I want to visualize the magnetic field of a wire with the quiver function.
#Calculation of a magnetic field of a wire
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from pylab import *
I = 100000000000
constant = 1e-7/(4*np.pi)
# wire elements; always lenght one
coord = [(10,10,0), (11,10,0), (12,10,0), (13,10,0), (14,10,0), (15,10,0), (16,10,0), (17,10,0), (18,10,0),
(19,10,0), (19,11,0), (19,12,0), (19,13,0)]
xwidth = 3
ywidth = 3
z = 1
b = np.zeros((xwidth,ywidth))
# calculate the b-field
def bfield(x,y,z,c):
for x in range(xwidth):
for y in range(ywidth):
# number of wire elements
for i in range(1,12):
rx = x-(coord[i][0]+coord[i+1][0])/2.
ry = y-(coord[i][1]+coord[i+1][1])/2.
rz = z * 1.0 # = z-0
r = (rx**2+ry**2+rz**2)**0.5 # distance r between field and middle of the wire
dl = np.array([(coord[i+1][0]-coord[i][0]), (coord[i+1][1]-coord[i][1]), 0])
bb = np.cross(dl, np.array([rx,ry,rz]))
e = constant*I*bb/r**3
print e
#print e[0], e[1]
b[x,y] += e[c] # EDIT
return b
X,Y = meshgrid(arange(0,xwidth,1),arange(0,ywidth,1))
U = bfield(X,Y,z,0)
V = bfield(X,Y,z,1)
quiver(X,Y,U,V)
xlim(0,xwidth)
ylim(0,ywidth)
show()
EDIT 2: How can I plot lines of the coords in the plot?
EDIT 3: I want to use quiver, but it doesn't work.
it looks like quiver only supports 2d plots right now, but you could make it 3d by plotting multiple 2d layers into a 3d plot. You can follow my example to see how to do these layers.
ValueError: too many values to unpack
That means you have more values on the RHS than variables on the LHS
Related
I wrote some code that creates randomised patches from graphs in matplotlib. Basically how it works is that you create a graph from nodes taken from a circle using the parametric equation for a circle and then you randomly displace the nodes along the vector of (0,0) to the node point on the circumference of the circle. That way you can be certain to avoid lines from crossing each other once the circle is drawn. In the end you just append the first (x,y) coordinate to the list of coordinates to close the circle.
What I want to do next is to find a way to fill that circular graph with a solid colour so that I can create a "stamp" that can be used to make randomised patches on a canvas that hopefully will not create crossing edges. I want to use this to make procedural risk maps in svg format, because a lot of those are uploaded with terrible edges using raster image formats using jpeg.
I am pretty sure that my information of the nodes should be sufficient to make that happen but I have no idea how to implement that. Can anyone help?
import numpy as np
import matplotlib.pyplot as plt
def node_circle(r=0.5,res=100):
# Create arrays (x and y coordinates) for the nodes on the circumference of a circle. Use parametric equation.
# x = r cos(t) y = r sin(t)
t = np.linspace(0,2*np.pi,res)
x = r*np.cos(t)
y = r*np.sin(t)
return t,x,y
def sgn(x,x_shift=-0.5,y_shift=1):
# A shifted sign function to use as a switching function
# in order to avoid shifts lower than -0.5 which is
# the radius of the circle.
return -0.5*(np.abs(x -x_shift)/(x -x_shift)) +y_shift
def displacer(x,y,low=-0.5,high=0.5,maxrad=0.5):
# Displaces the node points of the circle
shift = 0
shift_increment = 0
for i in range(len(x)):
shift_increment = np.random.uniform(low,high)
shift += shift_increment*sgn(maxrad)
x[i] += x[i]*shift
y[i] += y[i]*shift
x = np.append(x,x[0])
y = np.append(y,y[0])
return x,y
def plot():
# Actually visualises everything
fig, ax = plt.subplots(figsize=(4,4))
# np.random.seed(1)
ax.axis('off')
t,x,y = node_circle(res=100)
a = 0
x,y = displacer(x,y,low=-0.15,high=0.15)
ax.plot(x,y,'r-')
# ax.scatter(x,y,)
plt.show()
plot()
got it: the answer is to use matplotlib.Patches.Polygon
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
def node_circle(r=0.5,res=100):
