 0], [-1, 0, 0]) except: # print("insert(): cannot cut", [a]) pass self.AddPart(a) self.actors.append(a) return self
Inherited members
class Histogram1D (data, weights=None, bins=None, errors=False, density=False, logscale=False, fill=True, radius=0.1, c='olivedrab', gap=0.02, alpha=1, outline=False, lw=2, lc='k', texture='', marker='', ms=None, mc=None, ma=None, like=None, xlim=None, ylim=(0, None), aspect=1.3333333333333333, padding=(0.0, 0.0, 0.0, 0.05), title='', xtitle=' ', ytitle=' ', ac='k', grid=False, ztolerance=None, label='', **fig_kwargs)-
Creates a
Histogram1D(Figure)object.Parameters
weights:list- An array of weights, of the same shape as
data. Each value indataonly contributes its associated weight towards the bin count (instead of 1). bins:int- number of bins
density:bool- normalize the area to 1 by dividing by the nr of entries and bin size
logscale:bool- use logscale on y-axis
fill:bool- fill bars woth solid color
c gap:float- leave a small space btw bars
radius:float- border radius of the top of the histogram bar. Default value is 0.1.
texture:str- url or path to an image to be used as texture for the bin
outline:bool- show outline of the bins
errors:bool- show error bars
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
aspect:float- the desired aspect ratio of the histogram. Default is 4/3.
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True) ztolerance:float- a tolerance factor to superimpose objects (along the z-axis).
Hint: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
Expand source code
class Histogram1D(Figure): """ Creates a `Histogram1D(Figure)` object. Parameters ---------- weights : list An array of weights, of the same shape as `data`. Each value in `data` only contributes its associated weight towards the bin count (instead of 1). bins : int number of bins density : bool normalize the area to 1 by dividing by the nr of entries and bin size logscale : bool use logscale on y-axis fill : bool fill bars woth solid color `c` gap : float leave a small space btw bars radius : float border radius of the top of the histogram bar. Default value is 0.1. texture : str url or path to an image to be used as texture for the bin outline : bool show outline of the bins errors : bool show error bars xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. aspect : float the desired aspect ratio of the histogram. Default is 4/3. grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` ztolerance : float a tolerance factor to superimpose objects (along the z-axis). .. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py .. image:: https://vedo.embl.es/images/pyplot/histo_1D.png """ def __init__( self, data, weights=None, bins=None, errors=False, density=False, logscale=False, fill=True, radius=0.1, c="olivedrab", gap=0.02, alpha=1, outline=False, lw=2, lc="k", texture="", marker="", ms=None, mc=None, ma=None, # Figure and axes options: like=None, xlim=None, ylim=(0, None), aspect=4/3, padding=(0., 0., 0., 0.05), title="", xtitle=" ", ytitle=" ", ac="k", grid=False, ztolerance=None, label="", **fig_kwargs, ): if like is not None: xlim = like.xlim ylim = like.ylim aspect = like.aspect padding = like.padding if bins is None: bins = like.bins if bins is None: bins = 20 if utils.isSequence(xlim): # deal with user passing eg [x0, None] _x0, _x1 = xlim if _x0 is None: _x0 = data.min() if _x1 is None: _x1 = data.max() xlim = [_x0, _x1] # purge NaN from data validIds = np.all(np.logical_not(np.isnan(data))) data = np.array(data[validIds]).ravel() fs, edges = np.histogram(data, bins=bins, weights=weights, range=xlim) binsize = edges[1] - edges[0] ntot = data.shape[0] fig_kwargs["title"] = title fig_kwargs["xtitle"] = xtitle fig_kwargs["ytitle"] = ytitle fig_kwargs["ac"] = ac fig_kwargs["ztolerance"] = ztolerance fig_kwargs["grid"] = grid unscaled_errors = np.sqrt(fs) if density: scaled_errors = unscaled_errors / (ntot * binsize) fs = fs / (ntot * binsize) if ytitle == " ": ytitle = f"counts / ( {ntot}~x~{utils.precision(binsize,3)} )" fig_kwargs["ytitle"] = ytitle elif logscale: se_up = np.log10(fs + unscaled_errors / 2 + 1) se_dw = np.log10(fs - unscaled_errors / 2 + 1) scaled_errors = np.c_[se_up, se_dw] fs = np.log10(fs + 1) if ytitle == " ": ytitle = "log_10 (counts+1)" fig_kwargs["ytitle"] = ytitle x0, x1 = np.min(edges), np.max(edges) y0, y1 = ylim[0], np.max(fs) _errors = [] if errors: if density: y1 += max(scaled_errors) / 2 _errors = scaled_errors elif logscale: y1 = max(scaled_errors[:, 0]) _errors = scaled_errors else: y1 += max(unscaled_errors) / 2 _errors = unscaled_errors if like is None: ylim = list(ylim) if xlim is None: xlim = [x0, x1] if ylim[1] is None: ylim[1] = y1 if ylim[0] != 0: ylim[0] = y0 self.entries = ntot self.frequencies = fs self.errors = _errors self.edges = edges self.centers = (edges[0:-1] + edges[1:]) / 2 self.mean = data.mean() self.std = data.std() self.bins = edges # internally used by "like" ############################### stats legend as htitle addstats = False if not title: if "axes" not in fig_kwargs: addstats = True axesopts = dict() fig_kwargs["axes"] = axesopts elif fig_kwargs["axes"] is False: pass else: axesopts = fig_kwargs["axes"] if "htitle" not in axesopts: addstats = True if addstats: htitle = f"Entries:~~{int(self.entries)} " htitle += f"Mean:~~{utils.precision(self.mean, 4)} " htitle += f"STD:~~{utils.precision(self.std, 4)} " axesopts["htitle"] = htitle axesopts["hTitleJustify"] = "bottom-left" axesopts["hTitleSize"] = 0.016 axesopts["hTitleOffset"] = [-0.49, 0.01, 0] if mc is None: mc = lc if ma is None: ma = alpha if label: nlab = LabelData() nlab.text = label nlab.tcolor = ac nlab.marker = marker nlab.mcolor = mc if not marker: nlab.marker = "s" nlab.mcolor = c fig_kwargs["label"] = nlab ############################################### Figure init Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs) if not self.yscale: return None if utils.isSequence(bins): myedges = np.array(bins) bins = len(bins) - 1 else: myedges = edges bin_centers = [] for i in range(bins): x = (myedges[i] + myedges[i + 1]) / 2 bin_centers.append([x, fs[i], 0]) rs = [] maxheigth = 0 if not fill and not outline and not errors and not marker: outline = True # otherwise it's empty.. if fill: ##################### if outline: gap = 0 for i in range(bins): F = fs[i] if not F: continue p0 = (myedges[i] + gap * binsize, 0, 0) p1 = (myedges[i + 1] - gap * binsize, F, 0) if radius: if gap: rds = np.array([0, 0, radius, radius]) else: rd1 = 0 if i < bins - 1 and fs[i + 1] >= F else radius / 2 rd2 = 0 if i > 0 and fs[i - 1] >= F else radius / 2 rds = np.array([0, 0, rd1, rd2]) p1_yscaled = [p1[0], p1[1]*self.yscale, 0] r = shapes.Rectangle(p0, p1_yscaled, radius=rds*binsize, res=6) r.scale([1, 1/self.yscale, 1]) r.radius = None # so it doesnt get recreated and rescaled by insert() else: r = shapes.Rectangle(p0, p1) if texture: r.texture(texture) c = "w" # if texture: # causes Segmentation