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dem.cpp
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//The Expectation Maximum Algorithm
//the plot is right
//add the weight to the optics part
//the microcluster is a core microcluster when the sum of its neighbors' weight exceed the minimum density
//add in competing learning
//the graph seems to be right, but not good enough
//try to reduce the usage of memory
//different out file
#include <fstream>
#include <iomanip>
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <errno.h>
#include <math.h>
#include <time.h>
#include <sys/timeb.h>
#include "mytime.h"
#define FALSE 0
#define TRUE 1
#define eigeneps 0.000001
#define pagesize 50
#define minprob 0.001
#define compressratio 1
#define compressratio2 1
#define iterationtime 5
#define BIGENOUGH_FLOAT 10000
//iterationtimeSetting: quadratic(3),cubic(3),ovalhelixes(10),iris(8),image(8),aml(3),Iyer(20)
struct S_BigEnoughItem
{
int ItemNO;
short *ItemList;
};
class EM{
public:
EM(char *ufile, int pnumcluster, int pdimension, int ppagecap);
~EM();
int pagecap;
void EMCluster(char *pinfile, char *poutfile, char *porderfile, double pepsilon, double pdistepsilon, double pmindensity);
private:
int processedcluster;
double * eigmem;
double *PRlx;
double *uXXT;
double *uX;
double * tempmem;
double *resultmem;
double *N;
double Det(double *matrix, int pdim);
double setcoredistance(double pN, double pmindensity, int pneighcount, double *pneighdif, int *pneighindex);
void popseedlist(int *pseedlist, double *pseeddif, int *pcluster2seed, int seedcount);
void expandclusterorder(int pclusternum, double pdisteps, double pmindenstiy, int *pprocessed, FILE *pofp);
void orderseedlist(int pseedcount, int *pseedlist, double *pseeddif, int *pcluster2seed);
int updatedif(int *pseedflag, int *pcluster2seed, int *pseedlist, double *pseeddif, int *pneighindex, double *pneighdif, int pseedcount, int pneighcount);
int neighbour(int clusternum, double pdistepsi, int *pneighindex, double *pneighdif, int *pprocessed);
void optics(char *poutfile, double pdistepsi, double pmindensity);
double probdifference(int numcluster1, int numcluster2);
void filewrite(char *poutfile, double *pu, double *psigma, int pdim, int pnumcluster);
int dim;
int numcluster;
double *RS;
char *infile, *outfile;
double weight;
double *u;
double *sigma;
double *PRxl;
double *determinant;
char * clusterfile;
int sigmasize;
double *dist;
int samplesize;
S_BigEnoughItem *tmp_ItemList;
void eigenvalue(FILE *pofp, double *matrix, int pdim);
void InverseMatrix(double *pmatrix,int pmatrixdim, int pnumcluster);
};
void main(int argc, char **argv) {
char *minfile, *moutfile, *meanfile, *orderfile;
int mdimension;
int mnumcluster;
int mpagecap;
double mepsilon, mdistepsilon, mmindensity;
Timer excutetime;
printf("\nClustering with EM algorithm\n");
/*
if(argc != 11) {
printf(" ** Usage: %s <in-file> <num of cluster> <dimension> <page capacity> <epsilon> <minimum density> <distepsilon> <meanfile> <out-file> <ordered file>\n\n",argv[0]); exit(-2);
