flouble *he_read_healpix_map(char *fname,long *nside,int nfield)
{
//////
// Reads a healpix map from file fname. The map will be
// read from column #nfield. It also returns the map's nside.
int status=0,hdutype,nfound,anynul;
long naxes,*naxis,npix;
fitsfile *fptr;
flouble *map,nulval;
char order_in_file[32];
int nested_in_file=0;
fits_open_file(&fptr,fname,READONLY,&status);
fits_movabs_hdu(fptr,2,&hdutype,&status);
fits_read_key_lng(fptr,"NAXIS",&naxes,NULL,&status);
naxis=(long *)malloc(naxes*sizeof(long));
fits_read_keys_lng(fptr,"NAXIS",1,naxes,naxis,&nfound,&status);
fits_read_key_lng(fptr,"NSIDE",nside,NULL,&status);
npix=12*(*nside)*(*nside);
if(npix%naxis[1]!=0) {
fprintf(stderr,"CRIME: WTFFF\n");
exit(1);
}
if (fits_read_key(fptr, TSTRING, "ORDERING", order_in_file, NULL, &status)) {
fprintf(stderr, "WARNING: Could not find %s keyword in in file %s\n",
"ORDERING",fname);
exit(1);
}
if(!strncmp(order_in_file,"NEST",4))
nested_in_file=1;
map=(flouble *)my_malloc(npix*sizeof(flouble));
#ifdef _SPREC
fits_read_col(fptr,TFLOAT,nfield+1,1,1,npix,&nulval,map,&anynul,&status);
#else //_SPREC
fits_read_col(fptr,TDOUBLE,nfield+1,1,1,npix,&nulval,map,&anynul,&status);
#endif //_SPREC
free(naxis);
fits_close_file(fptr,&status);
flouble *map_ring;
if(nested_in_file) {
long ipring,ipnest;
printf("read_healpix_map: input is nested. Transforming to ring.\n");
map_ring=(flouble *)my_malloc(npix*sizeof(flouble));
for(ipnest=0;ipnest<npix;ipnest++) {
nest2ring(*nside,ipnest,&ipring);
map_ring[ipring]=map[ipnest];
}
free(map);
}
else
map_ring=map;
return map_ring;
}
/* Read only part (N "spectra" in time) of the DATA column from the
* current subint from the set of files described by the psrfits
* struct. Put the data into the buffer "buffer". It is assumed that
* all files form a consistent set. Read automatically goes to the
* next file when one ends. Arrays should be allocated outside this
* routine. Counters are _not_ updated as they are in
* psrfits_read_subint().
*/
int psrfits_read_part_DATA(struct psrfits *pf, int N, int numunsigned,
float *fbuffer) {
struct hdrinfo *hdr = &(pf->hdr);
int colnum = 0, *status = &(pf->status);
// See if we need to move to next file
if (pf->rownum > pf->rows_per_file) {
printf("Closing file '%s'\n", pf->filename);
fits_close_file(pf->fptr, status);
pf->filenum++;
psrfits_open(pf);
if (*status==FILE_NOT_OPENED) {
printf("Finished with all input files.\n");
pf->filenum--;
*status = 1;
return *status;
}
}
int nivals = hdr->nchan * hdr->npol;
long long numdata = (long long) nivals * (long long) N;
long long bytes_to_read = (hdr->nbits * numdata) / 8L;
float *offsets = (float *)malloc(sizeof(float) * nivals);
float *scales = (float *)malloc(sizeof(float) * nivals);
unsigned char *buffer = (unsigned char *)malloc(numdata);
unsigned char *rawbuffer = buffer;
if (hdr->nbits==4) {
rawbuffer = (unsigned char *)malloc(bytes_to_read);
}
// Now read the data
fits_get_colnum(pf->fptr, 0, "DAT_OFFS", &colnum, status);
fits_read_col(pf->fptr, TFLOAT, colnum, pf->rownum, 1, nivals,
NULL, offsets, NULL, status);
fits_get_colnum(pf->fptr, 0, "DAT_SCL", &colnum, status);
fits_read_col(pf->fptr, TFLOAT, colnum, pf->rownum, 1, nivals,
NULL, scales, NULL, status);
fits_get_colnum(pf->fptr, 0, "DATA", &colnum, status);
fits_read_col(pf->fptr, TBYTE, colnum, pf->rownum, 1, bytes_to_read,
NULL, rawbuffer, NULL, status);
if (hdr->nbits==4) {
convert_4bit_to_8bit(rawbuffer, (unsigned char *)buffer, numdata);
free(rawbuffer);
}
// Now convert the 8-bit data to floats using the scales and offsets
apply_scales_and_offsets(hdr->nchan, hdr->npol, N, numunsigned,
scales, offsets, buffer, fbuffer);
free(offsets);
free(scales);
free(buffer);
// Complain on error
fits_report_error(stderr, *status);
