How to make tight bounding boxes respect an invisible artist? - matplotlib

I want to export a figure whose bounding boxes should be tight, but accounting for an artist that is invisible.
(I want to unveil that artist in a later variant of the plot, which shall have the same bounding boxes.)
My approach to this is:
from matplotlib import pyplot as plt
plt.plot([0,1])
title = plt.title("my invisible title")
title.set_visible(False)
plt.savefig(
"invisible_artist.png",
bbox_inches="tight", pad_inches=0,
bbox_extra_artists=[title],
facecolor="grey", # just to visualise the bbox
)
This produces:
For comparison, here is the output with the title left visible, which is what I would expect in this case:
Obviously, when the title is made invisible, no space is left for it, while additional space is added in other directions.
Why does this happen and how can I achieve the desired result, i.e., have the same bounding box in both cases?

Invisible artists are not taken into account for tight bbox calculations. Some workaround could be to make the title transparent,
title.set_alpha(0)
Or to use a whitespace as title
plt.title(" ")
More generally, you can of course get the tight bounding box before making the title invisible, then turn the title invisible and finally save the figure with the previously stored bbox.
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.plot([0,1])
title = ax.set_title("my invisible title")
bbox = fig.get_tightbbox(fig.canvas.get_renderer())
title.set_visible(False)
plt.savefig(
"invisible_artist.png",
bbox_inches=bbox,
facecolor="grey", # just to visualise the bbox
)
plt.show()
The drawback is that pad_inches only works for bbox_inches="tight". So to achieve the effect of pad_inches for such manually specified bbox one would need to manipulate the Bbox itself.

Just specify the color of the title to be the same as the facecolor, i.e., 'grey' in your case. Now you don't need title.set_visible(False). I make it more general by using a variable col to specify the color
from matplotlib import pyplot as plt
col = 'grey'
plt.plot([0,1])
title = plt.title("my invisible title", color=col)
plt.savefig(
"invisible_artist.png",
bbox_inches="tight", pad_inches=0,
bbox_extra_artists=[title],
facecolor=col, # just to visualise the bbox
)

Related

Matplotlib issue x and y label for multi axes figure

import matplotlib
import matplotlib.pyplot as plt
import numpy as nm
x = nm.linspace(start=0,stop=20,num=30)
fig=plt.figure()
ax1 = fig.add_axes([0,0.6,0.6,0.4])
ax2 = fig.add_axes([0,0,0.8,0.4])
ax1.plot(x,nm.sin(x))
ax1.set_xlabel('x',fontsize=15,color='r')
ax1.set_ylabel('sin(x)',fontsize=15,color='r')
ax2.plot(x,nm.cos(x))
ax2.set_xlabel('x',fontsize=15,color='r')
ax2.set_ylabel('cos(x)',fontsize=15,color='r')
plt.show()
The output I am not able to see the xlabel for ax2 and not able to see both y label for ax1 and ax2..The image is present below:
enter code hereenter image description here
This is expected as you are asking to create an axes that is aligned with the left edge of the figure by using fig.add_axes([0,...]). Same thing for the bottom axes, which you have aligned to the bottom-left of the figure using fig.add_axes([0,0,...]).
Increase the first value e.g. fig.add_axes([0.125,...]) to leave room for the axes decorations on the left or bottom of the axes.
It is generally recommended to use the subplots functions (such as add_subplot, plt.subplots or GridSpec) so that these details are handled automatically.

Is there a convenient way to add a scale indicator to a plot in matplotlib?

