--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mds_plot.py	Thu Aug 15 03:39:14 2013 -0400
@@ -0,0 +1,29 @@
+#!/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 )