void plot_add_model(plot *p, model_func *f, const mat *x_0, const size_t j, \
const mat *par, void *f_param, const double xmin, \
const double xmax, const size_t npt, const strbuf title,\
const strbuf color)
{
mat *x,*y,*X;
size_t i;
double x_i,y_i;
x = mat_create(npt,1);
y = mat_create(npt,1);
X = mat_create_from_mat(x_0);
for (i=0;i<npt;i++)
{
x_i = xmin + (xmax-xmin)*DRATIO(i,npt-1);
mat_set(X,j,0,x_i);
y_i = f(X,par,f_param);
mat_set(x,i,0,x_i);
mat_set(y,i,0,y_i);
}
plot_add_line(p,x,y,title,color);
mat_destroy(x);
mat_destroy(y);
mat_destroy(X);
}
int main(void)
{
Item x = 5, y = 2, x2 = 6, y2 = 3;
mat m1, m2, k1, k2;
int i, j;
printf("\nItems: ");
item_print(x);
printf(" ");
item_print(y);
printf("\n");
printf("Item Addition: ");
item_print(item_add(x, y));
printf("\n");
printf("Item Multiplication: ");
item_print(item_mul(x, y));
printf("\n");
printf("Item Substraction: ");
item_print(item_sub(x, y));
printf("\n");
printf("Item Division: ");
item_print(item_div(x, y));
printf("\n\n");
m1 = mat_create(3, 2);
m2 = mat_create(2, 3);
k1 = mat_create(2, 2);
k2 = mat_create(2, 2);
for (i = 0; i < mat_rows(m1); i++)
for (j = 0; j < mat_cols(m1); j++)
mat_add_elem(m1, i, j, x);
for (i = 0; i < mat_rows(m2); i++)
for (j = 0; j < mat_cols(m2); j++)
mat_add_elem(m2, i, j, y);
for (i = 0; i < mat_rows(k1); i++)
for (j = 0; j < mat_cols(k1); j++)
{
mat_add_elem(k1, i, j, x2);
mat_add_elem(k2, i, j, y2);
}
printf("k1 Matrix: \n");
mat_print(k1);
printf("k2 Matrix: \n");
mat_print(k2);
printf("Addition: \n");
mat_print(mat_add(k1, k2));
printf("Substraction: \n");
mat_print(mat_sub(k1, k2));
printf("m1 Matrix: \n");
mat_print(m1);
printf("m2 Matrix: \n");
mat_print(m2);
printf("Multiplication: \n");
mat_print(mat_mul(m1, m2));
return 0;
}
MatrixFile *matrix_create(const char *fname, Main_header * proto_mhptr) {
MatrixFile *mptr = NULL;
FILE *fptr, *mat_create();
matrix_errno = MAT_OK;
matrix_errtxt[0] = '\0';
fptr = mat_create(fname, proto_mhptr);
if (!fptr) return( NULL );
mptr = (MatrixFile *) calloc(1, sizeof(MatrixFile));
if (!mptr) {
fclose( fptr );
return( NULL );
}
mptr->fptr = fptr;
mptr->fname = (char *) malloc(strlen(fname) + 1);
if (!mptr->fname) {
free( mptr );
fclose( fptr );
return( NULL );
}
strcpy(mptr->fname, fname);
mptr->mhptr = (Main_header *) malloc(sizeof(Main_header));
if (!mptr->mhptr) {
free( mptr->fname );
free( mptr );
fclose( fptr );
return( NULL );
}
memcpy(mptr->mhptr, proto_mhptr, sizeof(Main_header));
mptr->dirlist = mat_read_directory(mptr);
if (!mptr->dirlist) {
free( mptr->fname );
free( mptr->mhptr );
free( mptr );
fclose( fptr );
return( NULL );
}
return mptr;
}
void plot_add_fit_predband(plot *p, const fit_data *d, const size_t ky,\
const mat *x_ex, const size_t kx, \
const rs_sample *par, const double xmin, \
const double xmax, const size_t npt, \
const strbuf color)
{
mat *x,*yp,*ym,*y_i_err,*X;
rs_sample *s_y_i;
size_t i;
double x_i,yp_i,ym_i;
x = mat_create(npt,1);
yp = mat_create(npt,1);
ym = mat_create(npt,1);
y_i_err = mat_create(1,1);
s_y_i = rs_sample_create(1,1,rs_sample_get_nsample(par));
X = mat_create_from_mat(x_ex);
for (i=0;i<npt;i++)
{
x_i = xmin + (xmax-xmin)*DRATIO(i,npt-1);
mat_set(X,kx,0,x_i);
fit_data_model_rs_xeval(s_y_i,d,ky,X,par);
rs_sample_var(y_i_err,s_y_i);
mat_eqsqrt(y_i_err);
yp_i = mat_get(rs_sample_pt_cent_val(s_y_i),0,0) + mat_get(y_i_err,0,0);
ym_i = mat_get(rs_sample_pt_cent_val(s_y_i),0,0) - mat_get(y_i_err,0,0);
mat_set(yp,i,0,yp_i);
mat_set(ym,i,0,ym_i);
mat_set(x,i,0,x_i);
}
plot_add_line(p,x,yp,"",color);
plot_add_line(p,x,ym,"",color);
mat_destroy(x);
mat_destroy(yp);
mat_destroy(ym);
mat_destroy(y_i_err);
rs_sample_destroy(s_y_i);
mat_destroy(X);
}
void next_step_cal(FLUX *flux, PCS *pcs, TCONF *tconf, MAPPER *mapper, MESH *mesh, CDAT4 *vsf_lst)
{
size_t eg_size = mapper->eg_size;
size_t rt_size = mapper->rt_size;
CDAT4 *vsf = mesh->vsf;
FLUX *flux_lst = flux_create(mapper);
flux_copy(flux_lst, flux);
CDAT4 *sr_rvs = cdat4_create(mapper);
sr_rvs_cal(sr_rvs, tconf, mesh);
MAT *M = mat_create(eg_size*rt_size);
MAT *S = mat_create(eg_size*rt_size);
MAT *F = mat_create(eg_size*rt_size);
EDAT4 *DFDM = edat4_create(mapper);
EDAT4 *DNOD = edat4_create(mapper);
cal_DFDM(DFDM, mesh);
cal_m(M, DFDM, DNOD, mapper, mesh, sr_rvs);
CDAT4 *chi_bar = cdat4_create(mapper);
cal_chi_bar(chi_bar, tconf, mesh);
cal_s(S, mapper, mesh);
cal_f(F, mapper, mesh, chi_bar);
mat_adds(M, S, -1.0);
mat_adds(M, F, -1.0);
VEC *src_eff = vec_create(eg_size*rt_size);
src_eff_cal(src_eff,tconf,mesh,vsf_lst,flux_lst,pcs);
VEC *sol = vec_ref_create(eg_size*rt_size, flux->data);
(*mat_solver)(sol,M,src_eff,1024);
vec_ref_free(sol);
pcs_cal(pcs,flux,flux_lst,vsf,vsf_lst,tconf);
cdat4_free(chi_bar);
vec_free(src_eff);
edat4_free(DNOD);
edat4_free(DFDM);
mat_free(F);
mat_free(S);
mat_free(M);
cdat4_free(sr_rvs);
flux_free(flux_lst);
}
void plot_add_func(plot *p, univar_func *f, void *f_param, const double xmin,\
const double xmax, const size_t npt, const strbuf title, \
const strbuf color)
{
mat *x,*y;
size_t i;
double x_i,y_i;
x = mat_create(npt,1);
y = mat_create(npt,1);
for (i=0;i<npt;i++)
{
x_i = xmin + (xmax-xmin)*DRATIO(i,npt-1);
y_i = f(x_i,f_param);
mat_set(x,i,0,x_i);
mat_set(y,i,0,y_i);
}
plot_add_line(p,x,y,title,color);
mat_destroy(x);
mat_destroy(y);
}
static
void
setupSeqProblem__ (int m, int n, int k,
double** p_A, double** p_B,
double** p_C, double** p_C_bound)
{
if (p_A) {
*p_A = mat_create (m, k);
mat_randomize (m, k, *p_A);
}
if (p_B) {
*p_B = mat_create (k, n);
mat_randomize (k, n, *p_B);
}
if (p_C) {
*p_C = mat_create (m, n);
mat_setZero (m, n, *p_C);
}
if (p_C_bound) {
*p_C_bound = mat_create (m, n);
mat_setZero (m, n, *p_C_bound);
}
}
void icaTransformInverse(double** S, int rows, int cols, int comp, int comp_rm,
double** X, double** K, double** W, double** RowData, int startEb,
int stopEb) {
double **A;
double *Total;
FILE * OutputFile;
int i, j;
A = mat_create(comp, comp);
Total = malloc(cols * sizeof(double));
for (j = 0; j < cols; j++) {
Total[j] = 0;
for (i = 0; i < rows; i++)
Total[j] = Total[j] + RowData[i][j];
Total[j] = Total[j] / rows;
}
puts("Before");
for (j = startEb; j < stopEb; j++)
//for (j = 40; j < 90; j++)
S[j][comp_rm] = 0;//////////////////////////////////////////////////////////////////////////////////
puts("Debug");
mat_mult(K, cols, comp, W, comp, comp, A); //A[cols, comp]
mat_inverse(A, comp, W);
mat_mult(S, rows, comp, W, comp, comp, X);
//strcat(pPathFile, "_recontruction");
OutputFile = fopen("/home/truongnh/eeg-lab411/SignalProcessing/RemoveEyeblink/Data/Output.txt",
"wb");
for (i = 0; i < rows; i++) {
for (j = 0; j < cols; j++) {
if(j == comp_rm)
fprintf(OutputFile, "%f\n", X[i][j] + Total[j]);
}
//fprintf(OutputFile, "\n");
}
fclose(OutputFile);
for (j = 0; j < cols; j++) {
for (i = 0; i < rows; i++)
X[i][j] = X[i][j] + Total[j];
}
free(Total);
}
int main(void)
{
mat *m;
size_t dim[2];
m = mat_create(6,6);
io_init();
io_set_fmt(IO_ASCII);
mat_load(m,dim,"ex_io.dat:m");
printf("%dx%d matrix loaded from %s:\n",(int)(dim[0]),(int)(dim[1]),FNAME);
mat_print(m,"% .15e");
io_set_fmt(IO_XML);
mat_save("ex_io.xml:m",'w',m);
io_finish();
mat_destroy(m);
return EXIT_SUCCESS;
}
void icaTransform(double** X, int rows, int cols, int comp, double **S,
double** K, double** W) {
double **A;
FILE * OutputFile;
int i, j;
A = mat_create(comp, comp);
//thuc hien ICA
fastICA(X, rows, cols, comp, K, W, A, S);
puts(">>>>>>>>>>...run ica complete.");
//In cac thanh phan doc lap
FILE * file = fopen("/home/truongnh/eeg-lab411/SignalProcessing/RemoveEyeblink/Data/outICA.txt", "w+");
for(i=0; i<rows; i++) {
for(j=0; j<cols; j++) {
fprintf(file, "%lf\t", S[i][j]);
}
fprintf(file, "\n");
}
fclose(file);
/*
//in cac thanh phan doc lap ra
for (j = 0; j < comp; j++) {
if(j==0)
OutputFile = fopen("/storage/sdcard0/NickGun/EEG/Liec-len-xuong/DataICA", "wb");
else
OutputFile = fopen("/storage/sdcard0/NickGun/EEG/Liec-len-xuong/DataICA", "at");
fprintf(OutputFile, "********************Comp %i\n", j);
for (i = 0; i < rows; i++) {
fprintf(OutputFile, "%f\n", S[i][j]);
}
fclose(OutputFile);
}*/
mat_delete(A, comp, comp);
}
int main(int argc, char *argv[])
{
int i,j;
rs_sample *s1,*s2,*res;
size_t s1_dim[2],s2_dim[2],s1_nsample,s2_nsample;
mat *sig;
bool do_save_res, show_usage;
strbuf out_elname,out_fname,in_elname[2],in_fname[2],in_path[2],out_path;
char *spt[2];
io_fmt_no fmt;
/* argument parsing */
i = 1;
j = 0;
show_usage = false;
do_save_res = false;
fmt = io_get_fmt();
if (argc <= 1)
