Fixed memory management, Add more datasets, Fixed Processing script

data/run_helper.txt

@@ -0,0 +1,46 @@
+Dataset X {
+	int NUMBER_OF_POINTS = 600;
+	int DIMENSIONS = 2;
+	char* POINTS_FILENAME = "data/X.bin";
+	
+	A good h is 1
+	For Processing script:
+		float maxX = 17.124000;
+		float minX = 3.402000;
+		float maxY = 14.996000;
+		float minY = 3.178000;
+
+	12 iterations
+}
+
+Dataset s1 {
+	int NUMBER_OF_POINTS = 5000;
+	int DIMENSIONS = 2;
+	char* POINTS_FILENAME = "data/s1";
+	
+	A good h is 30000
+	For Processing script:
+		float maxX = 961951;
+		float minX = 19835;
+		float maxY = 970756;
+		float minY = 51121;
+
+	~28 iterations
+}
+
+Dataset s4 {
+	int NUMBER_OF_POINTS = 5000;
+	int DIMENSIONS = 2;
+	char* POINTS_FILENAME = "data/s4";
+	
+	A good h is 30000-35000
+	For Processing script:
+		float maxX = 932954;
+		float minX = 89604;
+		float maxY = 977215;
+		float minY = 35412;
+
+	122 iterations with epsilon = 0.0001 and h = 30000
+	110 iterations with epsilon = 0.01 and h = 30000
+	108 iterations with epsilon = 1 and h = 31000
+}

output/visualization/visualization.pde

@@ -2,20 +2,24 @@ int frame = 1;
 PShape frameS;
 
 void setup() {
-  size(1280, 720);
+  size(720, 720);
   frameRate(12);
 }
 
-int scale = 40;
+int scale = 1;
 float radius = 2;
+float maxX = 17.124000;
+float minX = 3.402000;
+float maxY = 14.996000;
+float minY = 3.178000;
 
 void draw() {
   background(255);
   stroke(0);
-  translate(220, 0);
   //scale(scale);
   
   fill(0);
+  System.out.println("frame = " + frame);
   String[] lines;
   lines = loadStrings("../output_" + frame);
   if (lines == null){
@@ -24,11 +28,14 @@ void draw() {
   } else {
     for (int i = 0; i < lines.length; i++) {
       String[] pieces = split(lines[i], ",");
-      frameS = createShape(ELLIPSE, Float.parseFloat(pieces[0])*scale,Float.parseFloat(pieces[1])*scale, radius, radius);
+      float mapedX = map(Float.parseFloat(pieces[0]), minX, maxX, 0, 720);
+      float mapedY = map(Float.parseFloat(pieces[1]), minY, maxY, 0, 720);
+      frameS = createShape(ELLIPSE, mapedX*scale, mapedY*scale, radius, radius);
       shape(frameS, 0, 0);
     }
   }
   frame++;
+  
   //Uncomment to save each frame to a jpg file
   //saveFrame("out-######.jpg");
   delay(600);

serial.c

@@ -68,5 +68,5 @@ int main(int argc, char **argv){
     printf("%s wall clock time = %f\n","Mean Shift", seq_time);
 
     //TODO write output points to file -> plot later
-    //save_matrix(vectors, iterations);
+    //save_matrix(shifted_points, iterations);
 }

serial_declarations.c

@@ -70,24 +70,35 @@ int meanshift(double **original_points, double ***shifted_points, int h
     }
 
     // create new y vector
-    double **y_new = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
+    double **new_shift = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
-
+    // build nominator
-    multiply(kernel_matrix, original_points, y_new);
+    multiply(kernel_matrix, original_points, new_shift);
     // divide element-wise
     for (int i=0; i<NUMBER_OF_POINTS; i++){
         for (int j=0; j<DIMENSIONS; j++){
-            y_new[i][j] = y_new[i][j] / denominator[i];
+            new_shift[i][j] = new_shift[i][j] / denominator[i];
-            // calculate mean-shift vector
+            // calculate mean-shift vector at the same time
-            mean_shift_vector[i][j] = y_new[i][j] - (*shifted_points)[i][j];
+            mean_shift_vector[i][j] = new_shift[i][j] - (*shifted_points)[i][j];
         }
     }
-    shifted_points = &y_new;
+
+    // frees previously shifted points, they're now garbage
+    free((*shifted_points)[0]);
+    // updates shifted points pointer to the new array address
+    shifted_points = &new_shift;
 
     save_matrix((*shifted_points), iteration);
 
     double current_norm = norm(mean_shift_vector, NUMBER_OF_POINTS, DIMENSIONS);
     printf("Iteration n. %d, error %f \n", iteration, current_norm);
 
+    // clean up this iteration's allocates
+    free(mean_shift_vector[0]);
+    free(mean_shift_vector);
+    free(kernel_matrix[0]);
+    free(kernel_matrix);
+    free(denominator);
+
     /** iterate until convergence **/
     if (current_norm > opt->epsilon) {
         return meanshift(original_points, shifted_points, h, opt, ++iteration);