}
minfile = argv[1];
//printf("the input file: %s \n", minfile);
mnumcluster = atoi(argv[2]);
// printf("the number of clusters: %d \n",mnumcluster);
mdimension = atoi(argv[3]);
// printf("the number of dimesion: %d \n",mdimension);
mpagecap = atoi(argv[4]);
// printf("the pagecap of the file: %d \n",mpagecap);
mepsilon = atof(argv[5]);
// printf("the epsilon: %f \n",mepsilon);
mmindensity = atof(argv[6]);
// printf("the mininum density: %f \n", mmindensity);
mdistepsilon = atof(argv[7]);
// printf("the distepsilon: %f \n", mdistepsilon);
meanfile = argv[8];
// printf("the mean file: %s\n",meanfile);
moutfile = argv[9];
// printf("the output file: %s\n",moutfile);
orderfile = argv[10];
// printf("the ordered file: %s\n",orderfile);
*/
/*
minfile="Release\\image\\image.ascii";
mnumcluster=500;
mdimension=19;
mpagecap=2310;
//mp=0.5;
mmindensity = 0;
mepsilon=10;
mdistepsilon = 0;
moutfile="Release\\image\\image.out";
meanfile="Release\\image\\image_500.ascii";
orderfile="Release\\image\\image_500.clu"; */
/* quadratic sample
minfile="sample.ascii";
mnumcluster=186;
mdimension=2;
mpagecap=3720;
mepsilon=0;
mmindensity = 20;
mdistepsilon = 0;
meanfile="sample_seed.ascii";
moutfile="sample_out.ascii";
orderfile="sample_clu.ascii";*/
/* quadratic
minfile="quadratic.txt";
mnumcluster=150;
mdimension=2;
mpagecap=2354;
mepsilon=0;
mmindensity = 0;
mdistepsilon = 0;
meanfile="quadratic_seed.txt";
moutfile="quadratic_out.ascii";
orderfile="quadratic_clu.ascii";*/
/* cubic
minfile="cubic589.ascii";
mnumcluster=150;
mdimension=2;
mpagecap=589;
mepsilon=0;
mmindensity = 20;
mdistepsilon = 0;
meanfile="cubic_seed.txt";
moutfile="cubic_out.ascii";
orderfile="cubic_clu.ascii";*/
/* sin
minfile="sin.txt";
mnumcluster=250;
mdimension=2;
mpagecap=2500;
mepsilon=0;
mmindensity = 0;
mdistepsilon = 0;
meanfile="sin_seed.txt";
moutfile="sin_out.ascii";
orderfile="sin_clu.ascii";*/
/* helix
minfile="ovalhelixes.txt";
mnumcluster=450;
mdimension=9;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="ovalhelixes_seed450_ordered.txt";
moutfile="ovalhelixes_out.ascii";
orderfile="ovalhelixes_clu.ascii"; */
/* iris
minfile="iris.ascii";
mnumcluster=150;
mdimension=4;
mpagecap=150;
mepsilon=0;
mmindensity = 50;
mdistepsilon = 0;
meanfile="iris_seed150.ascii";
moutfile="iris_out.ascii";
orderfile="iris_clu.ascii";*/
/* image
minfile="imagenew.ascii";
mnumcluster=500;
mdimension=16;
mpagecap=2310;
mepsilon=0;
mmindensity = 30;
mdistepsilon = 0;
meanfile="imagenew_seed500.ascii";
moutfile="imagenew_out.ascii";
orderfile="imagenew_clu.ascii";*/
/* combined
minfile="combined4628.ascii";
mnumcluster=594;
mdimension=3;
mpagecap=4628;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="combined594.ascii";
moutfile="combined_out.ascii";
orderfile="combined_clu.ascii";*/
/* compresscombined3d
minfile="compresscombined3d.txt";
mnumcluster=500;
mdimension=3;
mpagecap=3628;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="compresscombined3d_seed500.txt";