{
show_usage = true;
}
else
{
while (i < argc)
{
if (strcmp(argv[i],"-o") == 0)
{
if (i == argc - 1)
{
show_usage = true;
break;
}
else
{
strbufcpy(out_path,argv[i+1]);
do_save_res = true;
i += 2;
}
}
else if (strcmp(argv[i],"-f") == 0)
{
if (i == argc - 1)
{
show_usage = true;
break;
}
else
{
if (strcmp(argv[i+1],"xml") == 0)
{
fmt = IO_XML;
}
else if (strcmp(argv[i+1],"ascii") == 0)
{
fmt = IO_ASCII;
}
else
{
fprintf(stderr,"error: format %s unknown\n",argv[i+1]);
return EXIT_FAILURE;
}
i += 2;
}
}
else
{
if (j < 2)
{
strbufcpy(in_path[j],argv[i]);
j++;
i++;
}
else
{
show_usage = true;
break;
}
}
}
}
if (show_usage)
{
fprintf(stderr,"usage: %s <in sample 1> <in sample 2> [-o <out sample>] [-f {ascii|xml}]\n",\
argv[0]);
return EXIT_FAILURE;
}
/* I/O init */
io_set_fmt(fmt);
io_init();
/* getting sizes */
rs_sample_load(NULL,&s1_nsample,s1_dim,in_path[0]);
rs_sample_load(NULL,&s2_nsample,s2_dim,in_path[1]);
/* allocation */
s1 = rs_sample_create(s1_dim[0],s1_dim[1],s1_nsample);
s2 = rs_sample_create(s2_dim[0],s2_dim[1],s2_nsample);
res = rs_sample_create(s1_dim[0],s1_dim[1],s1_nsample);
sig = mat_create(s1_dim[0],s1_dim[1]);
/* loading samples */
printf("-- loading sample from %s...\n",in_path[0]);
rs_sample_load(s1,NULL,NULL,in_path[0]);
printf("-- loading sample from %s...\n",in_path[1]);
rs_sample_load(s2,NULL,NULL,in_path[1]);
/* multiplying samples */
printf("-- executing operation on samples...\n");
rs_sample_binop(res,s1,s2,&BINOP);
/* result output */
rs_sample_varp(sig,res);
mat_eqsqrt(sig);
printf("central value:\n");
mat_print(rs_sample_pt_cent_val(res),"%e");
printf("standard deviation:\n");
mat_print(sig,"%e");
if (do_save_res)
{
get_elname(out_fname,out_elname,out_path);
if (strlen(out_elname) == 0)
{
get_elname(in_fname[0],in_elname[0],in_path[0]);
get_elname(in_fname[1],in_elname[1],in_path[1]);
spt[0] = (strlen(in_elname[0]) == 0) ? in_fname[0] : in_elname[0];
spt[1] = (strlen(in_elname[1]) == 0) ? in_fname[1] : in_elname[1];
sprintf(out_path,"%s%c%s_%s_%s",out_fname,LATAN_PATH_SEP,argv[0],\
spt[0],spt[1]);
}
rs_sample_save(out_path,'w',res);
}
/* desallocation */
rs_sample_destroy(s1);
rs_sample_destroy(s2);
rs_sample_destroy(res);
mat_destroy(sig);
/* I/O finish */
io_finish();
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
rs_sample *s1,*res,*buf;
size_t s1_dim[2],res_dim[2],s1_nsample,a,b,s,k,l;
int i,j;
mat *sig;
bool do_save_res, show_usage, have_s;
char *spt;
strbuf out_elname,out_fname,in_elname,in_fname,in_path,out_path;
io_fmt_no fmt;
/* argument parsing */
i = 1;
j = 0;
a = 0;
b = 0;
s = 1;
show_usage = false;
do_save_res = false;
have_s = false;
fmt = io_get_fmt();
if (argc <= 3)
{
show_usage = true;
}
else
{
while (i < argc)
{
if (strcmp(argv[i],"-o") == 0)
{
if (i == argc - 1)
{
show_usage = true;
break;
}
else
{
strbufcpy(out_path,argv[i+1]);
do_save_res = true;
i += 2;
}
}
else if (strcmp(argv[i],"-f") == 0)
{
if (i == argc - 1)
{
show_usage = true;
break;
}
else
{
if (strcmp(argv[i+1],"xml") == 0)
{
fmt = IO_XML;
}
else if (strcmp(argv[i+1],"ascii") == 0)
{
fmt = IO_ASCII;
}
else
{
fprintf(stderr,"error: format %s unknown\n",argv[i+1]);
return EXIT_FAILURE;
}
i += 2;
}
}
else if (strcmp(argv[i],"-s") == 0)
{
if (i == argc - 1)
{
show_usage = true;
break;
}
else
{
s = (size_t)atol(argv[i+1]);
have_s = true;
i += 2;
}
}
else
{
if (j == 0)
{
strbufcpy(in_path,argv[i]);
j++;
i++;
}
else if (j == 1)
{
a = (size_t)atol(argv[i]);
j++;
i++;
}
else if (j == 2)
{
b = (size_t)atol(argv[i]);
j++;
i++;
}
else
{
show_usage = true;
break;
}
}
}
}
if (show_usage)
{
fprintf(stderr,"usage: %s <in sample> <a> <b> [-o <out sample>] [-f {ascii|xml}]\n",\
argv[0]);
return EXIT_FAILURE;
}
/* I/O init */
io_set_fmt(fmt);
io_init();
/* getting sizes */
rs_sample_load(NULL,&s1_nsample,s1_dim,in_path);
l = b - a + 1;
s = (have_s) ? s : l;
res_dim[0] = s;
res_dim[1] = s1_dim[1];
/* allocation */
s1 = rs_sample_create(s1_dim[0],s1_dim[1],s1_nsample);
buf = rs_sample_create(1,s1_dim[1],s1_nsample);
res = rs_sample_create(res_dim[0],res_dim[1],s1_nsample);
sig = mat_create(res_dim[0],res_dim[1]);
/* loading samples */
printf("-- loading sample from %s...\n",in_path);
rs_sample_load(s1,NULL,NULL,in_path);
/* multiplying samples */
printf("-- taking subsample [%d,%d]...\n",(int)a,(int)b);
for (k=0;k<s;k++)
{
rs_sample_get_subsamp(buf,s1,a+(k%l),0,a+(k%l),s1_dim[1]-1);
rs_sample_set_subsamp(res,buf,k,0,k,s1_dim[1]-1);
}
/* result output */
rs_sample_varp(sig,res);
mat_eqsqrt(sig);
printf("central value:\n");
mat_print(rs_sample_pt_cent_val(res),"%e");
printf("standard deviation:\n");
mat_print(sig,"%e");
if (do_save_res)
{
get_elname(out_fname,out_elname,out_path);
if (strlen(out_elname) == 0)
{
get_elname(in_fname,in_elname,in_path);
spt = (strlen(in_elname) == 0) ? in_fname : in_elname;
sprintf(out_path,"%s%c%s_%s",out_fname,LATAN_PATH_SEP,argv[0],spt);
}
rs_sample_save(out_path,'w',res);
}
/* desallocation */
rs_sample_destroy(s1);
rs_sample_destroy(res);
rs_sample_destroy(buf);
mat_destroy(sig);
/* I/O finish */
io_finish();
return EXIT_SUCCESS;
}
int main(void)
{
mat *a,*b,*c,*d,*e,*f,*g,*h,*i,*j;
const double b_init[] =
{
2.5,\
2.0,\
5.0
};
const double c_init[] =
{
1.0,10.0,6.7
};
a = mat_create(3,3);
b = mat_create_from_ar(b_init,3,1);
c = mat_create_from_ar(c_init,1,3);
d = mat_create(2,2);
e = mat_create(3,3);
f = mat_create(3,3);
g = mat_create(5,3);
h = mat_create(3,5);
i = mat_create(5,3);
j = mat_create(3,1);
randgen_init(12);
latan_set_verb(DEBUG1);
printf("---------- %-30s ----------\n","matrix product");
printf("b =\n");
mat_print(b,"%8.2f");
printf("\n");
printf("c =\n");
mat_print(c,"%8.2f");
printf("\n");
printf("a <- b*c\n");
mat_mul(a,b,'n',c,'n');
printf("a =\n");
mat_print(a,"%8.2f");
printf("\n");
printf("\n---------- %-30s ----------\n","sub-matrices");
printf("d <- a(1:2,0:1)\n");
mat_get_subm(d,a,1,0,2,1);
printf("d =\n");
mat_print(d,"%9.2f");
printf("\n");
printf("a(1,0:2) <- c\n");
mat_set_subm(a,c,1,0,1,2);
printf("a =\n");
mat_print(a,"%8.2f");
printf("\n");
printf("\n---------- %-30s ----------\n","symmetric matrix product");
printf("e <- a*t(a)\n");
mat_mul(e,a,'n',a,'t');
mat_print(e,"%8.2f");
printf("\n");
printf("e is assumed symmetric\n\n");
mat_assume(e,MAT_SYM);
printf("j <- e*b\n");
mat_mul(j,e,'n',b,'t');
mat_print(j,"%8.2f");
printf("\n");
printf("f <- a*e\n");
mat_mul(f,a,'n',e,'n');
mat_print(f,"%8.2f");
printf("\n");
printf("f <- e*t(a)\n");
mat_mul(f,e,'n',a,'t');
mat_print(f,"%8.2f");
printf("\n");
printf("g <- random(-1.0,1.0)\n");
mat_rand_u(g,-1.0,1.0);
mat_print(g,"%8.2f");
printf("\n");
printf("h <- e*t(g) (buffer should be created)\n");
mat_mul(h,e,'n',g,'t');
mat_print(h,"%8.2f");
printf("\n");
printf("i <- g*e\n");
mat_mul(i,g,'n',e,'n');
mat_print(i,"%8.2f");
printf("\n");
printf("e is not assumed symmetric anymore\n");
mat_reset_assump(e);
printf("\n---------- %-30s ----------\n","matrix inversion");
printf("*** LU decomposition\n");
printf("a <- random(-6.0,6.0)\n");
mat_rand_u(a,-6.0,6.0);
printf("a =\n");
mat_print(a,"%8.2f");
printf("\n");
printf("e <- a^(-1)\n");
mat_inv_LU(e,a);
printf("e =\n");
mat_print(e,"%8.2f");
printf("\n");
printf("f <- e*a\n");
mat_mul(f,e,'n',a,'n');
printf("f =\n");
mat_print(f,"%8.2f");
printf("\n");
printf("*** pseudo-inverse with good-conditioned matrix\n");
printf("a =\n");
mat_print(a,"%8.2f");
printf("\n");
printf("e <- a^+\n");
mat_pseudoinv(e,a);
printf("e =\n");
mat_print(e,"%8.2f");
printf("\n");
printf("f <- e*a\n");
mat_mul(f,e,'n',a,'n');
printf("f =\n");
mat_print(f,"%8.2f");
printf("\n");
printf("*** symmetric pseudo-inverse with good-conditioned matrix\n");
printf("a <- a*t(a)\n");
mat_mul(a,a,'n',a,'t');
mat_print(a,"%8.2f");
printf("\n");
printf("a is assumed symmetric and positive\n\n");
mat_assume(a,(mat_flag)(MAT_SYM|MAT_POS));
printf("e <- a^+\n");
mat_pseudoinv(e,a);
printf("e =\n");
mat_print(e,"%8.2f");
printf("\n");
printf("f <- e*a\n");
mat_mul(f,e,'n',a,'n');
printf("f =\n");
mat_print(f,"%8.2f");
printf("\n");
printf("*** Cholesky decomposition\n");
printf("e <- a^(-1)\n");
mat_inv_symChol(e,a);
printf("e =\n");
mat_print(e,"%8.2f");
printf("\n");
printf("f <- e*a\n");
mat_mul(f,e,'n',a,'n');
printf("f =\n");
mat_print(f,"%8.2f");
printf("\n");
mat_destroy(a);
mat_destroy(b);
mat_destroy(c);
mat_destroy(d);
mat_destroy(e);
mat_destroy(f);
mat_destroy(g);
mat_destroy(h);
mat_destroy(i);
mat_destroy(j);
return EXIT_SUCCESS;
}
/**
* ICA function. Computes the W matrix from the
* preprocessed data.
