Add header documentation

Add Processing script for visualizing results
Change camelCase strings to _underscore notation

Makefile

@@ -6,8 +6,8 @@ SHELL := /bin/bash
 CC = gcc
 RM = rm -f
 CFLAGS=-lm -O3 -Wall -I.
-OBJ=serial.o serialDeclarations.o
+OBJ=serial.o serial_declarations.o
-DEPS=serialDeclarations.h
+DEPS=serial_declarations.h
 
 # ==========================================
 # TARGETS

output/visualization/visualization.pde

@@ -0,0 +1,35 @@
+int frame = 1;
+PShape frameS;
+
+void setup() {
+  size(1280, 720);
+  frameRate(12);
+}
+
+int scale = 40;
+float radius = 2;
+
+void draw() {
+  background(255);
+  stroke(0);
+  translate(220, 0);
+  //scale(scale);
+  
+  fill(0);
+  String[] lines;
+  lines = loadStrings("../output_" + frame);
+  if (lines == null){
+    delay(5000);
+    exit();
+  } 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);
+      shape(frameS, 0, 0);
+    }
+  }
+  frame++;
+  //Uncomment to save each frame to a jpg file
+  //saveFrame("out-######.jpg");
+  delay(600);
+}

serial.c

@@ -2,7 +2,7 @@
 #include <stdlib.h>
 #include <sys/time.h>
 
-#include "serialDeclarations.h"
+#include "serial_declarations.h"
 
 int NUMBER_OF_POINTS = 600;
 int DIMENSIONS = 2;
@@ -56,11 +56,11 @@ int main(int argc, char **argv){
     parameters *opt;
     opt = &params;
 
-    double **shiftedPoints;
+    double **shifted_points;
     // tic
     gettimeofday (&startwtime, NULL);
 
-    int iterations = meanshift(vectors, &shiftedPoints, h, opt, 1);
+    int iterations = meanshift(vectors, &shifted_points, h, opt, 1);
 
     // toc
     gettimeofday (&endwtime, NULL);

serialDeclarations.h

@@ -1,28 +0,0 @@
-#ifndef SERIAL_DECLARATIONS_H	/*	Include guard	*/
-#define SERIAL_DECLARATIONS_H
-
-#include <stdbool.h>
-
-extern int NUMBER_OF_POINTS;
-extern int DIMENSIONS;
-extern char* POINTS_FILENAME;
-extern char* LABELS_FILENAME;
-
-typedef struct parameters {
-    double epsilon;
-    bool verbose;
-    bool display;
-} parameters;
-
-void get_args(int argc, char **argv, int *h);
-int meanshift(double **originalPoints, double ***shiftedPoints, int h
-    , parameters *opt, int iteration);
-double norm(double ** m, int rows, int cols);
-void multiply(double ** matrix1, double ** matrix2, double ** output);
-double calculateDistance(double *, double *);
-double **alloc_2d_double(int rows, int cols);
-double **duplicate(double **a, double **b, int rows, int cols);
-void print_matrix(double ** array, int rows, int cols);
-void save_matrix(double **matrix,int iteration);
-
-#endif //SERIAL_DECLARATIONS_H

serialDeclarations.c → serial_declarations.c

@@ -4,7 +4,7 @@
 #include <float.h>
 #include <string.h>
 
-#include "serialDeclarations.h"
+#include "serial_declarations.h"
 
 void get_args(int argc, char **argv, int *h){
     if (argc != 6) {
@@ -24,47 +24,47 @@ void get_args(int argc, char **argv, int *h){
     LABELS_FILENAME = argv[5];
 }
 
-int meanshift(double **originalPoints, double ***shiftedPoints, int h
+int meanshift(double **original_points, double ***shifted_points, int h
     , parameters *opt, int iteration){
 
     // allocates space and copies original points on first iteration
     if (iteration == 1){
-        (*shiftedPoints) = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
+        (*shifted_points) = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
-        (*shiftedPoints) = duplicate(originalPoints, (*shiftedPoints)
+        duplicate(original_points, NUMBER_OF_POINTS, DIMENSIONS, shifted_points);
-            , NUMBER_OF_POINTS, DIMENSIONS);
     }
 