return *status;
}
void get_PSRFITS_subint(float *fdata, unsigned char *cdata, struct spectra_info *s)
{
unsigned char *ctmp = cdata;
int ii, status = 0, anynull;
int numtoread = s->samples_per_subint;
// The following allows us to read byte-packed data
if (s->bits_per_sample < 8) {
numtoread = (s->samples_per_subint * s->bits_per_sample) / 8;
ctmp = gen_bvect(numtoread);
}
// or 16-bit data that is listed as being bytes
if (s->bits_per_sample == 16 && s->FITS_typecode == 11)
numtoread = s->samples_per_subint * 2;
// Read the weights, offsets, and scales if required
if (s->apply_weight)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_wts_col, cur_subint, 1L,
s->num_channels, 0, weights, &anynull, &status);
if (s->apply_offset)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_offs_col, cur_subint,
1L, s->num_channels * s->num_polns, 0, offsets, &anynull,
&status);
if (s->apply_scale)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_scl_col, cur_subint, 1L,
s->num_channels * s->num_polns, 0, scales, &anynull, &status);
// Now actually read the subint into the temporary buffer
fits_read_col(s->fitsfiles[cur_file], s->FITS_typecode,
s->data_col, cur_subint, 1L, numtoread,
0, ctmp, &anynull, &status);
if (status) {
fprintf(stderr, "Error!: Problem reading record from PSRFITS data file\n"
"\tfilename = '%s', subint = %d. FITS status = %d. Exiting.\n",
s->filenames[cur_file], cur_subint, status);
exit(1);
}
// The following converts that byte-packed data into bytes
if (s->bits_per_sample == 4) {
#ifdef _OPENMP
#pragma omp parallel for default(none) shared(numtoread,cdata,ctmp)
#endif
for (ii = 0; ii < numtoread; ii++) {
const unsigned char uctmp = ctmp[ii];
const int jj = 2 * ii;
cdata[jj] = uctmp >> 4;
cdata[jj + 1] = uctmp & 0x0F;
}
} else if (s->bits_per_sample == 2) {
int get_fqtable(fitsfile *fptr, int hdu, struct uvf_header *header)
{
int status = 0, i;
int hdutype, col_iff, type_iff;
long nrows, rpt_iff, wid_iff;
double f;
fits_movabs_hdu(fptr, hdu, &hdutype, &status);
fits_get_num_rows(fptr, &nrows, &status);
fits_get_colnum(fptr, CASEINSEN, "IF FREQ", &col_iff, &status);
fits_get_coltype(fptr, col_iff, &type_iff, &rpt_iff, &wid_iff,
&status);
if (status || type_iff != TDOUBLE || nrows != 1 || rpt_iff !=
header->nif)
fprintf(stderr, " Warning: Invalid AIPS frequency table\n");
for (i=0; i < rpt_iff; i++) {
fits_read_col(fptr, TDOUBLE, col_iff, 1, i+1, 1,
NULL, &f, NULL, &status);
header->iffreq[i] = header->freq + f;
}
fprintf(stderr, " %d IFs ", header->nif);
for (i=0; i < header->nif; i++)
fprintf(stderr, " %.2f", header->iffreq[i]*1e-9);
fprintf(stderr, "\n");
return status ? 1 : 0;
}
void FitsFile::ReadTableCell(int row, int col, double *output, size_t size)
{
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TDOUBLE, col, row, 1, size, &nulValue, output, &anynul, &status);
}
void FitsFile::ReadTableCell(int row, int col, char *output)
{
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TSTRING, col, row, 1, 1, &nulValue, &output, &anynul, &status);
}
int LFIIOSource::readField( double *v, const QString& field, int s, int n )
{
double dNan = strtod( "nan", NULL );
fitsfile* ffits;
bool bOk;
int i;
int iCol;
int iRead = -1;
int iStatus = 0;
int iAnyNull;
int iResult = 0;
if( n < 0 )
{
n = 1; /* n < 0 means read one sample, not frame - irrelavent here */
}
if( field == "INDEX" )
{
for( i = 0; i < n; i++ )
{
v[i] = (double)( s + i );
}
iRead = n;
}
else
{
memset( v, 0, n * sizeof( double ) );
bOk = getColNumber( field, &iCol );
if( bOk )
{
_valid = false;
if( !_filename.isNull( ) && !_filename.isEmpty( ) )
{
iResult = fits_open_table( &ffits, _filename.ascii( ), READONLY, &iStatus );
if( iResult == 0 )
{
_valid = true;
//
// copy the data...
