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;
}
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";
}
}
/* 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];
double epochs[MAX_OBSN];
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
double mean=0.0;
// Create a set of corrections.
toasim_corrections_t* corr = (toasim_corrections_t*)malloc(sizeof(toasim_corrections_t));
double f1_1;
double f1_2;
double t0 = 0;
double t;
double phaseStart=0;
double phase0=0;
double f0;
double phase;
double nudot;
double nu;
int nStep;
double stepTime[MAX_STEP];
int sw;
int nSwitch;
double nu0,initialT,nudot_now;
double nuSwitch[MAX_STEP+1];
double fa,fb;
double deltaT;
int ii;
nStep = 0;
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: add2state\n");
printf("Author: G. Hobbs\n");
printf("Version: 1.0\n");
/* Obtain all parameters from the command line */
for (i=2;i<argc;i++)
{
if (strcmp(argv[i],"-nreal")==0){
nit=atoi(argv[++i]);
}
if (strcmp(argv[i],"-step")==0){
sscanf(argv[++i],"%lf",&stepTime[nStep]);
nStep++;
}
if (strcmp(argv[i],"-fa")==0){
sscanf(argv[++i],"%lf",&f1_1);
}
if (strcmp(argv[i],"-fb")==0){
sscanf(argv[++i],"%lf",&f1_2);
}
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[++i]);
strcpy(timFile[*npsr],argv[++i]);
(*npsr)++;
}
if (strcmp(argv[i],"-seed")==0){
sscanf(argv[++i],"%d",&seed);
}
}
if (seed > 0)seed=-seed;
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// Now read in all the .tim files
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
preProcess(psr,*npsr,argc,argv);
for (p=0;p<*npsr;p++)
{
f0 = (double)psr[p].param[param_f].val[0];
printf("NTOA = %d\n",psr[p].nobs);
header = toasim_init_header();
strcpy(header->short_desc,"add2state");
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.add2state",timFile[p]);
file = toasim_write_header(header,fname);
for (i=0;i<nit;i++)
{
mean=0;
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);
}
t0 = (double)psr[p].obsn[0].sat;
for (j=0;j<psr[p].nobs;j++)
{
t= (psr[p].obsn[j].sat-t0)*86400.0;
// Calculate nudot at time t
sw=1;
for (ii=0;ii<nStep;ii++)
{
if (psr[p].obsn[j].sat > stepTime[ii])
sw*=-1;
}
if (sw == 1)
nudot = f1_1;
else
nudot = f1_2;
// Calculate nu at time t
// Integrate from time t0 to the current time
// Find necessary number of switches
nSwitch=0;
for (ii=0;ii<nStep;ii++)
{
if (stepTime[ii] < psr[p].obsn[j].sat) {nSwitch++;}
}
nu0 = f0;
initialT = t0;
nudot_now = f1_1;
sw=1;
nuSwitch[0] = nu0;
for (ii=0;ii<nSwitch;ii++)
{
nu0 = nu0 + nudot_now*(stepTime[ii]-initialT)*86400.0;
nuSwitch[ii+1] = nu0;
sw*=-1;
if (sw==1)
nudot_now = f1_1;
else
nudot_now = f1_2;
initialT = stepTime[ii];
}
// Now do the last bit
nu = nu0 + nudot_now*(psr[p].obsn[j].sat - initialT)*86400.0;
// Now calculate phase at time t
// Dealing with all the switches
phase = phaseStart;
fb = f0;
initialT = t0;
nudot_now = f1_1;
sw=1;
for (ii=0;ii<nSwitch;ii++)
{
fa = nuSwitch[ii];
fb = nuSwitch[ii+1];
if (ii>0)
deltaT = stepTime[ii]-stepTime[ii-1];
else
deltaT = stepTime[ii] - t0;
sw*=-1;
if (sw==1)
nudot_now = f1_1;
else
nudot_now = f1_2;
phase += (deltaT*86400.0*fb)+0.5*deltaT*86400.0*fabs(fa-fb);