*/
static mat ICA_compute(mat X, int rows, int cols)
{
mat TXp, GWX, W, Wd, W1, D, TU, TMP;
vect d, lim;
int i, it;
// matrix creation
TXp = mat_create(cols, rows);
GWX = mat_create(rows, cols);
W = mat_create(rows, rows);
Wd = mat_create(rows, rows);
D = mat_create(rows, rows);
TMP = mat_create(rows, rows);
TU = mat_create(rows, rows);
W1 = mat_create(rows, rows);
d = vect_create(rows);
// W rand init
mat_apply_fx(W, rows, rows, fx_rand, 0);
// sW <- La.svd(W)
mat_copy(W, rows, rows, Wd);
svdcmp(Wd, rows, rows, d, D);
// W <- sW$u %*% diag(1/sW$d) %*% t(sW$u) %*% W
mat_transpose(Wd, rows, rows, TU);
vect_apply_fx(d, rows, fx_inv, 0);
mat_diag(d, rows, D);
mat_mult(Wd, rows, rows, D, rows, rows, TMP);
mat_mult(TMP, rows, rows, TU, rows, rows, D);
mat_mult(D, rows, rows, W, rows, rows, Wd); // W = Wd
// W1 <- W
mat_copy(Wd, rows, rows, W1);
// lim <- rep(1000, maxit); it = 1
lim = vect_create(MAX_ITERATIONS);
for (i=0; i<MAX_ITERATIONS; i++)
lim[i] = 1000;
it = 0;
// t(X)/p
mat_transpose(X, rows, cols, TXp);
mat_apply_fx(TXp, cols, rows, fx_div_c, cols);
while (lim[it] > TOLERANCE && it < MAX_ITERATIONS) {
// wx <- W %*% X
mat_mult(Wd, rows, rows, X, rows, cols, GWX);
// gwx <- tanh(alpha * wx)
mat_apply_fx(GWX, rows, cols, fx_tanh, 0);
// v1 <- gwx %*% t(X)/p
mat_mult(GWX, rows, cols, TXp, cols, rows, TMP); // V1 = TMP
// g.wx <- alpha * (1 - (gwx)^2)
mat_apply_fx(GWX, rows, cols, fx_1sub_sqr, 0);
// v2 <- diag(apply(g.wx, 1, FUN = mean)) %*% W
mat_mean_rows(GWX, rows, cols, d);
mat_diag(d, rows, D);
mat_mult(D, rows, rows, Wd, rows, rows, TU); // V2 = TU
// W1 <- v1 - v2
mat_sub(TMP, TU, rows, rows, W1);
// sW1 <- La.svd(W1)
mat_copy(W1, rows, rows, W);
svdcmp(W, rows, rows, d, D);
// W1 <- sW1$u %*% diag(1/sW1$d) %*% t(sW1$u) %*% W1
mat_transpose(W, rows, rows, TU);
vect_apply_fx(d, rows, fx_inv, 0);
mat_diag(d, rows, D);
mat_mult(W, rows, rows, D, rows, rows, TMP);
mat_mult(TMP, rows, rows, TU, rows, rows, D);
mat_mult(D, rows, rows, W1, rows, rows, W); // W1 = W
// lim[it + 1] <- max(Mod(Mod(diag(W1 %*% t(W))) - 1))
mat_transpose(Wd, rows, rows, TU);
mat_mult(W, rows, rows, TU, rows, rows, TMP);
lim[it+1] = fabs(mat_max_diag(TMP, rows, rows) - 1);
// W <- W1
mat_copy(W, rows, rows, Wd);
it++;
}
// clean up
mat_delete(TXp, cols, rows);
mat_delete(GWX, rows, cols);
mat_delete(W, rows, rows);
mat_delete(D, rows, rows);
mat_delete(TMP, rows, rows);
mat_delete(TU, rows, rows);
mat_delete(W1, rows, rows);
vect_delete(d);
return Wd;
}
/**
* Main FastICA function. Centers and whitens the input
* matrix, calls the ICA computation function ICA_compute()
* and computes the output matrixes.
*/
void fastICA(mat X, int rows, int cols, int compc, mat K, mat W, mat A, mat S)
{
mat XT, V, TU, D, X1, _A;
vect scale, d;
// matrix creation
XT = mat_create(cols, rows);
X1 = mat_create(compc, rows);
V = mat_create(cols, cols);
D = mat_create(cols, cols);
TU = mat_create(cols, cols);
scale = vect_create(cols);
d = vect_create(cols);
/*
* CENTERING
*/
mat_center(X, rows, cols, scale);
/*
* WHITENING
*/
// X <- t(X); V <- X %*% t(X)/rows
mat_transpose(X, rows, cols, XT);
mat_apply_fx(X, rows, cols, fx_div_c, rows);
mat_mult(XT, cols, rows, X, rows, cols, V);
// La.svd(V)
svdcmp(V, cols, cols, d, D); // V = s$u, d = s$d, D = s$v
// D <- diag(c(1/sqrt(d))
vect_apply_fx(d, cols, fx_inv_sqrt, 0);
mat_diag(d, cols, D);
// K <- D %*% t(U)
mat_transpose(V, cols, cols, TU);
mat_mult(D, cols, cols, TU, cols, cols, V); // K = V
// X1 <- K %*% X
mat_mult(V, compc, cols, XT, cols, rows, X1);
/*
* FAST ICA
*/
_A = ICA_compute(X1, compc, rows);
/*
* OUTPUT
*/
// X <- t(x)
mat_transpose(XT, cols, rows, X);
mat_decenter(X, rows, cols, scale);
// K
mat_transpose(V, compc, cols, K);
// w <- a %*% K; S <- w %*% X
mat_mult(_A, compc, compc, V, compc, cols, D);
mat_mult(D, compc, cols, XT, cols, rows, X1);
// S
mat_transpose(X1, compc, rows, S);
// A <- t(w) %*% solve(w * t(w))
mat_transpose(D, compc, compc, TU);
mat_mult(D, compc, compc, TU, compc, compc, V);
mat_inverse(V, compc, D);
mat_mult(TU, compc, compc, D, compc, compc, V);
// A
mat_transpose(V, compc, compc, A);
// W
mat_transpose(_A, compc, compc, W);
// cleanup
mat_delete(XT, cols, rows);
mat_delete(X1, compc, rows);
mat_delete(V, cols, cols);
mat_delete(D, cols, cols);
mat_delete(TU,cols, cols);
vect_delete(scale);
vect_delete(d);
}
int main (int argc, char *argv[]) {
uint32_t nincvxls;
uint32_t *incvxls;
analyze_volume_t vol;
mat_t *mat;
dsr_t lblhdr;
dsr_t *hdrs[2];
uint8_t *lblimg;
char *imgmsg;
char *hdrdata;
args_t args;
struct argp argp = {options, _parse_opt, "INPUT OUTPUT", doc};
lblimg = NULL;
incvxls = NULL;
mat = NULL;
imgmsg = NULL;
hdrdata = NULL;
memset(&args, 0, sizeof(args));
startup("tsmat", argc, argv, &argp, &args);
if (analyze_open_volume(args.input, &vol)) {
printf("error opening analyze volume from %s\n", args.input);
goto fail;
}
nincvxls = _create_mask(&vol, &incvxls, &args);
if (nincvxls < 0) {
printf("error masking voxels\n");
goto fail;
}
if (nincvxls == 0) {
printf("All voxels have been thresholded - relax your constraints\n");
goto fail;
}
/*
* if a label file was not provided, but a mask file
* was, use the mask file to set row/column labels
*/
if ((args.labelf == NULL) && (args.maskf != NULL)) {
args.labelf = args.maskf;
}
if (args.labelf != NULL) {
if (analyze_load(args.labelf, &lblhdr, &lblimg)) {
printf("error loading label file %s\n", args.labelf);
goto fail;
}
hdrs[0] = vol.hdrs;
hdrs[1] = &lblhdr;
if (analyze_hdr_compat_ptr(2, hdrs, 1)) {
printf(
"label file %s does not match volume files in %s\n",
args.labelf, args.input);
goto fail;
}
}
mat = mat_create(
args.output, nincvxls, nincvxls,
(1 << MAT_IS_SYMMETRIC) | (1 << MAT_HAS_ROW_LABELS),
MAT_HDR_DATA_SIZE,
sizeof(graph_label_t));
if (mat == NULL) {
printf("error creating mat file %s\n", args.output);
goto fail;
}
imgmsg = malloc(200);
if (imgmsg == NULL) {
printf("out of memory?\n");
goto fail;
}
sprintf(
imgmsg,
"vol dims: %u (%0.6f), y: %u (%0.6f), z: %u (%0.6f), t: %u (%0.6f)",
analyze_dim_size( vol.hdrs, 0),
analyze_pixdim_size(vol.hdrs, 0),
analyze_dim_size( vol.hdrs, 1),
analyze_pixdim_size(vol.hdrs, 1),
analyze_dim_size( vol.hdrs, 2),
analyze_pixdim_size(vol.hdrs, 2),
vol.nimgs,
args.sampletime);
if (args.hdrmsg != NULL)
hdrdata = malloc(strlen(imgmsg) + strlen(args.hdrmsg) + 3);
else
hdrdata = malloc(strlen(imgmsg) + 2);