// N.B. fitsio column indices are 1 based, so we ask for iCol+1 instead of just iCol
//
iResult = fits_read_col( ffits, TDOUBLE, iCol+1, s+1, 1, n, &dNan, v, &iAnyNull, &iStatus );
if( iResult == 0 )
{
iRead = n;
}
iStatus = 0;
fits_close_file( ffits, &iStatus );
}
}
}
}
return iRead;
}
void InputFileFITS::_readv(int ncol, std::vector< std::vector<T> >& buff, int type, long frow, long lrow, int vsize) {
int status = 0;
if(!isOpened())
throwException("Error in InputFileFITS::_readv() ", status);
int anynull;
long nelem = (lrow - frow + 1);
long null = 0;
T* buffptr = new T[nelem*vsize];
fits_read_col(infptr, type, ncol+1, frow+1, 1, nelem*vsize, &null, buffptr, &anynull, &status);
// conversion from row pointers to std::vector< std::vector<T> >
buff.resize(nelem);
for(unsigned int i=0; i<nelem; i++)
buff[i].resize(vsize);
for(unsigned int row = frow; row < lrow+1; row++)
memcpy(&buff[row][0], &buffptr[row*vsize], vsize*sizeof(T));
delete[] buffptr;
if(status)
throwException("Error in InputFileFITS::_readv() ", status);
}
void get_PSRFITS_subint(float *fdata, unsigned char *cdata,
struct spectra_info *s)
{
float *fptr;
unsigned char *cptr;
short *sptr;
float *ftptr;
int ii, jj, status = 0, anynull;
int numtoread = s->samples_per_subint;
// The following allows us to read byte-packed data
if (s->bits_per_sample < 8)
numtoread = s->samples_per_subint * s->bits_per_sample / 8;
// Read the weights, offsets, and scales if required
if (s->apply_weight)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_wts_col, cur_subint, 1L,
s->num_channels, 0, weights, &anynull, &status);
if (s->apply_offset)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_offs_col, cur_subint, 1L,
s->num_channels*s->num_polns, 0, offsets, &anynull, &status);
if (s->apply_scale)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_scl_col, cur_subint, 1L,
s->num_channels*s->num_polns, 0, scales, &anynull, &status);
// Now actually read the subint into the temporary buffer
fits_read_col(s->fitsfiles[cur_file], s->FITS_typecode,
s->data_col, cur_subint, 1L, numtoread,
0, cdata, &anynull, &status);
if (status) {
fprintf(stderr, "Error!: Problem reading record from PSRFITS data file\n"
"\tfilename = '%s', subint = %d. FITS status = %d. Exiting.\n",
s->filenames[cur_file], cur_subint, status);
exit(1);
}
// The following converts that byte-packed data into bytes, in place
if (s->bits_per_sample == 4) {
unsigned char uctmp;
for (ii = numtoread - 1, jj = 2 * numtoread - 1 ;
ii >= 0 ; ii--, jj -= 2) {
uctmp = (unsigned char)cdata[ii];
cdata[jj] = uctmp & 0x0F;
cdata[jj-1] = uctmp >> 4;
}
} else if (s->bits_per_sample == 2) {
static int read_row_value (fitsfile *f, int row, int col, double *val)
{
int status = 0;
int anynul = 0;
if (0 == fits_read_col (f, TDOUBLE, col, row, 1, 1, NULL, val, &anynul, &status))
return 0;
/* dump_fits_error (status); */
return -1;
}
static int read_row_value_short (fitsfile *f, int row, int col, short *val)
{
int status = 0;
int anynul = 0;
if (0 == fits_read_col (f, TSHORT, col, row, 1, 1, NULL, val, &anynul, &status))
return 0;
/* dump_fits_error (status); */
return -1;
}
static int read_row_value_long (fitsfile *f, int row, int col, long *val)
{
int status = 0;
int anynul = 0;
if (0 == fits_read_col (f, TLONG, col, row, 1, 1, NULL, val, &anynul, &status))
return 0;
/* dump_fits_error (status); */
return -1;
}
/*
初始化整个aa+bb序列，为了省内存，用unsigned char类型存储，并除2使之不超过范围
*/
void initTotalAABB(fitsfile* fptr,struct Fitsinfo* fi,unsigned char** abptr,int* status) {
int n = fi->nROW;int k = fi->nSBLK; int m = fi->nCHAN;
int step = fi->nCHAN*fi->nPOL; int start;
unsigned char aa[m]; unsigned char bb[m];
int dataCol; int nulval = 0; int anynull; int i,j,p;
fits_get_colnum(fptr,CASEINSEN,"DATA",&dataCol,status);
for (i=0; i<n; i++) {
for (j=0; j<k; j++) {
start = 1+j*step;
fits_read_col(fptr,TBYTE,dataCol,i+1,start,m,&nulval,aa,&anynull,status);
fits_read_col(fptr,TBYTE,dataCol,i+1,start+m,m,&nulval,bb,&anynull,status);
for (p=0; p<m; p++) {
abptr[j+i*k][p] = (aa[p]+bb[p])/2;
}
}
printf("All Freq AABB init:Totalrow %d,row completed %d\n",n,i);
}
return;
}
void FitsFile::ReadTableCell(int row, int col, long double *output, size_t size)
