void TKfit_getPulsarDesignMatrix(double *x,double *y,int n,int nf,void (*fitFuncs)(double, double [], int,pulsar *,int,int), pulsar *psr, int* ip, double **uinv,int ipsr,double ***OUT_designMatrix,double ***OUT_white_designMatrix,double** OUT_b, double** OUT_wb){
//double precision arrays for matrix algebra.
double **designMatrix, **white_designMatrix;
double basisFunc[nf];
double *b,*white_b;
int i,j;
int nrows=get_blas_rows(uinv);
int ncols=get_blas_cols(uinv);
if (ncols!=n){
logmsg("n=%d ncols=%d",n,ncols);
logerr("uinv error. Either you did not use malloc_uinv() to create uinv or np!=ncols");
exit(1);
}
if (nrows!=n && nrows != 1){
logmsg("n=%d nrows=%d",n,nrows);
logerr("uinv error. Either you did not use malloc_uinv() to create uinv or np!=nrows");
exit(1);
}
// double arrays
white_designMatrix=malloc_blas(n,nf);
designMatrix=malloc_blas(n,nf);
b=(double*)malloc(sizeof(double)*n);
white_b=(double*)malloc(sizeof(double)*n);
/* This routine has been developed from Section 15 in Numerical Recipes */
/* Determine the design matrix - eq 15.4.4
* and the vector 'b' - eq 15.4.5
*/
for (i=0;i<n;i++)
{
// fitFuncs is not threadsafe!
fitFuncs(x[i],basisFunc,nf,psr,ip[i],ipsr);
for (j=0;j<nf;j++) designMatrix[i][j] = basisFunc[j];
b[i] = y[i];
}
// Take into account the data covariance matrix
if(nrows==1){
// we have only diagonal elements
for (i=0;i<n;i++){
white_b[i]=b[i]*uinv[0][i];
for (j=0;j<nf;j++){
white_designMatrix[i][j] = designMatrix[i][j]*uinv[0][i];
}
}
} else {
TKmultMatrix_sq(uinv,designMatrix,n,nf,white_designMatrix);
TKmultMatrixVec_sq(uinv,b,n,white_b);
}
*OUT_designMatrix=designMatrix;
*OUT_white_designMatrix=white_designMatrix;
*OUT_b=b;
*OUT_wb=white_b;
}
/*
* Derive a covariance matrix from the given filename.
*
* input:
* univ (double[np][np] empty matrix that will be filled with the "Cholesky matrix"
* fname (char[*]) Input filename to read
* psr (*pulsar) pointer to pulsar structure that univ is used for
* resx (double[np]) X values of residuals (+ 0 for constraints)
* resy (double[np]) Y values of residuals (+ 0 for constraints)
* rese (double[np]) Error on residuals (+ eta for constraints)
* np (int) Number of data points in fit (nres+nc)
* nc (int) Number of constraints in fit
* ip (int) Mapping from fit point to observation number in pulsar struct.
*/
void getCholeskyMatrix(double **uinv, char* fname, pulsar *psr, double *resx,double *resy,double *rese, int np, int nc,int* ip){
FILE* modelDescriptionFile;
char modelFileName[1024];
char tmp[1024];
double **m;
int i,j;
int nrows=get_blas_rows(uinv);
int ncols=get_blas_cols(uinv);
if (ncols!=np){
logmsg("np=%d ncols=%d",ncols,np);
logerr("uinv error. Either you did not use malloc_uinv() to create uinv or np!=ncols");
exit(1);
}
if (nrows==1){
// we are just adding the errors to a diagonal matrix.
getCholeskyDiagonals(uinv,psr,resx,resy, rese, np, nc,ip);
return;
}
if (nrows!=np){
logmsg("np=%d nrows=%d",ncols,np);
logerr("uinv error. Either you did not use malloc_uinv() to create uinv or np!=nrows");
exit(1);
}
if(uinv[np-1] != uinv[0]+(np-1)*np){
logerr("uinv matrix not declared as consecutive memory.");
logmsg("Please use malloc_uinv() and free_uinv() from cholesky.C");
#ifdef ACCEL_UINV
// if we are using the accelerated code then it will crash... otherwise it's just a warning
exit(1);
#endif
}
logmsg("Reading Cholesky model '%s' for pulsar %s",fname,psr->name);
m=(double**)malloc(sizeof(double*)*(np+1));
if(!m)logerr("Could not allocate enough memory");
for(i=0;i<np+1;i++){
m[i]=(double*)malloc(sizeof(double)*(np+1));
if(!m[i])logerr("Could not allocate enough memory");
}
if (strcmp(fname,"PSRJ")==0){
// this is the old method where the covariance function is read based on pulsar name.
// There is no model description file.
// This method is depricated
logdbg("Reading covariance function using 'PSRJ' is now depricated");
sprintf(modelFileName,"covarFunc.dat_%s",psr->name);
cholesky_readFromCovarianceFunction(m,modelFileName,resx,resy,rese,np,nc);
} else {
cholesky_readT2CholModel(m,fname,resx,resy,rese,np,nc,ip,psr);
}
if(psr->ToAextraCovar!=NULL){
logmsg("adding extra covar function to m");
for (i=0;i<np;i++)
{
for (j=0;j<np;j++){
m[i][j]+=psr->ToAextraCovar[i][j];
}
}
}
logdbg("mbefore = ");
for (i=0;i<5;i++)
{
for (j=0;j<5;j++) fprintf(LOG_OUTFILE,"%10g ",m[i][j]);
fprintf(LOG_OUTFILE,"\n");
}
fprintf(LOG_OUTFILE,"\n");
// make sure constraints are not covariant with anything.
logdbg("Ensuring constraints have zero co-variance, np = %d, nc = %d",np,nc);
for (i=np-nc; i < np; i++){
for (j=0; j < np; j++){
m[i][j]=0;
m[j][i]=0;
}
}
logdbg("Adding errors");
for(i=0;i<np;i++){
m[i][i]+=rese[i]*rese[i];
}
if (debugFlag)
{
logdbg("m = ");
for (i=0;i<5;i++)
{
for (j=0;j<5;j++) fprintf(LOG_OUTFILE,"%10g ",m[i][j]);
fprintf(LOG_OUTFILE,"\n");
}
fprintf(LOG_OUTFILE,"\n");
FILE* mFile = fopen("chol.covarMatrix","w");
for (i=0;i<np;i++)
{
for (j=0;j<np;j++) fprintf(mFile,"%d %d %g\n",i,j,m[i][j]);
fprintf(mFile,"\n");
}
fclose(mFile);
}
logdbg("Form uinv from cholesky matrix 'm'");
int ret = cholesky_formUinv(uinv,m,np);
if (ret!=0) {
logerr("Error with formUinv");
exit(ret);
}
for(i=0;i<np+1;i++)free(m[i]);
free(m);
}