initialT = stepTime[ii];
}
// Now do last bit
deltaT = (psr[p].obsn[j].sat-initialT)*86400.0;
fa = fb;
fb = fa+deltaT*nudot_now;
phase += fb*deltaT+0.5*deltaT*fabs(fa-fb);
// phase = phase - floor(phase);
printf("initial %g %g %d %.15f %.15f %g\n",(double)psr[p].obsn[j].sat,nudot,nSwitch,nu,phase,f0);
epochs[j] = (double)(psr[p].obsn[j].sat-psr[p].param[param_pepoch].val[0]);
offsets[j] = (double)(phase);
mean+=offsets[j];
}
for (j=0;j<psr[p].nobs;j++)
offsets[j]-=mean/(double)psr[p].nobs;
TKremovePoly_d(epochs,offsets,psr[p].nobs,3);
for (j=0;j<psr[p].nobs;j++)
printf("value = %g %.15f\n",epochs[j],offsets[j]);
// // printf("Error = %g\n",(double)psr[p].obsn[j].toaErr);
// }
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;
}
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
// 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],"-nreal")==0){
nit=atoi(argv[++i]);
}
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[++i]);
strcpy(timFile[*npsr],argv[++i]);
(*npsr)++;
}
if (strcmp(argv[i],"-seed")==0){
sscanf(argv[++i],"%d",&seed);
}
}
if (seed > 0)seed=-seed;
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// Now read in all the .tim files
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
preProcess(psr,*npsr,argc,argv);
for (p=0;p<*npsr;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++){
offsets[j] = (double)(psr[p].obsn[j].toaErr*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;
}
extern "C" int graphicalInterface(int argc,char *argv[],pulsar *psr,int *npsr)
{
char parFile[MAX_PSR][MAX_FILELEN];
char oparFile[MAX_PSR][MAX_FILELEN]; // Overlay files
char timFile[MAX_PSR][MAX_FILELEN];
char otimFile[MAX_PSR][MAX_FILELEN];
char tpar[MAX_PSR][MAX_FILELEN];
char ttim[MAX_PSR][MAX_FILELEN];
int i;
int plotUs=0;
float scale[1000];
int nScale=0;
char grDev[100]="/vps";
// char grDev[100]="/xs";
FILE *pin;
FILE *fin;
char str[1000];
float fontsize = 1.2;
float centreMJD=54500;
int ptStyle=16;
float ptSize = 1;
int reverse=0;
int error=1;
float miny=-1;
float maxy=-1;
float minx=-1;
float maxx=-1;
int nOverlay=0;
float labelsize=-1;
float fracX = 0.85;
*npsr = 0;
strcpy(covarFuncFile2,"NULL");
printf("Graphical Interface: plotMany\n");
printf("Author: George Hobbs\n");
printf("Version: 1.0\n");
/* Obtain the .par and the .tim file from the command line */
for (i=1;i<argc;i++)
{
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[i+1]);
strcpy(timFile[*npsr],argv[i+2]);
(*npsr)++;
if (*npsr > MAX_PSR)
{
printf("Error, npsr > MAX_PSR. Must increase MAX_PSR\n");
exit(1);
}
}
else if (strcmp(argv[i],"-overlay")==0)
sscanf(argv[i+1],"%d",&nOverlay);
else if (strcmp(argv[i],"-dcf")==0){
strcpy(covarFuncFile2,argv[++i]);
}
else if (strcmp(argv[i],"-g")==0)
strcpy(grDev,argv[++i]);
else if (strcmp(argv[i],"-h")==0)
help();
else if (strcmp(argv[i],"-scale")==0)
{
sscanf(argv[i+1],"%f",&scale[nScale]);
nScale++;
}
else if (strcmp(argv[i],"-fontsize")==0)
sscanf(argv[i+1],"%f",&fontsize);
else if (strcasecmp(argv[i],"-fracX")==0)
sscanf(argv[i+1],"%f",&fracX);
else if (strcasecmp(argv[i],"-labelSize")==0)
sscanf(argv[i+1],"%f",&labelsize);