moutfile="compresscombined3d_out.ascii";
orderfile="compresscombined3d_clu.ascii";*/
/* compresscombined4d (seed800 and seed200)
minfile="compresscombined4d.txt";
mnumcluster=200;
mdimension=4;
mpagecap=3628;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="compresscombined4d_seed200.txt";
moutfile="compresscombined4d_out.ascii";
orderfile="compresscombined4d_clu.ascii";*/
/* ovalcombined3d seed800 seed200 seed500
minfile="ovalcombined3d.txt";
mnumcluster=800;
mdimension=3;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="ovalcombined3d_seed800.txt";
moutfile="ovalcombined3d_out.ascii";
orderfile="ovalcombined3d_clu.ascii";*/
/* ovalcombined4d seed800 seed200 seed500
minfile="ovalcombined4d.txt";
mnumcluster=500;
mdimension=4;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="ovalcombined4d_seed500.txt";
moutfile="ovalcombined4d_out.ascii";
orderfile="ovalcombined4d_clu.ascii"; */
/* noisecombined3d seed500
minfile="noisecombined3d.txt";
mnumcluster=500;
mdimension=3;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="noisecombined3d_seed500.txt";
moutfile="noisecombined3d_out.ascii";
orderfile="noisecombined3d_clu.ascii"; */
/* combined7dnoise05 seed500 seed400 seed300
minfile="combined7dnoise05.txt";
mnumcluster=300;
mdimension=7;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="combined7dnoise05_seed300.txt";
moutfile="combined7dnoise05_out.ascii";
orderfile="combined7dnoise05_clu.ascii"; */
/* combined7dnoise30 seed500 seed400 seed300
minfile="combined7dnoise30.txt";
mnumcluster=500;
mdimension=7;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="combined7dnoise30_seed500.txt";
moutfile="combined7dnoise30_out.ascii";
orderfile="combined7dnoise30_clu.ascii"; */
/* testcombined6d seed500 seed400 seed300
minfile="testcombined6d.txt";
mnumcluster=500;
mdimension=6;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="testcombined6d_seed500.txt";
moutfile="testcombined6d_out.ascii";
orderfile="testcombined6d_clu.ascii"; */
/* testcombined5d seed500 seed400 seed300
minfile="testcombined5d.txt";
mnumcluster=500;
mdimension=5;
mpagecap=3000;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="testcombined5d_seed500.txt";
moutfile="testcombined5d_out.ascii";
orderfile="testcombined5d_clu.ascii"; */
/*
minfile="aml72grainratiogene10n5.ascii";
mnumcluster=72;
mdimension=10;
mpagecap=72;
mepsilon=0;
mmindensity = 0;
mdistepsilon = 0;
meanfile="aml72grainratiogene10n5_seed72.ascii";
moutfile="aml_out.ascii";
orderfile="aml_clu.ascii";*/
/* Iyer517V2_seed360
minfile="Iyer517V2.ascii";
mnumcluster=360;
mdimension=18;
mpagecap=517;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="Iyer517V2_seed360.ascii";
moutfile="Iyer_out.ascii";
orderfile="Iyer_clu.ascii";*/
/* wdbc */
/* minfile="wdbcn5.txt";
mnumcluster=200;
mdimension=30;
mpagecap=569;
mepsilon=0;
mmindensity = 10;
mdistepsilon = 0;
meanfile="wdbcn5_seed200.txt";
moutfile="wdbc_out.txt";
orderfile="wdbc_clu.txt";*/
minfile="data_norm.txt"; // Data file