{
std::vector<double> data(size);
int status = 0;
double nulValue = std::numeric_limits<double>::quiet_NaN();
int anynul = 0;
fits_read_col(_fptr, TDOUBLE, col, row, 1, size, &nulValue, data.data(), &anynul, &status);
for(size_t i = 0;i<size;++i)
output[i] = data[i];
}
void initFreqDataWithZeroDm(fitsfile* fptr,struct FreqData* fd,unsigned char** ptr,int freqIndex,long samNum,int chanNum,int* status) {
int freqCol; int nulval = 0; int anynull; float tmpFreq; int i;
fits_get_colnum(fptr,CASEINSEN,"DAT_FREQ",&freqCol,status);
fits_read_col(fptr,TFLOAT,freqCol,1,freqIndex+1,1,&nulval,&tmpFreq,&anynull,status);
fd->freq = tmpFreq;
for (i=0; i<samNum; i++) {
fd->data[i] = ptr[i][freqIndex]-calcZeroDm(ptr,chanNum,i);
}
return;
}
void FitsFile::ReadTableCell(int row, int col, bool *output, size_t size)
{
std::vector<char> data(size);
int status = 0;
char nulValue = 0;
int anynul = 0;
fits_read_col(_fptr, TBIT, col, row, 1, size, &nulValue, data.data(), &anynul, &status);
for(size_t i = 0;i<size;++i)
output[i] = data[i]!=0;
}
void FitsFile::ReadTableCell(int row, int col, bool *output, size_t size)
{
char *data = new char[size];
int status = 0;
char nulValue = 0;
int anynul = 0;
fits_read_col(_fptr, TBIT, col, row, 1, size, &nulValue, data, &anynul, &status);
for(size_t i = 0;i<size;++i)
output[i] = data[i]!=0;
delete[] data;
}
float *
supcam_read_data( fitsfile * fits, size_t * numRows, size_t * numChans, int * status ) {
int colnum = 0; /* DATA column */
int fitsStatus = 0; /* CFITSIO status */
long nRows = 0;
long nChans = 0;
long dummy;
float * data = NULL;
int typecode = 0;
/* Initialise the return values */
*numChans = 0;
*numRows = 0;
if (*status != SAI__OK) return NULL;
/* Prepare to read the Binary Table */
/* Check number of rows */
CALLCFITSIO( fits_get_num_rows(fits, &nRows, &fitsStatus), "Error getting number of rows" );
/* Find DATA column and check its repeat count */
/* cast because cfitsio does not use const */
CALLCFITSIO( fits_get_colnum(fits, CASEINSEN, (char *)"DATA", &colnum, &fitsStatus),
"Error getting column number for DATA" );
CALLCFITSIO( fits_get_coltype(fits, colnum, &typecode, &nChans, &dummy, &fitsStatus),
"Error getting column information" );
if (*status != SAI__OK) return NULL;
/* Get some memory */
data = astMalloc( nChans * nRows * sizeof(*data) );
/* Read DATA column */
CALLCFITSIO( fits_read_col(fits, TFLOAT, colnum, 1, 1,
nChans*nRows, NULL, data, NULL, &fitsStatus),
"Error reading spectra from Binary Column DATA" );
if (*status == SAI__OK) {
/* It looks like there is a bad value of (-1)*VAL__BADI */
size_t i;
size_t nelems = nChans * nRows;
for (i = 0; i < nelems; i++ ) {
if (data[i] >= (float)(VAL__MAXI - 1)) {
data[i] = VAL__BADR;
}
}
*numChans = nChans;
*numRows = nRows;
}
return data;
}
int get_antable(fitsfile *fptr, int hdu, struct uvf_header *header)
{
int status = 0, i;
int hdutype, col_name, col_xyz, type_name, type_xyz;
long nrows, rpt_name, rpt_xyz, wid_name, wid_xyz;
char *string[1];
int anynull;
fits_movabs_hdu(fptr, hdu, &hdutype, &status);
fits_get_num_rows(fptr, &nrows, &status);
header->n_antennas = (int) nrows;
fits_get_colnum(fptr, CASEINSEN, "ANNAME", &col_name, &status);
fits_get_coltype(fptr, col_name, &type_name, &rpt_name, &wid_name,
&status);
fits_get_colnum(fptr, CASEINSEN, "STABXYZ", &col_xyz, &status);
fits_get_coltype(fptr, col_xyz, &type_xyz, &rpt_xyz, &wid_xyz,
&status);
if (status || type_name != TSTRING ||
type_xyz != TDOUBLE || rpt_xyz != 3)
fprintf(stderr, " Warning: Invalid AIPS antenna table: %d %ld %d %ld\n",
type_name, rpt_name, type_xyz, rpt_xyz);
for (i=0; i < nrows; i++) {
string[0] = header->antenna[i].name;
fits_read_col(fptr, TSTRING, col_name, i+1, 1, 1,
"NONAME", string, &anynull, &status);
fits_read_col(fptr, TDOUBLE, col_xyz, i+1, 1, 1,
NULL, &(header->antenna[i].x), NULL, &status);
fits_read_col(fptr, TDOUBLE, col_xyz, i+1, 2, 1,
NULL, &(header->antenna[i].y), NULL, &status);
fits_read_col(fptr, TDOUBLE, col_xyz, i+1, 3, 1,
NULL, &(header->antenna[i].z), NULL, &status);
if (DEBUG)
fprintf(stderr, " %s %8.3f %8.3f %8.3f\n", header->antenna[i].name,
header->antenna[i].x, header->antenna[i].y, header->antenna[i].z);
}