     // mean shift vector
-    double **meanShiftVector;
+    double **mean_shift_vector;
-    meanShiftVector = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
+    mean_shift_vector = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
-    // initialize elements of meanShiftVector to inf
+    // initialize elements of mean_shift_vector to inf
     for (int i=0;i<NUMBER_OF_POINTS;i++){
         for (int j=0;j<DIMENSIONS;j++){
-            meanShiftVector[i][j] = DBL_MAX;
+            mean_shift_vector[i][j] = DBL_MAX;
         }
     }
 
-    double **kernelMatrix = alloc_2d_double(NUMBER_OF_POINTS, NUMBER_OF_POINTS);
+    double **kernel_matrix = alloc_2d_double(NUMBER_OF_POINTS, NUMBER_OF_POINTS);
     double *denominator = malloc(NUMBER_OF_POINTS * sizeof(double));
 
     // find pairwise distance matrix (inside radius)
     // [I, D] = rangesearch(x,y,h);
     for (int i=0; i<NUMBER_OF_POINTS; i++){
-        double sum =0;
+        double sum = 0;
         for (int j=0; j<NUMBER_OF_POINTS; j++){
-            double dist = calculateDistance((*shiftedPoints)[i],originalPoints[j]);
+            double dist = calculateDistance((*shifted_points)[i]
+                , original_points[j]);
 
             if (i == j){
-                kernelMatrix[i][j] = 1;
+                kernel_matrix[i][j] = 1;
             } else if (dist < h*h){
-                kernelMatrix[i][j] = dist * dist;
+                kernel_matrix[i][j] = dist * dist;
                 // compute kernel matrix
-                double pow = ((-1)*(kernelMatrix[i][j]))/(2*(h*h));
+                double pow = ((-1)*(kernel_matrix[i][j]))/(2*(h*h));
-                kernelMatrix[i][j] = exp(pow);
+                kernel_matrix[i][j] = exp(pow);
             } else {
-                kernelMatrix[i][j] = 0;
+                kernel_matrix[i][j] = 0;
             }
-            sum = sum + kernelMatrix[i][j];
+            sum = sum + kernel_matrix[i][j];
         }
         denominator[i] = sum;
     }
@@ -72,25 +72,25 @@ int meanshift(double **originalPoints, double ***shiftedPoints, int h
     // create new y vector
     double **y_new = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
 
-    multiply(kernelMatrix, originalPoints, y_new);
+    multiply(kernel_matrix, original_points, y_new);
     // 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];
             // calculate mean-shift vector
-            meanShiftVector[i][j] = y_new[i][j] - (*shiftedPoints)[i][j];
+            mean_shift_vector[i][j] = y_new[i][j] - (*shifted_points)[i][j];
         }
     }
-    shiftedPoints = &y_new;
+    shifted_points = &y_new;
 
-    save_matrix((*shiftedPoints), iteration);
+    save_matrix((*shifted_points), iteration);
 
-    double current_norm = norm(meanShiftVector, NUMBER_OF_POINTS, DIMENSIONS);
+    double current_norm = norm(mean_shift_vector, NUMBER_OF_POINTS, DIMENSIONS);
     printf("Iteration n. %d, error %f \n", iteration, current_norm);
 
     /** iterate until convergence **/
     if (current_norm > opt->epsilon) {
-        return meanshift(originalPoints, shiftedPoints, h, opt, ++iteration);
+        return meanshift(original_points, shifted_points, h, opt, ++iteration);
     }
 
     return iteration;
@@ -98,11 +98,11 @@ int meanshift(double **originalPoints, double ***shiftedPoints, int h
 
