int cfits_read_string_col (char **array, long num_values,
long firstrow, const char *colname, cfitsfile *fptr)
{
char nulval[CFLEN_VALUE];
int status = 0;
long firstelem = 1;
int anynul, colnum;
nulval[0] = '\0';
if (-1 == cfits_get_colnum (&colnum, colname, fptr))
{
array = NULL;
return -1;
}
(void) fits_read_col_str ((fitsfile *) fptr, colnum, firstrow, firstelem,
num_values, nulval, array, &anynul, &status);
cfits_report_error (status);
if (status != 0) return -1;
return 0;
}
void loadPrimaryHeader(fitsfile *fp,dSet *data)
{
int status=0;
int nkey=-1;
int morekeys=-1;
int i;
char keyname[128],val[128],comment[128];
fits_get_hdrspace(fp,&nkey,&morekeys,&status);
data->pheaderSet = 1;
data->phead.nhead = nkey;
// Allocate memory
data->phead.keyname = (char **)malloc(sizeof(char *)*nkey);
data->phead.val = (char **)malloc(sizeof(char *)*nkey);
data->phead.comment = (char **)malloc(sizeof(char *)*nkey);
for (i=0;i<nkey;i++)
{
data->phead.keyname[i] = (char *)malloc(sizeof(char)*128);
data->phead.val[i] = (char *)malloc(sizeof(char)*128);
data->phead.comment[i] = (char *)malloc(sizeof(char)*128);
}
data->pheaderSet=1;
// Complete allocating memory
for (i=1;i<=nkey;i++)
{
fits_read_keyn(fp,i+1,data->phead.keyname[i-1],data->phead.val[i-1],data->phead.comment[i-1],&status);
if (strcmp(data->phead.keyname[i-1],"OBSFREQ")==0)
sscanf(data->phead.val[i-1],"%f",&(data->phead.freq));
else if (strcmp(data->phead.keyname[i-1],"STT_IMJD")==0)
sscanf(data->phead.val[i-1],"%d",&(data->phead.imjd));
else if (strcmp(data->phead.keyname[i-1],"STT_SMJD")==0)
sscanf(data->phead.val[i-1],"%f",&(data->phead.smjd));
else if (strcmp(data->phead.keyname[i-1],"STT_OFFS")==0)
sscanf(data->phead.val[i-1],"%f",&(data->phead.stt_offs));
else if (strcmp(data->phead.keyname[i-1],"OBSBW")==0)
sscanf(data->phead.val[i-1],"%f",&(data->phead.bw));
}
// Read specific parameters
fits_read_key(fp,TSTRING,"OBS_MODE",data->phead.obsMode,NULL,&status);
fits_read_key(fp,TSTRING,"SRC_NAME",data->phead.source,NULL,&status);
if (status)
{
fits_report_error(stderr,status);
exit(1);
}
// Now load information from the subintegration table
fits_movnam_hdu(fp,BINARY_TBL,"SUBINT",1,&status);
if (status)
{
printf("No subintegration table\n");
data->subintTable=0;
status=0;
}
else
{
data->subintTable=1;
fits_read_key(fp,TINT,"NAXIS2",&(data->phead.nsub),NULL,&status);
if (status)
{
printf("Reading naxis2\n");
fits_report_error(stderr,status);
exit(1);
}
fits_read_key(fp,TINT,"NCHAN",&(data->phead.nchan),NULL,&status);
if (status)
{
printf("Reading nchan\n");
fits_report_error(stderr,status);
exit(1);
}
fits_read_key(fp,TFLOAT,"ZERO_OFF",&(data->phead.zeroOff),NULL,&status);
if (status)
{
printf("Reading zero_off\n");
fits_report_error(stderr,status);
data->phead.zeroOff = 0;
status=0;
}
fits_read_key(fp,TINT,"NBITS",&(data->phead.nbits),NULL,&status);
if (status)
{
printf("Reading nbits\n");
fits_report_error(stderr,status);
exit(1);
}
fits_read_key(fp,TINT,"NPOL",&(data->phead.npol),NULL,&status);
if (status)
{
printf("Reading npol\n");
fits_report_error(stderr,status);
exit(1);
