Develop Reference

Rotate matplotlib colourmap

The ProPlot Python package adds additional features to the Matplotlib library, including colourmap manipulations. One feature that is particularly attractive to me is the ability to rotate/shift colourmaps. To give you an example:
import proplot as pplot
import matplotlib.pyplot as plt
import numpy as np
state = np.random.RandomState(51423)
data = state.rand(30, 30).cumsum(axis=1)
fig, axes = plt.subplots(ncols=3, figsize=(9, 4))
fig.patch.set_facecolor("white")
axes[0].pcolormesh(data, cmap="Blues")
axes[0].set_title("Blues")
axes[1].pcolormesh(data, cmap="Blues_r")
axes[1].set_title("Reversed Blues")
axes[2].pcolormesh(data, cmap="Blues_s")
axes[2].set_title("Rotated Blues")
plt.tight_layout()
plt.show()
In the third column, you see the 180° rotated version of Blues. Currently ProPlot suffers from a bug that doesn't allow the user to revert the plotting style to Matplotlib's default style, so I was wondering if there was an easy way to rotate a colourmap in Matplotlib without resorting to ProPlot. I always found cmap manipulations in Matplotlib a bit arcane, so any help would be much appreciated.

If what you are trying to do is shift the colormaps, this can be done (relatively) easily:
def shift_cmap(cmap, frac):
"""Shifts a colormap by a certain fraction.
Keyword arguments:
cmap -- the colormap to be shifted. Can be a colormap name or a Colormap object
frac -- the fraction of the colorbar by which to shift (must be between 0 and 1)
"""
N=256
if isinstance(cmap, str):
cmap = plt.get_cmap(cmap)
n = cmap.name
x = np.linspace(0,1,N)
out = np.roll(x, int(N*frac))
new_cmap = matplotlib.colors.LinearSegmentedColormap.from_list(f'{n}_s', cmap(out))
return new_cmap
demonstration:
x = np.linspace(0,1,100)
x = np.vstack([x,x])
cmap1 = plt.get_cmap('Blues')
cmap2 = shift_cmap(cmap1, 0.25)
fig, (ax1, ax2) = plt.subplots(2,1)
ax1.imshow(x, aspect='auto', cmap=cmap1)
ax2.imshow(x, aspect='auto', cmap=cmap2)

To reverse a ListedColormap, there is a built-in reversed() but for the intended rotation, we have to create our own function.
#fake data generation
import numpy as np
np.random.seed(123)
#numpy array containing x, y, and color
arr = np.random.random(30).reshape(3, 10)
from matplotlib import pyplot as plt
from matplotlib.colors import ListedColormap
def rotate_cm(co_map, deg=180):
#define a function where the colormap is rotated by a certain degree
#180° shifts by 50%, 360° no change
n = co_map.N
#if rotating in the opposite direction feels more intuitive, reverse the sign here
deg = -deg%360
if deg < 0:
deg += 360
cutpoint = n * deg // 360
new_col_arr = [co_map(i) for i in range(cutpoint, n)] + [co_map(i) for i in range(cutpoint)]
return ListedColormap(new_col_arr)
fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(21,7))
#any listed colormap
my_cm = plt.cm.get_cmap("inferno")
#normal color map
cb1 = ax1.scatter(*arr[:2,:], c=arr[2,:], cmap=my_cm, marker="o")
plt.colorbar(cb1, ax=ax1)
ax1.set_title("regular colormap")
#reversed colormap
cb2 = ax2.scatter(*arr[:2,:], c=arr[2,:], cmap=my_cm.reversed(), marker="o")
plt.colorbar(cb2, ax=ax2)
ax2.set_title("reversed colormap")
#rotated colormap
cb3 = ax3.scatter(*arr[:2,:], c=arr[2,:], cmap=rotate_cm(my_cm, 90), marker="o")
#you can also combine the rotation with reversed()
#cb3 = ax3.scatter(*arr[:2,:], c=arr[2,:], cmap=rotate_cm(my_cm, 90).reversed(), marker="o")
plt.colorbar(cb3, ax=ax3)
ax3.set_title("colormap rotated by 90°")
plt.show()
Sample output:

