March 1, 2015

Implementation problem

Forums: 

Hello, I want to implement k-means algo on LEACH protocol in ns2.34 in centos for that i don`t have any idea how to implement it with given code? Please help me ? Please guide me for that.I have installed leach in ns2.34.

// kmeans.h
// Ethan Brodsky
// October 2011

void kmeans(
int dim, // dimension of data

double *X, // pointer to data
int n, // number of elements

int k, // number of clusters
double *cluster_centroid, // initial cluster centroids
int *cluster_assignment_final // output
);

// kmeans.c
// Ethan Brodsky
// October 2011

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

#define sqr(x) ((x)*(x))

#define MAX_CLUSTERS 16

#define MAX_ITERATIONS 100

#define BIG_double (INFINITY)

void fail(char *str)
{
printf(str);
exit(-1);
}

double calc_distance(int dim, double *p1, double *p2)
{
double distance_sq_sum = 0;

for (int ii = 0; ii < dim; ii++)
distance_sq_sum += sqr(p1[ii] - p2[ii]);

return distance_sq_sum;

}

void calc_all_distances(int dim, int n, int k, double *X, double *centroid, double *distance_output)
{
for (int ii = 0; ii < n; ii++) // for each point
for (int jj = 0; jj < k; jj++) // for each cluster
{
// calculate distance between point and cluster centroid
distance_output[ii*k + jj] = calc_distance(dim, &X[ii*dim], &centroid[jj*dim]);
}
}

double calc_total_distance(int dim, int n, int k, double *X, double *centroids, int *cluster_assignment_index)
// NOTE: a point with cluster assignment -1 is ignored
{
double tot_D = 0;

// for every point
for (int ii = 0; ii < n; ii++)
{
// which cluster is it in?
int active_cluster = cluster_assignment_index[ii];

// sum distance
if (active_cluster != -1)
tot_D += calc_distance(dim, &X[ii*dim], &centroids[active_cluster*dim]);
}

return tot_D;
}

void choose_all_clusters_from_distances(int dim, int n, int k, double *distance_array, int *cluster_assignment_index)
{
// for each point
for (int ii = 0; ii < n; ii++)
{
int best_index = -1;
double closest_distance = BIG_double;

// for each cluster
for (int jj = 0; jj < k; jj++)
{
// distance between point and cluster centroid

double cur_distance = distance_array[ii*k + jj];
if (cur_distance < closest_distance)
{
best_index = jj;
closest_distance = cur_distance;
}
}

// record in array
cluster_assignment_index[ii] = best_index;
}
}

void calc_cluster_centroids(int dim, int n, int k, double *X, int *cluster_assignment_index, double *new_cluster_centroid)
{
int cluster_member_count[MAX_CLUSTERS];

// initialize cluster centroid coordinate sums to zero
for (int ii = 0; ii < k; ii++)
{
cluster_member_count[ii] = 0;

for (int jj = 0; jj < dim; jj++)
new_cluster_centroid[ii*dim + jj] = 0;
}

// sum all points
// for every point
for (int ii = 0; ii < n; ii++)
{
// which cluster is it in?
int active_cluster = cluster_assignment_index[ii];

// update count of members in that cluster
cluster_member_count[active_cluster]++;

// sum point coordinates for finding centroid
for (int jj = 0; jj < dim; jj++)
new_cluster_centroid[active_cluster*dim + jj] += X[ii*dim + jj];
}

// now divide each coordinate sum by number of members to find mean/centroid
// for each cluster
for (int ii = 0; ii < k; ii++)
{
if (cluster_member_count[ii] == 0)
printf("WARNING: Empty cluster %d! \n", ii);

// for each dimension
for (int jj = 0; jj < dim; jj++)
new_cluster_centroid[ii*dim + jj] /= cluster_member_count[ii]; /// XXXX will divide by zero here for any empty clusters!