mnumcluster=200;
mdimension=36; // Number of columns
mpagecap=67336; // Number of rows
mepsilon=0;
mmindensity = 20;
mdistepsilon = 0;
meanfile="data_seed.txt";
moutfile="data_out.txt";
orderfile="data_ord.txt";
excutetime.start();
EM em(meanfile, mnumcluster, mdimension, mpagecap);
em.EMCluster(minfile, moutfile, orderfile, mepsilon, mdistepsilon, mmindensity);
excutetime.end();
}
EM::EM(char *ufile, int pnumcluster, int pdimension, int ppagecap){
int i=0,j=0,k=0;
FILE *ufp;
double meanval;
int index;
/* set the members of EM */
sigmasize = pdimension * (pdimension + 1) / 2;
samplesize = pnumcluster * compressratio;//*pnumcluster;
pagecap = ppagecap;
dim = pdimension;
numcluster = pnumcluster;
clusterfile = "sample1_170.clu";
RS = (double *) malloc (sizeof (double) * dim);
u = (double * ) malloc ( sizeof (double) * pnumcluster * dim);
sigma = (double * ) malloc (sizeof (double) * pnumcluster * sigmasize);
determinant = (double * ) malloc (sizeof (double) * pnumcluster);
N = (double *) malloc (sizeof(double) * pnumcluster);
tempmem = (double *) malloc (sizeof(double) * dim * dim);
resultmem = (double *) malloc (sizeof(double) * dim * dim);
eigmem = (double *) malloc (sizeof(double) * dim * (dim+4));
//test the memory allocation
if (RS == NULL){
printf("Not enough memory for RS!!\n");
exit(0);
}
if (u == NULL){
printf("Not enough memory for u!!\n");
exit(0);
}
if (sigma == NULL){
printf("Not enough memory for sigma!!\n");
exit(0);
}
if (determinant == NULL){
printf("Not enough memory for determinant!!\n");
exit(0);
}
if (N == NULL){
printf("Not enough memory for N!!\n");
exit(0);
}
if (tempmem == NULL){
printf("Not enough memory for tempmem!!\n");
exit(0);
}
if (eigmem == NULL){
printf("Not enough memory for eigmem!!\n");
exit(0);
}
/* open the mean value file */
if ((ufp = fopen(ufile, "r"))==NULL)
{
printf("Mean File Not Opened!");
exit(0);
}
/* read the initial mean value */
for (i = 0; i < pnumcluster; i++)
{
for (j = 0; j < dim; j++){
fscanf(ufp, "%lf\t", &meanval);
u[i * dim + j] = meanval;
}
fscanf(ufp, "\n");
}
/* initialize the sigma matrix */
for (i = 0; i < pnumcluster; i++){
index = 0;
for (j = 0; j < dim; j++){
for (k = 0; k < j + 1; k++){
if (k == j) {
sigma[i * sigmasize + index] = 1;
index = index + 1;
}
else {
sigma[i * sigmasize + index] = 0;
index = index + 1;
}
}
}
}
}
EM::~EM(){
//free(RS);
//free(u);
//free(sigma);
//free(determinant);
free(N);
free(tempmem);
free(resultmem);
free(eigmem);
}
void EM::InverseMatrix(double *pmatrix, int pmatrixdim, int pnumcluster){
double *tempmatrix;
int i,j,k,m;
int count;
double temp;
int mat_index;
int matrixsize;
double *resultmatrix;
short *IS, *JS;
double largest;
matrixsize = pmatrixdim * (pmatrixdim + 1) / 2;
/*0 0*1/2+0 */
/*1, 2 1*2/2+0 or 1 */
/*3, 4, 5 2*3/2+0 or 1 or 2 */
/*6, 7, 8, 9 3*4/2+0 or 1 or 2 or 3 */
count = pmatrixdim * pmatrixdim * pnumcluster;
tempmatrix = tempmem;
resultmatrix = resultmem;
// tempmatrix = (double *) malloc (sizeof(double) * pmatrixdim * pmatrixdim);
