cm_xml_to_matplotlib.py

#!/usr/bin/env python
#
## This script converts the .xml(ParaView compatible format) colormaps into Matplotlib or MATLAB format
import sys
import os
import matplotlib as mpl
import numpy as np
from lxml import etree

## load source xml file
def load_xml(xml):
    try:
        xmldoc = etree.parse(xml)
    except IOError as e:
        print('The input file is invalid. It must be a colormap xml file. Go to https://sciviscolor.org/home/colormaps/ for some good options')
        print('Go to https://sciviscolor.org/matlab-matplotlib-pv44/ for an example use of this script.')
        sys.exit()
    data_vals=[]
    color_vals=[]
    for s in xmldoc.getroot().findall('.//Point'):
        data_vals.append(float(s.attrib['x']))
        color_vals.append((float(s.attrib['r']),float(s.attrib['g']),float(s.attrib['b'])))
    return {'color_vals':color_vals, 'data_vals':data_vals}

## source of this function: http://schubert.atmos.colostate.edu/~cslocum/custom_cmap.html#code
def make_cmap(xml):
    vals = load_xml(xml)
    colors = vals['color_vals']
    position = vals['data_vals']
    if len(position) != len(colors):
        sys.exit('position length must be the same as colors')
    cdict = {'red':[], 'green':[], 'blue':[]}
    if position[0] != 0:
        cdict['red'].append((0, colors[0][0], colors[0][0]))
        cdict['green'].append((0, colors[0][1], colors[0][1]))
        cdict['blue'].append((0, colors[0][2], colors[0][2]))
    for pos, color in zip(position, colors):
        cdict['red'].append((pos, color[0], color[0]))
        cdict['green'].append((pos, color[1], color[1]))
        cdict['blue'].append((pos, color[2], color[2]))
    if position[-1] != 1:
        cdict['red'].append((1, colors[-1][0], colors[-1][0]))
        cdict['green'].append((1, colors[-1][1], colors[-1][1]))
        cdict['blue'].append((1, colors[-1][2], colors[-1][2]))
    cmap = mpl.colors.LinearSegmentedColormap('my_colormap',cdict,256)
    return cmap

## Print MATLAB compatible matrix
def print_cmap_matrix(colormap):
    c = 0
    print('')
    print('matlab-colormap = [')
    while c <= 255:
        if c == 0: pass
        else: 
            print('')
        print(str(colormap(c)[0:3]).replace('(','').replace(')',''))
        c = c + 1
    print('];')
    
## This is a quick example plotting the 8 by 1 gradient of the colormap 
## with Matplotlib
def plot_cmap(colormap):
    gradient = np.linspace(0, 1, 256)
    gradient = np.vstack((gradient, gradient))
    fig=plt.figure(figsize=(8,1))
    map=fig.add_subplot(111)
    map.set_frame_on(False)
    map.get_xaxis().set_visible(False)
    map.get_yaxis().set_visible(False)
    fig.tight_layout(pad=0)
    map.imshow(gradient, aspect='auto', cmap=plt.get_cmap(colormap))
    plt.show(fig)

## check for correct file type
def is_xml(string):
    if os.path.isfile(string):
        return string
    else:
        raise argparse.ArgumentTypeError('The file %s does not exist!' % string)

## Example usage
if __name__ == '__main__':
    import argparse
    
    parser = argparse.ArgumentParser(description='Convert ParaView compatible colormaps to Matplotlib or MATLAB compatible colormaps.')
    parser.add_argument('-f', '--file-path', dest='path', required=True, type=lambda s: is_xml(s), help='Input file path of .xml colormap with position starting at 0 and ending at 1.')
    parser.add_argument('-m', '--make-matrix', dest='matrix', action='store_true', required=False, help='Print a 3xn matrix of rgb values to copy and paste into MATLAB.')

    args = parser.parse_args()

    ## construct the colormap
    mycmap = make_cmap(args.path)
    print('converted successfully!')

    ## mycmap is matplotlib compatible object. to query color value out of it:
    print('example rgba value for data value 0 is: ' + str(mycmap(0.0)))

    ## MATLAB Users: This fuction will output a RGB matrix to use in MATLAB
    if args.matrix == True:
        print_cmap_matrix(mycmap)

    ## Plotting the colormap to test the conversion
    plot_cmap(mycmap)