Wednesday, August 29, 2012

Nonlinear colormap in Matplotlib

One of the difficulties I deal with is data that is not evenly distributed across a particular range. Sometimes, I want to highlight a particularly small set of values with great color contrasts and leave other portions of the range to be much less distinguished. For this, I went looking for a way to have a non-linear colormap in matplotlib. To be clear, I didn't want the data itself to be transformed, rather I wanted the color mapping to progress through a normal colormap like cm.jet but expand and contract portions of the map across the entire of values to provide granular resolution at a specific range of values. The graphs below show the difference when using a linear colormap and a transformed colormap:

Image before:

Image after:

I found a script to perform this mapping. It allows the user to set a number of levels that get used to transform the colormap. My modified version of the script is below:

nlcmap - a nonlinear cmap from specified levels

Copyright (c) 2006-2007, Robert Hetland <>
Release under MIT license.

Some hacks added 2012 noted in code (@MRR)

from pylab import *
from numpy import *
from matplotlib.colors import LinearSegmentedColormap

class nlcmap(LinearSegmentedColormap):
    """A nonlinear colormap"""
    name = 'nlcmap'
    def __init__(self, cmap, levels):
        self.cmap = cmap
        # @MRR: Need to add N for backend
        self.N = cmap.N
        self.monochrome = self.cmap.monochrome
        self.levels = asarray(levels, dtype='float64')
        self._x = self.levels / self.levels.max()
        self._y = linspace(0.0, 1.0, len(self.levels))
    #@MRR Need to add **kw for 'bytes'
    def __call__(self, xi, alpha=1.0, **kw):
        """docstring for fname"""
        # @MRR: Appears broken? 
        # It appears something's wrong with the
        # dimensionality of a calculation intermediate
        #yi = stineman_interp(xi, self._x, self._y)
        yi = interp(xi, self._x, self._y)
        return self.cmap(yi, alpha)

if __name__ == '__main__':
    y, x = mgrid[0.0:3.0:100j, 0.0:5.0:100j]
    H = 50.0 * exp( -(x**2 + y**2) / 4.0 )
    levels = [0, 1, 2, 3, 6, 9, 20, 50]
    cmap_lin = cm.jet
    cmap_nonlin = nlcmap(cmap_lin, levels)
    contourf(x, y, H, levels, cmap=cmap_nonlin)
    contourf(x, y, H, levels, cmap=cmap_lin)
Some of the comments above point to changes that I had to make to get the script to work. Specifically:
  • pylab.stineman_interp gave an error relating to the dimensionality of some of the intermediate calculations
  • one of the backends requested the colormaps N member, which wasn't set in the original
  • the **kw parameter wasn't passed to the __call__ method, causing problems when optional parameters such as bytes were passed.
I'm not entirely sure if the script works correctly at this point, so use at your own risk.