TEST(testEndToEnd,checkIdeal){
pulsar _psr;
pulsar *psr = &_psr;
MAX_PSR=1;
char timFile[MAX_PSR][MAX_FILELEN],parFile[MAX_PSR][MAX_FILELEN];
char** argv=NULL;
int npsr=1;
initialise(psr,0); /* Initialise all */
strcpy(parFile[0],DATDIR "/test3.par");
strcpy(timFile[0],DATDIR "/test3.tim");
readParfile(psr,parFile,timFile,npsr);
readTimfile(psr,timFile,npsr);
preProcessSimple(psr);
psr->noWarnings=2;
formBatsAll(psr,npsr);
formResiduals(psr,npsr,0);
for(int iobs = 0; iobs < psr->nobs; iobs++){
ASSERT_LT(static_cast<double>(fabsl(psr->obsn[iobs].residual)),TEST_DELTA) << DATDIR "/test3.par test3.tim do not give idealised ToAs";
}
doFitAll(psr,npsr,"NULL");
formBatsAll(psr,npsr);
formResiduals(psr,npsr,0);
for(int iobs = 0; iobs < psr->nobs; iobs++){
ASSERT_LT(static_cast<double>(fabsl(psr->obsn[iobs].residual)),TEST_DELTA) << "Fitting has caused error in ideal";
}
}
TEST(testEndToEnd,gracefulBadFit){
pulsar _psr;
pulsar *psr = &_psr;
MAX_PSR=1;
char timFile[MAX_PSR][MAX_FILELEN],parFile[MAX_PSR][MAX_FILELEN];
char** argv=NULL;
int npsr=1;
initialise(psr,0); /* Initialise all */
strcpy(parFile[0],DATDIR "/test3c.par");
strcpy(timFile[0],DATDIR "/test3.tim");
readParfile(psr,parFile,timFile,npsr);
readTimfile(psr,timFile,npsr);
preProcessSimple(psr);
psr->noWarnings=2;
formBatsAll(psr,npsr);
formResiduals(psr,npsr,0);
TK_errorCount=0;
doFitAll(psr,npsr,"NULL");
// ASSERT_GT(TK_errorCount,1u);
ASSERT_EQ(1,1);
TK_errorCount=0;
}
void callFit(pulsar *psr,int npsr)
{
int iteration;
double globalParameter = 0.0;
for (iteration=0;iteration<2;iteration++)
{
formBatsAll(psr,npsr);
formResiduals(psr,npsr,1);
/* Do the fitting */
if (iteration==0) doFitAll(psr,npsr,covarFuncFile2);
else textOutput(psr,npsr,globalParameter,0,0,0,"");
}
}
/* The main function has to be called this, even if no
* graphics are involved ;)
*/
extern "C" int graphicalInterface(int argc, char *argv[],
pulsar *psr, int *npsr)
{
char parFile[MAX_PSR][MAX_FILELEN];
char timFile[MAX_PSR][MAX_FILELEN];
*npsr = 1; // Necessary, I guess?
printf("Chi2 grid plugin for tempo2\n");
printf("Author: Paul Demorest\n");
printf("Version: 0.0\n");
parFile[0][0]='\0';
timFile[0][0]='\0';
// Parse command line.. there has to be a better way to do this..