if (hdrdata == NULL) {
printf("out of memory?\n");
goto fail;
}
if (args.hdrmsg != NULL)
sprintf(hdrdata, "%s\n%s\n", args.hdrmsg, imgmsg);
else
sprintf(hdrdata, "%s\n", imgmsg);
if (mat_write_hdr_data(mat, hdrdata, strlen(hdrdata)+1)) {
printf("error writing header message \"%s\" to %s\n",
hdrdata, args.output);
goto fail;
}
if (lblimg != NULL) {
if (_write_labels(&lblhdr, lblimg, mat, incvxls, nincvxls)) {
printf("error writing labels to %s\n", args.output);
goto fail;
}
}
if (_mk_corr_matrix(&vol, mat, args.corrtype, incvxls, nincvxls)) {
printf("error creating correlation matrix\n");
goto fail;
}
mat_close(mat);
analyze_free_volume(&vol);
free(imgmsg);
free(hdrdata);
free(lblimg);
free(incvxls);
return 0;
fail:
if (mat != NULL) mat_close(mat);
return 1;
}
void plot_add_fit(plot *p, const fit_data *d, const size_t ky, const mat *x_ex,\
const size_t kx, const mat *par, const double xmin, \
const double xmax, const size_t npt, const bool do_sub, \
const unsigned int obj, const strbuf dat_title, \
const strbuf fit_title, const strbuf dat_color, \
const strbuf fit_color)
{
mat *x,*x_err,*y,*y_err,*cor_data;
bool have_x_err;
size_t nfitpt,ndata;
size_t i,j;
nfitpt = fit_data_fit_point_num(d);
ndata = fit_data_get_ndata(d);
j = 0;
have_x_err = fit_data_have_x_covar(d,kx);
x = mat_create(nfitpt,1);
y = mat_create(nfitpt,1);
x_err = mat_create(nfitpt,1);
y_err = mat_create(nfitpt,1);
cor_data = mat_create(ndata,1);
if (par != NULL)
{
if (obj & PF_FIT)
{
plot_add_model(p,d->model->func[ky],x_ex,kx,par,d->model_param,\
xmin,xmax,npt,fit_title,fit_color);
}
if ((obj & PF_DATA)&&(do_sub))
{
fit_partresidual(cor_data,d,ky,x_ex,kx,par);
}
else
{
fit_data_get_y_k(cor_data,d,ky);
}
}
else
{
fit_data_get_y_k(cor_data,d,ky);
}
if (obj & PF_DATA)
{
for (i=0;i<ndata;i++)
{
if (fit_data_is_fit_point(d,i))
{
mat_set(x,j,0,fit_data_get_x(d,i,kx));
if (have_x_err)
{
mat_set(x_err,j,0, \
sqrt(mat_get(fit_data_pt_x_covar(d,kx,kx),i,i)));
}
mat_set(y,j,0,mat_get(cor_data,i,0));
mat_set(y_err,j,0, \
sqrt(mat_get(fit_data_pt_y_covar(d,ky,ky),i,i)));
j++;
}
}
if (have_x_err)
{
plot_add_dat(p,x,y,x_err,y_err,dat_title,dat_color);
}
else
{
plot_add_dat(p,x,y,NULL,y_err,dat_title,dat_color);
}
}
mat_destroy(x);
mat_destroy(x_err);
mat_destroy(y);
mat_destroy(y_err);
mat_destroy(cor_data);
}
void plot_fit(const rs_sample *s_fit, fit_data *d, fit_param *param, const plot_flag f)
{
plot *p[N_EX_VAR];
double *xb[N_EX_VAR] = {NULL,NULL,NULL,NULL,NULL,NULL,NULL};
double x_range[N_EX_VAR][2],b_int[2],dbind,a;
size_t bind,vind,eind,k,phy_ind,s;
strbuf color,gtitle,title,xlabel,ylabel;
mat *phy_pt,*x_k,*fit,*cordat,**vol_av_corr,*yerrtmp;
ens *ept;
phy_pt = mat_create(N_EX_VAR,1);
x_k = mat_create(param->nens,1);
cordat = mat_create(param->nens,1);
MALLOC(vol_av_corr,mat **,param->nbeta);
for (bind=0;bind<param->nbeta;bind++)
{
vol_av_corr[bind] = mat_create(param->nvol[bind],1);
}
for (k=0;k<N_EX_VAR;k++)
{
p[k] = plot_create();
}
param->scale_model = 1;
fit = rs_sample_pt_cent_val(s_fit);
if (IS_AN(param,AN_PHYPT)&&IS_AN(param,AN_SCALE))
{
phy_ind = 1;
s = fm_scaleset_taylor_npar(param);
}
else
{
phy_ind = 0;
s = 0;
}
for (k=0;k<N_EX_VAR;k++)
{
if (k == i_vind)
{
fit_data_get_x_k(x_k,d,i_Linv);
}
else
{
fit_data_get_x_k(x_k,d,k);
}
if ((k == i_a)||(k == i_ud)||(k == i_Linv)||(k == i_alpha)\
||(k == i_vind))
{
x_range[k][0] = 0.0;
}
else
{
x_range[k][0] = mat_get_min(x_k)-0.15*fabs(mat_get_min(x_k));
}
x_range[k][1] = mat_get_max(x_k)+0.15*fabs(mat_get_min(x_k));
plot_set_scale_xmanual(p[k],x_range[k][0],x_range[k][1]);
}
if (f == Q)
{
sprintf(gtitle,"quantity: %s -- scale: %s -- datasets: %s -- ensembles: %s",\
param->q_name,param->scale_part,param->dataset_cat,param->manifest);
mat_set(phy_pt,i_ud,0,SQ(param->M_ud));
mat_set(phy_pt,i_s,0,SQ(param->M_s));
mat_set(phy_pt,i_umd,0,param->M_umd_val);
mat_set(phy_pt,i_alpha,0,param->alpha);
mat_set(phy_pt,i_bind,0,0.0);
mat_set(phy_pt,i_vind,0,0.0);
mat_set(phy_pt,i_a,0,0.0);
mat_set(phy_pt,i_Linv,0,0.0);
mat_set(phy_pt,i_fvM,0,param->qed_fvol_mass);
/* regular plots */
PLOT_ADD_FIT(PF_FIT,i_ud,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_ud,phy_ind,"rgb 'black'");
PLOT_ADD_FIT(PF_FIT,i_s,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_s,phy_ind,"rgb 'black'");
PLOT_ADD_FIT(PF_FIT,i_umd,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_umd,phy_ind,"rgb 'black'");
PLOT_ADD_FIT(PF_FIT,i_alpha,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_alpha,phy_ind,"rgb 'black'");
PLOT_ADD_FIT(PF_FIT,i_a,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_a,phy_ind,"rgb 'black'");
PLOT_ADD_FIT(PF_FIT,i_Linv,phy_ind,"","rgb 'black'");
PLOT_ADD_PB(i_Linv,phy_ind,"rgb 'black'");
for (bind=0;bind<param->nbeta;bind++)
{
dbind = (double)(bind);
b_int[0] = dbind - 0.1;
b_int[1] = dbind + 0.1;
xb[i_bind] = b_int;
fit_data_fit_region(d,xb);
sprintf(color,"%d",1+(int)bind);
sprintf(title,"beta = %s",param->beta[bind]);
PLOT_ADD_FIT(PF_DATA,i_ud,phy_ind,title,color);
PLOT_ADD_FIT(PF_DATA,i_s,phy_ind,title,color);
PLOT_ADD_FIT(PF_DATA,i_umd,phy_ind,title,color);
PLOT_ADD_FIT(PF_DATA,i_alpha,phy_ind,title,color);
PLOT_ADD_FIT(PF_DATA,i_a,phy_ind,title,color);
PLOT_ADD_FIT(PF_DATA,i_Linv,phy_ind,title,color);
fit_data_fit_all_points(d,true);
}
/* volume averages plot */
plot_add_fit(p[i_vind],d,phy_ind,phy_pt,i_Linv,fit,x_range[i_Linv][0],\
x_range[i_Linv][1],MOD_PLOT_NPT,true,PF_FIT,"","", \
"rgb 'black'","rgb 'black'");
plot_add_fit_predband(p[i_vind],d,phy_ind,phy_pt,i_Linv,s_fit,\
x_range[i_Linv][0],x_range[i_Linv][1], \
MOD_PLOT_NPT/4,"rgb 'black'");
fit_partresidual(cordat,d,phy_ind,phy_pt,i_Linv,fit);
for(bind=0;bind<param->nbeta;bind++)
{
mat_zero(vol_av_corr[bind]);
}
for(eind=0;eind<param->nens;eind++)
{
ept = param->point + eind;
bind = (size_t)ind_beta(ept->beta,param);
vind = (size_t)ind_volume((unsigned int)ept->L,(int)bind,param);
mat_inc(vol_av_corr[bind],vind,0,mat_get(cordat,eind,0));
}
for (bind=0;bind<param->nbeta;bind++)
for (vind=0;vind<param->nvol[bind];vind++)
{
mat_set(vol_av_corr[bind],vind,0, \
mat_get(vol_av_corr[bind],vind,0) \
/((double)(param->nenspvol[bind][vind])));
}
for(bind=0;bind<param->nbeta;bind++)
{
yerrtmp = mat_create(param->nvol[bind],1);
rs_sample_varp(yerrtmp,param->s_vol_av[bind]);
mat_eqsqrt(yerrtmp);
sprintf(color,"%d",1+(int)bind);