ArtistAnimation of subplots with different framerates

Consider the following code which implements ArtistAnimation to animate two different subplots within the same figure object.
import numpy as np
import itertools
import matplotlib.pyplot as plt
import matplotlib.mlab as ml
import matplotlib.animation as animation
def f(x,y,a):
return ((x/a)**2+y**2)
avals = np.linspace(0.1,1,10)
xaxis = np.linspace(-2,2,9)
yaxis = np.linspace(-2,2,9)
xy = itertools.product(xaxis,yaxis)
xy = list(map(list,xy))
xy = np.array(xy)
x = xy[:,0]
y = xy[:,1]
fig, [ax1,ax2] = plt.subplots(2)
ims = []
for a in avals:
xi = np.linspace(min(x), max(x), len(x))
yi = np.linspace(min(y), max(y), len(y))
zi = ml.griddata(x, y, f(x, y, a), xi, yi, interp='linear') # turn it into grid data, this is what imshow takes
title = plt.text(35,-4,str(a), horizontalalignment = 'center')
im1 = ax1.imshow(zi, animated = True, vmin = 0, vmax = 400)
im2 = ax2.imshow(zi, animated=True, vmin=0, vmax=400)
ims.append([im1,im2, title])
ani = animation.ArtistAnimation(fig, ims, interval = 1000, blit = False)
plt.show()
In this case the number of items in im1 and im2 are the same, and the frame rate for each subplot is identical.
Now, imagine I have 2 lists with different numbers of items, and that I wish ArtistAnimate to go through the frames in the same total time. Initially I thought of manipulating the interval keyword in the ArtistAnimation call but this implies that you can set different intervals for different artists, which I don't think is possible.
Anyway, I think the basic idea is pretty clear len(im1) is not equal to len(im2), but the animation needs to go through them all in the same amount of time.
Is there any way to do this please? Thanks
EDIT
While I try out the answer provided below, I should add that I would rather use ArtistAnimation due to the structure of my data. If there are no alternatives I will revert to the solution below.

Yes that is possible, kinda, using Funcanimation and encapsulating your data inside func.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
arr1 = np.random.rand(300,3,4)
arr2 = np.random.rand(200,5,6)
fig, (ax1, ax2) = plt.subplots(1,2)
img1 = ax1.imshow(arr1[0])
img2 = ax2.imshow(arr2[0])
# set relative display rates
r1 = 2
r2 = 3
def animate(ii):
if ii % r1:
img1.set_data(arr1[ii/r1])
if ii % r2:
img2.set_data(arr2[ii/r2])
return img1, img2
ani = animation.FuncAnimation(fig, func=animate, frames=np.arange(0, 600))
plt.show()

Square root scale using matplotlib/python

I want to make a plot with square root scale using Python:
However, I have no idea how to make it. Matplotlib allows to make log scale but in this case I need something like power function scale.

