I have a function that produces triangles and quadrilaterals (called 'trisq') in red or green, resp. My goal is to make an arrangement of these shapes on the same plot by running a loop over my drawing function.
I can draw multiple shapes and call plt.show() on it which works fine but after that I won't be able to add more shapes as it gives me a blank output.
I think my issue is that I don't know how to control subplot command. Please see my inline comment in the code for how it goes wrong. What would be the cleanest way to do this? Thanks!
(Btw, this is my first time posting here. I think my question is basic but I hope that at least I've posed it in a clear way).
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
fig, ax = plt.subplots()
def trisq(points):
inf = 20
plt.xlim(-inf, inf)
plt.ylim(-inf, inf)
plt.gca().set_aspect('equal', adjustable='box')
ver = np.array(points)
polygon = Polygon(ver, True)
patches = []
patches.append(polygon)
if len(points) == 3:
color = 'red'
elif len(points) == 4:
color = 'green'
p = PatchCollection(patches, color = color,cmap=matplotlib.cm.jet, alpha=0.4)
ax.add_collection(p)
trisq([(4,18),(6,16),(5,-1),(-5,9)]
trisq([(4,-8),(1,7),(15,9)])
# this works as expected
plt.show()
trisq([(4,8),(12,3),(0,0),(1,9)])
# but this one returns a blank plot
plt.show()
Update:
My concrete question is: how do I show a graph, then add more elements to it and show it again in the above context and possibly repeat inside a loop? Apparently, plt.show() can only be called once and not in an ongoing manner.
Plt.show() shows the active figures. After your first call to plt.show() there is no active figure any more.
Unfortunately the question is not clear about what the actual goal is.
You may call plt.show only once at the end. You may also create a new figure in between.
Make sure to add the collection inside the trisq function.
Related
So I'm trying to expand on this code, which is the only code I could find to display Markov Chains as a diagram of nodes and arrows. Specifically, I needed it to work for more than 4 states and I have been editing it to suit my needs. Since right now I want to use it for n=7 where any two states have a transition probability, it can get very messy with all the arrows, which is why I wanted to use the parameter alpha in the matplotlib.patches.FancyArrow() function.
However, I have tested it and while I get an error if I give it a value outside of the interval [0,1], any value in that interval seems to do nothing, whether it's 0.001 or 0.999. The documentation isn't great, it includes alpha as a possible kwarg but the description just says "unknown". In the "Arrow Guide" there is no mention of this parameter at all. So does anyone know how I can make my arrows more transparent?
Here is a code example where you can change alpha and see no change:
import matplotlib.patches as mpatches
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
fig, ax = plt.subplots(figsize=(20,20))
plt.xlim(-10,10)
plt.ylim(-10,10)
coords = [(5,7),(3,-6),(0,5),(-2,-4)]
for (x,y) in coords:
arrow = mpatches.FancyArrow(0,0,x,y,
width = .2,
head_width = 1,
length_includes_head = True,
alpha = 0.1)
p = PatchCollection(
[arrow],
edgecolor = '#a3a3a3',
facecolor = '#a3a3a3'
)
ax.add_collection(p)
plt.axis("off")
plt.show()
Ok I just realized my mistake (well sort of, I don't really understand the mechanics of why this works). I have to pass the alpha keyword in the PatchCollection() function. Then it works. Thank you to myself for figuring this out lol
This is a slightly tricky one to explain. Basically, I want to make an inset plot and then utilize the convenience of mpl_toolkits.axes_grid1.inset_locator.mark_inset, but I want the data in the inset plot to be completely independent of the data in the parent axes.
Example code with the functions I'd like to use:
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from mpl_toolkits.axes_grid1.inset_locator import mark_inset
from mpl_toolkits.axes_grid1.inset_locator import InsetPosition
data = np.random.normal(size=(2000,2000))
plt.imshow(data, origin='lower')
parent_axes = plt.gca()
ax2 = inset_axes(parent_axes, 1, 1)
ax2.plot([900,1100],[900,1100])
# I need more control over the position of the inset axes than is given by the inset_axes function
ip = InsetPosition(parent_axes,[0.7,0.7,0.3,0.3])
ax2.set_axes_locator(ip)
# I want to be able to control where the mark is connected to, independently of the data in the ax2.plot call
mark_inset(parent_axes, ax2, 2,4)
# plt.savefig('./inset_example.png')
plt.show()
The example code produces the following image:
So to sum up: The location of the blue box is entire controlled by the input data to ax2.plot(). I would like to manually place the blue box and enter whatever I want into ax2. Is this possible?
quick edit: to be clear, I understand why inset plots would have the data linked, as that's the most likely usage. So if there's a completely different way in matplotlib to accomplish this, do feel free to reply with that. However, I am trying to avoid manually placing boxes and lines to all of the axes I would place, as I need quite a few insets into a large image.