sprintf(title,"beta = %s",param->beta[bind]);
plot_add_dat_yerr(p[i_vind], \
rs_sample_pt_cent_val(param->s_vol_Linv[bind]),\
vol_av_corr[bind],yerrtmp,title,color);
mat_destroy(yerrtmp);
}
/* display plots */
switch (param->q_dim)
{
case 0:
strbufcpy(ylabel,param->q_name);
break;
case 1:
sprintf(ylabel,"%s (MeV)",param->q_name);
break;
default:
sprintf(ylabel,"%s^%d (MeV^%d)",param->q_name,param->q_dim,\
param->q_dim);
break;
}
sprintf(xlabel,"M_%s^2 (MeV^2)",param->ud_name);
PLOT_ADD_EX(i_ud,s);
PLOT_DISP(i_ud,"ud");
sprintf(xlabel,"M_%s^2 (MeV^2)",param->s_name);
PLOT_ADD_EX(i_s,s);
PLOT_DISP(i_s,"s");
strbufcpy(xlabel,"a (MeV^-1)");
PLOT_ADD_EX(i_a,s);
PLOT_DISP(i_a,"a");
if (param->have_umd)
{
sprintf(xlabel,"%s (MeV^2)",param->umd_name);
PLOT_ADD_EX(i_umd,s);
PLOT_DISP(i_umd,"umd");
}
if (param->have_alpha)
{
strbufcpy(xlabel,"alpha");
PLOT_ADD_EX(i_alpha,s);
PLOT_DISP(i_alpha,"alpha");
}
strbufcpy(xlabel,"1/L (MeV)");
PLOT_ADD_EX(i_Linv,s);
PLOT_DISP(i_Linv,"Linv");
PLOT_ADD_EX(i_vind,s);
PLOT_DISP(i_vind,"Linv_av");
}
else if (f == SCALE)
{
sprintf(gtitle,"scale setting: %s -- datasets: %s -- ensembles: %s",
param->scale_part,param->dataset_cat,param->manifest);
for (bind=0;bind<param->nbeta;bind++)
{
dbind = (double)(bind);
b_int[0] = dbind - 0.1;
b_int[1] = dbind + 0.1;
xb[i_bind] = b_int;
a = mat_get(fit,bind,0);
fit_data_fit_region(d,xb);
mat_set(phy_pt,i_ud,0,SQ(a*param->M_ud));
mat_set(phy_pt,i_s,0,SQ(a*param->M_s));
mat_set(phy_pt,i_umd,0,SQ(a)*param->M_umd_val);
mat_set(phy_pt,i_bind,0,bind);
mat_set(phy_pt,i_a,0,a);
mat_set(phy_pt,i_Linv,0,0.0);
sprintf(color,"%d",1+(int)bind);
sprintf(title,"beta = %s",param->beta[bind]);
PLOT_ADD_FIT(PF_DATA|PF_FIT,i_ud,0,title,color);
PLOT_ADD_FIT(PF_DATA|PF_FIT,i_s,0,title,color);
PLOT_ADD_FIT(PF_DATA|PF_FIT,i_umd,0,title,color);
PLOT_ADD_FIT(PF_DATA|PF_FIT,i_Linv,0,title,color);
fit_data_fit_all_points(d,true);
}
sprintf(ylabel,"(a*M_%s)^2",param->scale_part);
sprintf(xlabel,"(a*M_%s)^2",param->ud_name);
PLOT_DISP(i_ud,"ud");
sprintf(xlabel,"(a*M_%s)^2",param->s_name);
PLOT_DISP(i_s,"s");
if (param->have_umd)
{
sprintf(xlabel,"a^2*%s",param->umd_name);
PLOT_DISP(i_umd,"umd");
}
strbufcpy(xlabel,"a/L");
PLOT_DISP(i_Linv,"Linv");
}
param->scale_model = 0;
mat_destroy(phy_pt);
mat_destroy(x_k);
mat_destroy(cordat);
for (bind=0;bind<param->nbeta;bind++)
{
mat_destroy(vol_av_corr[bind]);
}
free(vol_av_corr);
for (k=0;k<N_EX_VAR;k++)
{
plot_destroy(p[k]);
}
}
int ProcessData(){
int i, j, ii;
int comp = 14; //so thanh phan doc lap
//khai bao matrix X la ma tran dung de luu eegData doc tu file Edf
mat X;
int rows_X, cols_X;//so hang, cot cua ma tran
mat K, W, A, S;
double *Af3; //du lieu kenh AF3
double *EyeBlink;//dang tin hieu eyeblink
double *Component;
double *Comp_Wavelet;
double Mean_X, Mean_Y, S_X, S_Y, Denom, Cr_Correlate;
FILE *FileOut;
X = mat_create(SAMPLE_MAX, CHANNEL_NUMBER);//cap phat bo nho cho X
/**
* READ DATA
*/
printf("\nStart read EEG data..........\n");
rows_X = readData(X);//goi ham doc file edf, luu du lieu vao ma tran X
cols_X = CHANNEL_NUMBER;
rows_X = 128;
//END READ DATA
/**
* RUN ICA
*/
printf("\nStart run ICA..........\n");
//cap phat vung nho cho cac matrix
W = mat_create(comp, comp);
A = mat_create(comp, comp);
K = mat_create(cols_X, comp);
S = mat_create(rows_X, comp);
fastICA(X, rows_X, cols_X, comp, K, W, A, S);//run ICA, matrix output: S
#ifdef DEBUG
//kiem tra xem matrix S thu ve co dung khong
FileOut = fopen("/home/nick_gun/Desktop/Lab-2013/SAMSUNG_2013_2014/Code/EEGProject/Debug/ICA_Out.txt", "wb");
for(i=0; i<rows_X; i++){
for(j=0;j<1;j++)
fprintf(FileOut, "%f ", S[i][3]);
fprintf(FileOut, "\n");
}
fclose(FileOut);
#endif
//END RUN ICA
/**
* RUN WAVELET
* Compute Wavelet and Recontruction Detail/Aprroximation
* with AF3(for recontruction eyeblink) and each component(ICA)
* Then use Cross Correlation for Detect EyeBlink Component
*
* Ref: http://paulbourke.net/miscellaneous/correlate/
*/
printf("\nStart run Wavelet..........\n");
//1.RUN WAVELET FOR FA3
//copy du lieu sang Af3
Af3 = malloc(SAMPLE*sizeof(double));
for(i=0;i<SAMPLE;i++)
Af3[i]=X[i][5];
//chay wavelet daub4 cho Af3 va tai tao tin hieu eyeblink
EyeBlink = reWavelet(SAMPLE, 32, 64, Af3);
//compute mean of EyeBlink and absolute EyeBlink
S_X=0; Mean_X=0;
for(i=0;i<SAMPLE;i++){
//if(EyeBlink[i]<0) EyeBlink[i]=-EyeBlink[i];
Mean_X+=EyeBlink[i];
}
Mean_X=Mean_X/SAMPLE;
for(i=0;i<SAMPLE;i++)
S_X+=(EyeBlink[i]-Mean_X)*(EyeBlink[i]-Mean_X);
#ifdef DEBUG
//print eyeblink
FileOut = fopen("/home/nick_gun/Desktop/Lab-2013/SAMSUNG_2013_2014/Code/EEGProject/Debug/Eyeblink.txt", "wb");
for(i=0; i<SAMPLE; i++)
fprintf(FileOut, "%f\n", EyeBlink[i]);
fclose(FileOut);
#endif
//2.RUN WAVELET FOR COMPONENT ICA
Comp_Wavelet = malloc(SAMPLE*sizeof(double));
Component = malloc(SAMPLE*sizeof(double));
//loop load one of all channel
for(ii=0;ii<comp;ii++){
//2.1.COMPUTE WAVELET FOR EACH COMPONENT
for(j=0;j<SAMPLE;j++)
Component[j]=S[j][ii];
Comp_Wavelet = reWavelet(SAMPLE, 16, 32, Component);
#ifdef DEBUG
if(ii==0) FileOut = fopen("/home/nick_gun/Desktop/Lab-2013/SAMSUNG_2013_2014/Code/EEGProject/Debug/Comp_Wavelet.txt", "wb");
else FileOut = fopen("/home/nick_gun/Desktop/Lab-2013/SAMSUNG_2013_2014/Code/EEGProject/Debug/Comp_Wavelet.txt", "at");
fprintf(FileOut, "Comp_Wavelet %d ***************\n", ii);
for(j=0; j<SAMPLE; j++){
//if(Comp_Wavelet[j]<0) Comp_Wavelet[j]=-Comp_Wavelet[j];
fprintf(FileOut, "%f\n", Comp_Wavelet[j]);
}
fclose(FileOut);
#endif
//2.2.COMPUTE WITH EYEBLINK USE CROSS CORRELATION
//compute mean and absolute Component
S_Y=0; Mean_Y=0;
for(j=0;j<SAMPLE;j++){
//if(Comp_Wavelet[j]<0) Comp_Wavelet[j]=-Comp_Wavelet[j];
Mean_Y+=Comp_Wavelet[j];
}
Mean_Y=Mean_Y/SAMPLE;
for(j=0;j<SAMPLE;j++)
S_Y+=(Comp_Wavelet[j]-Mean_Y)*(Comp_Wavelet[j]-Mean_Y);
Denom = sqrt(S_X*S_Y);
//compute cross correlate at delay = 0
Cr_Correlate=0;
for(j=0;j<SAMPLE;j++){
Cr_Correlate+=EyeBlink[j]*Comp_Wavelet[j];
}
Cr_Correlate=Cr_Correlate/Denom;
printf("==%d===%f===\n",ii, Cr_Correlate);
}
//END RUN WAVELET
free(Af3);
free(EyeBlink);
free(Component);
free(Comp_Wavelet);
mat_delete(X, SAMPLE_MAX, CHANNEL_NUMBER);//giai phong ma tran X
mat_delete(W, comp, comp);
mat_delete(A, comp, comp);
mat_delete(K, cols_X, comp);
mat_delete(S, rows_X, comp);
return rows_X;
}
/**
* ICA function. Computes the W matrix from the
* preprocessed data.