fprintf(stderr, " %d antennas ", (int) nrows);
for (i=0; i < nrows; i++)
fprintf(stderr, " %s", header->antenna[i].name);
fprintf(stderr, "\n");
return status ? 1 : 0;
}
int read_data(const char *filename,const char *extname, int colnum, long firstelem, long nelements, double *data)
{
firstelem++; //from 0 to 1 based
int status = 0, anynul;
double doublenull = 0.;
fitsfile *fptr;
fits_open_file(&fptr, filename, READONLY, &status);
fits_movnam_hdu(fptr, BINARY_TBL, extname, 0, &status);
fits_read_col(fptr, TDOUBLE, colnum, firstelem, 1, nelements, &doublenull, data, &anynul, &status);
fits_close_file(fptr, &status);
if (status) /* print any error messages */
fits_report_error(stderr, status);
return(status);
}
int read_offs ( char *name, int subint, double *offs, int nchan, int npol)
//int main (int argc, char *argv[] )
{
fitsfile *fptr; // pointer to the FITS file, defined in fitsio.h
int status;
int colnum;
status = 0;
if ( fits_open_file(&fptr, name, READONLY, &status) ) // open the file
//if ( fits_open_file(&fptr, argv[1], READONLY, &status) ) // open the file
{
printf( "error while openning file\n" );
}
if ( fits_get_colnum(fptr, CASEINSEN, "DAT_OFFS", &colnum, &status) ) // get the colnum number
{
printf( "error while getting the colnum number\n" );
//fits_get_colnum(fptr, CASEINSEN, "DATA", &colnum, &status);
}
//printf ("%d\n", colnum);
int frow;
int felem = 1;
int nelem = nchan*npol;
int null = 0;
int anynull = 0;
//int subint = 1;
//int nchan = 8;
//double wts[nchan];
frow = subint;
fits_read_col(fptr, TDOUBLE, colnum, frow, felem, nelem, &null, offs, &anynull, &status); // read the column
//int i;
//for (i = 0; i < nchan; i++) // print the results
//{
//puts(line[0]);
// printf("%lf\n", wts[i]);
//fprintf (fp, "%s\n", line[0]);
//}
if ( fits_close_file(fptr, &status) )
{
printf( " error while closing the file \n" );
}
return 0;
}
void WMAPSource::addToMetadata( fitsfile *ffits, const int iNumCols, int &iStatus )
{
QString str;
char charTemplate[ FLEN_CARD ];
char charName[ FLEN_CARD ];
long lRepeat;
long lWidth;
int iTypeCode;
int iColNumber;
int iResult;
int entry;
int col;
for( col=0; col<iNumCols; col++ )
{
iResult = fits_get_coltype( ffits, col+1, &iTypeCode, &lRepeat, &lWidth, &iStatus );
if( iResult == 0 )
{
sprintf( charTemplate, "%d", col+1 );
iResult = fits_get_colname( ffits, CASEINSEN, charTemplate, charName, &iColNumber, &iStatus );
if( iResult == 0 )
{
if( lRepeat == 3 )
{
QString strValue;
double dNan = strtod( "nan", NULL );
double value;
int iAnyNull;
for( entry=0; entry<lRepeat; entry++ )
{
iResult = fits_read_col( ffits, TDOUBLE, iColNumber, 1, entry+1, 1, &dNan, &value, &iAnyNull, &iStatus );
if( iResult == 0 )
{
KstString *metaString;
QString keyname = QString("%1_%2").arg(charName).arg(QChar('X'+entry));
KstObjectTag newTag( keyname, tag( ) );
strValue = QString("%1").arg(value);
metaString = new KstString( newTag, this, strValue );
_metaData.insert( keyname, metaString );
}
}
}
}
}
}
}
void InputFileFITS::_read(int ncol, std::vector<T>& buff, int type, long frow, long lrow) {
int status = 0;
if(!isOpened())
throwException("Error in InputFileFITS::read() ", status);
int anynull;
long nelem = lrow - frow + 1;
long null = 0;
buff.resize(nelem);
fits_read_col(infptr, type, ncol+1, frow+1, 1, nelem, &null, &buff[0], &anynull, &status);
if(status)
throwException("Error in InputFileFITS::read() ", status);
}
/*
如果是IQUV模式，则按此函数来初始化一个二维unsigned char型数组
*/
void initTotalI(fitsfile* fptr,struct Fitsinfo* fi,unsigned char** iptr,int* status) {
int n = fi->nROW; int k = fi->nSBLK; int m = fi->nCHAN;
int step = fi->nCHAN*fi->nPOL; int start;
unsigned char fluxI[m];
int dataCol; int nulval = 0; int anynull; int i,j,p;
fits_get_colnum(fptr,CASEINSEN,"DATA",&dataCol,status);
for (i=0; i<n; i++) {
for (j=0; j<k; j++) {
start = 1+j*step;
fits_read_col(fptr,TBYTE,dataCol,i+1,start,m,&nulval,fluxI,&anynull,status);
for (p=0; p<m; p++) {
iptr[j+i*k][p] = fluxI[p];
}
}
printf("All Freq I init:Totalrow %d,row completed %d\n",n,i);
}
}
/**
* Function: get_lcolumn_from_SPC_opened
* The function reads the values from a column with long specified
* by its name into a array of type long. The array is returned.