// resultmatrix = (double *) malloc (sizeof(double) * pmatrixdim * pmatrixdim);
IS = (short *) malloc (sizeof(short) * pmatrixdim);
JS = (short *) malloc (sizeof(short) * pmatrixdim);
/* the number of clusters stored in pmatrix is pnumcluster */
for (i = 0; i < pnumcluster; i++){
for (j = 0; j < pmatrixdim; j++){
IS[j] = j;
JS[j] = j;
}
/* tempmatrix: read the data for the current cluster from pmatrix */
for (j = 0; j < pmatrixdim; j++)
for (k = 0; k < pmatrixdim; k++){
if (j < k)
mat_index = (k + 1) * k / 2 + j;
else
mat_index = (j + 1) * j / 2 + k;
tempmatrix[j * pmatrixdim + k] = pmatrix[i * matrixsize + mat_index];
}
/* resultmatrix: set the element at diagonal as 1, else as 0 */
for (j = 0; j < pmatrixdim; j++)
for (k = 0; k < pmatrixdim; k++)
if (j == k)
resultmatrix[j * pmatrixdim + k] = 1;
else
resultmatrix[j * pmatrixdim + k] = 0;
/* tempmatrix: move the largest element to the diagonal */
for (j = 0; j < pmatrixdim; j++){
/* find the largest element in tempmatrix */
largest = fabs(tempmatrix[IS[j] * pmatrixdim + JS[j]]);
for (k = 0; k < pmatrixdim; k++)
for (m = 0; m < pmatrixdim; m++)
if (fabs(tempmatrix[k * pmatrixdim + m]) > largest){
largest = fabs(tempmatrix[k * pmatrixdim + m]);
IS[j] = k;
JS[j] = m;
}
/* exchange the rows */
if (IS[j] != j){
for (k = 0; k < pmatrixdim; k++){
temp = tempmatrix[IS[j] * pmatrixdim + k];
tempmatrix[IS[j] * pmatrixdim + k] = tempmatrix[j * pmatrixdim + k];
tempmatrix[j * pmatrixdim + k] = temp;
}
}
/* exchange the cols */
if (JS[j] != j){
for (k = 0; k < pmatrixdim; k++){
temp = tempmatrix[JS[j] + k * pmatrixdim];
tempmatrix[JS[j] + k * pmatrixdim] = tempmatrix[j + k * pmatrixdim];
tempmatrix[j + k * pmatrixdim] = temp;
}
}
/* normalize row j */
tempmatrix[j * pmatrixdim + j] = 1 / tempmatrix[j * pmatrixdim + j];
for (k = 0; k < pmatrixdim; k++)
if (k != j)
tempmatrix[j * pmatrixdim + k] = tempmatrix[j * pmatrixdim + k] * tempmatrix[j * pmatrixdim + j];
/* adjust elements not in row j and column j */
for (k = 0; k < pmatrixdim; k++)
for (m = 0; m < pmatrixdim; m++)
if ((k != j) && (m != j))
tempmatrix[k * pmatrixdim + m] = tempmatrix[k * pmatrixdim + m] -
tempmatrix[k * pmatrixdim + j] * tempmatrix[j * pmatrixdim + m];
/* adjust elements in column j */
for (k = 0; k < pmatrixdim; k++)
if (k != j)
tempmatrix[k * pmatrixdim + j] = - tempmatrix[k * pmatrixdim + j] * tempmatrix[j * pmatrixdim + j];
}//j<pmatrixdim
for (j = pmatrixdim-1; j >= 0;j--){
/* exchange the rows */
if (JS[j] != j){
for (k = 0; k < pmatrixdim; k++){
temp = tempmatrix[JS[j] * pmatrixdim + k];
tempmatrix[JS[j] * pmatrixdim + k] = tempmatrix[j * pmatrixdim + k];
tempmatrix[j * pmatrixdim + k] = temp;
}
}
/* exchange the cols */
if (IS[j] != j){
for (k = 0; k < pmatrixdim; k++){
temp = tempmatrix[IS[j] + k * pmatrixdim];
tempmatrix[IS[j] + k * pmatrixdim] = tempmatrix[j + k * pmatrixdim];
tempmatrix[j + k * pmatrixdim] = temp;
}
}
}// j>=0
/* resultmatrix=>pmatrix */
for (j = 0; j < pmatrixdim; j++)
for (k = 0; k <=j; k++)