*/
static mat ICA_compute(mat X, int rows, int cols) {
mat TXp, GWX, W, Wd, W1, D, TU, TMP;
vect d, lim;
int i, it;
FILE *OutputFile;
clock_t clock1, clock2;
float time;
//char ascii_path[512];
//strcpy(ascii_path, "/storage/sdcard0/NickGun/EEG/Log.txt");
//FILE *Log;
// matrix creation
TXp = mat_create(cols, rows);
GWX = mat_create(rows, cols);
W = mat_create(rows, rows);
Wd = mat_create(rows, rows);
D = mat_create(rows, rows);
TMP = mat_create(rows, rows);
TU = mat_create(rows, rows);
W1 = mat_create(rows, rows);
d = vect_create(rows);
// W rand init
mat_apply_fx(W, rows, rows, fx_rand, 0);
// sW <- La.svd(W)
mat_copy(W, rows, rows, Wd);
svdcmp(Wd, rows, rows, d, D);
// W <- sW$u %*% diag(1/sW$d) %*% t(sW$u) %*% W
mat_transpose(Wd, rows, rows, TU);
vect_apply_fx(d, rows, fx_inv, 0);
mat_diag(d, rows, D);
mat_mult(Wd, rows, rows, D, rows, rows, TMP);
mat_mult(TMP, rows, rows, TU, rows, rows, D);
mat_mult(D, rows, rows, W, rows, rows, Wd); // W = Wd
// W1 <- W
mat_copy(Wd, rows, rows, W1);
// lim <- rep(1000, maxit); it = 1
lim = vect_create(MAX_ITERATIONS);
for (i = 0; i < MAX_ITERATIONS; i++)
lim[i] = 1000;
it = 0;
// t(X)/p
mat_transpose(X, rows, cols, TXp);
mat_apply_fx(TXp, cols, rows, fx_div_c, cols);
while (lim[it] > TOLERANCE && it < MAX_ITERATIONS) {
// wx <- W %*% X
mat_mult(Wd, rows, rows, X, rows, cols, GWX);
// gwx <- tanh(alpha * wx)
mat_apply_fx(GWX, rows, cols, fx_tanh, 0);
// v1 <- gwx %*% t(X)/p
mat_mult(GWX, rows, cols, TXp, cols, rows, TMP); // V1 = TMP
// g.wx <- alpha * (1 - (gwx)^2)
mat_apply_fx(GWX, rows, cols, fx_1sub_sqr, 0);
// v2 <- diag(apply(g.wx, 1, FUN = mean)) %*% W
mat_mean_rows(GWX, rows, cols, d);
mat_diag(d, rows, D);
mat_mult(D, rows, rows, Wd, rows, rows, TU); // V2 = TU
// W1 <- v1 - v2
mat_sub(TMP, TU, rows, rows, W1);
// sW1 <- La.svd(W1)
mat_copy(W1, rows, rows, W);
svdcmp(W, rows, rows, d, D);
// W1 <- sW1$u %*% diag(1/sW1$d) %*% t(sW1$u) %*% W1
mat_transpose(W, rows, rows, TU);
vect_apply_fx(d, rows, fx_inv, 0);
mat_diag(d, rows, D);
mat_mult(W, rows, rows, D, rows, rows, TMP);
mat_mult(TMP, rows, rows, TU, rows, rows, D);
mat_mult(D, rows, rows, W1, rows, rows, W); // W1 = W
// lim[it + 1] <- max(Mod(Mod(diag(W1 %*% t(W))) - 1))
mat_transpose(Wd, rows, rows, TU); //chuyen vi
mat_mult(W, rows, rows, TU, rows, rows, TMP); //TMP=WxTU
lim[it + 1] = fabs(mat_max_diag(TMP, rows, rows) - 1);
if(lim[it+1]<0.1)
break;
/*
OutputFile = fopen("/storage/sdcard0/Nickgun/EEG/data/lim",
"at");
fprintf(OutputFile, "%f \n", lim[it+1]);
fclose(OutputFile);
// W <- W1
*/
mat_copy(W, rows, rows, Wd);
it++;
}
// clean up
mat_delete(TXp, cols, rows);
mat_delete(GWX, rows, cols);
mat_delete(W, rows, rows);
mat_delete(D, rows, rows);
mat_delete(TMP, rows, rows);
mat_delete(TU, rows, rows);
mat_delete(W1, rows, rows);
vect_delete(d);
return Wd;
}
void print_result(const rs_sample *s_fit, fit_param *param)
{
size_t i;
int j;
mat *fit,*fit_var;
strbuf buf;
i = 0;
fit = rs_sample_pt_cent_val(s_fit);
fit_var = mat_create(fit_model_get_npar(&(param->fm),param),1);
rs_sample_varp(fit_var,s_fit);
mpi_printf("\n");
mpi_printf("fit parameters :\n");
if (IS_AN(param,AN_SCALE))
{
for(j=0;j<(int)param->nbeta;j++)
{
sprintf(buf,"a_%s",param->beta[j]);
PRINT_SCALE(buf);
}
if (param->s_M_ud_deg > 0)
{
for (j=0;j<param->s_M_ud_deg;j++)
{
sprintf(buf,"s_p_ud_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->s_M_s_deg > 0)
{
for (j=0;j<param->s_M_s_deg;j++)
{
sprintf(buf,"s_p_s_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->s_with_a2ud)
{
PRINT_PAR("s_a2ud");
}
if (param->s_with_a2s)
{
PRINT_PAR("s_a2s");
}
if (param->s_umd_deg > 0)
{
for (j=0;j<param->s_umd_deg;j++)
{
sprintf(buf,"s_p_umd_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->s_with_qed_fvol)
{
PRINT_PAR("s_p_fvol_L");
}
}
if (IS_AN(param,AN_PHYPT))
{
if (param->with_const)
{
PRINT_PAR("const");
}
if (param->M_ud_deg > 0)
{
for (j=0;j<param->M_ud_deg;j++)
{
sprintf(buf,"p_ud_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->M_s_deg > 0)
{
for (j=0;j<param->M_s_deg;j++)
{
sprintf(buf,"p_s_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->with_a2 > 0)
{
PRINT_PAR("p_a2");
}
if (param->with_alpha_sa > 0)
{
PRINT_PAR("p_alpha_sa");
}
if (param->with_a2ud)
{
PRINT_PAR("p_a2ud");
}
if (param->with_a2s)
{
PRINT_PAR("p_a2s");
}
if (param->umd_deg)
{
PRINT_PAR("p_umd");
}
if (param->with_udumd)
{
for (j=0;j<param->with_udumd;j++)
{
sprintf(buf,"p_udumd_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->with_sumd)
{
for (j=0;j<param->with_sumd;j++)
{
sprintf(buf,"p_sumd_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->with_a2umd)
{
PRINT_PAR("p_a2umd");
}
if (param->with_alpha_saumd)
{
PRINT_PAR("p_alpha_saumd");
}
if (param->alpha_deg)
{
PRINT_PAR("p_alpha");
}
if (param->with_udalpha)
{
for (j=0;j<param->with_udalpha;j++)
{
sprintf(buf,"p_udalpha_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->with_salpha)
{
for (j=0;j<param->with_salpha;j++)
{
sprintf(buf,"p_salpha_%d",j+1);
PRINT_PAR(buf);
}
}
if (param->with_aalpha)
{
PRINT_PAR("p_aalpha");
}
if (param->with_qed_fvol)
{
if (param->with_qed_fvol_monopmod)
{
if (param->with_qed_fvol == 2)
{
PRINT_PAR("p_Linv_2");
}
}
else
{
for (j=0;j<param->with_qed_fvol;j++)
{
sprintf(buf,"p_Linv_%d",j+1);
PRINT_PAR(buf);
}
}
}
if (IS_AN(param,AN_PHYPT)&&!IS_AN(param,AN_SCALE)&&\
(strbufcmp(param->with_ext_a,"") != 0))
{
for(j=0;j<(int)param->nbeta;j++)
{
sprintf(buf,"corr_a_%s",param->beta[j]);
PRINT_SCALE(buf);
}
}
}
mpi_printf("\n");
mat_destroy(fit_var);
}
void fprint_table(FILE* stream, rs_sample *s_x[N_EX_VAR], rs_sample *s_q[2],\
const mat *res, const fit_param *param, const plot_flag f)
{
mat **x_err,*q_err;
const rs_sample *s_q_pt;
size_t nens,ydim;
size_t ens_ind;
nens = param->nens;
ydim = (f == SCALE) ? 0 : 1;
s_q_pt = s_q[ydim];
x_err = mat_ar_create(N_EX_VAR,nens,1);
q_err = mat_create(nens,1);
/* computing errors */
rs_sample_varp(x_err[i_ud],s_x[i_ud]);
mat_eqsqrt(x_err[i_ud]);
rs_sample_varp(x_err[i_s],s_x[i_s]);
mat_eqsqrt(x_err[i_s]);
rs_sample_varp(x_err[i_a],s_x[i_a]);
mat_eqsqrt(x_err[i_a]);
rs_sample_varp(x_err[i_umd],s_x[i_umd]);
mat_eqsqrt(x_err[i_umd]);
rs_sample_varp(x_err[i_Linv],s_x[i_Linv]);
mat_eqsqrt(x_err[i_Linv]);
rs_sample_varp(q_err,s_q_pt);
mat_eqsqrt(q_err);
/* display */
fprintf(stream,"#%49s ","ensemble");
PRINT_DLABEL_WERR(param->ud_name);
PRINT_DLABEL_WERR(param->s_name);
if (f == Q)
{
PRINT_DLABEL_WERR("a");
}
if (param->have_umd)
{
PRINT_DLABEL_WERR(param->umd_name);
}
if (param->have_alpha)
{
PRINT_DLABEL("alpha");
}
PRINT_DLABEL_WERR("1/L");
if (f == Q)
{
PRINT_DLABEL_WERR(param->q_name);
}
else if (f == SCALE)
{
PRINT_DLABEL_WERR(param->scale_part);
}
PRINT_DLABEL("residuals");
fprintf(stream,"\n");
for(ens_ind=0;ens_ind<nens;ens_ind++)
{
fprintf(stream,"%50s ",param->point[ens_ind].dir);
PRINT_X_WERR(i_ud);
PRINT_X_WERR(i_s);
if (f == Q)
{
PRINT_X_WERR(i_a);
}
if (param->have_umd)
{
PRINT_X_WERR(i_umd);
}
if (param->have_alpha)
{
PRINT_X(i_alpha);
}
PRINT_X_WERR(i_Linv);
PRINT_CV_WERR(s_q_pt,q_err);
PRINT_D(mat_get(res,ens_ind,0));
fprintf(stream,"\n");
}
fprintf(stream,"\n");
mat_ar_destroy(x_err,N_EX_VAR);
mat_destroy(q_err);
}
int main(int argc, char* argv[])
{
/* parsing arguments */
/********************************************/
double latspac_nu;
qcd_options *opt;
strbuf name[3],manf_name,unit,sink[3],source[3];
size_t binsize,nboot,propdim[2],nt;
char *cpt1,*cpt2;
