benmaier / cividis

Register `cividis` with matplotlib, a color map optimized for color vision deficiency, as published in Nuñez, et al. (2018), PLoS ONE 13(7): e0199239 .

cividis

Register the color map cividis for matplotlib, as described in

Nuñez JR, Anderton CR, Renslow RS (2018) Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data. PLoS ONE 13(7): e0199239.

Install

pip install cividis

Usage

After installation, just import cividis once and it's registered and usable

import cividis

Afterwards, you can use it like any other color map.

import matplotlib.pyplot as pl
import numpy as np

x = np.arange(0, 2*np.pi, 0.07)
y = np.arange(0, 2*np.pi, 0.07)
X, Y = np.meshgrid(x,y)
Z = np.cos(X) * np.sin(Y) * 20
Z += np.random.randn(*Z.shape)

pl.figure(figsize=(4,3.375))
pl.imshow(Z,cmap='cividis')
pl.colorbar()
pl.gcf().savefig('xmpl.png',dpi=150)

pl.show()

More examples

Register cividis as default

This has to be done once in your matplotlibrc file, or you call the corresponding function from the package.

import cividis
cividis.make_default()

 ...

pl.imshow(Z)

Will give equal results to the above.

Get an array of N cividis colors

import cividis
color_list = cividis.get_colors(10,n_start=2,n_end=200)

Where the function is implemented as

def get_colors(N, n_start=0, n_end=255):
    """Get a color array of `N` entries, where the `N` entries
    are taken at equidistance from the `cividis` array between
    `n_start` and `n_end`"""

    indices = np.linspace(n_start, n_end, N)
    indices = np.array(indices, dtype=int)
    return cividis[indices]