}
fits_read_key(fp,TINT,"NSBLK",&(data->phead.nsblk),NULL,&status);
if (status)
{
printf("Reading nsblk\n");
fits_report_error(stderr,status);
exit(1);
}
fits_read_key(fp,TINT,"NBIN",&(data->phead.nbin),NULL,&status);
if (status)
{
printf("Reading nbin\n");
fits_report_error(stderr,status);
exit(1);
}
// printf("nbin = %d (%d)\n",data->phead.nbin,status);
fits_read_key(fp,TFLOAT,"CHAN_BW",&(data->phead.chanbw),NULL,&status);
if (data->phead.chanbw < 0 && data->phead.bw > 0)
data->phead.bw*=-1;
fits_read_key(fp,TFLOAT,"TBIN",&(data->phead.tsamp),NULL,&status);
}
fits_movnam_hdu(fp,BINARY_TBL,"PSRPARAM",1,&status);
if (status)
{
printf("No PSRPARM table\n");
data->psrparamTable=0;
status=0;
}
else
{
int len,i,colnum;
char **line,str1[1024],str2[1024];
data->psrparamTable=1;
char nval[128]="UNKNOWN";
int anynul=0;
float tt;
fits_read_key(fp,TINT,"NAXIS2",&len,NULL,&status);
fits_get_colnum(fp,CASEINSEN,"PARAM",&colnum,&status);
if (status) {
printf("Unable to find data in the psrparam table in FITS file\n");
exit(1);
}
line = (char **)malloc(sizeof(char *));
line[0] = (char *)malloc(sizeof(char)*1024);
for (i=0;i<len;i++)
{
fits_read_col_str(fp,colnum,i+1,1,1,nval,line,&anynul,&status);
if (sscanf(line[0],"%s %s",str1,str2)==2)
{
if (strcasecmp(str1,"DM")==0)
sscanf(str2,"%f",&(data->phead.dm));
if (strcasecmp(str1,"F0")==0)
{
sscanf(str2,"%f",&tt);
data->phead.period = 1.0/tt;
}
}
// printf("Read: %s\n",line[0]);
}
// printf("Lenght = %d\n",len);
free(line[0]);
free(line);
}
}
void c_tbegtt (const IRAFPointer tp, const IRAFPointer cp, int row, char *buffer,
int maxch) {
/* Read a string value from a table column.
arguments:
IRAFPointer tp i: table descriptor
IRAFPointer cp i: column descriptor
int row i: row number (one indexed)
char *buffer o: value read from table
int maxch i: maximum length of the string (not incl NULL)
*/
TableDescr *tbl_descr;
ColumnDescr *col_descr;
int anynul=0;
long firstelem=1, nelem=1;
char *value;
int len;
int status = 0;
tbl_descr = (TableDescr *)tp;
col_descr = (ColumnDescr *)cp;
if (col_descr->datatype < 0) {
if (col_descr->width >= maxch)
len = col_descr->width;
else
len = maxch;
} else {
len = SZ_FITS_STR;
}
value = (char *)calloc (len+1, sizeof(char));
if (col_descr->datatype == IRAF_BOOL) {
Bool b_value;
c_tbegtb (tp, cp, row, &b_value);
if (b_value == True)
strcpy (value, "yes");
else
strcpy (value, "no");
} else if (col_descr->datatype == IRAF_DOUBLE) {
double d_value;
c_tbegtd (tp, cp, row, &d_value);
if (d_value == IRAF_INDEFD)
strcpy (value, "INDEF");
else
sprintf (value, "%.16g", d_value);
} else if (col_descr->datatype == IRAF_REAL) {
float r_value;
c_tbegtr (tp, cp, row, &r_value);
if (r_value >= 0.99999 * IRAF_INDEFR &&
r_value <= 1.00001 * IRAF_INDEFR) {
strcpy (value, "INDEF");
} else {
sprintf (value, "%.7g", r_value);
}
} else if (col_descr->datatype == IRAF_INT) {
int i_value;
c_tbegti (tp, cp, row, &i_value);
if (i_value == IRAF_INDEFI)
strcpy (value, "INDEF");
else
sprintf (value, "%d", i_value);
} else if (col_descr->datatype == IRAF_SHORT) {
short si_value;
c_tbegts (tp, cp, row, &si_value);