corr_no lastc;
fit_model *fm_pt;
opt = qcd_arg_parse(argc,argv,A_PLOT|A_SAVE_RS|A_LOAD_RG|A_PROP_NAME\
|A_PROP_LOAD|A_LATSPAC|A_QCOMP|A_FIT,2,0);
cpt1 = strtok(opt->ss,"/");
printf("%s\n",cpt1);
if (cpt1)
{
cpt2 = strchr(cpt1,':');
if (cpt2 == NULL)
{
fprintf(stderr,"error: sink/source option %s is invalid\n",\
cpt1);
exit(EXIT_FAILURE);
}
strbufcpy(source[PP],cpt2+1);
*cpt2 = '\0';
strbufcpy(sink[PP],cpt1);
}
else
{
fprintf(stderr,"error: sink/source option %s is invalid\n",\
opt->ss);
exit(EXIT_FAILURE);
}
cpt1 = strtok(NULL,"/");
if (cpt1)
{
cpt2 = strchr(cpt1,':');
if (cpt2 == NULL)
{
fprintf(stderr,"error: sink/source option %s is invalid\n",\
cpt1);
exit(EXIT_FAILURE);
}
strbufcpy(source[AP],cpt2+1);
*cpt2 = '\0';
strbufcpy(sink[AP],cpt1);
}
else
{
strbufcpy(sink[AP],sink[PP]);
strbufcpy(source[AP],source[PP]);
}
cpt1 = strtok(NULL,"/");
if (cpt1)
{
cpt2 = strchr(cpt1,':');
if (cpt2 == NULL)
{
fprintf(stderr,"error: sink/source option %s is invalid\n",\
cpt1);
exit(EXIT_FAILURE);
}
strbufcpy(source[AA],cpt2+1);
*cpt2 = '\0';
strbufcpy(sink[AA],cpt1);
}
else
{
strbufcpy(sink[AA],sink[PP]);
strbufcpy(source[AA],source[PP]);
}
cpt1 = strtok(opt->channel[0],"/");
if (cpt1)
{
sprintf(name[PP],"%s_%s_%s_%s",cpt1,opt->quark[0],sink[PP],source[PP]);
}
else
{
fprintf(stderr,"error: channel option %s is invalid\n",\
opt->channel[0]);
exit(EXIT_FAILURE);
}
cpt1 = strtok(NULL,"/");
if (cpt1)
{
sprintf(name[AP],"%s_%s_%s_%s",cpt1,opt->quark[0],sink[AP],source[AP]);
}
else
{
fprintf(stderr,"error: channel option %s is invalid\n",\
opt->channel[0]);
exit(EXIT_FAILURE);
}
cpt1 = strtok(NULL,"/");
if (cpt1)
{
sprintf(name[AA],"%s_%s_%s_%s",cpt1,opt->quark[0],sink[AA],source[AA]);
lastc = AA;
fm_pt = &fm_pseudosc3;
}
else
{
lastc = AP;
fm_pt = &fm_pseudosc2;
}
strbufcpy(manf_name,opt->manf_name);
binsize = opt->binsize;
nboot = opt->nboot;
latspac_nu = opt->latspac_nu;
if (opt->have_latspac)
{
strbufcpy(unit," (MeV)");
}
else
{
strbufcpy(unit,"");
}
latan_set_verb(opt->latan_verb);
minimizer_set_alg(opt->minimizer);
mat_ar_loadbin(NULL,propdim,manf_name,name[PP],1);
nt = propdim[0];
io_set_fmt(opt->latan_fmt);
io_init();
/* loading datas */
/********************************************/
size_t ndat,nbdat;
mat **prop[3];
corr_no c;
ndat = (size_t)get_nfile(manf_name);
nbdat = ndat/binsize + ((ndat%binsize == 0) ? 0 : 1);
for (c=PP;c<=lastc;c++)
{
prop[c] = mat_ar_create(nbdat,propdim[0],propdim[1]);
qcd_printf(opt,"-- loading %s datas from %s...\n",name[c],manf_name);
mat_ar_loadbin(prop[c],NULL,manf_name,name[c],binsize);
}
/* propagator */
/********************************************/
rs_sample *s_mprop[3];
mat *mprop[3],*sigmprop[3];
for (c=PP;c<=lastc;c++)
{
s_mprop[c] = rs_sample_create(propdim[0],propdim[1],nboot);
sigmprop[c] = mat_create(propdim[0],propdim[1]);
qcd_printf(opt,"-- resampling %s mean propagator...\n",name[c]);
randgen_set_state(opt->state);
resample(s_mprop[c],prop[c],nbdat,&rs_mean,BOOT,NULL);
mprop[c] = rs_sample_pt_cent_val(s_mprop[c]);
rs_sample_varp(sigmprop[c],s_mprop[c]);
mat_eqsqrt(sigmprop[c]);
}
/* effective mass */
/********************************************/
rs_sample *s_effmass[3];
mat *tem,*em[3],*sigem[3];
size_t emdim[2];
get_effmass_size(emdim,mprop[PP],1,EM_ACOSH);
tem = mat_create(emdim[0],1);
for (c=PP;c<=lastc;c++)
{
s_effmass[c] = rs_sample_create(emdim[0],emdim[1],nboot);
sigem[c] = mat_create(emdim[0],emdim[1]);
qcd_printf(opt,"-- resampling %s effective mass...\n",name[c]);
rs_sample_effmass(s_effmass[c],tem,s_mprop[c],1,EM_ACOSH);
em[c] = rs_sample_pt_cent_val(s_effmass[c]);
rs_sample_varp(sigem[c],s_effmass[c]);
mat_eqsqrt(sigem[c]);
}
/* fit mass */
/********************************************/
fit_data *d;
rs_sample *s_fit;
mat *fit,*limit,*sigfit,*scanres_t,*scanres_chi2,*scanres_mass,\
*scanres_masserr;
size_t npar,nti,tibeg,range[2],ta;
size_t i,j;
strbuf buf,range_info,latan_path;
double pref_i,mass_i;
d = fit_data_create(nt,1,(size_t)(lastc+1));
tibeg = (size_t)(opt->range[0][0]);
range[0] = 0;
range[1] = 0;
npar = fit_model_get_npar(fm_pt,&nt);
s_fit = rs_sample_create(npar,1,nboot);
fit = rs_sample_pt_cent_val(s_fit);
limit = mat_create(npar,2);
sigfit = mat_create(npar,1);
/** print operation **/
if (!opt->do_range_scan)
{
qcd_printf(opt,"-- fitting and resampling...\n");
}
else
{
qcd_printf(opt,"-- scanning ranges [ti,%u] from ti= %u\n",\
opt->range[0][1],opt->range[0][0]);
opt->nmanrange = 1;
}
/** check ranges **/
strbufcpy(range_info,"");
qcd_printf(opt,"%-20s: ","corrected range(s)");
fit_data_fit_all_points(d,false);
for (i=0;i<opt->nmanrange;i++)
{
sprintf(buf,"_%u_%u",opt->range[i][0],opt->range[i][1]);
strbufcat(range_info,buf);
range[0] = (size_t)(opt->range[i][0]);
range[1] = (size_t)(opt->range[i][1]);
correct_range(range,mprop[PP],sigmprop[PP],opt);
fit_data_fit_range(d,range[0],range[1],true);
}
qcd_printf(opt,"\n");
nti = MAX(range[1] - 1 - tibeg,1);
scanres_t = mat_create(nti,1);
scanres_chi2 = mat_create(nti,1);
scanres_mass = mat_create(nti,1);
scanres_masserr = mat_create(nti,1);
/** set model **/
fit_data_set_model(d,fm_pt,&nt);
/** set correlation filter **/
if (opt->corr == NO_COR)
{
for (i=0;i<nt;i++)
for (j=0;j<nt;j++)
{
if (i != j)
{
fit_data_set_data_cor(d,i,j,false);
}
}
}
/** set initial parameter values **/
ta = nt/8-(size_t)(mat_get(tem,0,0));
mass_i = mat_get(em[PP],ta,0);
if (latan_isnan(mass_i))
{
mass_i = 0.3;
}
mat_set(fit,0,0,mass_i);
pref_i = mat_get(mprop[PP],ta,0)/(exp(-mass_i*ta)+exp(-mass_i*(nt-ta)));
if (latan_isnan(pref_i))
{
pref_i = 1.0;
}
mat_set(fit,1,0,sqrt(pref_i));
mat_set(fit,2,0,sqrt(pref_i));
qcd_printf(opt,"%-22smass= %e -- prefactor_0= %e\n","initial parameters: ",\
mat_get(fit,0,0),pref_i);
/** set parameter limits **/
mat_cst(limit,latan_nan());
mat_set(limit,0,0,0.0);
mat_set(limit,1,0,0.0);
mat_set(limit,2,0,0.0);
/** positive AP correlator **/
rs_sample_eqabs(s_mprop[AP]);
/** set x **/
for (i=0;i<nt;i++)
{
fit_data_set_x(d,i,0,(double)(i)-opt->tshift);
}
/** regular correlator fit... **/
if (!opt->do_range_scan)
{
latan_set_warn(false);
rs_data_fit(s_fit,limit,NULL,s_mprop,d,NO_COR,NULL);
latan_set_warn(true);
rs_data_fit(s_fit,limit,NULL,s_mprop,d,opt->corr,NULL);
rs_sample_varp(sigfit,s_fit);
mat_eqsqrt(sigfit);
if (fit_data_get_chi2pdof(d) > 2.0)
{
fprintf(stderr,"warning: bad final fit (chi^2/dof= %.2e)\n",\
fit_data_get_chi2pdof(d));
}
qcd_printf(opt,"-- results:\n");
qcd_printf(opt,"%-10s= %.8f +/- %.8e %s\n","mass",\
mat_get(fit,0,0)/latspac_nu, \
mat_get(sigfit,0,0)/latspac_nu,unit);
qcd_printf(opt,"%-10s= %.8f +/- %.8e %s\n","decay",\
mat_get(fit,1,0)/latspac_nu, \
mat_get(sigfit,1,0)/latspac_nu,unit);
qcd_printf(opt,"%-10s= %.8f +/- %.8e %s\n","norm",\
mat_get(fit,2,0)/latspac_nu, \
mat_get(sigfit,2,0)/latspac_nu,unit);
qcd_printf(opt,"%-10s= %d\n","dof",fit_data_get_dof(d));
qcd_printf(opt,"%-10s= %e\n","chi^2/dof",fit_data_get_chi2pdof(d));
if (opt->do_save_rs_sample)
{
sprintf(latan_path,"%s_pseudosc_fit%s_%s.boot:%s_pseudosc_fit%s_%s",\
opt->quark[0],range_info,manf_name,opt->quark[0],\
range_info,manf_name);
rs_sample_save_subsamp(latan_path,'w',s_fit,0,0,1,0);
}
}
/** ...or fit range scanning **/
else
{
qcd_printf(opt,"\n%-5s %-12s a*M_%-8s %-12s","ti/a","chi^2/dof",\
opt->quark[0],"error");
for (i=tibeg;i<range[1]-1;i++)
{
latan_set_warn(false);
rs_data_fit(s_fit,limit,NULL,s_mprop,d,NO_COR,NULL);
latan_set_warn(true);