You can make your own ScaleBase class to do this. I have modified the example from here (which made a square-scale, not a square-root-scale) for your purposes. Also, see the documentation here.
Note that to do this properly, you should probably also create your own custom tick locator; I haven't done that here though; I just manually set the major and minor ticks using ax.set_yticks().
import matplotlib.scale as mscale
import matplotlib.pyplot as plt
import matplotlib.transforms as mtransforms
import matplotlib.ticker as ticker
import numpy as np
class SquareRootScale(mscale.ScaleBase):
"""
ScaleBase class for generating square root scale.
"""
name = 'squareroot'
def __init__(self, axis, **kwargs):
# note in older versions of matplotlib (<3.1), this worked fine.
# mscale.ScaleBase.__init__(self)
# In newer versions (>=3.1), you also need to pass in `axis` as an arg
mscale.ScaleBase.__init__(self, axis)
def set_default_locators_and_formatters(self, axis):
axis.set_major_locator(ticker.AutoLocator())
axis.set_major_formatter(ticker.ScalarFormatter())
axis.set_minor_locator(ticker.NullLocator())
axis.set_minor_formatter(ticker.NullFormatter())
def limit_range_for_scale(self, vmin, vmax, minpos):
return max(0., vmin), vmax
class SquareRootTransform(mtransforms.Transform):
input_dims = 1
output_dims = 1
is_separable = True
def transform_non_affine(self, a):
return np.array(a)**0.5
def inverted(self):
return SquareRootScale.InvertedSquareRootTransform()
class InvertedSquareRootTransform(mtransforms.Transform):
input_dims = 1
output_dims = 1
is_separable = True
def transform(self, a):
return np.array(a)**2
def inverted(self):
return SquareRootScale.SquareRootTransform()
def get_transform(self):
return self.SquareRootTransform()
mscale.register_scale(SquareRootScale)
fig, ax = plt.subplots(1)
ax.plot(np.arange(0, 9)**2, label='$y=x^2$')
ax.legend()
ax.set_yscale('squareroot')
ax.set_yticks(np.arange(0,9,2)**2)
ax.set_yticks(np.arange(0,8.5,0.5)**2, minor=True)
plt.show()

This is old, but I made a quick-fix because i didn't want to bother with creating a custom tick-locator. If you are making a lot of plots with custom scales that is probably the way to go. Just plotting the function with the scale you want, then setting the ticks and changing the labels is quicker if you just need a plot or two.
Nx = 100
x = np.linspace(0,50,Nx)
y = np.sqrt(x)
fig, ax = plt.subplots(1, 1)
plt.plot(np.sqrt(x), y)
ax.set_xticks([np.sqrt(x[i]) for i in range(0, Nx, Nx // 10)])
ax.set_xticklabels([str(round(x[i],0))[:-2] for i in range(0, Nx, Nx // 10)])
plt.xlabel('x')
plt.ylabel(r'y = $\sqrt{x}$')
plt.grid()
plt.show()
produces the plot

I like lolopop's comment and tom's answer, a more quick and dirty solution would be using set_yticks and set_yticklabels as in the following:
x = np.arange(2, 15, 2)
y = x * x
fig = plt.figure()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
ax1.plot(x,y)
ax2.plot(x, np.sqrt(y))
ax2.set_yticks([2,4,6,8,10,12,14])
ax2.set_yticklabels(['4','16','36','64','100','144','196'])

Matplotlib now offers a powlaw norm. Thus setting power to 0.5 should do the trick!
C.f. Matplotlib Powerlaw norm
And their example:
"""
Demonstration of using norm to map colormaps onto data in non-linear ways.
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from matplotlib.mlab import bivariate_normal
N = 100
X, Y = np.mgrid[-3:3:complex(0, N), -2:2:complex(0, N)]
'''
PowerNorm: Here a power-law trend in X partially obscures a rectified
sine wave in Y. We can remove gamma to 0.5 should do the trick using PowerNorm.
'''
X, Y = np.mgrid[0:3:complex(0, N), 0:2:complex(0, N)]
Z1 = (1 + np.sin(Y * 10.)) * X**(2.)
fig, ax = plt.subplots(2, 1)
pcm = ax[0].pcolormesh(X, Y, Z1, norm=colors.PowerNorm(gamma=1./2.),
cmap='PuBu_r')
fig.colorbar(pcm, ax=ax[0], extend='max')
pcm = ax[1].pcolormesh(X, Y, Z1, cmap='PuBu_r')
fig.colorbar(pcm, ax=ax[1], extend='max')
fig.show()