double m2_min = 0.0, m2_max = 2.0;
double sini_min = 0.5, sini_max = 1.0;
int m2_steps = 128, sini_steps = 128;
for (unsigned i=1; i<argc; i++) {
if (strcmp(argv[i], "-f")==0) {
strcpy(parFile[0], argv[i+1]);
strcpy(timFile[0], argv[i+2]);
} else if (strcmp(argv[i], "-sini_min")==0) {
sini_min = atof(argv[i+1]);
} else if (strcmp(argv[i], "-sini_max")==0) {
sini_max = atof(argv[i+1]);
} else if (strcmp(argv[i], "-sini_steps")==0) {
sini_steps = atoi(argv[i+1]);
} else if (strcmp(argv[i], "-m2_min")==0) {
m2_min = atof(argv[i+1]);
} else if (strcmp(argv[i], "-m2_max")==0) {
m2_max = atof(argv[i+1]);
} else if (strcmp(argv[i], "-m2_steps")==0) {
m2_steps = atoi(argv[i+1]);
}
}
if (parFile[0][0]=='\0' || timFile[0][0]=='\0') {
fprintf(stderr, "Please provide .par and .tim files using -f\n");
fprintf(stderr, "Optional arguments:\n");
fprintf(stderr, " -sini_min N Minimum sin(i) value (0.5)\n");
fprintf(stderr, " -sini_max N Maximum sin(i) value (1.0)\n");
fprintf(stderr, " -sini_steps N Number of sin(i) steps (128)\n");
fprintf(stderr, " -m2_min N Minimum m2 value (0.0)\n");
fprintf(stderr, " -m2_max N Maximum m2 value (2.0)\n");
fprintf(stderr, " -m2_steps N Number of m2 steps (128)\n");
exit(1);
}
// Read the stuff
readParfile(psr, parFile, timFile, *npsr);
readTimfile(psr, timFile, *npsr);
preProcess(psr, *npsr, argc, argv);
// Do an initial fit to get best-fit params to use as a starting
// place.
formBatsAll(psr, *npsr);
formResiduals(psr, *npsr, 0); // Final arg is "removeMean"
doFit(psr, *npsr, 0); // Final arg is "writeModel"
formBatsAll(psr, *npsr); // Run these again to get post-fit
formResiduals(psr, *npsr, 0); // residuals.
// Get initial chi2, etc.
double init_chi2 = psr_chi2(psr);
// step size, etc
double delta_m2 = (m2_max - m2_min)/(double)m2_steps;
double delta_sini = (sini_max - sini_min)/(double)sini_steps;
// Store current parameters in psr[1], trial params in psr[0]
store_params(psr);
// Print header lines
printf("# chi2_0=%.5e\n", init_chi2);
printf("# SINI M2 chi2-chi2_0\n");
// Main iteration loop
signal(SIGINT, cc);
double cur_m2, cur_sini, cur_chi2;
for (cur_sini=sini_min; cur_sini<sini_max; cur_sini+=delta_sini) {
for (cur_m2=m2_min; cur_m2<m2_max; cur_m2+=delta_m2) {
reset_params(psr);
psr[0].param[param_sini].val[0] = cur_sini;
psr[0].param[param_sini].paramSet[0] = 1;
psr[0].param[param_m2].val[0] = cur_m2;
psr[0].param[param_m2].paramSet[0] = 1;
// updateBats or FormBats?
int ok=1;
updateBatsAll(psr, *npsr);
try {
formResiduals(psr, *npsr, 0);
doFit(psr, *npsr, 0);
} catch (int e) {
// Note, this is a hack to ignore spots in
// M2-sini parameter space where the fit does not
// converge. Plain tempo2 exit()'s here, killing
// the whole process. I've modified my copy to
// throw an error instead so we can continue on
// with the gridding.
if (e==5) { ok=0; }
}
if (ok) {
updateBatsAll(psr, *npsr);
formResiduals(psr, *npsr, 0);
cur_chi2 = psr_chi2(psr);
} else {
cur_chi2 = 1e6;
}
printf("%.9f %.5f %.10e\n", cur_sini, cur_m2, cur_chi2-init_chi2);
if (run==0) break;
}
if (run==0) break;
}
}
extern "C" int graphicalInterface(int argc,char *argv[],pulsar *psr,int *npsr)
{
char parFile[MAX_PSR][MAX_FILELEN];
char timFile[MAX_PSR][MAX_FILELEN];
int i,nit,j,p;
char fname[MAX_FILELEN];
double globalParameter;
long double result;
long seed = TKsetSeed();
//
// For the output file
//
toasim_header_t* header;
toasim_header_t* read_header;
FILE* file;
double offsets[MAX_OBSN]; // Will change to doubles - should use malloc
char incdm=0; // include the dm error?
// Create a set of corrections.
toasim_corrections_t* corr = (toasim_corrections_t*)malloc(sizeof(toasim_corrections_t));
corr->offsets=offsets;
corr->params=""; // Normally leave as NULL. Can store this along with each realisation.
