authParallelAndDistributedSystemsCourseExercise3/mean-shift.c

#include <stdio.h>
#include <stdlib.h>
#include <sys/time.h>

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <float.h>
#include <string.h>


#include "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);

int NUMBER_OF_POINTS = 600;
int DIMENSIONS = 2;
char* POINTS_FILENAME = "data/X.bin";
char* LABELS_FILENAME = "data/L.bin";

struct timeval startwtime, endwtime;
double seq_time;

int main(int argc, char **argv){
    int h = 1;

    //get_args(argc, argv, &h); commented out while in development

    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/DIMENSIONS;
//    //printf("points : %d \n", points);
    f = fopen(POINTS_FILENAME, "rb");
    double **vectors;
    vectors = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
    for (int i=0; i<NUMBER_OF_POINTS; i++){
        int out = fread(vectors[i], sizeof(double), DIMENSIONS, f);
    }

    save_matrix(vectors, 0);

    // initializing file that will contain the labels (train)
    f = fopen(LABELS_FILENAME, "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);
    long int 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
    parameters params;
    params.epsilon = 0.0001;
    params.verbose = false;
    params.display = false;
    parameters *opt;
    opt = &params;

    double **shifted_points;
    // tic
    gettimeofday (&startwtime, NULL);

    int iterations = meanshift(vectors, &shifted_points, h, opt, 1);

    // 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
    //save_matrix(shifted_points, iterations);
}

void get_args(int argc, char **argv, int *h){
    if (argc != 6) {
        printf("Usage: %s h N D Pd Pl\nwhere:\n", argv[0]);
        printf("\th is the variance\n");
        printf("\tN is the the number of points\n");
        printf("\tD is the number of dimensions of each point\n");
        printf("\tPd is the path of the dataset file\n");
        printf("\tPl is the path of the labels file\n");
        exit(1);
    }

    *h = atoi(argv[1]);
    NUMBER_OF_POINTS = atoi(argv[2]);
    DIMENSIONS = atoi(argv[3]);
    POINTS_FILENAME = argv[4];
    LABELS_FILENAME = argv[5];
}

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){
        (*shifted_points) = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
        duplicate(original_points, NUMBER_OF_POINTS, DIMENSIONS, shifted_points);
    }

    // mean shift vector
    double **mean_shift_vector;
    mean_shift_vector = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
    // initialize elements of mean_shift_vector to inf
    for (int i=0;i<NUMBER_OF_POINTS;i++){
        for (int j=0;j<DIMENSIONS;j++){
            mean_shift_vector[i][j] = DBL_MAX;
        }
    }

    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;
        for (int j=0; j<NUMBER_OF_POINTS; j++){
            double dist = calculateDistance((*shifted_points)[i]
                    , original_points[j]);

            if (i == j){
                kernel_matrix[i][j] = 1;
            } else if (dist < h*h){
                kernel_matrix[i][j] = dist * dist;
                // compute kernel matrix
                double pow = ((-1)*(kernel_matrix[i][j]))/(2*(h*h));
                kernel_matrix[i][j] = exp(pow);
            } else {
                kernel_matrix[i][j] = 0;
            }
            sum = sum + kernel_matrix[i][j];
        }
        denominator[i] = sum;
    }

    // create new y vector
    double **new_shift = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
    // build nominator
    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++){
            new_shift[i][j] = new_shift[i][j] / denominator[i];
            // calculate mean-shift vector at the same time
            mean_shift_vector[i][j] = new_shift[i][j] - (*shifted_points)[i][j];
        }
    }

    // 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);
    }

    return iteration;
}

// 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, temp_mul=0;
    for (int i=0; i<rows; i++) {
        for (int j=0; j<cols; j++) {
            temp_mul = matrix[i][j] * matrix[i][j];
            sum = sum + temp_mul;
        }
    }
    double norm = sqrt(sum);
    return norm;
}

void multiply(double **matrix1, double **matrix2, double **output){
    // W dims are NUMBER_OF_POINTS NUMBER_OF_POINTS
    // and x dims are NUMBER_OF_POINTS DIMENSIONS

    for (int i=0; i<NUMBER_OF_POINTS; i++){
        for (int j=0; j<DIMENSIONS; j++){
            output[i][j] = 0;
            for (int k=0; k<NUMBER_OF_POINTS; k++){
                output[i][j] += matrix1[i][k] * matrix2[k][j];
            }
        }
    }
}

double calculateDistance(double *y, double *x){
    double sum = 0, dif;
    for (int i=0; i<DIMENSIONS; i++){
        dif = y[i]-x[i];
        sum += dif * dif;
    }
    double distance = sqrt(sum);
    return distance;
}

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;
}

void duplicate(double **source, int rows, int cols, double ***dest){
    for (int i=0; i<rows; i++){
        for (int j=0; j<cols; j++){
            (*dest)[i][j] = source[i][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");
    }
}

void save_matrix(double **matrix, int iteration){
    char filename[18];
    snprintf(filename, sizeof(filename), "%s%d", "output/output_", iteration);
    FILE *file;
    file = fopen(filename, "w");
    for (int rows=0; rows<NUMBER_OF_POINTS; ++rows){
        for (int cols=0; cols<DIMENSIONS; ++cols){
            fprintf(file, "%f", matrix[rows][cols]);
            if (cols != DIMENSIONS - 1){
                fprintf(file, ",");
            }
        }
        fprintf(file, "\n");
    }
}