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author | bgruening |
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date | Thu, 15 Aug 2013 03:39:14 -0400 |
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#!/usr/bin/env python import argparse import os import sklearn.manifold import numpy import math import pylab if __name__ == "__main__": parser = argparse.ArgumentParser( description="""2D multidimenisnal scaling of NxN matrices with scatter plot""" ) parser.add_argument("-i", "--input", dest="sm", required=True, help="Path to the input file.") parser.add_argument("--oformat", default='png', help="Output format (png, svg)") parser.add_argument("-o", "--output", dest="output_path", help="Path to the output file.") args = parser.parse_args() mds = sklearn.manifold.MDS( n_components=2, max_iter=300, eps=1e-6, dissimilarity='precomputed' ) data = numpy.fromfile( args.sm ) d = math.sqrt( len(data) ) sm = numpy.reshape( data, ( d,d )) pos = mds.fit( sm ).embedding_ pylab.scatter( pos[:,0],pos[:,1] ) pylab.savefig( args.output_path, format=args.oformat )