else if (strcmp(argv[i],"-ptstyle")==0)
sscanf(argv[i+1],"%d",&ptStyle);
else if (strcmp(argv[i],"-ptsize")==0)
sscanf(argv[i+1],"%f",&ptSize);
else if (strcmp(argv[i],"-miny")==0)
sscanf(argv[i+1],"%f",&miny);
else if (strcmp(argv[i],"-maxy")==0)
sscanf(argv[i+1],"%f",&maxy);
else if (strcmp(argv[i],"-minx")==0)
sscanf(argv[i+1],"%f",&minx);
else if (strcmp(argv[i],"-maxx")==0)
sscanf(argv[i+1],"%f",&maxx);
else if (strcmp(argv[i],"-reverse")==0)
reverse=1;
else if (strcmp(argv[i],"-centremjd")==0)
sscanf(argv[i+1],"%f",¢reMJD);
else if (strcmp(argv[i],"-plotus")==0)
plotUs=1;
else if (strcmp(argv[i],"-noerror")==0)
error=0;
}
if (*npsr==0) /* Select all files */
{
printf("Using all available .par and .tim files\n");
sprintf(str,"ls `ls *.par | sed s/par/tim/` | sed s/.tim/\"\"/");
pin = popen(str,"r");
while (!feof(pin))
{
if (fscanf(pin,"%s",str)==1)
{
sprintf(parFile[*npsr],"%s.par",str);
sprintf(timFile[*npsr],"%s.tim",str);
(*npsr)++;
}
}
pclose(pin);
printf("Obtained files for %d pulsars\n",*npsr);
}
if (reverse==1) // Reverse order of .par and .tim files
{
for (i=0;i<*npsr;i++)
{
strcpy(tpar[i],parFile[i]);
strcpy(ttim[i],timFile[i]);
}
for (i=0;i<*npsr;i++)
{
// printf("Have %d %d %d >%s< >%s<\n",i,*npsr,(*npsr)-i-1,tpar[(*npsr)-i-1],ttim[(*npsr)-i-1]);
strcpy(parFile[i],tpar[(*npsr)-i-1]);
strcpy(timFile[i],ttim[(*npsr)-i-1]);
// strcpy(timFile[i],"J0900-3144.new2.tim");
}
}
printf("Starting plugin1\n");
// initialise(psr,0); /* Initialise the structures */
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
printf("Starting plugin2\n");
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
printf("Starting plugin3\n");
preProcess(psr,*npsr,argc,argv);
printf("Starting plugin4\n");
callFit(psr,*npsr); /* Do all the fitting routines */
printf("Starting plugin5\n");
doPlot(psr,*npsr,scale,nScale,grDev,plotUs,fontsize,centreMJD,ptStyle,ptSize,error,miny,maxy,minx,maxx,nOverlay,labelsize,fracX); /* Do plot */
printf("Starting plugin6\n");
}
extern "C" int graphicalInterface(int argc,char *argv[],pulsar *psr,int *npsr)
{
longdouble imjd=-1.0,fmjd=-1.0,ra,grms=0.0;
longdouble toa,ha0,almst,amjd,hnobs,mjd,trmjd,tstep=0.0;
longdouble times[MAX_OBSN];
longdouble out[MAX_OBSN];
longdouble lowFreq,highFreq,alpha=-3.0,ampPL=1.0e-16;
int setref=0;
int nshots,npts;
int j,count=0,i,k,ii,jj,kk;
longdouble solsid = 1.002737909;
longdouble obslong = 149.0; /* Longitude of Parkes */
longdouble freq = 1440.0;
long iseed;
int site = 7,p;
int endit=0;
long idum = 0;
int nday = -1;
float ngap=-1.0;
char parFile[MAX_PSR][MAX_FILELEN];
char timFile[MAX_PSR][MAX_FILELEN];
char str[MAX_FILELEN],str2[MAX_FILELEN];
double hamax =-1.0;
char random[100];
char read_f=0;
FILE *fout,*fin;
char addCubic[100]="n",temp[100];
char formstr[50]="tempo2";
char smooth[100]="n";
int psrNum,giveRMS=-1,setrand=-1,setred=-1,Npsr=0;
int timesFile=0;
char fake_fname[100];
char have_outfile=0;
char outfile[100];
char timesfname[100];
char telID[128]="7"; // Hardcode to Parkes
int bunching=0; // flag on whether or not observations occur in groups
// size of gap between observing runs, and length of observing runs.
