Matplotlib: plotting images with special valuesΒΆ

Image plotting requires data, a colormap, and a normalization. A common desire is to show missing data or other values in a specified color. The following code shows an example of how to do this.

The code creates a new Colormap subclass and a norm subclass.

The initialization takes a dictionary of value, color pairs. The data is already assumed to be normalized (except for the sentinels which are preserved). The RGB values at the sentinel values are replaced by the specified colors.

The class normalizes the data in the standard way except for one sublety. takes an “ignore” argument. The ignored values need to be excluded from the normalization so that they do not skew the results.

I use a not particularly wonderful algorithm of explicitly sorting the data and using the first non-sentinel values to define the min and max. This can probably be improved, but for my purposes was easy and sufficient. The data is then normalized including the sentinels. Finally, the sentinels are replaced.

from matplotlib.colors import Colormap, normalize
import matplotlib.numerix as nx
from types import IntType, FloatType, ListType

class SentinelMap(Colormap):
        def __init__(self, cmap, sentinels={}):
                # boilerplate stuff
                self.N = cmap.N
       = 'SentinelMap'
                self.cmap = cmap
                self.sentinels = sentinels
                for rgb in sentinels.values():
                        if len(rgb)!=3:
                                raise ValueError('sentinel color must be RGB')

        def __call__(self, scaledImageData, alpha=1):
                # assumes the data is already normalized (ignoring sentinels)
                # clip to be on the safe side
                rgbaValues = self.cmap(nx.clip(scaledImageData, 0.,1.))

                #replace sentinel data with sentinel colors
                for sentinel,rgb in self.sentinels.items():
                        r,g,b = rgb
                        rgbaValues[:,:,0] =  nx.where(scaledImageData==sentinel, r, rgbaValues[:,:,0])
                        rgbaValues[:,:,1] =  nx.where(scaledImageData==sentinel, g, rgbaValues[:,:,1])
                        rgbaValues[:,:,2] =  nx.where(scaledImageData==sentinel, b, rgbaValues[:,:,2])
                        rgbaValues[:,:,3] =  nx.where(scaledImageData==sentinel, alpha, rgbaValues[:,:,3])

                return rgbaValues

class SentinelNorm(normalize):
        Leave the sentinel unchanged
        def __init__(self, ignore=[], vmin=None, vmax=None):

                if type(ignore) in [IntType, FloatType]:
                        self.ignore = [ignore]
                        self.ignore = list(ignore)

        def __call__(self, value):

                vmin = self.vmin
                vmax = self.vmax

                if type(value) in [IntType, FloatType]:
                        vtype = 'scalar'
                        val = array([value])
                        vtype = 'array'
                        val = nx.asarray(value)

                # if both vmin is None and vmax is None, we'll automatically
                # norm the data to vmin/vmax of the actual data, so the
                # clipping step won't be needed.
                if vmin is None and vmax is None:
                        needs_clipping = False
                        needs_clipping = True

                if vmin is None or vmax is None:
                        rval = nx.ravel(val)
                        #do this if sentinels (values to ignore in data)
                        if self.ignore:
                                if vmin is None:
                                        # find the lowest non-sentinel value
                                        for thisVal in sortValues:
                                                if thisVal not in self.ignore:
                                                        vmin=thisVal #vmin is the lowest non-sentinel value
                                if vmax is None:
                                        for thisVal in sortValues[::-1]:
                                                if thisVal not in self.ignore:
                                                        vmax=thisVal #vmax is the greatest non-sentinel value
                                if vmin is None: vmin = min(rval)
                                if vmax is None: vmax = max(rval)
                if vmin > vmax:
                        raise ValueError("minvalue must be less than or equal to maxvalue")
                elif vmin==vmax:
                        return 0.*value
                        if needs_clipping:
                                val = nx.clip(val,vmin, vmax)
                        result = (1.0/(vmax-vmin))*(val-vmin)

                # replace sentinels with original (non-normalized) values
                for thisIgnore in self.ignore:
                        result = nx.where(val==thisIgnore,thisIgnore,result)

                if vtype == 'scalar':
                        result = result[0]
                return result

if __name__=="__main__":
        import pylab
        import matplotlib.colors

        # create a random array
        X = nx.mlab.rand(n,n)
        cmBase =

        # plot it array as an image
        pylab.imshow(X, cmap=cmBase, interpolation='nearest')

        # define the sentinels
        sentinel1 = -10
        sentinel2 = 10

        # replace some data with sentinels
        X[int(.1*n):int(.2*n), int(.5*n):int(.7*n)]  = sentinel1
        X[int(.6*n):int(.8*n), int(.2*n):int(.3*n)]  = sentinel2

        # define the colormap and norm
        rgb1 = (0.,0.,0.)
        rgb2 = (1.,0.,0.)
        cmap = SentinelMap(cmBase, sentinels={sentinel1:rgb1,sentinel2:rgb2,})
        norm = SentinelNorm(ignore=[sentinel1,sentinel2])

        # plot with the modified colormap and norm
        pylab.imshow(X, cmap = cmap, norm=norm, interpolation='nearest')

If the preceeding code is run from a prompt, two images are generated. The first is a pristine image of random data. The second image is the data modified by setting some blocks to sentinel values and then plotting the sentinels in specific colors. A sample result is shown below.

Section author: AndrewStraw