# Create arrays (x and y coordinates) for the nodes on the circumference of a circle. Use parametric equation.
# x = r cos(t) y = r sin(t)
t = np.linspace(0,2*np.pi,res)
x = r*np.cos(t)
y = r*np.sin(t)
return x,y
def sgn(x,x_shift=-0.5,y_shift=1):
# A shifted sign function to use as a switching function
# in order to avoid shifts lower than -0.5 which is
# the radius of the circle.
return -0.5*(np.abs(x -x_shift)/(x -x_shift)) +y_shift
def displacer(x,y,low=-0.5,high=0.5,maxrad=0.5):
# Displaces the node points of the circle
shift = 0
shift_increment = 0
for i in range(len(x)):
shift_increment = np.random.uniform(low,high)
shift += shift_increment*sgn(maxrad)
x[i] += x[i]*shift
y[i] += y[i]*shift
x = np.append(x,x[0])
y = np.append(y,y[0])
return x,y
def patch_distributor(M,N,res,grid='square'):
# Distribute Patches based on a specified pattern/grid.
if grid == 'square':
data = np.zeros(shape=(M,N,2,res+1))
for i in range(M):
for j in range(N):
x,y = displacer(*node_circle(res=res),low=-0.2,high=0.2)
data[i,j,0,:] = x
data[i,j,1,:] = y
return data
def plot(res):
# Actually visualises everything
fig, ax = plt.subplots(figsize=(4,4))
# np.random.seed(1)
ax.axis('off')
# x,y = node_circle(res=res)
# x,y = displacer(x,y,low=-0.15,high=0.15)
# xy = np.zeros((len(x),2))
# xy[:,0] = x
# xy[:,1] = y
patch_data = patch_distributor(10,10,res)
for i in range(patch_data.shape[0]):
for j in range(patch_data.shape[1]):
x,y = patch_data[i,j]
x += i*0.5
y += j*0.5
xy = np.zeros((len(x),2))
xy[:,0] = x
xy[:,1] = y
patch = Polygon(xy,fc='w',ec='k',lw=2,zorder=np.random.randint(2),antialiased=False)
ax.add_patch(patch)
ax.autoscale_view()
# ax.plot(x,y,'r-')
# ax.scatter(x,y,)
plt.savefig('lol.png')
plot(res=40)
# Displace circle along the line of (0,0) -> (cos(t),sin(t))
# Make the previous step influence the next to avoid jaggedness
# limit displacement level to an acceptable amount
# Random displaced cubic grid as placing points for stamps.
Aim
I would like to create a 3D Streamtube Plot with Plotly.
Here is a cross-section of the vector field in the middle of the plot to give you an idea of how it looks like:
The final vector field should have rotational symmetry.
My Attempt
Download the data here: https://filebin.net/x6ywfuo6v4851v74
Run the code bellow:
Code:
import plotly.graph_objs as go
import plotly.express as px
import pandas as pd
import numpy as np
import plotly.io as pio
pio.renderers.default='browser'
# Import data to pandas
df = pd.read_csv("data.csv")
# Plot
X = np.linspace(0,1,101)
Y = np.linspace(0,1,10)
Z = np.linspace(0,1,101)
# Points from which the streamtubes should originate
xpos,ypos = np.meshgrid(X[::5],Y, indexing="xy")
xpos = xpos.reshape(1,-1)[0]
ypos = ypos.reshape(1,-1)[0]
starting_points = px.scatter_3d(
x=xpos,
y=ypos,
z=[-500]*len(xpos)
)
starting_points.show()
# Streamtube Plot
data_plot = [go.Streamtube(
x = df['x'],
y = df['y'],
z = df['z'],
u = df['u'],
v = df['v'],
w = df['w'],
starts = dict( #Determines the streamtubes starting position.
x=xpos,
y=ypos,
z=[-500]*len(xpos)
),
#sizeref = 0.3,
colorscale = 'jet',
showscale = True,
maxdisplayed = 300 #Determines the maximum segments displayed in a streamtube.