 // TODO check why there's is a difference in the norm calculate in matlab
 double norm(double **matrix, int rows, int cols){
-    double sum=0, tempMul=0;
+    double sum=0, temp_mul=0;
     for (int i=0; i<rows; i++) {
         for (int j=0; j<cols; j++) {
-            tempMul = matrix[i][j] * matrix[i][j];
+            temp_mul = matrix[i][j] * matrix[i][j];
-            sum = sum + tempMul;
+            sum = sum + temp_mul;
         }
     }
     double norm = sqrt(sum);
@@ -133,7 +133,6 @@ double calculateDistance(double *y, double *x){
     return distance;
 }
 
-// allocates a 2d array in continuous memory positions
 double **alloc_2d_double(int rows, int cols) {
     double *data = (double *) malloc(rows*cols*sizeof(double));
     double **array = (double **) malloc(rows*sizeof(double*));
@@ -142,14 +141,12 @@ double **alloc_2d_double(int rows, int cols) {
     return array;
 }
 
-// copy the values of a 2d double array to another
+void duplicate(double **source, int rows, int cols, double ***dest){
-double **duplicate(double **a, double **b, int rows, int cols){
     for (int i=0; i<rows; i++){
         for (int j=0; j<cols; j++){
-            b[i][j] = a[i][j];
+            (*dest)[i][j] = source[i][j];
         }
     }
-    return b;
 }
 
 void print_matrix(double **array, int rows, int cols){
@@ -164,15 +161,15 @@ void print_matrix(double **array, int rows, int cols){
 void save_matrix(double **matrix, int iteration){
     char filename[18];
     snprintf(filename, sizeof(filename), "%s%d", "output/output_", iteration);
-    FILE *iterOutput;
+    FILE *file;
-    iterOutput = fopen(filename, "w");
+    file = fopen(filename, "w");
     for (int rows=0; rows<NUMBER_OF_POINTS; ++rows){
         for (int cols=0; cols<DIMENSIONS; ++cols){
-            fprintf(iterOutput, "%f", matrix[rows][cols]);
+            fprintf(file, "%f", matrix[rows][cols]);
             if (cols != DIMENSIONS - 1){
-                fprintf(iterOutput, ",");
+                fprintf(file, ",");
             }
         }
-        fprintf(iterOutput, "\n");
+        fprintf(file, "\n");
     }
 }

serial_declarations.h

@@ -0,0 +1,50 @@
+#ifndef SERIAL_DECLARATIONS_H    /*    Include guard    */
+#define SERIAL_DECLARATIONS_H
+
+#include <stdbool.h>
+
+extern int NUMBER_OF_POINTS;
+extern int DIMENSIONS;
+extern char* POINTS_FILENAME;
+extern char* LABELS_FILENAME;
+
+typedef struct parameters {
+    double epsilon;
+    bool verbose;
+    bool display;
+} parameters;
+
+//Function get_args parses command line arguments.
+void get_args(int argc, char **argv, int *h);
+
+//Function meanshift recursively shifts original points according to th
+//mean-shift algorithm saving the result to shiftedPoints. Struct opt has user
+//options, h is the desirable deviation, iteration is this call's iteration
+//number.
+int meanshift(double **original_points, double ***shifted_points, int h
+	, parameters *opt, int iteration);
+
+//Function norm returns the second norm of matrix of dimensions rowsXcols.
+double norm(double **matrix, int rows, int cols);
+
+//Function multiply calculates the product of matrices 1 and 2 into output.
+void multiply(double **matrix1, double **matrix2, double **output);
+
+//Function calculateDistance returns the distance between x and y vectors.
+double calculateDistance(double *y, double *x);
+
+//Function alloc_2d_double allocates rows*cols bytes of continuous memory.
+double **alloc_2d_double(int rows, int cols);
+
+//Function duplicate copies the values of source array to dest array.
+void duplicate(double **source, int rows, int cols, double ***dest);
+
+//Function print_matrix prints array of dimensions rowsXcols to the console.
+void print_matrix(double **array, int rows, int cols);
+
+//Function save_matrix prints matrix in a csv file with path/filename
+//"output/output_iteration". If a file already exists new lines are concatenated.
+void save_matrix(double **matrix
+	, int iteration);
+
+#endif //SERIAL_DECLARATIONS_H