fault vtk9.0.3 # if i>0 and rs[i-1].GetTexture(): # reuse the same texture obj # r.texture(rs[i-1].GetTexture()) # else: # r.texture(texture) # c = 'w' r.PickableOff() maxheigth = max(maxheigth, p1[1]) if c in colors.cmaps_names: col = colors.colorMap((p0[0]+p1[0])/2, c, myedges[0], myedges[-1]) else: col = c r.color(col).alpha(alpha).lighting("off") r.z(self.ztolerance) rs.append(r) if outline: ##################### lns = [[myedges[0], 0, 0]] for i in range(bins): lns.append([myedges[i], fs[i], 0]) lns.append([myedges[i + 1], fs[i], 0]) maxheigth = max(maxheigth, fs[i]) lns.append([myedges[-1], 0, 0]) outl = shapes.Line(lns, c=lc, alpha=alpha, lw=lw) outl.z(self.ztolerance * 2) rs.append(outl) if errors: ##################### for i in range(bins): x = self.centers[i] f = fs[i] if not f: continue err = _errors[i] if utils.isSequence(err): el = shapes.Line([x, err[0], 0], [x, err[1], 0], c=lc, alpha=alpha, lw=lw) else: el = shapes.Line([x, f-err/2, 0], [x, f+err/2, 0], c=lc, alpha=alpha, lw=lw) el.z(self.ztolerance*3) rs.append(el) if marker: ##################### # remove empty bins (we dont want a marker there) bin_centers = np.array(bin_centers) bin_centers = bin_centers[bin_centers[:, 1] > 0] if utils.isSequence(ms): ### variable point size mk = shapes.Marker(marker, s=1) mk.scale([1, 1 / self.yscale, 1]) msv = np.zeros_like(bin_centers) msv[:, 0] = ms marked = shapes.Glyph( bin_centers, glyphObj=mk, c=mc, orientationArray=msv, scaleByVectorSize=True, ) else: ### fixed point size if ms is None: ms = (xlim[1] - xlim[0]) / 100.0 else: ms = (xlim[1] - xlim[0]) / 100.0 * ms if utils.isSequence(mc): mk = shapes.Marker(marker, s=ms) mk.scale([1, 1 / self.yscale, 1]) msv = np.zeros_like(bin_centers) msv[:, 0] = 1 marked = shapes.Glyph( bin_centers, glyphObj=mk, c=mc, orientationArray=msv, scaleByVectorSize=True, ) else: mk = shapes.Marker(marker, s=ms) mk.scale([1, 1 / self.yscale, 1]) marked = shapes.Glyph(bin_centers, glyphObj=mk, c=mc) marked.alpha(ma) marked.z(self.ztolerance * 4) rs.append(marked) self.insert(*rs, as3d=False) self.name = "Histogram1D"Ancestors
- Figure
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- Base3DProp
Inherited members
class Histogram2D (xvalues, yvalues=None, bins=25, weights=None, cmap='cividis', alpha=1, gap=0, scalarbar=True, like=None, xlim=None, ylim=(None, None), zlim=(None, None), aspect=1, title='', xtitle=' ', ytitle=' ', ztitle='', ac='k', **fig_kwargs)-
Input data formats
[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]are both valid.Use keyword
like=...if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message.Parameters
bins:list- binning as (nx, ny)
weights:list- array of weights to assign to each entry
cmap:str, lookuptable- color map name or look up table
alpha:float- opacity of the histogram
gap:float- separation between adjacent bins as a fraction for their size
scalarbar:bool- add a scalarbar to right of the histogram
like:Figure- grab and use the same format of the given Figure (for superimposing)
xlim:list- [x0, x1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored.
ylim:list- [y0, y1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored.
aspect:float- the desired aspect ratio of the figure.
title:str- title of the plot to appear on top. If left blank some statistics will be shown.
xtitle:str- x axis title
ytitle:str- y axis title
ztitle:str- title for the scalar bar
ac:str- axes color, additional keyword for Axes can also be added
using e.g.