)]
fig = go.Figure(data=data_plot)
fig.show()
The initial points (starting points) of the streamtubes seem to be nicely defined:
...but the resulting 3D streamtube plot is very weird:
Edit
I tried normalizing the field plot, but the result is still not satisfactory:
import plotly.graph_objs as go
import pandas as pd
import numpy as np
import plotly.io as pio
pio.renderers.default='browser'
# Import data to pandas
df = pd.read_csv("data.csv")
# NORMALIZE VECTOR FIELD -> between [0,1]
df["u"] = (df["u"]-df["u"].min()) / (df["u"].max()-df["u"].min())
df["v"] = (df["v"]-df["v"].min()) / (df["v"].max()-df["v"].min())
df["w"] = (df["w"]-df["w"].min()) / (df["w"].max()-df["w"].min())
# Plot
X = np.linspace(0,1,101)
Y = np.linspace(0,1,10)
Z = np.linspace(0,1,101)
# Points from which the streamtubes should originate
xpos,ypos = np.meshgrid(X[::5],Y, indexing="xy")
xpos = xpos.reshape(1,-1)[0]
ypos = ypos.reshape(1,-1)[0]
# Streamtube Plot
data_plot = [go.Streamtube(
x = df['x'],
y = df['y'],
z = df['z'],
u = df['u'],
v = df['v'],
w = df['w'],
starts = dict( #Determines the streamtubes starting position.
x=xpos,
y=ypos,
z=[0]*len(xpos)
),
#sizeref = 0.3,
colorscale = 'jet',
showscale = True,
maxdisplayed = 300 #Determines the maximum segments displayed in a streamtube.
)]
fig = go.Figure(data=data_plot)
fig.show()
Data
As for the data itself:
It is created from 10 slices (y-direction). For each slice (y), [u,v,w] on a regular xz mesh (101x101) was computed. The whole was then assembled into the dataframe which you can download, and which has 101x101x10 data points.
Edit 2
It may be that I am wrongly converting my original data (download here: https://filebin.net/tlgkz3fy1h3j6h5o) into the format suitable for plotly, hence I was wondering if you know how this can be done correctly?
Here some code to visualize the data in a 3D vector plot correctly:
# %%
import pickle
import numpy as np
import matplotlib.pyplot as plt
# Import Full Data
with open("full_data.pickle", 'rb') as handle:
full_data = pickle.load(handle)
# Axis
X = np.linspace(0,1,101)
Y = np.linspace(0,1,10)
Z = np.linspace(-500,200,101)
# Initialize List of all fiels
DX = []
DY = []
DZ = []
for cross_section in list(full_data["cross_sections"].keys()):
# extract field components in x, y, and z
dx,dy,dz = full_data["cross_sections"][cross_section]
# Make them numpy imediatley
dx = np.array(dx)
dy = np.array(dy)
dz = np.array(dz)
# Apppend
DX.append(dx)
DY.append(dy)
DZ.append(dz)
#Convert to numpy
DX = np.array(DX)
DY = np.array(DY)
DZ = np.array(DZ)
# Create 3D Quiver Plot with color gradient
# Source: https://stackoverflow.com/questions/65254887/how-to-plot-with-matplotlib-a-3d-quiver-plot-with-color-gradient-for-length-giv
def plot_3d_quiver(x, y, z, u, v, w):
# COMPUTE LENGTH OF VECTOR -> MAGNITUDE
c = np.sqrt(np.abs(v) ** 2 + np.abs(u) ** 2 + np.abs(w) ** 2)
c = (c.ravel() - c.min()) / c.ptp()
# Repeat for each body line and two head lines
c = np.concatenate((c, np.repeat(c, 2)))
# Colormap
c = plt.cm.jet(c)
fig = plt.figure(dpi =300)
ax = fig.gca(projection='3d')
ax.quiver(x, y, z, u, v, w, colors=c, length=0.2, arrow_length_ratio=0.7)
plt.gca().invert_zaxis()
plt.show()
# Create Mesh !
xi, yi, zi = np.meshgrid(X, Y, Z, indexing='xy')
skip_every = 5
skip_slice = 2
skip3D=(slice(None,None,skip_slice),slice(None,None,skip_every),slice(None,None,skip_every))
# Source: https://stackoverflow.com/questions/68690442/python-plotting-3d-vector-field
plot_3d_quiver(xi[skip3D], yi[skip3D], zi[skip3D]/1000, DX[skip3D], DY[skip3D],
np.moveaxis(DZ[skip3D],2,1))
As you can see there are some long downward vectors in the middle of the 3D space, which is not shown in the plotly tubes.