I want to add a scale indicator to a plot like the one labelled '10kpc' in the (otherwise) empty plot below. So basically, the axis use one unit of measure and I want to indicate a length in the plot in a different unit. It has to have the same style as below, i.e. a |----| bar with text above.
Is there a convenient way in matplotlib to do that or do I have to draw three lines (two small vertical, one horizontal) and add the text? An ideal solution would not even require me to set coordinates in the data dimensions, i.e. I just say something along the line of horizontalalignment='left', verticalalignment='bottom', transform=ax.transAxes and specify only the width in data coordinates.
I fought with annotate() and arrow() and their documentations for quiet a bit until I concluded, they were not exactly useful, but I might be wrong.
Edit:
The code below is the closest, I have come so far. I still don't like having to specify the x-coordinates in the data coordinate system. The only thing I want to specify in data is the width of the bar. The rest should be placed in the plot system and ideally the bar should be placed relative to the text (a few pixels above).
import matplotlib.pyplot as plt
import matplotlib.transforms as tfrms
plt.imshow(somedata)
plt.colorbar()
ax = plt.gca()
trans = tfrms.blended_transform_factory( ax.transData, ax.transAxes )
plt.errorbar( 5, 0.06, xerr=10*arcsecperkpc/2, color='k', capsize=5, transform=trans )
plt.text( 5, 0.05, '10kpc', horizontalalignment='center', verticalalignment='top', transform=trans )
Here is a code that adds a horizontal scale bar (or scale indicator or scalebar) to a plot. The bar's width is given in data units, while the height of the edges is in fraction of axes units.
The solution is based on an AnchoredOffsetbox, which contains a VPacker. The VPacker has a label in its lower row, and an AuxTransformBox in its upper row.
The key here is that the AnchoredOffsetbox is positioned relative to the axes, using the loc argument similar to the legend positioning (e.g. loc=4 denotes the lower right corner). However, the AuxTransformBox contains a set of elements, which are positioned inside the box using a transformation. As transformation we can choose a blended transform which transforms x coordinates according to the data transform of the axes and y coordinates according to the axes transform. A tranformation which does this is actually the xaxis_transform of the axes itself. Supplying this transform to the AuxTransformBox allows us to specify the artists within (which are Line2Ds in this case) in a useful way, e.g. the line of the bar will be Line2D([0,size],[0,0]).
All of this can be packed into a class, subclassing the AnchoredOffsetbox, such that it is easy to be used in an existing code.
import matplotlib.pyplot as plt
import matplotlib.offsetbox
from matplotlib.lines import Line2D
import numpy as np; np.random.seed(42)
x = np.linspace(-6,6, num=100)
y = np.linspace(-10,10, num=100)
X,Y = np.meshgrid(x,y)
Z = np.sin(X)/X+np.sin(Y)/Y
fig, ax = plt.subplots()
ax.contourf(X,Y,Z, alpha=.1)
ax.contour(X,Y,Z, alpha=.4)
class AnchoredHScaleBar(matplotlib.offsetbox.AnchoredOffsetbox):
""" size: length of bar in data units
extent : height of bar ends in axes units """
def __init__(self, size=1, extent = 0.03, label="", loc=2, ax=None,
pad=0.4, borderpad=0.5, ppad = 0, sep=2, prop=None,
frameon=True, linekw={}, **kwargs):
if not ax:
ax = plt.gca()
trans = ax.get_xaxis_transform()
size_bar = matplotlib.offsetbox.AuxTransformBox(trans)
line = Line2D([0,size],[0,0], **linekw)
vline1 = Line2D([0,0],[-extent/2.,extent/2.], **linekw)
vline2 = Line2D([size,size],[-extent/2.,extent/2.], **linekw)
size_bar.add_artist(line)
size_bar.add_artist(vline1)
size_bar.add_artist(vline2)
txt = matplotlib.offsetbox.TextArea(label, minimumdescent=False)
self.vpac = matplotlib.offsetbox.VPacker(children=[size_bar,txt],
align="center", pad=ppad, sep=sep)
matplotlib.offsetbox.AnchoredOffsetbox.__init__(self, loc, pad=pad,
borderpad=borderpad, child=self.vpac, prop=prop, frameon=frameon,
**kwargs)
ob = AnchoredHScaleBar(size=3, label="3 units", loc=4, frameon=True,
pad=0.6,sep=4, linekw=dict(color="crimson"),)
ax.add_artist(ob)
plt.show()
In order to achieve a result as desired in the question, you can set the frame off and adjust the linewidth. Of course the transformation from the units you want to show (kpc) into data units (km?) needs to be done by yourself.
ikpc = lambda x: x*3.085e16 #x in kpc, return in km
ob = AnchoredHScaleBar(size=ikpc(10), label="10kpc", loc=4, frameon=False,
pad=0.6,sep=4, linekw=dict(color="k", linewidth=0.8))

