matlab version with variable lengths and init with medoid

DBA.m

@@ -1,27 +1,71 @@
-/*******************************************************************************
- * Copyright (C) 2013 Francois PETITJEAN, Ioannis PAPARRIZOS
- * 
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, version 3 of the License.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.well
- * 
- * You should have received a copy of the GNU General Public License
- * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- ******************************************************************************/ 
+%*******************************************************************************
+ % Copyright (C) 2013 Francois PETITJEAN, Ioannis PAPARRIZOS
+ % This program is free software: you can redistribute it and/or modify
+ % it under the terms of the GNU General Public License as published by
+ % the Free Software Foundation, version 3 of the License.
+ % 
+ % This program is distributed in the hope that it will be useful,
+ % but WITHOUT ANY WARRANTY; without even the implied warranty of
+ % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ % GNU General Public License for more details.well
+ % 
+ % You should have received a copy of the GNU General Public License
+ % along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ %*****************************************************************************/ 
+
+% function average = DBA(sequences)
+% 	index=randi(length(sequences),1);
+% 	average=repmat(sequences{index},1);
+% 	for i=1:15
+% 		average=DBA_one_iteration(average,sequences);
+% 	end
+% end
 
 function average = DBA(sequences)
-	index=randi(size(sequences,1),1);
-	average=sequences(index,:);
+    average = repmat(sequences{medoidIndex(sequences)},1);
 	for i=1:15
 		average=DBA_one_iteration(average,sequences);
 	end
 end
 
+function sos = sumOfSquares(s,sequences)
+    sos = 0.0;
+    for i=1:length(sequences)
+        dist = dtw(s,sequences{i});
+        sos = sos + dist * dist;
+    end
+end
+
+function score = dtw(S,T)
+    costM = zeros(length(S),length(T));
+
+    costM(1,1) = (S(1)-T(1))^2;
+    for i=2:length(S)
+        costM(i,1)= costM(i-1,1)+ (S(i)-T(1))^2;
+    end
+    for i=2:length(T)
+        costM(1,i)= costM(1,i-1)+ (S(1)-T(i))^2;
+    end
+    for i=2:length(S)
+        for j=2:length(T)
+            costM(i,j)=min(min(costM(i-1,j-1),costM(i,j-1)),costM(i-1,j))+(S(i)-T(j))^2;
+        end
+    end
+    score = sqrt(costM(length(S),length(T)));
+end
+
+function index = medoidIndex(sequences) 
+	index = -1;
+    lowestInertia = Inf;
+	for i=1:length(sequences)
+        tmpInertia = sumOfSquares(sequences{i},sequences);
+        if (tmpInertia < lowestInertia)
+            index = i;
+            lowestInertia = tmpInertia;
+        end
+    end
+end
+
 
 function average = DBA_one_iteration(averageS,sequences)
 
@@ -30,11 +74,11 @@
 		tupleAssociation{t}=[];
 	end
 
-	costMatrix = [];
-	pathMatrix = [];
+	costMatrix = zeros(1000,1000);
+	pathMatrix = zeros(1000,1000);
 
-	for k=1:size(sequences,1)
-	    sequence = sequences(k,:);
+	for k=1:length(sequences)
+	    sequence = sequences{k};
 	    costMatrix(1,1) = distanceTo(averageS(1),sequence(1));
 	    pathMatrix(1,1) = -1;
 	    for i=2:size(averageS,2)
@@ -118,8 +162,16 @@
 function dist = distanceTo(a,b)
     dist=(a-b)*(a-b);
 end
-
-sequences=rand(100,20);
-mean=DBA(sequences)
-plot(mean);
+
+function ex = test()
+    sequences = {};
+    sequences{100}=[];
+    for i=1:100
+        length = randi(100);
+        sequences{i}=rand(1,length);
+    end
+    mean=DBA(sequences);
+end
+
+