Edit 3
Using the code from the answer, I get this:
This is a huge improvement. This looks almost perfect and is in accordance to what I expect.
A few more questions:
Is there a way to also show some tubes at the lower part of the plot?
Is there a way to flip the z-axis, such that the tubes are coming down from -z to +z (like shown in the cross-section streamline plot) ?
How does the data need to be structured to be organized correctly for the plotly plot? I ask that because of the use of np.moveaxis()?
I have rewritten my answer to reflect the history of conversation but in a disciplined manner.
The situation is:
len(np.unique(df['x']))
>>> 101
that when compared with:
len(np.unique(df['y']))
>>> 10
Seems data in y-direction are much coarser than that of x-direction!
But in z-direction the situation is even worse because the range of data are way more than that of x and y:
df.min()
>>> x 0.000000
y 0.000000
z -500.000000
u -0.369106
v -0.259156
w -0.517652
df.max()
>>> x 1.000000
y 1.000000
z 200.000000
u 0.368312
v 0.238271
w 1.257869
The solution to the ill formed data-set comprises of three steps:
Normalize the vector field and sample points in each direction
Either reduce data density in x and z direction or increase density of data on y-axis.(This step is optional but generally recommended)
After making a plot based on the new data, change axis ticks to the real values.
To normalize a vector-field in this situation which apparently is an engineering one, it's important to maintain the relative length of vectors on every spacial point by doing it this way:
# NORMALIZE VECTOR FIELD -> between [0,1]
np_df = np.array([u, v, w])
vecf_norm = np.linalg.norm(np_df, 2, axis=0)
max_norm = np.max(vecf_norm)
min_norm = np.min(vecf_norm)
u = u * (vecf_norm - min_norm) / (max_norm - min_norm)
v = v * (vecf_norm - min_norm) / (max_norm - min_norm)
w = w * (vecf_norm - min_norm) / (max_norm - min_norm)
As you will see at the end, this formulation will be used to enhance the resulting tube-plot.
Please let me add some important details about using dimensionless data for engineering data visualisation:
First of all if this vector field is resulted from any sort of differential equations, it is highly recommended to reformulate your P.D.F. to a dimensionless equation before attempting to solve it numerically.
If the vector field is result of an already dimensionless differential equation, you need to plot it using dimensionless data (including geometry and u,v,w values).
Please consider plotly uses the local divergence values to determine the local diameter of the tubes. When changing the vector field (and the geometry) we are changing the divergence as well.
I tried to mix your initial and second codes to get this:
import plotly.graph_objs as go
import plotly.express as px
import pandas as pd
import numpy as np
import plotly.io as pio
import pickle
pio.renderers.default='browser'
# Import Full Data
with open("full_data.pickle", 'rb') as handle:
full_data = pickle.load(handle)
# Axis
X = np.linspace(0,1,101)
Y = np.linspace(0,1,10)
Z = np.linspace(-0.5,0.2,101)
xpos,ypos = np.meshgrid(X[::5],Y, indexing="ij")
#xpos = xpos.reshape(1,-1)[0]
#ypos = ypos.reshape(1,-1)[0]
xpos = np.ravel(xpos)
ypos = np.ravel(ypos)
# Initialize List of all fields
DX = []
DY = []
DZ = []
for cross_section in list(full_data["cross_sections"]):
# extract field components in x, y, and z
dx,dy,dz = full_data["cross_sections"][cross_section]
# Make them numpy imediatley
dx = np.array(dx)
dy = np.array(dy)
dz = np.array(dz)
# Apppend
DX.append(dx)
DY.append(dy)
DZ.append(dz)
#Convert to numpy
move_i = [0, 1, 2]
move_e = [1, 2, 0]
DX = np.moveaxis(np.array(DX), move_i, move_e)
DY = np.moveaxis(np.array(DY), move_i, move_e)
DZ = np.moveaxis(np.array(DZ), move_i, move_e)
# Create Mesh !
xi, yi, zi = np.meshgrid(X, Y, Z, indexing="ij")
data_plot = [go.Streamtube(
x = np.ravel(xi),
y = np.ravel(yi),
z = np.ravel(zi),
u = np.ravel(DX),
v = np.ravel(DY),
w = np.ravel(DZ),
starts = dict( #Determines the streamtubes starting position.