Coloring Intersection of Circles/Patches in Matplotlib

The following code:
# in ipython notebook, enable inline plotting with:
# %pylab inline --no-import-all
import matplotlib.pyplot as plt
# create some circles
circle1 = plt.Circle((-.5,0), 1, color='r', alpha=.2)
circle2 = plt.Circle(( .5,0), 1, color='b', alpha=.2)
# add them to the plot (bad form to use ;, but saving space)
# and control the display a bit
ax = plt.gca()
ax.add_artist(circle1); ax.add_artist(circle2)
ax.set_xlim(-2, 2); ax.set_ylim(-2, 2)
ax.set_aspect('equal')
# display it
plt.plot()
Produces the following plot:
I would like to specify the colors of the four regions (1) the background (currently white), (2 and 3) each individual event (the non-overlapping areas, currently blue and red), and (4) the intersection event (currently blended to purple). For example, I might color them red, green, blue, yellow -or- I might give them four different, precisely specified grayscale values (the later is more likely). [The colors will be generated based on characteristics of the underlying data.]
I specifically do not want to use alpha blending to "infer" a color in the intersection. I need to explicitly control the colors of all four regions.
I can think of a few strategies to solve this:
Ask mpl to extract the "primitive" patch objects that make up the three distinctly colored graphical regions (and do something similar to operate on the background) and then color them.
Given the circles, manually compute their intersections and color that intersection (somehow). Going point by point seems ugly.
Thanks!
I'm not 100% sure but I think matplotlib does not have the functionality to intersect polygons. But you could use shapely:
import shapely.geometry as sg
import matplotlib.pyplot as plt
import descartes
# create the circles with shapely
a = sg.Point(-.5,0).buffer(1.)
b = sg.Point(0.5,0).buffer(1.)
# compute the 3 parts
left = a.difference(b)
right = b.difference(a)
middle = a.intersection(b)
# use descartes to create the matplotlib patches
ax = plt.gca()
ax.add_patch(descartes.PolygonPatch(left, fc='b', ec='k', alpha=0.2))
ax.add_patch(descartes.PolygonPatch(right, fc='r', ec='k', alpha=0.2))
ax.add_patch(descartes.PolygonPatch(middle, fc='g', ec='k', alpha=0.2))
# control display
ax.set_xlim(-2, 2); ax.set_ylim(-2, 2)
ax.set_aspect('equal')
plt.show()

matplotlib text boxes automatic position

I would like to position a text box with keyword arguments like those used with legend 'loc' option, i.e. 'upper left', 'upper right', 'lower right', 'lower left'.
The basic purpose is to align the text box with legend.
I found a suggestion here : automatically position text box in matplotlib but it still uses coordinates with which I have to play to get what I want, especially if I want to put it on the right of the plot area depending on the length of the text put in the box. Unless I can set one of the right corner of the text box as the reference for coordinates.
You can do this with matplotlib's AnchoredText. As shown here:
automatically position text box in matplotlib
In brief:
from matplotlib.offsetbox import AnchoredText
anchored_text = AnchoredText("Test", loc=2)
ax.plot(x,y)
ax.add_artist(anchored_text)
Each loc number corresponds to a position within the axes, for example loc=2 is "upper left". The full list of positions is given here : http://matplotlib.org/api/offsetbox_api.html
How about setting the location of the text relative to the legend? The trick is, to find the location of the legend you have to draw it first then get the bbox. Here's an example:
import matplotlib.pyplot as plt
from numpy import random
# Plot some stuff
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(random.rand(10))
# Add a legend
leg = ax.legend('line', loc = 'upper right')
# Draw the figure so you can find the positon of the legend.
plt.draw()
# Get the Bbox
bb = leg.legendPatch.get_bbox().inverse_transformed(ax.transAxes)
# Add text relative to the location of the legend.
ax.text(bb.x0, bb.y0 - bb.height, 'text', transform=ax.transAxes)
plt.show()
On the other hand, if you only need to define the location of the text from the right you can set the horizontal alignment to right like this:
plt.text(x, y, 'text', ha = 'right')