axes=dict(xyGrid=True)
Hint: examples/pyplot/histo_2d.py
Expand source code
class Histogram2D(Figure): """ Input data formats `[(x1,x2,..), (y1,y2,..)] or [(x1,y1), (x2,y2),..]` are both valid. Use keyword `like=...` if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message. Parameters ---------- bins : list binning as (nx, ny) weights : list array of weights to assign to each entry cmap : str, lookuptable color map name or look up table alpha : float opacity of the histogram gap : float separation between adjacent bins as a fraction for their size scalarbar : bool add a scalarbar to right of the histogram like : Figure grab and use the same format of the given Figure (for superimposing) xlim : list [x0, x1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored. ylim : list [y0, y1] range of interest. If left to None will automatically choose the minimum or the maximum of the data range. Data outside the range are completely ignored. aspect : float the desired aspect ratio of the figure. title : str title of the plot to appear on top. If left blank some statistics will be shown. xtitle : str x axis title ytitle : str y axis title ztitle : str title for the scalar bar ac : str axes color, additional keyword for Axes can also be added using e.g. `axes=dict(xyGrid=True)` .. hint:: examples/pyplot/histo_2d.py .. image:: https://vedo.embl.es/images/pyplot/histo_2D.png """ def __init__( self, xvalues, yvalues=None, bins=25, weights=None, cmap="cividis", alpha=1, gap=0, scalarbar=True, # Figure and axes options: like=None, xlim=None, ylim=(None, None), zlim=(None, None), aspect=1, title="", xtitle=" ", ytitle=" ", ztitle="", ac="k", **fig_kwargs, ): if yvalues is None: # assume [(x1,y1), (x2,y2) ...] format yvalues = xvalues[:, 1] xvalues = xvalues[:, 0] padding = [0, 0, 0, 0] if like is not None: xlim = like.xlim ylim = like.ylim aspect = like.aspect padding = like.padding if bins is None: bins = like.bins if bins is None: bins = 20 if isinstance(bins, int): bins = (bins, bins) if utils.isSequence(xlim): # deal with user passing eg [x0, None] _x0, _x1 = xlim if _x0 is None: _x0 = xvalues.min() if _x1 is None: _x1 = xvalues.max() xlim = [_x0, _x1] if utils.isSequence(ylim): # deal with user passing eg [x0, None] _y0, _y1 = ylim if _y0 is None: _y0 = yvalues.min() if _y1 is None: _y1 = yvalues.max() ylim = [_y0, _y1] H, xedges, yedges = np.histogram2d( xvalues, yvalues, weights=weights, bins=bins, range=(xlim, ylim), ) xlim = np.min(xedges), np.max(xedges) ylim = np.min(yedges), np.max(yedges) dx, dy = xlim[1] - xlim[0], ylim[1] - ylim[0] fig_kwargs["title"] = title fig_kwargs["xtitle"] = xtitle fig_kwargs["ytitle"] = ytitle fig_kwargs["ac"] = ac self.entries = len(xvalues) self.frequencies = H self.edges = (xedges, yedges) self.mean = (xvalues.mean(), yvalues.mean()) self.std = (xvalues.std(), yvalues.std()) self.bins = bins # internally used by "like" ############################### stats legend as htitle addstats = False if not title: if "axes" not in fig_kwargs: addstats = True axesopts = dict() fig_kwargs["axes"] = axesopts elif fig_kwargs["axes"] is False: pass else: axesopts = fig_kwargs["axes"] if "htitle" not in fig_kwargs["axes"]: addstats = True if addstats: htitle = f"Entries:~~{int(self.entries)} " htitle += f"Mean:~~{utils.precision(self.mean, 3)} " htitle += f"STD:~~{utils.precision(self.std, 3)} " axesopts["htitle"] = htitle axesopts["hTitleJustify"] = "bottom-left" axesopts["hTitleSize"] = 0.0175 axesopts["hTitleOffset"] = [-0.49, 0.01, 0] ############################################### Figure init Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs) if not self.yscale: return None ##################### the grid acts = [] g = shapes.Grid( pos=[(xlim[0] + xlim[1]) / 2, (ylim[0] + ylim[1]) / 2, 0], s=(dx, dy), res=bins[:2], ) g.alpha(alpha).lw(0).wireframe(False).flat().lighting("off") g.cmap(cmap, np.ravel(H.T), on="cells", vmin=zlim[0], vmax=zlim[1]) if gap: g.shrink(abs(1 - gap)) if scalarbar: sc = g.addScalarBar3D(ztitle, c=ac).scalarbar sc.scale([self.yscale, 1, 1]) ## prescale trick sbnds = sc.xbounds() sc.x(self.x1lim + (sbnds[1] - sbnds[0]) * 0.75) acts.append(sc) acts.append(g) self.insert(*acts, as3d=False) self.name = "Histogram2D"Ancestors
- Figure
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- Base3DProp
Inherited members
class PlotBars (data, errors=False, logscale=False, fill=True, gap=0.02, radius=0.05, c='olivedrab', alpha=1, texture='', outline=False, lw=2, lc='k', like=None, xlim=(None, None), ylim=(0, None), aspect=1.3333333333333333, padding=(0.025, 0.025, 0, 0.05), title='', xtitle=' ', ytitle=' ', ac='k', grid=False, ztolerance=None, **fig_kwargs)-
Creates a
PlotBars(Figure)object.Input must be in format
[counts, labels, colors, edges]. Either or bothedgesandcolorsare optional and can be omitted.Use keyword
like=...if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message.Parameters
errors:bool- show error bars
logscale:bool- use logscale on y-axis
fill:bool- fill bars woth solid color
c gap:float- leave a small space btw bars
radius:float- border radius of the top of the histogram bar. Default value is 0.1.