If I understand correctly, you want an arbitrarily scaled axis at a given position that looks like a zoomed inset, but has no connection to the inset marker's position.
Following your approach you can simply add another axes to the plot and position it at the same spot of the true inset, using the set_axes_locator(ip) function. Since this axis is drawn after the original inset, it will be on top of it and you'll only need to hide the tickmarks of the original plot to let it disappear completely (set_visible(False) does not work here, as it would hide the lines between the inset and the marker position).
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes, mark_inset, InsetPosition
data = np.random.normal(size=(200,200))
plt.imshow(data, origin='lower')
parent_axes = plt.gca()
ax2 = inset_axes(parent_axes, 1, 1)
ax2.plot([60,75],[90,110])
# hide the ticks of the linked axes
ax2.set_xticks([])
ax2.set_yticks([])
#add a new axes to the plot and plot whatever you like
ax3 = plt.gcf().add_axes([0,0,1,1])
ax3.plot([0,3,4], [2,3,1], marker=ur'$\u266B$' , markersize=30, linestyle="")
ax3.set_xlim([-1,5])
ax3.set_ylim([-1,5])
ip = InsetPosition(parent_axes,[0.7,0.7,0.3,0.3])
ax2.set_axes_locator(ip)
# set the new axes (ax3) to the position of the linked axes
ax3.set_axes_locator(ip)
# I want to be able to control where the mark is connected to, independently of the data in the ax2.plot call
mark_inset(parent_axes, ax2, 2,4)
plt.show()
FWIW, I came up with a hack that works.
In the source code for inset_locator, I added a version of mark_inset that takes another set of axes used to define the TransformedBbox:
def mark_inset_hack(parent_axes, inset_axes, hack_axes, loc1, loc2, **kwargs):
rect = TransformedBbox(hack_axes.viewLim, parent_axes.transData)
pp = BboxPatch(rect, **kwargs)
parent_axes.add_patch(pp)
p1 = BboxConnector(inset_axes.bbox, rect, loc1=loc1, **kwargs)
inset_axes.add_patch(p1)
p1.set_clip_on(False)
p2 = BboxConnector(inset_axes.bbox, rect, loc1=loc2, **kwargs)
inset_axes.add_patch(p2)
p2.set_clip_on(False)
return pp, p1, p2
Then in my original-post code I make an inset axis where I want the box to be, pass it to my hacked function, and make it invisible:
# location of desired axes
axdesire = inset_axes(parent_axes,1,1)
axdesire.plot([100,200],[100,200])
mark_inset_hack(parent_axes, ax2, axdesire, 2,4)
axdesire.set_visible(False)
Now I have a marked box at a different location in data units than the inset that I'm marking:
It is certainly a total hack, and at this point I'm not sure it's cleaner than simply drawing lines manually, but I think for a lot of insets this will keep things conceptually cleaner.
Other ideas are still welcome.
I want to create a smooth cylinder using matplotlib/pyplot. I've adapted a tutorial online and produced the following minimal example:
from numpy import meshgrid,linspace,pi,sin,cos,shape
from matplotlib import pyplot
import matplotlib.tri as mtri
from mpl_toolkits.mplot3d import Axes3D
u,v = meshgrid(linspace(0,10,10),linspace(0,2*pi,20))
u = u.flatten()
v = v.flatten()
x = u
z = sin(v)
y = cos(v)
tri = mtri.Triangulation(u, v)
fig = pyplot.figure()
ax = fig.add_axes([0,0,1,1],projection='3d')
ax.plot_trisurf(x,y,z,triangles=tri.triangles,linewidth=0)
pyplot.show()
which produces a cylinder. I set linewidth=0 to remove the wireframe, however, there is now the "ghost" of the wireframe because the triangulation has (presumably) been spaced assuming the wireframe is there to fill in the gaps. This looks to be specific to plot_trisurf, because there are other 3d plotting examples (e.g., using plot_surface) which set linewidth=0 without these gaps showing up.
Doing an mtri.Triangulation?, it seems like it might not be possible to "perfectly" fill in the gaps, since it states
>Notes
> -----
> For a Triangulation to be valid it must not have duplicate points,
> triangles formed from colinear points, or overlapping triangles.
