diff pymf/laesa.py @ 0:26838b1f560f

initial commit of a segmenter project

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pymf/laesa.py	Thu Apr 02 18:09:27 2015 +0100
@@ -0,0 +1,87 @@
+#!/usr/bin/python
+#
+# Copyright (C) Christian Thurau, 2010. 
+# Licensed under the GNU General Public License (GPL). 
+# http://www.gnu.org/licenses/gpl.txt
+""" 
+PyMF LAESA
+"""
+
+
+import scipy.sparse
+import numpy as np
+
+from dist import *
+from sivm import SIVM
+
+__all__ = ["LAESA"]
+
+class LAESA(SIVM):
+    """      
+    LAESA(data, num_bases=4)
+    
+    
+    Simplex Volume Maximization. Factorize a data matrix into two matrices s.t.
+    F = | data - W*H | is minimal. H is restricted to convexity. W is iteratively
+    found by maximizing the volume of the resulting simplex (see [1]).
+    
+    Parameters
+    ----------
+    data : array_like, shape (_data_dimension, _num_samples)
+        the input data
+    num_bases: int, optional
+        Number of bases to compute (column rank of W and row rank of H).
+        4 (default)    
+    
+    Attributes
+    ----------
+    W : "data_dimension x num_bases" matrix of basis vectors
+    H : "num bases x num_samples" matrix of coefficients
+    ferr : frobenius norm (after calling .factorize())        
+    
+    Example
+    -------
+    Applying LAESA to some rather stupid data set:
+    
+    >>> import numpy as np
+    >>> data = np.array([[1.0, 0.0, 2.0], [0.0, 1.0, 1.0]])
+    >>> laesa_mdl = LAESA(data, num_bases=2)
+    >>> laesa_mdl.factorize()
+    
+    The basis vectors are now stored in laesa_mdl.W, the coefficients in laesa_mdl.H. 
+    To compute coefficients for an existing set of basis vectors simply    copy W 
+    to laesa_mdl.W, and set compute_w to False:
+    
+    >>> data = np.array([[1.5, 1.3], [1.2, 0.3]])
+    >>> W = np.array([[1.0, 0.0], [0.0, 1.0]])
+    >>> laesa_mdl = LAESA(data, num_bases=2)
+    >>> laesa_mdl.W = W
+    >>> laesa_mdl.factorize(niter=1, compute_w=False)
+    
+    The result is a set of coefficients laesa_mdl.H, s.t. data = W * laesa_mdl.H.
+    """
+    def update_w(self):    
+        # initialize some of the recursively updated distance measures     
+        self.init_sivm()
+        distiter = self._distance(self.select[-1])                
+        
+        for l in range(self._num_bases-1):                                        
+            d = self._distance(self.select[-1])                                
+        
+            # replace distances in distiter
+            distiter = np.where(d<distiter, d, distiter)
+            
+            # detect the next best data point                        
+            self.select.append(np.argmax(distiter))
+            self._logger.info('cur_nodes: ' + str(self.select))
+
+        # sort indices, otherwise h5py won't work
+        self.W = self.data[:, np.sort(self.select)]
+        
+        # but "unsort" it again to keep the correct order
+        self.W = self.W[:, np.argsort(np.argsort(self.select))]    
+                           
+                   
+if __name__ == "__main__":
+    import doctest  
+    doctest.testmod()