rs_data_fit(s_fit,limit,NULL,s_mprop,d,opt->corr,NULL);
rs_sample_varp(sigfit,s_fit);
mat_eqsqrt(sigfit);
mat_set(scanres_t,i-tibeg,0,(double)(i));
mat_set(scanres_chi2,i-tibeg,0,fit_data_get_chi2pdof(d));
mat_set(scanres_mass,i-tibeg,0,mat_get(fit,0,0));
mat_set(scanres_masserr,i-tibeg,0,mat_get(sigfit,0,0));
qcd_printf(opt,"\n% -4d % -.5e % -.5e % -.5e",(int)(i),\
fit_data_get_chi2pdof(d),mat_get(fit,0,0), \
mat_get(sigfit,0,0));
fit_data_fit_point(d,i,false);
}
qcd_printf(opt,"\n\n");
}
/* plot */
/********************************************/
if (opt->do_plot)
{
mat *mbuf,*em_i,*sigem_i,*par,*ft[3],*comp[3];
plot *p;
strbuf key,dirname,color;
size_t maxt,t,npoint;
double dmaxt,nmass;
mbuf = mat_create(1,1);
em_i = mat_create(nrow(em[PP]),1);
sigem_i = mat_create(nrow(em[PP]),1);
par = mat_create(2,1);
if (!opt->do_range_scan)
{
maxt = nt;
dmaxt = (double)maxt;
npoint = fit_data_fit_point_num(d);
/** chi^2 plot **/
p = plot_create();
i = 0;
for (c=PP;c<=lastc;c++)
{
ft[c] = mat_create(npoint,1);
comp[c] = mat_create(npoint,1);
for (t=0;t<nt;t++)
{
if (fit_data_is_fit_point(d,t))
{
mat_set(ft[c],i%npoint,0,(double)(t)+0.33*(double)(c));
mat_set(comp[c],i%npoint,0,mat_get(d->chi2_comp,i,0));
i++;
}
}
}
plot_set_scale_manual(p,-1.0,dmaxt,-5.0,5.0);
plot_add_plot(p,"0.0 lt -1 lc rgb 'black' notitle","");
plot_add_plot(p,"1.0 lt -1 lc rgb 'black' notitle","");
plot_add_plot(p,"-1.0 lt -1 lc rgb 'black' notitle","");
plot_add_plot(p,"2.0 lt -1 lc rgb 'dark-gray' notitle","");
plot_add_plot(p,"-2.0 lt -1 lc rgb 'dark-gray' notitle","");
plot_add_plot(p,"3.0 lt -1 lc rgb 'gray' notitle","");
plot_add_plot(p,"-3.0 lt -1 lc rgb 'gray' notitle","");
plot_add_plot(p,"4.0 lt -1 lc rgb 'light-gray' notitle","");
plot_add_plot(p,"-4.0 lt -1 lc rgb 'light-gray' notitle","");
plot_set_ylabel(p,"standard deviations");
for (c=PP;c<=lastc;c++)
{
sprintf(color,"%d",(int)(c)+1);
plot_add_points(p,ft[c],comp[c],c_name[c],color,"impulses");
}
plot_disp(p);
if (opt->do_save_plot)
{
sprintf(dirname,"%s_dev",opt->save_plot_dir);
plot_save(dirname,p);
}
plot_destroy(p);
for (c=PP;c<=lastc;c++)
{
/** propagator plot **/
p = plot_create();
fit_data_fit_all_points(d,true);
plot_set_scale_ylog(p);
plot_set_scale_xmanual(p,0,dmaxt);
sprintf(key,"%s %s propagator",opt->quark[0],c_name[c]);
mat_eqabs(mprop[c]);
plot_add_fit(p,d,c,mbuf,0,fit,0,dmaxt,1000,false,\
PF_FIT|PF_DATA,key,"","rgb 'red'","rgb 'red'");
plot_disp(p);
if (opt->do_save_plot)
{
sprintf(dirname,"%s_prop_%s",opt->save_plot_dir,c_name[c]);
plot_save(dirname,p);
}
plot_destroy(p);
/** effective mass plot **/
p = plot_create();
mat_eqmuls(em[c],1.0/latspac_nu);
mat_eqmuls(sigem[c],1.0/latspac_nu);
nmass = mat_get(fit,0,0)/latspac_nu;
plot_add_hlineerr(p,nmass, mat_get(sigfit,0,0)/latspac_nu,\
"rgb 'red'");
sprintf(key,"%s %s effective mass",opt->quark[0],c_name[c]);
plot_add_dat(p,tem,em[c],NULL,sigem[c],key,"rgb 'blue'");
plot_disp(p);
if (opt->do_save_plot)
{
sprintf(dirname,"%s_em_%s",opt->save_plot_dir,c_name[c]);
plot_save(dirname,p);
}
plot_destroy(p);
}
}
else
{
/* chi^2 plot */
p = plot_create();
plot_set_scale_manual(p,0,(double)(nt/2),0,5.0);
plot_add_hline(p,1.0,"rgb 'black'");
plot_add_dat(p,scanres_t,scanres_chi2,NULL,NULL,"chi^2/dof",\
"rgb 'blue'");
plot_disp(p);
if (opt->do_save_plot)
{
sprintf(dirname,"%s_chi2",opt->save_plot_dir);
plot_save(dirname,p);
}
plot_destroy(p);
/* mass plot */
p = plot_create();
plot_set_scale_xmanual(p,0,(double)(nt/2));
sprintf(key,"a*M_%s",opt->quark[0]);
plot_add_dat(p,scanres_t,scanres_mass,NULL,scanres_masserr,key,\
"rgb 'red'");
plot_disp(p);
if (opt->do_save_plot)
{
sprintf(dirname,"%s_mass",opt->save_plot_dir);
plot_save(dirname,p);
}
plot_destroy(p);
}
mat_destroy(em_i);
mat_destroy(sigem_i);
mat_destroy(mbuf);
mat_destroy(par);
for (c=PP;c<=lastc;c++)
{
mat_destroy(ft[c]);
mat_destroy(comp[c]);
}
}
/* desallocation */
/********************************************/
free(opt);
io_finish();
mat_ar_destroy(prop[0],nbdat);
mat_ar_destroy(prop[1],nbdat);
for (c=PP;c<=lastc;c++)
{
rs_sample_destroy(s_mprop[c]);
mat_destroy(sigmprop[c]);
rs_sample_destroy(s_effmass[c]);
mat_destroy(sigem[c]);
}
mat_destroy(tem);
fit_data_destroy(d);
rs_sample_destroy(s_fit);
mat_destroy(limit);
mat_destroy(sigfit);
mat_destroy(scanres_t);
mat_destroy(scanres_chi2);
mat_destroy(scanres_mass);
mat_destroy(scanres_masserr);
return EXIT_SUCCESS;
}
/**
* Main FastICA function. Centers and whitens the input
* matrix, calls the ICA computation function ICA_compute()
* and computes the output matrixes.
*/
void fastICA(mat X, int rows, int cols, int compc, mat K, mat W, mat A, mat S) {
mat XT, V, TU, D, X1, _A;
vect scale, d;
clock_t clock1, clock2;
float time;
//char ascii_path[512];
//strcpy(ascii_path, "/storage/sdcard0/NickGun/EEG/Log.txt");
//FILE *Log;
//chu thich voi truong hop 14 kenh, 2s (256mau) du lieu, 14 thanh phan doc lap>>> cols = 14, rows = 256, compc = 14
// matrix creation
XT = mat_create(cols, rows); //14x256
X1 = mat_create(compc, rows); //14x256
V = mat_create(cols, cols); //14x14
D = mat_create(cols, cols); //14x14
TU = mat_create(cols, cols); //14x14
scale = vect_create(cols); //14
d = vect_create(cols); //14
clock1 = clock();
/*
* CENTERING
*/
mat_center(X, rows, cols, scale); //tru di gia tri trung binh cua moi cot
clock2 = clock();
time = (clock2 - clock1) / CLOCKS_PER_SEC;
//Log = fopen(ascii_path, "wb");
//fprintf(Log, "CENTERING %f \n", time);
//fclose(Log);
clock1 = clock();
/*
* WHITENING
*/
// X <- t(X); V <- X %*% t(X)/rows
mat_transpose(X, rows, cols, XT); //XT la chuyen vi cua ma tran X[256][14] >>> XT[14][256]
mat_apply_fx(X, rows, cols, fx_div_c, rows); //lay tung gia tri cua X[i][j] chia cho 14
mat_mult(XT, cols, rows, X, rows, cols, V); //V=XT*X >>>V[14][14]
// La.svd(V)
svdcmp(V, cols, cols, d, D); // V = s$u, d = s$d, D = s$v
// D <- diag(c(1/sqrt(d))
vect_apply_fx(d, cols, fx_inv_sqrt, 0);
mat_diag(d, cols, D);
// K <- D %*% t(U)
mat_transpose(V, cols, cols, TU);
mat_mult(D, cols, cols, TU, cols, cols, V); // K = V
// X1 <- K %*% X
mat_mult(V, compc, cols, XT, cols, rows, X1);
clock2 = clock();
time = (clock2 - clock1) / CLOCKS_PER_SEC;
//Log = fopen(ascii_path, "at");
//fprintf(Log, "WHITENING %f \n", time);
//fclose(Log);
clock1 = clock();
/*
* FAST ICA
*/
_A = ICA_compute(X1, compc, rows);
clock2 = clock();
time = (clock2 - clock1) / CLOCKS_PER_SEC;
//Log = fopen(ascii_path, "at");
//fprintf(Log, "FASTICA %f \n", time);
//fclose(Log);
clock1 = clock();
/*
* OUTPUT
*/
// X <- t(x)
mat_transpose(XT, cols, rows, X);
mat_decenter(X, rows, cols, scale);
// K
mat_transpose(V, compc, cols, K);
// w <- a %*% K; S <- w %*% X
mat_mult(_A, compc, compc, V, compc, cols, D);
mat_mult(D, compc, cols, XT, cols, rows, X1);
// S
mat_transpose(X1, compc, rows, S);
// A <- t(w) %*% solve(w * t(w))
mat_transpose(D, compc, compc, TU);
mat_mult(D, compc, compc, TU, compc, compc, V);
mat_inverse(V, compc, D); //ham nay tinh mat tran ngich dao
mat_mult(TU, compc, compc, D, compc, compc, V);
// A
mat_transpose(V, compc, compc, A);
// W
mat_transpose(_A, compc, compc, W);
// cleanup
mat_delete(XT, cols, rows);
mat_delete(X1, compc, rows);
mat_delete(V, cols, cols);
mat_delete(D, cols, cols);
mat_delete(TU, cols, cols);
vect_delete(scale);
vect_delete(d);
clock2 = clock();
time = (clock2 - clock1) / CLOCKS_PER_SEC;
//Log = fopen(ascii_path, "at");
//fprintf(Log, "OUTPUT %f \n", time);
//fclose(Log);
}
