--- a/python/events.py	Sat Jul 25 23:28:52 2015 -0400
+++ b/python/events.py	Mon Aug 10 17:51:49 2015 -0400
@@ -295,13 +295,15 @@
         print('unknown type of point: '+pointType)
     return allPoints
 
-def prototypeCluster(interactions, similarityMatrix, alignmentMatrix, indicatorName, minSimilarity):
+def prototypeCluster(interactions, similarityMatrix, alignmentMatrix, indicatorName, minSimilarity, minClusterSize = None):
     '''Finds exemplar indicator time series for all interactions
     Returns the prototype indices (in the interaction list) and the label of each indicator (interaction)
 
     if an indicator profile (time series) is different enough (<minSimilarity), 
     it will become a new prototype. 
-    Non-prototype interactions will be assigned to an existing prototype'''
+    Non-prototype interactions will be assigned to an existing prototype
+    if minClusterSize is not None, the clusters will be refined by removing iteratively the smallest clusters
+    and reassigning all elements in the cluster until no cluster is smaller than minClusterSize'''
 
     # sort indicators based on length
     indices = range(similarityMatrix.shape[0])
@@ -320,13 +322,22 @@
              prototypeIndices.append(i)
 
     # assignment
-    labels = [-1]*similarityMatrix.shape[0]
     indices = [i for i in range(similarityMatrix.shape[0]) if i not in prototypeIndices]
-    for i in prototypeIndices:
-        labels[i] = i
-    for i in indices:
-        prototypeIndex = similarityMatrix[i][prototypeIndices].argmax()
-        labels[i] = prototypeIndices[prototypeIndex]
+    assign = True
+    while assign:
+        labels = [-1]*similarityMatrix.shape[0]
+        for i in prototypeIndices:
+            labels[i] = i
+        for i in indices:
+            prototypeIndex = similarityMatrix[i][prototypeIndices].argmax()
+            labels[i] = prototypeIndices[prototypeIndex]
+        clusterSizes = {i: sum(np.array(labels) == i) for i in prototypeIndices}
+        smallestClusterIndex = min(clusterSizes, key = clusterSizes.get) 
+        assign = (clusterSizes[smallestClusterIndex] < minClusterSize)
+        print prototypeIndices, smallestClusterIndex, clusterSizes[smallestClusterIndex]
+        if assign:
+            prototypeIndices.remove(smallestClusterIndex)
+            indices.append(smallestClusterIndex)
 
     return prototypeIndices, labels