}
}

void get_cluster_member_count(int n, int k, int *cluster_assignment_index, int *cluster_member_count)
{
// initialize cluster member counts
for (int ii = 0; ii < k; ii++)
cluster_member_count[ii] = 0;

// count members of each cluster
for (int ii = 0; ii < n; ii++)
cluster_member_count[cluster_assignment_index[ii&#91;&#91;++;
}

void update_delta_score_table(int dim, int n, int k, double *X, int *cluster_assignment_cur, double *cluster_centroid, int *cluster_member_count, double *point_move_score_table, int cc)
{
// for every point (both in and not in the cluster)
for (int ii = 0; ii < n; ii++)
{
double dist_sum = 0;
for (int kk = 0; kk < dim; kk++)
{
double axis_dist = X[ii*dim + kk] - cluster_centroid[cc*dim + kk];
dist_sum += sqr(axis_dist);
}

double mult = ((double)cluster_member_count[cc] / (cluster_member_count[cc] + ((cluster_assignment_cur[ii]==cc) ? -1 : +1)));

point_move_score_table[ii*dim + cc] = dist_sum * mult;
}
}

void perform_move(int dim, int n, int k, double *X, int *cluster_assignment, double *cluster_centroid, int *cluster_member_count, int move_point, int move_target_cluster)
{
int cluster_old = cluster_assignment[move_point];
int cluster_new = move_target_cluster;

// update cluster assignment array
cluster_assignment[move_point] = cluster_new;

// update cluster count array
cluster_member_count[cluster_old]--;
cluster_member_count[cluster_new]++;

if (cluster_member_count[cluster_old] <= 1)
printf("WARNING: Can't handle single-member clusters! \n");

// update centroid array
for (int ii = 0; ii < dim; ii++)
{
cluster_centroid[cluster_old*dim + ii] -= (X[move_point*dim + ii] - cluster_centroid[cluster_old*dim + ii]) / cluster_member_count[cluster_old];
cluster_centroid[cluster_new*dim + ii] += (X[move_point*dim + ii] - cluster_centroid[cluster_new*dim + ii]) / cluster_member_count[cluster_new];
}
}

void cluster_diag(int dim, int n, int k, double *X, int *cluster_assignment_index, double *cluster_centroid)
{
int cluster_member_count[MAX_CLUSTERS];

get_cluster_member_count(n, k, cluster_assignment_index, cluster_member_count);

printf(" Final clusters \n");
for (int ii = 0; ii < k; ii++)
printf(" cluster %d: members: %8d, centroid (%.1f %.1f) \n", ii, cluster_member_count[ii], cluster_centroid[ii*dim + 0], cluster_centroid[ii*dim + 1]);
}

void copy_assignment_array(int n, int *src, int *tgt)
{
for (int ii = 0; ii < n; ii++)
tgt[ii] = src[ii];
}

int assignment_change_count(int n, int a[], int b[])
{
int change_count = 0;

for (int ii = 0; ii < n; ii++)
if (a[ii] != b[ii])
change_count++;

return change_count;
}

void kmeans(
int dim, // dimension of data

double *X, // pointer to data
int n, // number of elements

int k, // number of clusters
double *cluster_centroid, // initial cluster centroids
int *cluster_assignment_final // output
)
{
double *dist = (double *)malloc(sizeof(double) * n * k);
int *cluster_assignment_cur = (int *)malloc(sizeof(int) * n);
int *cluster_assignment_prev = (int *)malloc(sizeof(int) * n);
double *point_move_score = (double *)malloc(sizeof(double) * n * k);

if (!dist || !cluster_assignment_cur || !cluster_assignment_prev || !point_move_score)
fail("Error allocating dist arrays");

// initial setup
calc_all_distances(dim, n, k, X, cluster_centroid, dist);
choose_all_clusters_from_distances(dim, n, k, dist, cluster_assignment_cur);
copy_assignment_array(n, cluster_assignment_cur, cluster_assignment_prev);

// BATCH UPDATE
double prev_totD = BIG_double;
int batch_iteration = 0;
while (batch_iteration < MAX_ITERATIONS)
{
// printf("batch iteration %d \n", batch_iteration);
// cluster_diag(dim, n, k, X, cluster_assignment_cur, cluster_centroid);

// update cluster centroids
calc_cluster_centroids(dim, n, k, X, cluster_assignment_cur, cluster_centroid);

// deal with empty clusters
// XXXXXXXXXXXXXX

// see if we've failed to improve
double totD = calc_total_distance(dim, n, k, X, cluster_centroid, cluster_assignment_cur);
if (totD > prev_totD)
// failed to improve - currently solution worse than previous
{
// restore old assignments
copy_assignment_array(n, cluster_assignment_prev, cluster_assignment_cur);