// These defaults give 7 observations every 28 days.
long double gapsize=21,hillsize=7,gapstartmjd;
// Flag whether or not to ask for red noise variables.
*npsr = 1;
strcpy(fake_fname,"fake.rf");
for (i=0;i<argc;i++){
if(strcmp(argv[i],"-ndobs")==0){
sscanf(argv[i+1],"%f",&ngap);
printf("Have >>%f<< days between observations\n",ngap);
}
if(strcmp(argv[i],"-nobsd")==0){
sscanf(argv[i+1],"%d",&nday);
printf("Have >>%d<< observations per day\n",nday);
}
if (strcmp(argv[i],"-idum")==0){
sscanf(argv[i+1],"%d",&idum);
printf("Have idum >>%d<<\n",idum);
}
if(strcmp(argv[i],"-ha")==0){
sscanf(argv[i+1],"%lf",&hamax);
printf("Have maximum absolute HA >>%lf<<\n",hamax);
}
if(strcmp(argv[i],"-randha")==0){
strcpy(&random[0],argv[i+1]);
printf("Have random >>%s<<\n",random);
setrand=1;
}
if(strcmp(argv[i],"-start")==0){
sscanf(argv[i+1],"%Lf",&imjd);
printf("Have initial MJD >>%lf<<\n",(double)imjd);
}
if(strcmp(argv[i],"-tel")==0){
sscanf(argv[i+1],"%s",telID);
}
if(strcmp(argv[i],"-end")==0){
sscanf(argv[i+1],"%Lf",&fmjd);
printf("Have final MJD >>%lf<<\n",(double)fmjd);
}
if(strcmp(argv[i],"-rms")==0){
sscanf(argv[i+1],"%Lf",&grms);
giveRMS=1;
printf("Have Gaussian noise rms >>%lf<<\n",(double)grms);
}
if(strcmp(argv[i],"-format")==0){
sscanf(argv[i+1],"%s",&formstr);
printf("Have output format >>%s<<\n",formstr);
}
if (strcmp(argv[i],"-times")==0){
timesFile=1;
sscanf(argv[i+1],"%s",×fname);
printf("Timesfile = %s\n",timesfname);
}
if (strcmp(argv[i],"-setref")==0)
setref=1;
if (strcmp(argv[i],"-o")==0){
have_outfile=1;
sscanf(argv[i+1],"%s",&outfile);
printf("outfile = %s\n",outfile);
}
if (strcmp(argv[i],"-readtim")==0){
read_f=1;
printf("Read name,freq,mjd\n");
}
if(strcmp(argv[i],"-group")==0){
bunching = 1;
sscanf(argv[i+1],"%Lf",&hillsize);
sscanf(argv[i+2],"%Lf",&gapsize);
printf("Will simulate runs of %lg observing days long and leave a gap of %lg days between runs.\n",
(double)hillsize,(double)gapsize);
}
if(strcmp(argv[i],"-h")==0){
printf("==========================================================================================\n");
printf(" fake Tempo2 plugin - usage instructions.\n");
printf(" tempo2 -gr fake -f file.par: The program will prompt you for parameters.\n");
printf("\n Command-line arguments:\n");
printf(" \t -f J0437-4715.par J1909-3744.par J1713+0747.par: specify a number of parfiles.\n");
printf(" \t -ndobs xxx: specify number of days between observations.\n");
printf(" \t -nobsd xxx: specify number of observations per day.\n");
printf(" \t -ha xxx: specify maximal absolute Hour Angle.\n");
printf(" \t -randha y: specify whether to use random HA coverage or not (y/n).\n");
printf(" \t -start xxxxx: specify start MJD.\n");
printf(" \t -end xxxxx: specify final MJD.\n");
printf(" \t -rms xxx: specify Gaussian noise rms (in ms).\n");
printf(" \t -times xxx: read observation times from specified file\n");