x=xpos,
y=ypos,
z=np.array([-0.5]*len(xpos)
)),
#sizeref = 0.3,
colorscale = 'jet',
showscale = True,
maxdisplayed = 300 #Determines the maximum segments displayed in a streamtube.
)]
fig = go.Figure(data=data_plot)
fig.show()
In this code I have removed the skipping thing, because I suspect the evil is happening there. The resulting plot which you have added to your question, seems similar to the 2D plot of your question, but it requires more work to have better result.
So using what have been told already in addition to the info below:
Yes, Tubes are started from the start points, so you need to define start points where you expect to see tubes there! but, the start points need to be geometrically inside the space defined by sample points, otherwise maybe plotly be forced to extrapolate data (I'm not sure about this) and it results in distorted and unexpected results. This means you can define start points both in upper and lower planes of the field to ensure that you have vectors which emit on both planes. Sometime the vectors are there but you can not see them because they are drawn too thin to see. It's because their local divergences are too low, may be if you normalize this vector field by the rules mentioned earlier, it gives you a better result.
According to plotly documentation:
You can tell plotly's automatic axis range calculation logic to reverse the direction of an axis by setting the autorange axis property to "reversed"
plotly reads data point-by-point, so the order of points doesn't really matter but in case of your problem, the issue happens when data became corrupted and disturbed during omitting of some of sample points. i.e. some of x,y,z and some of u,v,w data loosed their correct location which resulted in an entirely different unexpected data set.
I have tried to normalize the (u,v,w) vector-field(using the formulation provided earlier):
import plotly.graph_objs as go
import plotly.express as px
import pandas as pd
import numpy as np
import plotly.io as pio
import pickle
pio.renderers.default='browser'
# Import Full Data
with open("full_data.pickle", 'rb') as handle:
full_data = pickle.load(handle)
# Axis
X = np.linspace(0,1,101)
Y = np.linspace(0,1,10)
Z = np.linspace(-0.5,0.2,101)
xpos,ypos = np.meshgrid(X[::5],Y, indexing="ij")
#xpos = xpos.reshape(1,-1)[0]
#ypos = ypos.reshape(1,-1)[0]
xpos = np.ravel(xpos)
ypos = np.ravel(ypos)
# Initialize List of all fields
DX = []
DY = []
DZ = []
for cross_section in list(full_data["cross_sections"]):
# extract field components in x, y, and z
dx,dy,dz = full_data["cross_sections"][cross_section]
# Make them numpy imediatley
dx = np.array(dx)
dy = np.array(dy)
dz = np.array(dz)
# Apppend
DX.append(dx)
DY.append(dy)
DZ.append(dz)
#Convert to numpy
move_i = [0, 1, 2]
move_e = [1, 2, 0]
DX = np.moveaxis(np.array(DX), move_i, move_e)
DY = np.moveaxis(np.array(DY), move_i, move_e)
DZ = np.moveaxis(np.array(DZ), move_i, move_e)
u1 = np.ravel(DX)
v1 = np.ravel(DY)
w1 = np.ravel(DZ)
np_df = np.array([u1, v1, w1])
vecf_norm = np.linalg.norm(np_df, 2, axis=0)
max_norm = np.max(vecf_norm)
min_norm = np.min(vecf_norm)
u2 = u1 * (vecf_norm - min_norm) / (max_norm - min_norm)
v2 = v1 * (vecf_norm - min_norm) / (max_norm - min_norm)
w2 = w1 * (vecf_norm - min_norm) / (max_norm - min_norm)
# Create Mesh !
xi, yi, zi = np.meshgrid(X, Y, Z, indexing="ij")
data_plot = [go.Streamtube(
x = np.ravel(xi),
y = np.ravel(yi),
z = np.ravel(zi),
u = u2,
v = v2,
w = w2,
starts = dict( #Determines the streamtubes starting position.
x=xpos,
y=ypos,
z=np.array([-0.5]*len(xpos)
)),
#sizeref = 0.3,
colorscale = 'jet',
showscale = True,
maxdisplayed = 300 #Determines the maximum segments displayed in a streamtube.