// recalc centroids
calc_cluster_centroids(dim, n, k, X, cluster_assignment_cur, cluster_centroid);

printf(" negative progress made on this step - iteration completed (%.2f) \n", totD - prev_totD);

// done with this phase
break;
}

// save previous step
copy_assignment_array(n, cluster_assignment_cur, cluster_assignment_prev);

// move all points to nearest cluster
calc_all_distances(dim, n, k, X, cluster_centroid, dist);
choose_all_clusters_from_distances(dim, n, k, dist, cluster_assignment_cur);

int change_count = assignment_change_count(n, cluster_assignment_cur, cluster_assignment_prev);

printf("%3d %u %9d %16.2f %17.2f\n", batch_iteration, 1, change_count, totD, totD - prev_totD);
fflush(stdout);

// done with this phase if nothing has changed
if (change_count == 0)
{
printf(" no change made on this step - iteration completed \n");
break;
}

prev_totD = totD;

batch_iteration++;
}

cluster_diag(dim, n, k, X, cluster_assignment_cur, cluster_centroid);

// ONLINE UPDATE
/* The online update prtion of this code has never worked properly, but batch update has been adequate for our projects so far.
int online_iteration = 0;
int last_point_moved = 0;

int cluster_changed[MAX_CLUSTERS];
for (int ii = 0; ii < k; ii++)
cluster_changed[ii] = 1;

int cluster_member_count[MAX_CLUSTERS];
get_cluster_member_count(n, k, cluster_assignment_cur, cluster_member_count);

while (online_iteration < MAX_ITERATIONS)
{
// printf("online iteration %d \n", online_iteration);

// for each cluster
for (int ii = 0; ii < k; ii++)
if (cluster_changed[ii])
update_delta_score_table(dim, n, k, X, cluster_assignment_cur, cluster_centroid, cluster_member_count, point_move_score, ii);

// pick a point to move
// look at points in sequence starting at one after previously moved point
int make_move = 0;
int point_to_move = -1;
int target_cluster = -1;
for (int ii = 0; ii < n; ii++)
{
int point_to_consider = (last_point_moved + 1 + ii) % n;

// find the best target for it
int best_target_cluster = -1;
int best_match_count = 0;
double best_delta = BIG_double;

// for each possible target
for (int jj = 0; jj < k; jj++)
{
double cur_delta = point_move_score[point_to_consider*k + jj];

// is this the best move so far?
if (cur_delta < best_delta)
// yes - record it
{
best_target_cluster = jj;
best_delta = cur_delta;
best_match_count = 1;
}
else if (cur_delta == best_delta)
// no, but it's tied with the best one
best_match_count++;
}

// is the best cluster for this point its current cluster?
if (best_target_cluster == cluster_assignment_cur[point_to_consider])
// yes - don't move this point
continue;

// do we have a unique best move?
if (best_match_count > 1)
// no - don't move this point (ignore ties)
continue;
else
// yes - we've found a good point to move
{
point_to_move = point_to_consider;
target_cluster = best_target_cluster;
make_move = 1;
break;
}
}

if (make_move)
{
// where should we move it to?
printf(" %10d: moved %d to %d \n", point_to_move, cluster_assignment_cur[point_to_move], target_cluster);

// mark which clusters have been modified
for (int ii = 0; ii < k; ii++)
cluster_changed[ii] = 0;
cluster_changed[cluster_assignment_cur[point_to_move&#91;&#91; = 1;
cluster_changed[target_cluster] = 1;

// perform move
perform_move(dim, n, k, X, cluster_assignment_cur, cluster_centroid, cluster_member_count, point_to_move, target_cluster);

// count an iteration every time we've cycled through all the points
if (point_to_move < last_point_moved)
online_iteration++;

last_point_moved = point_to_move;
}

}

*/

// printf("iterations: %3d %3d \n", batch_iteration, online_iteration);

// write to output array
copy_assignment_array(n, cluster_assignment_cur, cluster_assignment_final);

free(dist);
free(cluster_assignment_cur);
free(cluster_assignment_prev);
free(point_move_score);
}

Click Here!