printf(" \t suppresses questions for red noise characteristics.\n");
printf(" \t -format parkes : sets the tim-file format to tempo. (Default: tempo2).\n");
printf(" \t -group 7 21 : simulate observations in groups of 7 days, with 21 days between groups.\n");
printf(" \t There will be nobsd observations every ndobs days during these 7 days.\n");
printf("\n\n \t -idum xxx: specify random number seed (default = set from clock)\n");
printf("\n The program will prompt you for the parameters not defined in the command line.\n");
printf("\n\n Have a nice day!\n\n");
printf("==========================================================================================\n");
exit(0);
}
if(strcmp(argv[i],"-f")==0){
Npsr=0;
while(argv[i+Npsr+1][0]!='-'){
strcpy(parFile[Npsr],argv[i+Npsr+1]);
printf("Have parfile %d: >>%s<<.\n",Npsr+1,parFile[Npsr]);
Npsr++;
if(i+Npsr+1>=argc) break;
}
printf("Have %d parameter files.\n",Npsr);
}
}
if (timesFile==1)
{
nday = 1;
ngap = 1;
hamax = 8;
setrand = 1;
imjd = 1;
fmjd = 1;
}
printf("Simulate arrival times for parameter file %s\n",argv[3]);
printf("----------------------------------------------------\n\n");
if(ngap<0){ printf("Enter number of days between observations . "); scanf("%f",&ngap);}
if(nday<0) { printf("Enter number of observations/day .......... "); scanf("%d",&nday);}
if(hamax<0 && nday!=1) {
printf("Enter max absolute HA...................... "); scanf("%lf", &hamax);}
if(setrand!=1){ printf("Random HA coverage? (y/n) ................. "); scanf("%s",&random);}
if(imjd<0) { printf("Enter initial MJD ......................... "); scanf("%Lf",&imjd);}
if(fmjd<0) { printf("Enter final MJD ........................... "); scanf("%Lf",&fmjd);}
if(giveRMS<0){
printf("Enter Gaussian noise rms (ms/auto)........ "); scanf("%s",temp);
giveRMS = sscanf(temp,"%Lf",&grms);
}
printf("GIVE RMS = %d\n",giveRMS);
if (idum==0)
{
printf("Setting random number seed from the clock\n");
idum = TKsetSeed();
}
iseed = idum;
psrNum = Npsr;
if (timesFile==1)
fin = fopen(timesfname,"r");
hnobs = nday/2.0;
for(ii=0;ii<Npsr;ii++){
count = 0;
strcpy(parFile[0],parFile[ii]);
printf("SET: %d\n",psr[0].param[param_pb].val[0]);
psr[0].nJumps=0;
psr[0].fitMode=0;
psr[0].eclCoord=0;
psr[0].nits=1;
psr[0].clockFromOverride[0] = '\0';
psr[0].nCompanion = 0;
psr[0].bootStrap = 0;
psr[0].units = SI_UNITS;
psr[0].ne_sw = NE_SW_DEFAULT;
psr[0].nWhite = 0; /* No whitening by default */
psr[0].timeEphemeris = IF99_TIMEEPH;
psr[0].dilateFreq = 1;
psr[0].planetShapiro = 1;
psr[0].correctTroposphere = 1;
psr[0].t2cMethod = T2C_IAU2000B;
psr[0].fixedFormat=0;
psr[0].nStorePrecision=0;
strcpy(psr[0].deleteFileName,"NONE");
strcpy(psr[0].tzrsite,"NULL");
psr[0].calcShapiro=1;
psr[0].ipm = 1;
psr[0].swm = 0;
psr[0].nPhaseJump=0;
for (i=0;i<MAX_PARAMS;i++)
{
for (j=0;j<psr[0].param[i].aSize;j++)
{
psr[0].param[i].fitFlag[j] = 0;
psr[0].param[i].paramSet[j] = 0;