*
* Parameters:
* @param SPC_ptr - pointer to the SPC extension
* @param count_col - name of the column to load
* @param nelems - number of elements in the column
*
* Returns:
* @return values - pointer to a filled array
*/
long *
get_lcolumn_from_SPC_opened(fitsfile *SPC_ptr, char colname[], int nelems)
{
int colnum=0;
int anynul;
int f_status=0;
long *values;
// allocate the return array;
// give an error if allocation fails
values = (long *) malloc(nelems * sizeof(long));
if (!values) {
aXe_message (aXe_M_ERROR, __FILE__, __LINE__,
"Memory allocation failed");
}
// get the desired column number;
// give an error if the column name
// can not be read
fits_get_colnum (SPC_ptr, CASEINSEN, colname, &colnum, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_dcolumn_from_SPC_opened: "
"Could not determine column %s in "
" table!\n", colname);
}
// read all data in the column
fits_read_col (SPC_ptr, TLONG, colnum, 1, 1, nelems, NULL, values,
&anynul, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_dcolumn_from_SPC_opened: "
"Could not read column %s"
" from BINARY table!",colname);
}
// return the filled array
return values;
}
// Reads a Healpix FITS file containing the map2alm weights into a double array:
int ReadHealpixWeights(int col, int nside, double *weights) {
char message[200];
std::string filename;
fitsfile *fpointer;
int status=0, anynul=0;
long i, firstrow=1, firstelem=1, nelements=2*nside;
double *nulval;
filename = HEALPIX_DATA;
if (filename.at(filename.length()-1)!='/') filename = filename+"/";
filename = filename+"weight_ring_n"+ZeroPad(nside, 10000)+".fits";
// Open file:
fits_open_table(&fpointer, filename.c_str(), READONLY, &status);
if (status!=0) {
sprintf(message, "ReadHealpixWeights: could not open table in FITS file, ERR=%d", status);
warning(message);
}
// Prepare to, read and check for errors:
nulval = vector<double>(0, nelements-1);
for(i=0; i<nelements; i++) nulval[i]=666.0;
fits_read_col(fpointer, TDOUBLE, col, firstrow, firstelem, nelements, nulval, weights, &anynul, &status);
if (status!=0) {
sprintf(message, "ReadHealpixWeights: problem reading column in FITS file table, ERR=%d", status);
warning(message);
}
if(anynul!=0) {
warning("ReadHealpixWeights: found NULL values in FITS table");
printf("They are:\n");
for (i=0; i<nelements; i++) printf("%g ",nulval[i]);
printf("\n");
}
free_vector(nulval, 0, nelements-1);
// Close file and exit:
fits_close_file(fpointer, &status);
if (status!=0) {
sprintf(message, "ReadHealpixWeights: could not close FITS file, ERR=%d", status);
warning(message);
}
return status;
}
int cfits_read_int_col (int *column_values, long num_values,
long firstrow, const char *colname, cfitsfile *fptr)
{
int datatype = TINT;
int nulval = 0;
int status = 0;
long firstelem = 1;
int anynul, colnum;
if (-1 == cfits_get_colnum (&colnum, colname, fptr))
{
column_values = NULL;
return -1;
}
(void) fits_read_col ((fitsfile *) fptr, datatype, colnum, firstrow,
firstelem, num_values, (void *) &nulval,
(void *) column_values, &anynul, &status);
cfits_report_error (status);
if (status != 0) return -1;
return 0;
}
int get_PSRFITS_rawblock(float *fdata, struct spectra_info *s, int *padding)
// This routine reads a single block (i.e subint) from the input files
// which contain raw data in PSRFITS format. If padding is
// returned as 1, then padding was added and statistics should not be
// calculated. Return 1 on success.