pmatrix[i * matrixsize + j * (j + 1) / 2 + k] = resultmatrix[j * pmatrixdim + k];
}//for i<pnumcluster
// free(tempmatrix);
// free(resultmatrix);
free(IS);
free(JS);
}
void EM::eigenvalue(FILE *pofp, double *matrix, int pdim){
int i, j, k;
double maxelement;
int p, q;
double *S;
double thita;
int sign;
double temp;
int matrix_index, matrix_index1, matrix_index2;
double m,n;
double *temprowp, *temprowq, *tempcolp, *tempcolq;
S = eigmem;
temprowp = &eigmem[pdim * pdim];
temprowq = &eigmem[pdim * pdim + pdim];
tempcolp = &eigmem[pdim * pdim + pdim * 2];
tempcolq = &eigmem[pdim * pdim + pdim * 3];
/* step 1:set S to be the identity matrix; */
for (i=0; i<pdim; i++)
for (j=0; j<pdim; j++)
if (i==j) S[i*pdim+j]=1;
else S[i*pdim+j]=0;
/* step2: get the maximun non-diagonal element apq of the matrix; */
/* 00 */
/* 10 11 */
/* 20 21 22 */
/* 30 31 32 33 */
/* ... */
maxelement=fabs(matrix[1]);
p=0; /* column index */
q=1; /* row index */
for (i=2; i<pdim; i++)
for (j=0; j<i; j++){
matrix_index = i * (i + 1) / 2 + j;
if (fabs(matrix[matrix_index])>maxelement){
p=j;
q=i;
maxelement=fabs(matrix[matrix_index]);
}
}
/* step3:if |apq|<eigeneps, terminates; */
/* step4: calculate sin(2*thita), sin(thita), cos(thita); */
while (fabs(maxelement)>eigeneps){
if (p > q){//?, we know p<q since j<i
matrix_index = p * (p + 1) / 2 + q;
}
else{
matrix_index = q * (q + 1) / 2 + p;
}
m=-matrix[matrix_index];
matrix_index1 = p * (p + 1) / 2 + p;/*diagonal element with row index p and col index p*/
matrix_index2 = q * (q + 1) / 2 + q;/*diagonal element with row index q and col index q*/
n=(matrix[matrix_index2]-matrix[matrix_index1])/2;
if (n>=0) sign=1;
else sign=-1;
thita=asin(sign*m/sqrt(pow(m,2)+pow(n,2))) / 2;
//step5: calculate the new element for the matrix;
for (i=0; i<pdim; i++){
//bpp,bpq,bqp
if (i==p){
matrix_index1 = p * (p + 1) / 2 + p;
matrix_index2 = q * (q + 1) / 2 + q;
if (p < q)
matrix_index = (q + 1) * q / 2+ p;
else
matrix_index = (p + 1) * p / 2+ q;
temprowp[i]=double(matrix[matrix_index1]*pow(cos(thita),2)
+matrix[matrix_index2]*pow(sin(thita),2)+matrix[matrix_index]*sin(2*thita));
tempcolp[i]=temprowp[i];
temprowq[i]=double((matrix[matrix_index2]-matrix[matrix_index1])*sin(2*thita)/2+matrix[matrix_index]*cos(2*thita));
tempcolq[i]=temprowq[i];
}
//bqq,bpq,bqp
else if (i==q){
matrix_index1 = p * (p + 1) / 2 + p;
matrix_index2 = q * (q + 1) / 2 + q;
if (p < q)
matrix_index = (q + 1) * q / 2+ p;
else
matrix_index = (p + 1) * p / 2+ q;
temprowq[i]=double(matrix[matrix_index1]*pow(sin(thita),2)
+matrix[matrix_index2]*pow(cos(thita),2)-matrix[matrix_index]*sin(2*thita));
tempcolq[i]=temprowq[i];
temprowp[i]=double((matrix[matrix_index2]-matrix[matrix_index1])*sin(2*thita)/2+matrix[matrix_index]*cos(2*thita));
tempcolp[i]=temprowp[i];
}
else{
if (p > i)
matrix_index1 = p * (p + 1) / 2 + i;
else
matrix_index1 = i * (i + 1) / 2 + p;
if (q > i)
matrix_index2 = q * (q + 1) / 2 + i;
else
matrix_index2 = i * (i + 1) / 2 + q;