texture:str- url or path to an image to be used as texture for the bin
outline:bool- show outline of the bins
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") ac:str- axes color
padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
aspect:float- the desired aspect ratio of the figure. Default is 4/3.
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True)
Hint: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py
Expand source code
class PlotBars(Figure): """ Creates a `PlotBars(Figure)` object. Input must be in format `[counts, labels, colors, edges]`. Either or both `edges` and `colors` are optional and can be omitted. Use keyword `like=...` if you want to use the same format of a previously created Figure (useful when superimposing Figures) to make sure they are compatible and comparable. If they are not compatible you will receive an error message. Parameters ---------- errors : bool show error bars logscale : bool use logscale on y-axis fill : bool fill bars woth solid color `c` gap : float leave a small space btw bars radius : float border radius of the top of the histogram bar. Default value is 0.1. texture : str url or path to an image to be used as texture for the bin outline : bool show outline of the bins xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` ac : str axes color padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. aspect : float the desired aspect ratio of the figure. Default is 4/3. grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` .. hint:: examples/pyplot/histo_1d_a.py histo_1d_b.py histo_1d_c.py histo_1d_d.py .. image:: https://vedo.embl.es/images/pyplot/histo_1D.png """ def __init__( self, data, errors=False, logscale=False, fill=True, gap=0.02, radius=0.05, c="olivedrab", alpha=1, texture="", outline=False, lw=2, lc="k", # Figure and axes options: like=None, xlim=(None, None), ylim=(0, None), aspect=4/3, padding=(0.025, 0.025, 0, 0.05), # title="", xtitle=" ", ytitle=" ", ac="k", grid=False, ztolerance=None, **fig_kwargs, ): ndata = len(data) if ndata == 4: counts, xlabs, cols, edges = data elif ndata == 3: counts, xlabs, cols = data edges = np.array(range(len(counts) + 1)) + 0.5 elif ndata == 2: counts, xlabs = data edges = np.array(range(len(counts) + 1)) + 0.5 cols = [c] * len(counts) else: m = "barplot error: data must be given as [counts, labels, colors, edges] not\n" vedo.logger.error(m + f" {data}\n bin edges and colors are optional.") raise RuntimeError() # sanity checks assert len(counts) == len(xlabs) assert len(counts) == len(cols) assert len(counts) == len(edges) - 1 counts = np.asarray(counts) edges = np.asarray(edges) if logscale: counts = np.log10(counts + 1) if ytitle == " ": ytitle = "log_10 (counts+1)" if like is not None: xlim = like.xlim ylim = like.ylim aspect = like.aspect padding = like.padding if utils.isSequence(xlim): # deal with user passing eg [x0, None] _x0, _x1 = xlim if _x0 is None: _x0 = np.min(edges) if _x1 is None: _x1 = np.max(edges) xlim = [_x0, _x1] x0, x1 = np.min(edges), np.max(edges) y0, y1 = ylim[0], np.max(counts) if like is None: ylim = list(ylim) if xlim is None: xlim = [x0, x1] if ylim[1] is None: ylim[1] = y1 if ylim[0] != 0: ylim[0] = y0 fig_kwargs["title"] = title fig_kwargs["xtitle"] = xtitle fig_kwargs["ytitle"] = ytitle fig_kwargs["ac"] = ac fig_kwargs["ztolerance"] = ztolerance fig_kwargs["grid"] = grid centers = (edges[0:-1] + edges[1:]) / 2 binsizes = (centers - edges[0:-1]) * 2 if "axes" not in fig_kwargs: fig_kwargs["axes"] = dict() _xlabs = [] for center, xlb in zip(centers, xlabs): _xlabs.append([center, str(xlb)]) fig_kwargs["axes"]["xValuesAndLabels"] = _xlabs ############################################### Figure self.statslegend = "" self.edges = edges self.centers = centers self.bins = edges # internal used by "like" Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs) if not self.yscale: return None rs = [] maxheigth = 0 if fill: ##################### if outline: gap = 0 for i in range(len(centers)): binsize = binsizes[i] p0 = (edges[i] + gap * binsize, 0, 0) p1 = (edges[i + 1] - gap * binsize, counts[i], 0) if radius: rds = np.array([0, 0, radius, radius]) p1_yscaled = [p1[0], p1[1]*self.yscale, 0] r = shapes.Rectangle(p0, p1_yscaled, radius=rds*binsize, res=6) r.scale([1, 1/self.yscale, 1]) r.radius = None # so it doesnt get recreated and rescaled by insert() else: r = shapes.Rectangle(p0, p1) if texture: r.texture(texture) c = "w" r.PickableOff() maxheigth = max(maxheigth, p1[1]) if c in colors.cmaps_names: col = colors.colorMap((p0[0] + p1[0]) / 2, c, edges[0], edges[-1]) else: col = cols[i] r.color(col).alpha(alpha).lighting("off") r.name = f"bar_{i}" r.z(self.ztolerance) rs.append(r) elif outline: ##################### lns = [[edges[0], 0, 0]] for i in range(len(centers)): lns.append([edges[i], counts[i], 0]) lns.append([edges[i + 1], counts[i], 0]) maxheigth = max(maxheigth, counts[i]) lns.append([edges[-1], 0, 0]) outl = shapes.Line(lns, c=lc, alpha=alpha, lw=lw).z(self.ztolerance) outl.name = f"bar_outline_{i}" rs.append(outl) if errors: ##################### for x, f in centers: err = np.sqrt(f) el = shapes.Line([x, f-err/2, 0], [x, f+err/2, 0], c=lc, alpha=alpha, lw=lw) el.z(self.ztolerance * 2) rs.append(el) self.insert(*rs, as3d=False) self.name = "PlotBars"Ancestors
- Figure
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- Base3DProp
Inherited members
class PlotXY (data, xerrors=None, yerrors=None, lw=2, lc='k', la=1, dashed=False, splined=False, elw=2, ec=None, errorBand=False, marker='', ms=None, mc=None, ma=None, like=None, xlim=None, ylim=(None, None), aspect=1.3333333333333333, padding=0.05, title='', xtitle=' ', ytitle=' ', ac='k', grid=True, ztolerance=None, label='', **fig_kwargs)-
Creates a
PlotXY(Figure)object.Parameters
xerrors:bool- show error bars associated to each point in x
yerrors:bool- show error bars associated to each point in y
lw:int- width of the line connecting points in pixel units. Set it to 0 to remove the line.
lc:str- line color
la:float- line "alpha", opacity of the line
dashed:bool- draw a dashed line instead of a continous line
splined:bool- spline the line joining the point as a countinous curve
elw:int- width of error bar lines in units of pixels
ec:color- color of error bar, by default the same as marker color
errorBand:bool- represent errors on y as a filled error band.
Use
eckeyword to modify its color. marker:str, int- use a marker for the data points
ms:float- marker size
mc:color- color of the marker
ma:float- opacity of the marker
xlim:list- set limits to the range for the x variable
ylim:list- set limits to the range for the y variable
aspect:float, str- Desired aspect ratio.
Use
aspect="equal"to force the same units in x and y. Scaling factor is saved in Figure.yscale. padding:float, list- keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers.
title:str- title to appear on the top of the frame, like a header.
xtitle:str- title for the x-axis, can also be set using
axes=dict(xtitle="my x axis") ytitle:str- title for the y-axis, can also be set using
axes=dict(ytitle="my y axis") ac:str- axes color
grid:bool- show the backgound grid for the axes, can also be set using
axes=dict(xyGrid=True) ztolerance:float- a tolerance factor to superimpose objects (along the z-axis).