{
int numtopad = 0, numtoread, status = 0, anynull;
float *fdataptr = fdata;
double offs_sub;
fdataptr = fdata + numbuffered * s->num_channels;
// numtoread is always this size since we need to read
// full PSRFITS subints...
numtoread = s->spectra_per_subint;
// If our buffer array is offset from last time,
// copy the previously offset part into the beginning.
// New data comes after the old data in the buffer.
if (numbuffered)
memcpy(fdata, fdata + numtoread * s->num_channels,
numbuffered * s->num_channels * sizeof(float));
// Make sure our current file number is valid
if (cur_file >= s->num_files) return 0;
// Read a subint of data from the DATA col
if (cur_subint <= s->num_subint[cur_file]) {
// Read the OFFS_SUB column value in case there were dropped blocks
fits_read_col(s->fitsfiles[cur_file], TDOUBLE,
s->offs_sub_col, cur_subint, 1L, 1L,
0, &offs_sub, &anynull, &status);
// Set last_offs_sub to proper value
if (cur_subint==1 && (offs_sub < s->time_per_subint)) {
if (cur_file==0) {
// This is for the first time
last_offs_sub = offs_sub - s->time_per_subint;
} else {
// And this is if we are combining observations
last_offs_sub = (s->start_spec[cur_file] -
(cur_spec + numbuffered)) * s->dt -
0.5 * s->time_per_subint;
}
}
// The following determines if there were lost blocks. We should
// always be within 0.5 sample (and only that big if we are putting
// two different observations together).
if (fabs((offs_sub - last_offs_sub) - s->time_per_subint) < 0.5 * s->dt) {
// if things look good, with no missing blocks, read the data
get_PSRFITS_subint(fdataptr, cdatabuffer, s);
last_offs_sub = offs_sub;
cur_subint++;
goto return_block;
} else {
if (offs_sub < last_offs_sub) { // Files out of order? Shouldn't get here.
fprintf(stderr, "Error!: Current subint has earlier time than previous!\n\n"
"\tfilename = '%s', subint = %d\n"
"\tlast_offs_sub = %20.15f offs_sub = %20.15f\n",
s->filenames[cur_file], cur_subint, last_offs_sub, offs_sub);
exit(1);
} else { // there is some missing data, use padding
numtopad = (int)round((offs_sub - last_offs_sub) / s->dt) - numbuffered;
if (numtopad > s->spectra_per_subint) numtopad = s->spectra_per_subint;
add_padding(fdataptr, s->padvals, s->num_channels, numtopad);
// Update the time of the last subs based on this padding
last_offs_sub += numtopad * s->dt;
// Update pointer into the buffer
numbuffered = (numbuffered + numtopad) % s->spectra_per_subint;
// Set the padding flag
*padding = 1;
// If we haven't gotten a full block, or completed the buffered one
// then recursively call get_PSRFITS_rawblock()
if (numbuffered)
return get_PSRFITS_rawblock(fdata, s, padding);
else
goto return_block;
}
}
} else {
// We can't read anymore... so read OFFS_SUB for the last row
// of the current file to see about padding
fits_read_col(s->fitsfiles[cur_file], TDOUBLE,
s->offs_sub_col, s->num_subint[cur_file], 1L, 1L,
0, &offs_sub, &anynull, &status);
}
if (s->num_pad[cur_file]==0 ||
(fabs(last_offs_sub - offs_sub) < 0.5 * s->dt)) {
// No padding is necessary. The second check means that the
// lack of data we noticed upon reading the file was due to
// dropped data in the middle of the file that we already
// fixed. So no padding is really necessary.
cur_file++;
cur_subint = 1;
return get_PSRFITS_rawblock(fdata, s, padding);
} else { // add padding
// Set offs_sub to the correct offs_sub time for the first
// row of the next file. Since that might or might not
// be from a different observation, use absolute times from
// the start of the observation for both offs_sub and last_offs_sub
offs_sub = s->start_spec[cur_file+1] * s->dt + 0.5 * s->time_per_subint;
last_offs_sub = (cur_spec + numbuffered) * s->dt - 0.5 * s->time_per_subint;
// Compute the amount of required padding
numtopad = (int)round((offs_sub - last_offs_sub) / s->dt) - numbuffered;
if (numtopad > s->spectra_per_subint) numtopad = s->spectra_per_subint;
add_padding(fdataptr, s->padvals, s->num_channels, numtopad);
// Update the time of the last subs based on this padding
last_offs_sub += numtopad * s->dt;
// Update pointer into the buffer
numbuffered = (numbuffered + numtopad) % s->spectra_per_subint;
// Set the padding flag
*padding = 1;
// If we haven't gotten a full block, or completed the buffered one
// then recursively call get_PSRFITS_rawblock()
if (numbuffered)
return get_PSRFITS_rawblock(fdata, s, padding);
else
goto return_block;
}
return_block:
// Apply the corrections that need a full block
// Invert the band if needed
if (s->apply_flipband) flip_band(fdata, s);
// Perform Zero-DMing if requested
if (s->remove_zerodm) remove_zerodm(fdata, s);
// Increment our static counter (to determine how much data we
// have written on the fly).
cur_spec += s->spectra_per_subint;
return 1;
}
void read_PSRFITS_files(struct spectra_info *s)
// Read and convert PSRFITS information from a group of files
// and place the resulting info into a spectra_info structure.