psr[0].param[i].err[j] = 0;
psr[0].param[i].val[j] = 0;
}
}
// initialise(psr,0); /* Initialise the structures */
// printf("SET AFTER 1: %d\n",psr[0].param[param_pb].val[0]);
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// printf("SET AFTER 2: %d %s\n",psr[0].param[param_pb].val[0],psr[0].name);
ra = (double)psr[0].param[param_raj].val[0]/2.0/M_PI;
/* Code based on fake1.f to calculate the TOA at transit for each of these observations */
trmjd = imjd;
/* 47892.0 = 1990??? */
almst = fortran_mod((trmjd-47892.0)*solsid+0.276105324+obslong/360.0,(longdouble)1.0);
/* Hour angle at 00h UT */
ha0 = almst - ra;
/* Approximate transit time */
if (ha0 < 0.0) ha0+=1.0;
trmjd += 1.0-ha0;
if (nday > 1)tstep = hamax/12.0/nday; /* Was 0.4/nday */
amjd = trmjd;
gapstartmjd = imjd+(hillsize)/solsid;
do {
for (j=0;j<nday;j++)
{
if (timesFile==1)
{
if (read_f){
if (fscanf(fin,"%s %Lf %Lf\n",fake_fname,&freq,&mjd)==3)
{
printf("Read %g %f\n",(double)mjd, (double)freq);
endit=0;
}
else
endit=1;
} else{
if (fscanf(fin,"%Lf",&mjd)==1)
{
printf("Read %g\n",(double)mjd);
endit=0;
}
else
endit=1;
}
}
else
{
if (random[0]=='y'||random[0]=='Y')
amjd=trmjd + (rand()/(longdouble)RAND_MAX - 0.5)*hamax/12.0;
else if (nday==1)
amjd=trmjd;
else
amjd=trmjd + ((j+1)-hnobs)*tstep;
mjd=amjd;
}
if (endit==0)
{
if (count==0 && setref==1)
{
psr[0].obsn[count].sat = psr[0].param[param_tzrmjd].val[0];
strcpy(psr[0].obsn[count].fname,"reference");
psr[0].obsn[count].freq = psr[0].param[param_tzrfrq].val[0];
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
// else grms=0.0;
psr[0].obsn[count].toaErr = grms*1000.0;
psr[0].obsn[count].origErr = grms*1000.0;
psr[0].obsn[count].phaseOffset = 0.0;
strcpy(psr[0].obsn[count].telID, psr[0].tzrsite);
psr[0].obsn[count].deleted = 0;
psr[0].obsn[count].clockCorr=1;
psr[0].obsn[count].delayCorr=1;
psr[0].obsn[count].efac=1;
count++;
}
psr[0].obsn[count].sat = mjd;
strcpy(psr[0].obsn[count].fname,fake_fname);
psr[0].obsn[count].freq = freq;
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
// else grms=0.0;
psr[0].obsn[count].toaErr = grms*1000.0;
psr[0].obsn[count].origErr = grms*1000.0;
psr[0].obsn[count].phaseOffset = 0.0;
strcpy(psr[0].obsn[count].telID, telID);
psr[0].obsn[count].deleted = 0;
psr[0].obsn[count].clockCorr=1;
psr[0].obsn[count].delayCorr=1;
psr[0].obsn[count].efac=1;
count++;
if (count>MAX_OBSN)
{
printf("Number of TOAs > MAX_OBSN.\n");
count--;
}
}
}
if((bunching == 1) && (trmjd >= (gapstartmjd-1))){
trmjd += gapsize/solsid;
gapstartmjd += (gapsize+hillsize)/solsid;
}
else{
trmjd+=ngap/solsid;
}
}while ((timesFile == 0 && amjd<fmjd) || (timesFile == 1 && endit==0));
if (timesFile==1)
fclose(fin);
psr[0].nobs=count;
if (have_outfile){
strcpy(str,outfile);
strcpy(timFile[0],outfile);
}else{
strcpy(str,parFile[0]);
str[strlen(str)-4]='\0';
strcat(str,".simulate");
strcpy(timFile[0],str);