if (si_value == IRAF_INDEFS)
strcpy (value, "INDEF");
else
sprintf (value, "%hd", si_value);
} else {
/* fits_read_col_str = ffgcvs */
fits_read_col_str (tbl_descr->fptr, col_descr->colnum,
(long)row, firstelem, nelem, "INDEF",
&value, &anynul, &status);
if (status != 0)
setError (status, "c_tbegtt: error reading element");
}
copyString (buffer, value, maxch);
free (value);
}
void processFile(char *fname,tmplStruct *tmpl,FILE *fout,int logit)
{
pheader *header;
ptime_observation *obs;
toaStruct toa;
fitsfile *fp;
int i;
float baselineFrac = 0.1;
int baselineType = 1;
int toaAlgorithm=1;
double dPhi;
double *offs_sub;
double *datFreq;
int nSub = 1;
FILE *fout_log;
char logFname[128];
long double period;
sprintf(logFname,"log.ptime.%s",fname);
fout_log = fopen(logFname,"w");
offs_sub = (double *)malloc(sizeof(double)*nSub);
obs = (ptime_observation *)malloc(sizeof(ptime_observation));
header = (pheader *)malloc(sizeof(pheader));
fp = openFitsFile(fname);
loadPrimaryHeader(fp,header);
datFreq= (double *)malloc(sizeof(double)*header->nchan);
allocateObsMemory(obs,header);
readData(obs,header,fp);
// Now get an array of subintegration times
readSubintOffs(obs,offs_sub,fp);
// Get an array of frequencies
readDatFreq(obs,datFreq,fp,header->nchan);
printf("offs_sub = %g\n",offs_sub[0]);
// Calculate the period
{
FILE *pred_out;
int status=0;
long nrows,row;
char nval[128]="UNKNOWN";
int anynul=0;
long double mjd0;
long double frequency;
char **line;
T2Predictor pred;
int ret;
line = (char **)malloc(sizeof(char *));
line[0] = (char *)malloc(sizeof(char)*1024);
if (!(pred_out = fopen("ptime.pred","w"))){
printf("Unable to open file >%s<\n","ptime.pred");
}
fits_movnam_hdu(fp,BINARY_TBL,(char *)"T2PREDICT",1,&status);
if (status)
{
printf("No predictor table in PSRFITS file\n");
status=0;
}
fits_get_num_rows(fp,&nrows,&status);
printf("NROWS = %d\n",nrows);
for (row = 1; row <= nrows ; row++){
fits_read_col_str(fp,1,row,1,1,nval,line,&anynul,&status);
printf("Have read %s\n",line[0]);
fprintf(pred_out,"%s\n",line[0]);
}
free(line[0]);
free(line);
fclose(pred_out);
T2Predictor_Init(&pred); // prepare the predictor
if (ret=T2Predictor_Read(&pred,(char *)"ptime.pred"))
{
printf("Error: unable to read predictor\n");
exit(1);
}
mjd0 = header->imjd + (header->smjd + header->stt_offs)/86400.0L;
frequency = datFreq[0]; //(freq in MHz) WHAT SHOULD THIS BE SET TO!!
period = 1.0/T2Predictor_GetFrequency(&pred,mjd0,frequency);
if (period==-1){
printf("Error: period returned from predictor = -1. This cannot be correct.\n");
exit(1);
}
T2Predictor_Destroy(&pred);
printf("Period = %.15Lf %.15Lf %.15Lf\n",period,mjd0,frequency);
}
closeFitsFile(fp);
// Must remove a baseline
removeBaseline(obs,header,baselineType,baselineFrac);
printf("Here\n");
// Now get the shift
if (toaAlgorithm == 1)
getTOA_alg1(obs,header,tmpl,&toa,fout_log);
strcpy(toa.fname,fname);
// Calculate the arrival time
calcArrivalTime(obs,header,tmpl,&toa,offs_sub,datFreq,period,fout,fout_log);
free(header);
free(obs);
free(offs_sub);
free(datFreq);
fclose(fout_log);
}