)]
fig = go.Figure(data=data_plot)
fig.show()
and get a better plot:
I have made the below in order to create a cube by giving different X, Y, Z values, but when I give for example (6,3,2) I don't receive 6 blocks on X-axis, 3 blocks on Y-axis, and 2 blocks on the Z-axis, but I received a cube 6x6x4, why?
import matplotlib.pyplot as plt
import numpy as np
def make(X,Y,Z):
x, y, z = np.indices((X,Y,Z))
cube2 = (x==0) & (y==0) & (z==0)
for i in range (X):
for j in range (Y):
for k in range(Z):
cube1 = (x==i) & (y==j) & (z==k)
cube2 = cube2|cube1
colors = np.ones(cube2.shape, dtype=object)
from matplotlib import cm
for i in range (X):
for j in range (Y):
for k in range(Z):
if 0<i<=3:
colors[i][j][k] = cm.gray(((i+j+k)/X),alpha=0.8)
elif 3<i<=6:
colors[i][j][k] = cm.winter(((i+j+k)/Y),alpha=0.8)
else:
colors[i][j][k] = cm.copper(((i+j+k)/Z),alpha=0.8)
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.voxels(cube2, facecolors=colors, edgecolor=None)
plt.show()
make(6,3,2,)
I also need your help with something else. I have created a bezier line according to the code.
#bezier line
import numpy as np
import matplotlib.pyplot as plt
A = np.array([10,20])
B = np.array([15,8])
C = np.array([8,22])
A = A.reshape(2,1)
B = B.reshape(2,1)
C = C.reshape(2,1)
t = np.arange(0.0, 1.0, 0.1).reshape(1,-1)
P0 = A * t + (1 - t) * B
P1 = B * t + (1 - t) * C
Pfinal = P0 * t + (1 - t) * P1
x=np.transpose(Pfinal)
x1= x[:, 0]
print(x1)
plt.plot(x1)
Is it possible to implement this to the above first code in order to choose different colors instead of what I have done in the if statement? For example, on the Z axis at the right of this bezier line to have cm.winter colors, at the left cm.copper or something similar.
Your code produces the expected plots. I don't see a problem. This is not an answer but a means of showing you the plot I get with your code. What are you looking for?
make(6,3,2)
I need to discriminate against non physical data in my heatmaps. I am using python(bokeh and holoviews).
Example Code:
import numpy as np
import holoviews as hv
import warnings\
warnings.filterwarnings("ignore")
hv.extension('bokeh')
%opts Image [colorbar=True tools=['hover']
%opts Image (cmap='rainbow')
%output max_frames=3000
import Definitions as def #these are my equations
a = 2
b = .2
c = .3
d = .4
e = 0
f = 0
g = 0
h = 0
i = .2
j = 0
l = .2
m = 1
N = 100 # number of points
yval = np.linspace(0.1,1,N)
xval = np.linspace(0,5,N)
bounds = (0,.1,5,1) #this sets the bounds from .1 to 1 on y axis and 0 to 5 on x axis
xval,yval = np.meshgrid(xval, yval, indexing 'xy')
v1val = def.v1(yval,b,a,m,l,xval) #Calling my these definitions from a seperate file
v2val = def.v2(b,m,a)
Zlist = def.Z(a,v2val/d,v2val/c,h,e,i,j,xval,l,v1val,f,g)
plot = hv.Image(np.flipud(Zlist), label = "Z Heat Map" \
,bounds = bounds, vdims = hv.Dimension('Z', range=(0,1))).redimlabel(x = 'x', y = 'y')
plot
This code makes a heat map where the value of the function Z is mapped as a color for a region of x and y. So Z depends on x and y and for different values of x and y, Z will have different colors.
My problem: I need to discriminate against any situations where v1val < c . The code I currently have plots all of the data but I need it to plot only the data for v1val > c and maybe assign a color like white or black to portion of the graph corresponding to v1val < c. I also similarly need to white out or blackout any region where v2val < d. Essentially I want to black out or white out regions of my heatmap that correspond to non physical data ie when v1val < c and when v2val < d.