}
/* Now run the tempo2 code */
preProcess(psr,*npsr,argc,argv);
callFit(psr,*npsr); /* Do all the fitting routines */
for (j=0;j<9;j++)
{
/* Now update the site arrival times depending upon the residuals */
for (i=0;i<psr[0].nobs;i++)
{
psr[0].obsn[i].sat -= psr[0].obsn[i].prefitResidual/SECDAY;
psr->obsn[i].nFlags = 0;
}
writeTim(str,psr,"tempo2");
// initialise(&psr[ii],0);
// Reset the jumps
psr[ii].nJumps = 0;
for(kk=0;kk<MAX_JUMPS;kk++){
psr[ii].jumpVal[kk] = 0.0;
psr[ii].jumpValErr[kk] = 0.0;
}
for(jj=0;jj<MAX_PARAMS;jj++){
psr[ii].param[jj].nLinkTo = 0;
psr[ii].param[jj].nLinkFrom = 0;
}
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
readTimfile(psr,timFile,*npsr);
preProcess(psr,1,argc,argv);
/* Now run the superTEMPO code again */
callFit(psr,*npsr); /* Do all the fitting routines */
}
printf("Complete 10 iterations\n");
for (i=0;i<psr[0].nobs;i++)
{
psr[0].obsn[i].sat -= psr[0].obsn[i].prefitResidual/SECDAY;
psr->obsn[i].nFlags = 0;
}
for (i=0;i<psr[0].nobs;i++)
{
times[i] = (psr[0].obsn[i].sat-psr[0].param[param_posepoch].val[0]);
}
npts = psr[0].nobs;
/* Add Gaussian noise */
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
if (grms>0.0)
{
printf("Adding Gaussian noise with rms = %f\n",(float)grms);
for (i=0;i<psr[0].nobs;i++)
psr[0].obsn[i].sat += TKgaussDev(&idum)*grms/1000.0/SECDAY;
}
printf("Output TOA file written to %s\n",str);
writeTim(str,psr,formstr);
}
}
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;
int overlay=0;
FILE *pin;
char str[1000];
*npsr = 0; /* This graphical interface will only show results for one pulsar */
strcpy(dcmFile,"NULL");
strcpy(covarFuncFile,"NULL");
printf("Graphical Interface: plk emulator\n");
printf("Author: George Hobbs (21 Dec 2003)\n");
printf("CVS Version: $Revision $\n");
/* Obtain the .par and the .tim file from the command line */
for (i=1;i<argc;i++)
{
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[i+1]);
strcpy(timFile[*npsr],argv[i+2]);
(*npsr)++;
if (*npsr > MAX_PSR)
{
printf("Error, npsr > MAX_PSR. Must increase MAX_PSR\n");
exit(1);
}
}
else if (strcmp(argv[i],"-dcm")==0)
strcpy(dcmFile,argv[++i]);
else if (strcmp(argv[i],"-dcf")==0)
strcpy(covarFuncFile,argv[++i]);
else if (strcmp(argv[i],"-overlay")==0)
overlay=1;
}
if (*npsr==0) /* Select all files */
{
printf("Using all available .par and .tim files\n");
sprintf(str,"ls `ls *.par | sed s/par/tim/` | sed s/.tim/\"\"/");
pin = popen(str,"r");
while (!feof(pin))
{
if (fscanf(pin,"%s",str)==1)
{
sprintf(parFile[*npsr],"%s.par",str);
sprintf(timFile[*npsr],"%s.tim",str);
(*npsr)++;
}
}
pclose(pin);
printf("Obtained files for %d pulsars\n",*npsr);
}
// initialise(psr,0); /* Initialise the structures */
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
preProcess(psr,*npsr,argc,argv);
callFit(psr,*npsr); /* Do all the fitting routines */
doPlot(psr,*npsr,overlay); /* Do plot */
return 0;
}