serial implementation of mean shift

serial.c

@@ -0,0 +1,269 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/time.h>
+#include <float.h>
+#include <stdbool.h>
+#include <sys/time.h>
+#include <math.h>
+
+#define X "data/X.bin"
+#define L "data/L.bin"
+#define COLUMNS     2
+#define ROWS        600
+
+struct parameters {
+    double epsilom;
+    bool verbose;
+    bool display;
+};
+struct timeval startwtime, endwtime;
+double seq_time;
+
+double **alloc_2d_double(int rows, int cols);
+double **duplicate(double **a, double **b, int rows, int cols);
+void meanshift(double **x, int h, struct parameters *opt);
+double norm(double ** m, int rows, int cols);
+void multiply(double ** matrix1, double ** matrix2, double ** output);
+double calculateDistance(double *, double *);
+void print_matrix(double ** array, int rows, int cols);
+
+int main(int argc, char **argv){
+
+//    if (argc<2){
+//        printf("%s\n", "Specify the k");
+//        return 1;
+//    }
+//    = atoi(argv[1]);  // the k-parameter
+
+
+    FILE *f;
+    f = fopen(X, "rb");
+    fseek(f, 0L, SEEK_END);
+    long int pos = ftell(f);
+    fclose(f);
+    int elements = pos / sizeof(double);  // number of total elements (points*dimension)
+    int points = elements/COLUMNS;
+    //printf("points : %d \n", points);
+    f = fopen(X, "rb");
+    double ** vectors;
+    vectors = alloc_2d_double(ROWS, COLUMNS);
+    for (int i=0; i<ROWS; i++){
+        int out = fread(vectors[i], sizeof(double), COLUMNS, f);
+    }
+    //printf("test : %f \n", vectors[0][0]);
+    //printf("test : %f \n", vectors[ROWS-1][COLUMNS-1]);
+
+    // initializing file that will contain the labels (train)
+    f = fopen(L, "rb");
+    // NOTE : Labels were classified as <class 'numpy.uint8'>
+    // variables of type uint8 are stored as 1-byte (8-bit) unsigned integers
+    fseek(f, 0L, SEEK_END);
+    pos = ftell(f);
+    rewind(f);
+    //printf("position : %ld \n", pos);
+    int label_elements = pos/ sizeof(char);
+    char *labels = (char*)malloc(label_elements* sizeof(char));
+    fseek(f, 0L, SEEK_SET);
+    int out = fread(labels, sizeof(char), label_elements, f);
+    fclose(f);
+
+    // MEAN SHIFT OPTIONS
+    int h = 1;
+    struct parameters params;
+    params.epsilom = 0.0001;
+    params.verbose = false;
+    params.display = false;
+    struct parameters *opt;
+    opt = &params;
+
+    // tic
+    gettimeofday (&startwtime, NULL);
+
+    meanshift(vectors, h, opt);
+
+    // toc
+    gettimeofday (&endwtime, NULL);
+    seq_time = (double)((endwtime.tv_usec - startwtime.tv_usec)/1.0e6 + endwtime.tv_sec - startwtime.tv_sec);
+    printf("%s wall clock time = %f\n","Mean Shift", seq_time);
+
+    //TODO write output points to file -> plot later
+
+}
+
+
+void meanshift(double **x, int h, struct parameters *opt){
+
+    double **y;
+    y = alloc_2d_double(ROWS, COLUMNS);
+    y = duplicate(x, y, ROWS, COLUMNS);
+
+    // mean shift vectors
+    double **m;
+    m = alloc_2d_double(ROWS, COLUMNS);
+    // initialize elements of m to inf
+    for (int i=0;i<ROWS;i++){
+        for (int j=0;j<COLUMNS;j++){
+            m[i][j] = DBL_MAX;
+        }
+    }
+
+    // initialize iteration counter
+    int iter = 0;
+
+    // printf("%f \n", opt->epsilom);
+    // TODO ITERATION
+    /** iterate until convergence **/
+    // printf("norm : %f \n", norm(m, ROWS, COLUMNS));
+
+    while (norm(m, ROWS, COLUMNS) > opt->epsilom) {
+//    while (iter < 1){
+        iter = iter +1;
+        // find pairwise distance matrix (inside radius)
+        // TODO write in C
+        /** allocate memory for inside iteration arrays **/
+        double ** W = alloc_2d_double(ROWS, ROWS);
+        double * l = malloc(ROWS * sizeof(double));
+        // [I, D] = rangesearch(x,y,h);
+        for (int i=0; i<ROWS; i++){
+            for (int j=0; j<ROWS; j++){