I have been trying different things but each time I have some idea I get an error like " The truth of a value of an array with more than one element is ambiguous. Use a.any() or a.all()"
Help with blacking out this non physical data would be much appreciated.
You can see how to black out or white out regions of a heatmap in http://pyviz.org/tutorial/01_Workflow_Introduction.html :
def nansum(a, **kwargs):
return np.nan if np.isnan(a).all() else np.nansum(a, **kwargs)
heatmap = df.hvplot.heatmap('Year', 'State', 'measles', reduce_function=nansum)
I already have a rectangle triangulated by a scipy.spatial.Delaunay() object. I manage to stretch and curve it around so that it looks like an annulus cut along a line. Here is some code to make something with the same topology:
from scipy.spatial import Delaunay
NR = 22
NTheta = 36
Rin = 1
Rout = 3
alphaFactor = 33/64
alpha = np.pi/alphaFactor # opening angle of wedge
u=np.linspace(pi/2, pi/2 + alpha, NTheta)
v=np.linspace(Rin, Rout, NR)
u,v=np.meshgrid(u,v)
u=u.flatten()
v=v.flatten()
#evaluate the parameterization at the flattened u and v
x=v*np.cos(u)
y=v*np.sin(u)
#define 2D points, as input data for the Delaunay triangulation of U
points2D=np.vstack([u,v]).T
xy0 = np.vstack([x,y]).T
triLattice = Delaunay(points2D) #triangulate the rectangle U
triSimplices = triLattice.simplices
plt.figure()
plt.triplot(x, y, triSimplices, linewidth=0.5)
Starting from this topology, I now want to join up the two open edges, and make a closed annulus (change the topology, that is). How do I manually add new triangles to the existing triangulation?
A solution is to merge the points around the gap. Here is a way to do this, by keeping track of the indexes of the corresponding points:
import matplotlib.pylab as plt
from scipy.spatial import Delaunay
import numpy as np
NR = 4
NTheta = 16
Rin = 1
Rout = 3
alphaFactor = 33/64 # -- set to .5 to close the gap
alpha = np.pi/alphaFactor # opening angle of wedge
u = np.linspace(np.pi/2, np.pi/2 + alpha, NTheta)
v = np.linspace(Rin, Rout, NR)
u_grid, v_grid = np.meshgrid(u, v)
u = u_grid.flatten()
v = v_grid.flatten()
# Get the indexes of the points on the first and last columns:
idx_grid_first = (np.arange(u_grid.shape[0]),
np.zeros(u_grid.shape[0], dtype=int))
idx_grid_last = (np.arange(u_grid.shape[0]),
(u_grid.shape[1]-1)*np.ones(u_grid.shape[0], dtype=int))
# Convert these 2D indexes to 1D indexes, on the flatten array:
idx_flat_first = np.ravel_multi_index(idx_grid_first, u_grid.shape)
idx_flat_last = np.ravel_multi_index(idx_grid_last, u_grid.shape)
# Evaluate the parameterization at the flattened u and v
x = v * np.cos(u)
y = v * np.sin(u)
# Define 2D points, as input data for the Delaunay triangulation of U
points2D = np.vstack([u, v]).T
triLattice = Delaunay(points2D) # triangulate the rectangle U
triSimplices = triLattice.simplices
# Replace the 'last' index by the corresponding 'first':
triSimplices_merged = triSimplices.copy()
for i_first, i_last in zip(idx_flat_first, idx_flat_last):
triSimplices_merged[triSimplices == i_last] = i_first
# Graph
plt.figure(figsize=(7, 7))
plt.triplot(x, y, triSimplices, linewidth=0.5)
plt.triplot(x, y, triSimplices_merged, linewidth=0.5, color='k')
plt.axis('equal');
plt.plot(x[idx_flat_first], y[idx_flat_first], 'or', label='first')
plt.plot(x[idx_flat_last], y[idx_flat_last], 'ob', label='last')
plt.legend();
which gives:
Maybe you will have to adjust the definition of the alphaFactor so that the gap has the right size.