comparison mds_plot.py @ 0:fe542273784f draft default tip

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author bgruening
date Thu, 15 Aug 2013 03:39:14 -0400
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-1:000000000000 0:fe542273784f
1 #!/usr/bin/env python
2
3 import argparse
4 import os
5 import sklearn.manifold
6 import numpy
7 import math
8 import pylab
9
10 if __name__ == "__main__":
11 parser = argparse.ArgumentParser(
12 description="""2D multidimenisnal scaling of NxN matrices with scatter plot"""
13 )
14
15 parser.add_argument("-i", "--input", dest="sm",
16 required=True,
17 help="Path to the input file.")
18 parser.add_argument("--oformat", default='png', help="Output format (png, svg)")
19 parser.add_argument("-o", "--output", dest="output_path",
20 help="Path to the output file.")
21
22 args = parser.parse_args()
23 mds = sklearn.manifold.MDS( n_components=2, max_iter=300, eps=1e-6, dissimilarity='precomputed' )
24 data = numpy.fromfile( args.sm )
25 d = math.sqrt( len(data) )
26 sm = numpy.reshape( data, ( d,d ))
27 pos = mds.fit( sm ).embedding_
28 pylab.scatter( pos[:,0],pos[:,1] )
29 pylab.savefig( args.output_path, format=args.oformat )