One partial solution is to just color the wireframe the same shade of blue, but after I've fixed this problem I also want to add a light source/shading on the surface, which would put me back at square one.
Is there a way to make this work? Or can someone suggest a different approach? Thanks for any help.
ax.plot_trisurf(x,y,z,triangles=tri.triangles,linewidth=0, antialiased=False)
Using Matplotlib I'd like to remove the grid lines inside the plot, while keeping the frame (i.e. the axes lines). I've tried the code below and other options as well, but I can't get it to work. How do I simply keep the frame while removing the grid lines?
I'm doing this to reproduce a ggplot2 plot in matplotlib. I've created a MWE below. Be aware that you need a relatively new version of matplotlib to use the ggplot2 style.
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
import numpy as np
if __name__ == '__main__':
values = np.random.uniform(size=20)
plt.style.use('ggplot')
fig = plt.figure()
_, ax1 = P.subplots()
weights = np.ones_like(values)/len(values)
plt.hist(values, bins=20, weights=weights)
ax1.set_xlabel('Value')
ax1.set_ylabel('Probability')
ax1.grid(b=False)
#ax1.yaxis.grid(False)
#ax1.xaxis.grid(False)
ax1.set_axis_bgcolor('white')
ax1.set_xlim([0,1])
P.savefig('hist.pdf', bbox_inches='tight')
OK, I think this is what you are asking (but correct me if I misunderstood):
You need to change the colour of the spines. You need to do this for each spine individually, using the set_color method:
for spine in ['left','right','top','bottom']:
ax1.spines[spine].set_color('k')
You can see this example and this example for more about using spines.
However, if you have removed the grey background and the grid lines, and added the spines, this is not really in the ggplot style any more; is that really the style you want to use?
EDIT
To make the edge of the histogram bars touch the frame, you need to either:
Change your binning, so the bin edges go to 0 and 1
n,bins,patches = plt.hist(values, bins=np.linspace(0,1,21), weights=weights)
# Check, by printing bins:
print bins[0], bins[-1]
# 0.0, 1.0
If you really want to keep the bins to go between values.min() and values.max(), you would need to change your plot limits to no longer be 0 and 1:
n,bins,patches = plt.hist(values, bins=20, weights=weights)
ax.set_xlim(bins[0],bins[-1])
I am working on using Matplotlib to produce plots of implicit equations (eg. y^x=x^y). With many thanks to the help I have already received I have got quite far with it. I have used a contour line to produce the plot. My remaining problem is with formatting the contour line eg width, color and especially zorder, where the contour appears behind my gridlines. These work fine when plotting a standard function of course.
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
import numpy as np
fig = plt.figure(1)
ax = fig.add_subplot(111)
# set up axis
ax.spines['left'].set_position('zero')
ax.spines['right'].set_color('none')
ax.spines['bottom'].set_position('zero')
ax.spines['top'].set_color('none')
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
# setup x and y ranges and precision
x = np.arange(-0.5,5.5,0.01)
y = np.arange(-0.5,5.5,0.01)
# draw a curve
line, = ax.plot(x, x**2,zorder=100,linewidth=3,color='red')
# draw a contour
X,Y=np.meshgrid(x,y)
F=X**Y
G=Y**X
ax.contour(X,Y,(F-G),[0],zorder=100,linewidth=3,color='green')
#set bounds
ax.set_xbound(-1,7)
ax.set_ybound(-1,7)
#add gridlines
ax.xaxis.set_minor_locator(MultipleLocator(0.2))
ax.yaxis.set_minor_locator(MultipleLocator(0.2))
ax.xaxis.grid(True,'minor',linestyle='-',color='0.8')
ax.yaxis.grid(True,'minor',linestyle='-',color='0.8')
plt.show()
This is rather hackish but...
Apparently in the current release Matplotlib does not support zorder on contours. This support, however, was recently added to the trunk.
So, the right way to do this is either to wait for the 1.0 release or just go ahead and re-install from trunk.
Now, here's the hackish part. I did a quick test and if I changed line 618 in
python/site-packages/matplotlib/contour.py
to add a zorder into the collections.LineCollection call, it fixes your specific problem.
col = collections.LineCollection(nlist,
linewidths = width,
linestyle = lstyle,
alpha=self.alpha,zorder=100)
Not the right way to do things, but might just work in a pinch.
Also off-topic, if you accept some responses to your previous questions, you probably get quicker help around here. People love those rep points :)