// Same length string in every iteration - defined in r_param_length see below
corr->a0=0; // constant
corr->a1=0; // a1*x
corr->a2=0; // a2*x*X
*npsr = 0;
nit = 1;
printf("Graphical Interface: addGaussian\n");
printf("Author: G. Hobbs, M. Keith\n");
printf("Version: 1.0\n");
/* Obtain all parameters from the command line */
for (i=2;i<argc;i++)
{
if (strcmp(argv[i],"-incdm")==0){
incdm=1;
printf("NOTICE: Including DM error in white noise\n");
}
if (strcmp(argv[i],"-nreal")==0){
nit=atoi(argv[++i]);
}
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[++i]);
strcpy(timFile[*npsr],argv[++i]);
(*npsr)++;
}
}
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// Now read in all the .tim files
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
if(incdm){
preProcess(psr,*npsr,argc,argv);
formBatsAll(psr,*npsr);
}
for (p=0;p<*npsr;p++)
{
if(incdm)updateDMvals(psr,p);
printf("NTOA = %d\n",psr[p].nobs);
header = toasim_init_header();
strcpy(header->short_desc,"addGaussian");
strcpy(header->invocation,argv[0]);
strcpy(header->timfile_name,timFile[p]);
strcpy(header->parfile_name,"Unknown");
header->idealised_toas="NotSet"; // What should this be
header->orig_parfile="NA";
header->gparam_desc=""; // Global parameters
header->gparam_vals="";
header->rparam_desc=""; // Desciprtion of the parameters
header->rparam_len=0; // Size of the string
header->seed = seed;
header->ntoa = psr[p].nobs;
header->nrealisations = nit;
// First we write the header...
sprintf(fname,"%s.addGauss",timFile[p]);
file = toasim_write_header(header,fname);
for (i=0;i<nit;i++)
{
if(i%10 == 0){
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("Iteration %d/%d",i+1,nit);
fflush(stdout);
}
for (j=0;j<psr[p].nobs;j++)
if(incdm)
offsets[j] = (double)(psr[p].obsn[j].toaErr*1.0e-6*TKgaussDev(&seed));
else
offsets[j] = (double)(psr[p].obsn[j].origErr*1.0e-6*TKgaussDev(&seed));
toasim_write_corrections(corr,header,file);
}
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("Iteration %d/%d\n",i,nit);
printf("Close file\n");
fclose(file);
}
return 0;
}
void polyco(pulsar *psr,int npsr,longdouble polyco_MJD1,longdouble polyco_MJD2,int nspan,int ncoeff,
longdouble maxha,char *sitename,longdouble freq,longdouble coeff[MAX_COEFF],int trueDM,char* polyco_file)
{
longdouble tsid = 1.0L/1.002737909L;
longdouble tmidMJD;
double doppler,rms;
int dspan;
char binPhase[32];
int i;
longdouble afmjd;
longdouble val[800];
char date[12];
longdouble tmin[800];
double globalParameter,utc;
int nsets;
const char *CVS_verNum = "$Revision: 1.8 $";
/* buffers for three polyco outputs -- any input from the user is
* prepended to the default file names */
char fname1[256];
char fname2[256];
char fname3[256];
strcpy(fname1,polyco_file);
strcpy(fname2,polyco_file);
strcpy(fname3,polyco_file);
strcat(fname1,"polyco_new.dat");
strcat(fname2,"newpolyco.dat");
strcat(fname3,"polyco.tim");
/* erase any existing files */
fclose(fopen(fname1,"w"));
fclose(fopen(fname2,"w"));
/* special flag for barycenter polycos */
bool bary = strcmp(sitename,"@")==0 || strcasecmp(sitename,"bat")==0;
if (displayCVSversion == 1) CVSdisplayVersion("polyco.C","polyco()",CVS_verNum);
binPhase[0]='\0';