This a simple way to graph
import numpy as np
from matplotlib import pyplot as plt
plt.rcParams["figure.dpi"] = 140
fig, ax = plt.subplots()
ax.spines["left"].set_position("zero")
ax.spines["bottom"].set_position("zero")
ax.spines["right"].set_color("none")
ax.spines["top"].set_color("none")
ax.xaxis.set_ticks_position("bottom")
ax.yaxis.set_ticks_position("left")
origin = [0, 0]
# 45
plt.plot(
np.linspace(0, 1, 1000),
np.sqrt(np.linspace(0, 1, 1000)),
color="k",
)
ax.set_aspect("equal")
plt.xlim(-0.25, 1)
plt.ylim(0, 1)
plt.yticks(ticks=np.linspace(0, 1, 6))
plt.show()

Setting discrete colormap corresponding to specific data range in Matplotlib

Some background
I have a 2-d array in the shape of (50,50), the data value are range from -40 ~ 40.
But I want to plot the data in three data range[<0], [0,20], [>20]
Then, I need to generate a colormap corresponding to the three section.
I have some thought now
## ratio is the original 2-d array
binlabel = np.zeros_like(ratio)
binlabel[ratio<0] = 1
binlabel[(ratio>0)&(ratio<20)] = 2
binlabel[ratio>20] = 3
def discrete_cmap(N, base_cmap=None):
base = plt.cm.get_cmap(base_cmap)
color_list = base(np.linspace(0, 1, N))
cmap_name = base.name + str(N)
return base.from_list(cmap_name, color_list, N)
fig = plt.figure()
ax = plt.gca()
plt.pcolormesh(binlabel, cmap = discrete_cmap(3, 'jet'))
divider = make_axes_locatable(ax)
cax = divider.append_axes("bottom", size="4%", pad=0.45)
cbar = plt.colorbar(ratio_plot, cax=cax, orientation="horizontal")
labels = [1.35,2,2.65]
loc = labels
cbar.set_ticks(loc)
cbar.ax.set_xticklabels(['< 0', '0~20', '>20'])
Is there any better approach? Any advice would be appreciate.

There are various answers to other questions using ListedColormap and BoundaryNorm, but here's an alternative. I've ignored the placement of your colorbar, as that's not relevant to your question.
You can replace your binlabel calculation with a call to np.digitize() and replace your discrete_cmap() function by using the lut argument to get_cmap(). Also, I find it easier to place the color bounds at .5 midpoints between the indexes rather than scale to awkward fractions of odd numbers:
import matplotlib.colors as mcol
import matplotlib.cm as cm
import matplotlib.pyplot as plt
import numpy as np
ratio = np.random.random((50,50)) * 50.0 - 20.0
fig2, ax2 = plt.subplots(figsize=(5,5))
# Turn the data into an array of N bin indexes (i.e., 0, 1 and 2).
bounds = [0,20]
iratio = np.digitize(ratio.flat,bounds).reshape(ratio.shape)
# Create a colormap containing N colors and a Normalizer that defines where
# the boundaries of the colors should be relative to the indexes (i.e., -0.5,
# 0.5, 1.5, 2.5).
cmap = cm.get_cmap("jet",lut=len(bounds)+1)
cmap_bounds = np.arange(len(bounds)+2) - 0.5
norm = mcol.BoundaryNorm(cmap_bounds,cmap.N)
# Plot using the colormap and the Normalizer.
ratio_plot = plt.pcolormesh(iratio,cmap=cmap,norm=norm)
cbar = plt.colorbar(ratio_plot,ticks=[0,1,2],orientation="horizontal")
cbar.set_ticklabels(["< 0","0~20",">20"])

