--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/breadcrumbs/src/MLPYDistanceAdaptor.py	Thu Jun 03 18:13:32 2021 +0000
@@ -0,0 +1,76 @@
+"""
+Author: Timothy Tickle
+Description: Allows KMedoids on a custom metric space.
+"""
+
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#####################################################################################
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = "MIT"
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+#External libraries
+from scipy.spatial.distance import squareform
+
+class MLPYDistanceAdaptor:
+    """
+    Allows one to use custom distance metrics with KMedoids in the MLPY package.
+    """
+
+    npaMatrix = None
+    """
+    Distance matrix to reference.
+    """
+
+    def __init__(self, npaDistanceMatrix, fIsCondensedMatrix):
+        """
+        Constructor requires a matrix of distances, could be condensed or square matrices
+
+    	:param	npaDistanceMatrix:	The distance matrix to be used
+	:type	Numpy array
+	:param	fIsCondensedMatrix:	Indicator of the matrix being square (true = condensed; false = square)
+	:type	Boolean
+        """
+
+        if fIsCondensedMatrix:
+            self.npaMatrix = squareform(npaDistanceMatrix)
+        else:
+            self.npaMatrix = npaDistanceMatrix
+
+    def compute(self,x,y):
+        """
+        This is the only method required in the interface to MLPY to be a distance metric.
+        Does NOT want values but positions, the positions will be used for accessing the distance matrix already provided.
+
+	:param	x:	X position as a array of 1 number
+	:type	Numpy array
+	:param	y:	Y position as a array of 1 number
+	:type	Boolean
+        """
+
+        if(self.npaMatrix == None):
+            raise Exception("".join(["MLPYDistanceAdaptor. Attempted to compute distance with out a distance matrix passed in during construction."]))
+        return self.npaMatrix[x[0],y[0]]