/* Set some defaults */
psr[0].param[param_track].paramSet[0]=0;
globalParameter=0;
// Zap the output files so we can append days to them later
fclose(fopen("polyco_new.dat","w"));
fclose(fopen("newpolyco.dat","w"));
for (afmjd=polyco_MJD1; afmjd <= polyco_MJD2; afmjd+=tsid)
{
/* Create some arrival times spread throughout the day */
atimfake(psr,npsr,nspan,ncoeff,maxha,sitename,freq,afmjd,tmin,&tmidMJD,&dspan,&nsets,val);
for (i=0;i<psr[0].nobs;i++)
{
psr->obsn[i].clockCorr=(!bary);
psr->obsn[i].delayCorr=(!bary);
psr->obsn[i].phaseOffset = 0.0;
}
/* Use reference phase TZR information unless at bary.*/
if (strcmp(psr->tzrsite,"@")!=0) {
psr->obsn[0].clockCorr=1;
psr->obsn[0].delayCorr=1;
}
else {
psr->obsn[0].clockCorr=0;
psr->obsn[0].delayCorr=0;
}
writeTim(fname3,psr,"tempo2");
formBatsAll(psr,npsr);
formResiduals(psr,npsr,0);
tzFit(psr,npsr,tmin,&doppler,&rms,&utc,tmidMJD,ncoeff,coeff,binPhase,nsets,afmjd,sitename,nspan,
freq,date,val,trueDM,polyco_file);
}
if (psr->tempo1==0)
printf("WARNING: Should probably use -tempo1 option\n");
}
extern "C" int pluginFitFunc(pulsar *psr,int npsr,int writeModel)
{
int p,i,k,j;
int count=0;
int flags[MAX_PSR];
longdouble* preobs[MAX_PSR];
printf(" <DMMODEL> Reset DM component of error to 0\n");
for (p=0; p < npsr; p++){
if (psr[p].param[param_dmmodel].fitFlag[0]==1){
flags[p]=1;
count++;
for(i=0; i < psr[p].nobs; i++){
psr[p].obsn[i].toaErr=psr[p].obsn[i].origErr;
psr[p].obsn[i].toaDMErr=0;
}
} else flags[p]=0;
}
strcpy(psr[0].fitFunc,"default");
printf(" <DMMODEL> First fit...\n");
if (strcmp(dcmFile,"NULL")==0 && strcmp(covarFuncFile,"NULL")==0)
doFit(psr,npsr,writeModel);
else
doFitDCM(psr,dcmFile,covarFuncFile,npsr,0);
for (p=0; p < npsr; p++){
char** labels = (char**)malloc(sizeof(char*)*MAX_PARAMS);
for (i=0;i<MAX_PARAMS;i++){
labels[i]= (char*)malloc(80);
strcpy(labels[i],"UNK_PARAM");
}
getFitLabels(psr,p,labels);
double** cvm=psr[p].covar;
int npol = psr[p].nFit - psr[p].fitNfree;
bool warn=false;
for (i=0;i<npol;i++){
for (j=0;j<i;j++){
double cv=fabs(cvm[i][j]/sqrt((cvm[j][j])*(cvm[i][i])));
if(cv > 0.5){
if(!warn){
printf(" <DMMODEL> Warning: highly covariant parameters in fit!\n");
warn=true;
}
printf(" % 15s % 15s %lg\n",labels[i],labels[j],cv);
}
}
}
for (i=0;i<MAX_PARAMS;i++)free(labels[i]);
free(labels);
}
if(count){
printf(" <DMMODEL> Disable DMMODEL\n");
// we also save the pre-fit residuals so it appears as if only one fit has happened
for (p=0; p < npsr; p++){
preobs[p] = (longdouble*)malloc(sizeof(longdouble)*psr[p].nobs);
for(i=0; i < psr[p].nobs; i++){
preobs[p][i]=psr[p].obsn[i].prefitResidual;
}
psr[p].param[param_dmmodel].fitFlag[0]=0;
}
formBatsAll(psr,npsr);
formResiduals(psr,npsr,0);
printf(" <DMMODEL> Second Fit...\n");
if (strcmp(dcmFile,"NULL")==0 && strcmp(covarFuncFile,"NULL")==0)
doFit(psr,npsr,writeModel);
else
doFitDCM(psr,dcmFile,covarFuncFile,npsr,0);
printf(" <DMMODEL> Enable DMMODEL\n");
for (p=0; p < npsr; p++){
psr[p].param[param_dmmodel].fitFlag[0]=flags[p];
// restore the pre-fit residuals
for(i=0; i < psr[p].nobs; i++){
psr[p].obsn[i].prefitResidual=preobs[p][i];
}
}
}
strcpy(psr[0].fitFunc,"dmmodel");
return 0;
}