temprowp[i]=double(matrix[matrix_index1]*cos(thita)+matrix[matrix_index2]*sin(thita));
temprowq[i]=double(-matrix[matrix_index1]*sin(thita)+matrix[matrix_index2]*cos(thita));
if (p > i)
matrix_index1 = p * (p + 1) / 2 + i;
else
matrix_index1 = i * (i + 1) / 2 + p;
if (q > i)
matrix_index2 = q * (q + 1) / 2 + i;
else
matrix_index2 = i * (i + 1) / 2 + q;
tempcolp[i]=double(matrix[matrix_index1]*cos(thita)+matrix[matrix_index2]*sin(thita));
tempcolq[i]=double(-matrix[matrix_index1]*sin(thita)+matrix[matrix_index2]*cos(thita));
}
}//for i<pdim
//update matrix A;
for (i=0; i<pdim; i++){
if (p > i)
matrix_index1 = p * (p + 1) / 2 + i;
else
matrix_index1 = i * (i + 1) / 2 + p;
if (q > i)
matrix_index2 = q * (q + 1) / 2 + i;
else
matrix_index2 = i * (i + 1) / 2 + q;
matrix[matrix_index1]=temprowp[i];
matrix[matrix_index2]=temprowq[i];
if (p > i)
matrix_index1 = p * (p + 1) / 2 + i;
else
matrix_index1 = i * (i + 1) / 2 + p;
if (q > i)
matrix_index2 = q * (q + 1) / 2 + i;
else
matrix_index2 = i * (i + 1) / 2 + q;
matrix[matrix_index1]=tempcolp[i];
matrix[matrix_index2]=tempcolq[i];
}
/* step6: update S=S*R(p,q,thita) */
for (i=0; i<pdim; i++){
tempcolp[i]=double(S[i*pdim+p]*cos(thita)+S[i*pdim+q]*sin(thita));
tempcolq[i]=double(S[i*pdim+p]*(-sin(thita))+S[i*pdim+q]*cos(thita));
}
for (i=0; i<pdim; i++){
S[i*pdim+p]=tempcolp[i];
S[i*pdim+q]=tempcolq[i];
}
/* step2: get the maximun non-diagonal element apq of the matrix; */
maxelement=fabs(matrix[1]);
p=0;
q=1;
for (i=0; i<pdim; i++)
for (j=0; j<i; j++){
matrix_index = i * (i + 1) / 2 + j;
if (fabs(matrix[matrix_index])>maxelement){
p=j;
q=i;
maxelement=fabs(matrix[matrix_index]);
}
}
}//while (fabs(maxelement)>eigeneps)
/* sort the eigenvalues */
for(i = 0; i < pdim; i++)
for (j = 0; j < pdim - i -1; j++)
if (fabs(matrix[j * (j + 1) / 2 + j]) > fabs(matrix[(j + 1) * (j + 2) / 2 + (j + 1)])){
temp = matrix[j * (j + 1) / 2 + j];
matrix[j * (j + 1) / 2 + j] = matrix[(j + 1) * (j + 2) / 2 + (j + 1)];
matrix[(j + 1) * (j + 2) / 2 + (j + 1)] = temp;
for (k = 0; k < pdim; k++){
temp = S[k * pdim + j];
S[k * pdim + j] = S[k * pdim + j + 1];
S[k * pdim + j + 1] = temp;
}
}
for (i = 0; i < pdim; i++)
for (j = 0; j < pdim; j++)
S[i * pdim + j] = S[i * pdim + j];
/*
printf("the eigenvalue is :\n");
for (i = 0; i < pdim; i++)
printf("%f ", matrix[i * (i + 1) / 2 + i]);
printf("\n");
printf("the S matrix:\n");
for (i=0; i<pdim; i++){
for (j=0; j<pdim; j++)
printf("%f, ",S[i*pdim+j]);
printf("\n");
}
*/
/* orientation sign (old) */
for (i=0; i<pdim; i++){
if (S[i] < 0)
for (j=0; j<pdim; j++)
S[j*pdim+i] = -S[j*pdim+i];
}
/* orientation sign (new)
//get the maximum variation dimension of the last eigenvector (the one with largest eigen value)
double maxvar=0, tempf;
int maxi=-1;
for (i=0; i<pdim; i++)
{
tempf=fabs(S[pdim-1+i*pdim]);
if (fabs(S[pdim-1+i*pdim])>maxvar)
{
maxvar=fabs(S[pdim-1+i*pdim]);
maxi=i;
}
}
printf("maxvar:%f, maxi:%d\n", maxvar, maxi);
for (i=0; i<pdim; i++){
if (maxi<3 && S[i+2*pdim] < 0)
for (j=0; j<pdim; j++)
S[j*pdim+i] = -S[j*pdim+i];