+                // TODO implement function to calculate distance calculateDistance(double *, double *)
+                double dist = calculateDistance(y[i],x[j]);
+
+                // 2sparse matrix
+                if (dist < h){
+                    W[i][j] = dist;
+                    //printf("%f \n", W[i][j]);
+                }else{
+                    W[i][j] = 0;
+                }
+            }
+        }
+
+
+        // for each element of W (x) do x^2
+        // size of W is [600 600]
+        // W is a sparse matrix -> apply to non-zero elements
+        for (int i=0; i<ROWS; i++){
+            double sum =0;
+            for (int j=0; j < ROWS; j++){
+                if (W[i][j] != 0){
+                    W[i][j] = W[i][j]*W[i][j];
+                    // compute kernel matrix
+                    // apply function to non zero elements of a sparse matrix
+                    double pow = ((-1)*(W[i][j]))/(2*(h*h));
+                    W[i][j] = exp(pow);
+                }
+                // make sure diagonal elements are 1
+                if (i==j){
+                    W[i][j] = W[i][j] +1;
+                }
+                // calculate sum(W,2)
+                sum = sum + W[i][j];
+            }
+            /** l array is correct**/
+            l[i] = sum;
+            // printf("l[%d] : %f \n", i, l[i]);
+        }
+        /** W is correct**/
+        //print_matrix(W, ROWS, ROWS);
+
+
+        // create new y vector
+        double** y_new = alloc_2d_double(ROWS, COLUMNS);
+        // TODO implement in C : y_new = W * x
+
+        // TODO implement function double ** multiply(double **, double **)
+        multiply(W, x, y_new);
+        /** y_new is CORRECT **/
+        // print_matrix(y_new, ROWS, COLUMNS);
+        // divide element-wise
+        for (int i=0; i<ROWS; i++){
+            for (int j=0; j<COLUMNS; j++){
+                y_new[i][j] = y_new[i][j] / l[i];
+            }
+        }
+
+        // calculate mean-shift vector
+        for (int i=0; i<ROWS; i++){
+            for (int j=0; j<COLUMNS; j++){
+                m[i][j] = y_new[i][j] - y[i][j];
+
+                // update y
+                y[i][j] = y_new[i][j];
+            }
+        }
+
+        printf("Iteration n. %d, error %f \n", iter, norm(m, ROWS, COLUMNS));
+        // TODO maybe keep y for live display later?
+    };
+
+
+
+}
+
+// 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*));
+    for (int i=0; i<rows; i++)
+        array[i] = &(data[cols*i]);
+    return array;
+}
+
+// copy the values of a 2d double array to another
+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];
+        }
+    }
+    return b;
+}
+
+// TODO check why there's is a difference in the norm calculate in matlab
+double norm(double ** m, int rows, int cols){
+    double sum=0, a=0;
+    for (int i = 0; i < rows; i++) {
+        for (int j = 0; j < cols; j++) {
+            a = m[i][j] * m[i][j];
+            sum = sum + a;
+        }
+    }
+    double norm = sqrt(sum);
+    return norm;
+}
+
+double calculateDistance(double *y, double *x){
+    double sum = 0, dif;
+    for (int i=0;i<COLUMNS;i++){
+        dif = y[i]-x[i];
+        sum += dif * dif;
+    }
+    double distance = sqrt(sum);
+    return distance;
+}
+
+void multiply(double ** matrix1, double ** matrix2, double ** output){
+    // W dims are ROWS ROWS and x dims are ROWS COLUMNS
+    // TODO CHECK
+    int i, j, k;
+    for (i=0; i<ROWS; i++){
+        for (j=0; j<COLUMNS; j++){
+            output[i][j] = 0;
+            for (k=0; k<ROWS; k++){
+                output[i][j] += matrix1[i][k] * matrix2[k][j];
+            }
+        }
+    }
+}
+
+void print_matrix(double ** array, int rows, int cols){
+    for (int i=0; i<cols; i++){
+        for (int j=0; j<rows; j++){
+            printf("%f ", array[j][i]);
+        }
+        printf("\n");
+    }
+}
+
+