Setting the size of a matplotlib ColorbarBase object

I have an patch collection that I'd like to display a color map for. Because of some manipulations I do on top of the colormap, it's not possible for me to define it using a matplotlib.colorbar instance. At least not as far as I can tell; doing so strips some manipulations I do with my colors that blank out patches lacking data:
cmap = matplotlib.cm.YlOrRd
colors = [cmap(n) if pd.notnull(n) else [1,1,1,1]
for n in plt.Normalize(0, 1)([nullity for _, nullity in squares])]
# Now we draw.
for i, ((min_x, max_x, min_y, max_y), _) in enumerate(squares):
square = shapely.geometry.Polygon([[min_x, min_y], [max_x, min_y],
[max_x, max_y], [min_x, max_y]])
ax0.add_patch(descartes.PolygonPatch(square, fc=colors[i],
ec='white', alpha=1, zorder=4))
So I define a matplotlib.colorbar.ColorbarBase instance instead, which works:
matplotlib.colorbar.ColorbarBase(ax1, cmap=cmap, orientation='vertical',
norm=matplotlib.colors.Normalize(vmin=0, vmax=1))
Which results in e.g.:
The problem I have is that I want to reduce the size of this colorbar (specifically, the shrink it down to a specific vertical size, say, 500 pixels), but I don't see any obvious way of doing this. If I had a colorbar instance, I could adjust this easily using its axis property arguments, but ColorbarBase lacks these.
For further reference:
The example my implementation is based on.
The source code in question (warning: lengthy).

The size and shape is defined with the axis. This is a snippet from code I have where I group 2 plots together and add a colorbar at the top independently. I played with the values in that add_axes instance until I got a size that worked for me:
cax = fig.add_axes([0.125, 0.925, 0.775, 0.0725]) #has to be as a list - starts with x, y coordinates for start and then width and height in % of figure width
norm = mpl.colors.Normalize(vmin = low_val, vmax = high_val)
mpl.colorbar.ColorbarBase(cax, cmap = self.cmap, norm = norm, orientation = 'horizontal')

The question may be a bit old, but I found another solution that can be of help for anyone who is not willing to manually create a colorbar axes for the ColorbarBase class.
The solution below uses the matplotlib.colorbar.make_axes class to create a dependent sub_axes from the given axes. That sub_axes can then be supplied for the ColorbarBase class for the colorbar creation.
The code is derived from the matplotlib code example describe in here
Here is a snippet code:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
import matplotlib.colorbar as mcbar
from matplotlib import ticker
import matplotlib.colors as mcolors
# Make some illustrative fake data:
x = np.arange(0, np.pi, 0.1)
y = np.arange(0, 2 * np.pi, 0.1)
X, Y = np.meshgrid(x, y)
Z = np.cos(X) * np.sin(Y) * 10
colors = [(1, 0, 0), (0, 1, 0), (0, 0, 1)] # R -> G -> B
n_bins = [3, 6, 10, 100] # Discretizes the interpolation into bins
cmap_name = 'my_list'
fig, axs = plt.subplots(2, 2, figsize=(9, 7))
fig.subplots_adjust(left=0.02, bottom=0.06, right=0.95, top=0.94, wspace=0.05)
for n_bin, ax in zip(n_bins, axs.ravel()):
# Create the colormap
cm = LinearSegmentedColormap.from_list(cmap_name, colors, N=n_bin)
# Fewer bins will result in "coarser" colomap interpolation
im = ax.imshow(Z, interpolation='nearest', origin='lower', cmap=cm)
ax.set_title("N bins: %s" % n_bin)
cax, cbar_kwds = mcbar.make_axes(ax, location = 'right',
fraction=0.15, shrink=0.5, aspect=20)
cbar = mcbar.ColorbarBase(cax, cmap=cm,
norm=mcolors.Normalize(clip=False),
alpha=None,
values=None,
boundaries=None,
orientation='vertical', ticklocation='auto', extend='both',
ticks=n_bins,
format=ticker.FormatStrFormatter('%.2f'),
drawedges=False,
filled=True,
extendfrac=None,
extendrect=False, label='my label')
if n_bin <= 10:
cbar.locator = ticker.MaxNLocator(n_bin)
cbar.update_ticks()
else:
cbar.locator = ticker.MaxNLocator(5)
cbar.update_ticks()
fig.show()