else if (maxi>=3 && maxi<6 && S[i+5*pdim] < 0)
for (j=0; j<pdim; j++)
S[j*pdim+i] = -S[j*pdim+i];
else if (maxi>=6 && S[i+8*pdim] < 0)
for (j=0; j<pdim; j++)
S[j*pdim+i] = -S[j*pdim+i];
}*/
for (i=0; i<pdim; i++)
for (j=0; j<pdim; j++)
fprintf(pofp, "%.18lf ",S[j*pdim+i] * 255);
fprintf(pofp, "\n");
}
/*******************************EM Clustering**************************************/
void EM::EMCluster(char *pinfile, char *poutfile, char *porderfile, double pepsilon, double pdistepsilon, double pmindensity){
/* file pointer to the data file */
FILE *ifp;
FILE *ofp;
/* the maximum liklyhood */
double epsilon;
/* iteration variable */
int i, j, k, m;
/* the number of points process as so far */
double NUM;
/* stopping criterion for RS set */
double E, newE;
/* local variable */
double tempresult;
double *tempPRlx;
double *tempv;
double PRx;
int count;
int sigma_index;
tempv = (double *) malloc (sizeof (double) * dim);
PRxl = (double *) malloc (sizeof (double) * numcluster);
PRlx = (double *) malloc (sizeof (double) * samplesize * pagecap);
uXXT = (double *) malloc (sizeof (double) * numcluster * dim * (dim+1)/2);
uX = (double *) malloc (sizeof (double) * numcluster * dim);
dist = (double *) malloc (sizeof (double) * numcluster * (numcluster-1)/2);
tempPRlx = (double *) malloc (sizeof (double) * numcluster);
/* memory allocation test */
if (tempv == NULL){
printf("Not enough memory for tempv!!\n");
exit(0);
}
if (PRxl == NULL){
printf("Not enough memory for PRxl!!\n");
exit(0);
}
if (PRlx == NULL){
printf("Not enough memory for PRlx!!\n");
exit(0);
}
if (uXXT == NULL){
printf("Not enough memory for uXXT!!\n");
exit(0);
}
if (uX == NULL){
printf("Not enough memory for uX!!\n");
exit(0);
}
if (dist == NULL){
printf("Not enough memory for dist!!\n");
exit(0);
}
if (tempPRlx == NULL){
printf("Not enough memory for tempPRlx!!\n");
exit(0);
}
/* initialization */
infile = pinfile;
outfile = poutfile;
epsilon = pepsilon;
E = 0;
newE = 100000;
NUM = 0;
int tmp_HowMany = samplesize;
int t, tmp_i, tmp_j, tmp_k;
double tmp_f;
tmp_ItemList = (struct S_BigEnoughItem*)malloc( pagecap * sizeof(struct S_BigEnoughItem) );
if (tmp_ItemList == NULL){
printf("Not enough memory for tmp_ItemList!\n");
exit(0);
}
/* open the file for recording cluster information */
if ((ofp = fopen(poutfile, "w")) == NULL)
{
printf("Outfile not opened!");
exit(0);
}
//initialization for the sumprob procedure, EM preparation
// Timer emtime;
// emtime.start();
int iterationnum=0;
/***********************the Outer Loop******************************************/
//if the stop criterion for outer loop is not satisfied
double g_Factor = double(pow(2 * 3.14, dim));
if (g_Factor > 1000000)
g_Factor = 10000000;
/* the outer iteration loop, begins */
while ((fabs(E - newE) > epsilon) && (iterationnum < iterationtime)){
iterationnum = iterationnum + 1;
printf("%dth iteration begin...\n", iterationnum);
E = newE;
newE = 0;
/* initialization for inner loop */
for (i = 0; i < numcluster; i++){