How to add a legend to matplotlib pie chart?

Using this example http://matplotlib.org/examples/pie_and_polar_charts/pie_demo_features.html
how could I add a legend to this pie chart?
My problem is that I have One big slice 88.4%, the second largest slice is 10.6%, and the other slices are 0.7 and 0.3%. The labels around the pie don't appear (except for the biggest slice) and neither the percentage values for the smaller slices. So I guess I can add a legend showing the names and the values. But I haven't found out how...
# -*- coding: UTF-8 -*-
import matplotlib.pyplot as plt
# The slices will be ordered and plotted counter-clockwise.
labels = 'Rayos X', 'RMN en solución', 'Microscopía electrónica', 'Otros'
sizes = [88.4, 10.6, 0.7, 0.3]
colors = ['yellowgreen', 'gold', 'lightskyblue', 'lightcoral']
explode = (0.1, 0, 0, 0)
plt.pie(sizes, explode=explode, labels=labels, colors=colors, shadow=True, startangle=90)
plt.legend(title="técnica")
# Set aspect ratio to be equal so that pie is drawn as a circle.
plt.axis('equal')
plt.show()
I checked your code, and the plt.legend() creates a legend, just how you want it to be; maybe set the loc="lower left", so it does not overlap with the relevant pieces of pie.
For me, the strings are displayed properly, besides the non standard chars - which might cause the problem that they are not displayed to you at all. Only the biggest slice and "Otros" do not contain special chars. Maybe also try to resize the figure, as they might be pushed out of the canvas. Please refer to how to write accents with matplotlib and try again with proper strings.
The percentages are not shown, because you did not set them to be shown. Please refer to the example posted by you, as you omitted autopct='%1.1f%%'which will plot the percentages. In this special case, I would rather not plot the percentages, as they will overlap just like the labels on the border, as some slices are too small. Maybe add these information to the legend.
Putting it all together (besides the special chars - I had some problems activating TeX), try the following code:
# -*- coding: UTF-8 -*-
import matplotlib.pyplot as plt
# The slices will be ordered and plotted counter-clockwise.
labels = [r'Rayos X (88.4 %)', r'RMN en solucion (10.6 %)',
r'Microscopia electronica (0.7 %)', r'Otros (0.3 %)']
sizes = [88.4, 10.6, 0.7, 0.3]
colors = ['yellowgreen', 'gold', 'lightskyblue', 'lightcoral']
patches, texts = plt.pie(sizes, colors=colors, startangle=90)
plt.legend(patches, labels, loc="best")
# Set aspect ratio to be equal so that pie is drawn as a circle.
plt.axis('equal')
plt.tight_layout()
plt.show()
You can change your legend following types-
best
upper right
upper left
lower left
lower right
right
center left
center right
lower center
upper center
center
state = stateData['State/UnionTerritory']
cases = stateData['ConfirmedIndianNational']
explode = stateData.ConfirmedIndianNational.apply(lambda x:x > 100)
explode = explode.apply(lambda x:0.2 if x == True else 0)
plt.title("Covid 19")
plt.pie(cases, explode=explode,autopct='%1.2f%%',shadow=True, radius=3)
plt.legend(state, loc="center")
plt.show()