Example
.. code-block:: python
import numpy as np from vedo.pyplot import plot x = np.arange(0, np.pi, 0.1) fig = plot(x, np.sin(2*x), 'r0-', aspect='equal') fig+= plot(x, np.cos(2*x), 'blue4 o-', like=fig) fig.show()Hint
examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py
Expand source code
class PlotXY(Figure): """ Creates a `PlotXY(Figure)` object. Parameters ---------- xerrors : bool show error bars associated to each point in x yerrors : bool show error bars associated to each point in y lw : int width of the line connecting points in pixel units. Set it to 0 to remove the line. lc : str line color la : float line "alpha", opacity of the line dashed : bool draw a dashed line instead of a continous line splined : bool spline the line joining the point as a countinous curve elw : int width of error bar lines in units of pixels ec : color color of error bar, by default the same as marker color errorBand : bool represent errors on y as a filled error band. Use ``ec`` keyword to modify its color. marker : str, int use a marker for the data points ms : float marker size mc : color color of the marker ma : float opacity of the marker xlim : list set limits to the range for the x variable ylim : list set limits to the range for the y variable aspect : float, str Desired aspect ratio. Use `aspect="equal"` to force the same units in x and y. Scaling factor is saved in Figure.yscale. padding : float, list keep a padding space from the axes (as a fraction of the axis size). This can be a list of four numbers. title : str title to appear on the top of the frame, like a header. xtitle : str title for the x-axis, can also be set using `axes=dict(xtitle="my x axis")` ytitle : str title for the y-axis, can also be set using `axes=dict(ytitle="my y axis")` ac : str axes color grid : bool show the backgound grid for the axes, can also be set using `axes=dict(xyGrid=True)` ztolerance : float a tolerance factor to superimpose objects (along the z-axis). Example: .. code-block:: python import numpy as np from vedo.pyplot import plot x = np.arange(0, np.pi, 0.1) fig = plot(x, np.sin(2*x), 'r0-', aspect='equal') fig+= plot(x, np.cos(2*x), 'blue4 o-', like=fig) fig.show() .. image:: https://user-images.githubusercontent.com/32848391/74363882-c3638300-4dcb-11ea-8a78-eb492ad9711f.png .. hint:: examples/pyplot/plot_errbars.py, plot_errband.py, plot_pip.py, scatter1.py, scatter2.py .. image:: https://vedo.embl.es/images/pyplot/plot_pip.png """ def __init__( self, # data, xerrors=None, yerrors=None, # lw=2, lc="k", la=1, dashed=False, splined=False, # elw=2, # error line width ec=None, # error line or band color errorBand=False, # errors in x are ignored # marker="", ms=None, mc=None, ma=None, # Figure and axes options: like=None, xlim=None, ylim=(None, None), aspect=4/3, padding=0.05, # title="", xtitle=" ", ytitle=" ", ac="k", grid=True, ztolerance=None, label="", **fig_kwargs, ): line = False if lw > 0: line = True if marker == "" and not line and not splined: marker = "o" if like is not None: xlim = like.xlim ylim = like.ylim aspect = like.aspect padding = like.padding if utils.isSequence(xlim): # deal with user passing eg [x0, None] _x0, _x1 = xlim if _x0 is None: _x0 = data.min() if _x1 is None: _x1 = data.max() xlim = [_x0, _x1] # purge NaN from data validIds = np.all(np.logical_not(np.isnan(data))) data = np.array(data[validIds])[0] fig_kwargs["title"] = title fig_kwargs["xtitle"] = xtitle fig_kwargs["ytitle"] = ytitle fig_kwargs["ac"] = ac fig_kwargs["ztolerance"] = ztolerance fig_kwargs["grid"] = grid x0, y0 = np.min(data, axis=0) x1, y1 = np.max(data, axis=0) if xerrors is not None and not errorBand: x0 = min(data[:, 0] - xerrors) x1 = max(data[:, 0] + xerrors) if yerrors is not None: y0 = min(data[:, 1] - yerrors) y1 = max(data[:, 1] + yerrors) if like is None: if xlim is None: xlim = (None, None) xlim = list(xlim) if xlim[0] is None: xlim[0] = x0 if xlim[1] is None: xlim[1] = x1 ylim = list(ylim) if ylim[0] is None: ylim[0] = y0 if ylim[1] is None: ylim[1] = y1 self.entries = len(data) self.mean = data.mean() self.std = data.std() ######### the PlotXY marker if mc is None: mc = lc if ma is None: ma = la if label: nlab = LabelData() nlab.text = label nlab.tcolor = ac nlab.marker = marker if line and marker == "": nlab.marker = "-" nlab.mcolor = mc fig_kwargs["label"] = nlab ############################################### Figure init Figure.__init__(self, xlim, ylim, aspect, padding, **fig_kwargs) if not self.yscale: return None acts = [] ######### the PlotXY Line or Spline if dashed: l = shapes.DashedLine(data, c=lc, alpha=la, lw=lw) acts.append(l) elif splined: l = shapes.KSpline(data).lw(lw).c(lc).alpha(la) acts.append(l) elif line: l = shapes.Line(data, c=lc, alpha=la).lw(lw) acts.append(l) if marker: pts = np.c_[data, np.zeros(len(data))] if utils.isSequence(ms): ### variable point size mk = shapes.Marker(marker, s=1) mk.scale([1, 1 / self.yscale, 1]) msv = np.zeros_like(pts) msv[:, 0] = ms marked = shapes.Glyph( pts, glyphObj=mk, c=mc, orientationArray=msv, scaleByVectorSize=True ) else: ### fixed point size if ms is None: ms = (xlim[1] - xlim[0]) / 100.0 if utils.isSequence(mc): fig_kwargs["marker_color"] = None # for labels mk = shapes.Marker(marker, s=ms) mk.scale([1, 1 / self.yscale, 1]) msv = np.zeros_like(pts) msv[:, 0] = 1 marked = shapes.Glyph( pts, glyphObj=mk, c=mc, orientationArray=msv, scaleByVectorSize=True, ) else: mk = shapes.Marker(marker, s=ms) mk.scale([1, 1 / self.yscale, 1]) marked = shapes.Glyph(pts, glyphObj=mk, c=mc) marked.name = "Marker" marked.alpha(ma) marked.z(3 * self.ztolerance) acts.append(marked) ######### the PlotXY marker errors if ec is None: if mc is None: ec = lc else: ec = mc ztol = self.ztolerance if errorBand: yerrors = np.abs(yerrors) du = np.array(data) dd = np.array(data) du[:, 1] += yerrors dd[:, 1] -= yerrors if splined: res = len(data) * 20 band1 = shapes.KSpline(du, res=res) band2 = shapes.KSpline(dd, res=res) band = shapes.Ribbon(band1, band2, res=(res, 2)) else: dd = list(reversed(dd.tolist())) band = shapes.Line(du.tolist() + dd, closed=True) band.triangulate().lw(0) if ec is None: band.c(lc) else: band.c(ec) band.lighting("off").alpha(la).z(ztol) acts.append(band) else: ## xerrors if xerrors is not None: if len(xerrors) == len(data): errs = [] for i, val in enumerate(data): xval, yval = val xerr = xerrors[i] / 2 el = shapes.Line((xval-xerr, yval, ztol), (xval+xerr, yval, ztol)) el.lw(elw) errs.append(el) mxerrs = merge(errs).c(ec).lw(lw).alpha(ma).z(2 * ztol) acts.append(mxerrs) else: vedo.logger.error("in PlotXY(xerrors=...): mismatch in array length") ## yerrors if yerrors is not None: if len(yerrors) == len(data): errs = [] for i, val in enumerate(data): xval, yval = val yerr = yerrors[i] el = shapes.Line((xval, yval-yerr, ztol), (xval, yval+yerr, ztol)) el.lw(elw) errs.append(el) myerrs = merge(errs).c(ec).lw(lw).alpha(ma).z(2 * ztol) acts.append(myerrs) else: vedo.logger.error("in PlotXY(yerrors=...): mismatch in array length") self.insert(*acts, as3d=False) self.name = "PlotXY"Ancestors
- Figure
- Assembly
- vtkmodules.vtkRenderingCore.vtkAssembly
- vtkmodules.vtkRenderingCore.vtkProp3D
- vtkmodules.vtkRenderingCore.vtkProp
- vtkmodules.vtkCommonCore.vtkObject
- vtkmodules.vtkCommonCore.vtkObjectBase
- Base3DProp
Inherited members