{
int IMJD, SMJD, itmp, ii, status = 0;
double OFFS, dtmp;
long double MJDf;
char ctmp[80], comment[120];
s->datatype = PSRFITS;
s->fitsfiles = (fitsfile **)malloc(sizeof(fitsfile *) * s->num_files);
s->start_subint = gen_ivect(s->num_files);
s->num_subint = gen_ivect(s->num_files);
s->start_spec = (long long *)malloc(sizeof(long long) * s->num_files);
s->num_spec = (long long *)malloc(sizeof(long long) * s->num_files);
s->num_pad = (long long *)malloc(sizeof(long long) * s->num_files);
s->start_MJD = (long double *)malloc(sizeof(long double) * s->num_files);
s->N = 0;
s->num_beams = 1;
s->get_rawblock = &get_PSRFITS_rawblock;
s->offset_to_spectra = &offset_to_PSRFITS_spectra;
// By default, don't flip the band. But don't change
// the input value if it is aleady set to flip the band always
if (s->apply_flipband==-1) s->apply_flipband = 0;
// Step through the other files
for (ii = 0 ; ii < s->num_files ; ii++) {
// Is the file a PSRFITS file?
if (!is_PSRFITS(s->filenames[ii])) {
fprintf(stderr,
"\nError! File '%s' does not appear to be PSRFITS!\n",
s->filenames[ii]);
exit(1);
}
// Open the PSRFITS file
fits_open_file(&(s->fitsfiles[ii]), s->filenames[ii], READONLY, &status);
// Is the data in search mode?
fits_read_key(s->fitsfiles[ii], TSTRING, "OBS_MODE", ctmp, comment, &status);
// Quick fix for Parkes DFB data (SRCH? why????)...
if (strcmp("SRCH", ctmp)==0) {
strncpy(ctmp, "SEARCH", 40);
}
if (strcmp(ctmp, "SEARCH")) {
fprintf(stderr,
"\nError! File '%s' does not contain SEARCH-mode data!\n",
s->filenames[ii]);
exit(1);
}
// Now get the stuff we need from the primary HDU header
fits_read_key(s->fitsfiles[ii], TSTRING, "TELESCOP", ctmp, comment, &status); \
// Quick fix for MockSpec data...
if (strcmp("ARECIBO 305m", ctmp)==0) {
strncpy(ctmp, "Arecibo", 40);
}
// Quick fix for Parkes DFB data...
{
char newctmp[80];
// Copy ctmp first since strlower() is in-place
strcpy(newctmp, ctmp);
if (strcmp("parkes", strlower(remove_whitespace(newctmp)))==0) {
strncpy(ctmp, "Parkes", 40);
}
}
if (status) {
printf("Error %d reading key %s\n", status, "TELESCOP");
if (ii==0) s->telescope[0]='\0';
if (status==KEY_NO_EXIST) status=0;
} else {
if (ii==0) strncpy(s->telescope, ctmp, 40);
else if (strcmp(s->telescope, ctmp)!=0)
printf("Warning!: %s values don't match for files 0 and %d!\n",
"TELESCOP", ii);
}
get_hdr_string("OBSERVER", s->observer);
get_hdr_string("SRC_NAME", s->source);
get_hdr_string("FRONTEND", s->frontend);
get_hdr_string("BACKEND", s->backend);
get_hdr_string("PROJID", s->project_id);
get_hdr_string("DATE-OBS", s->date_obs);
get_hdr_string("FD_POLN", s->poln_type);
get_hdr_string("RA", s->ra_str);
get_hdr_string("DEC", s->dec_str);
get_hdr_double("OBSFREQ", s->fctr);
get_hdr_int("OBSNCHAN", s->orig_num_chan);
get_hdr_double("OBSBW", s->orig_df);
//get_hdr_double("CHAN_DM", s->chan_dm);
get_hdr_double("BMIN", s->beam_FWHM);
/* This is likely not in earlier versions of PSRFITS so */
/* treat it a bit differently */
fits_read_key(s->fitsfiles[ii], TDOUBLE, "CHAN_DM",
&(s->chan_dm), comment, &status);
if (status==KEY_NO_EXIST) {
status = 0;
s->chan_dm = 0.0;
}
// Don't use the macros unless you are using the struct!
fits_read_key(s->fitsfiles[ii], TINT, "STT_IMJD", &IMJD, comment, &status);
s->start_MJD[ii] = (long double) IMJD;
fits_read_key(s->fitsfiles[ii], TINT, "STT_SMJD", &SMJD, comment, &status);
fits_read_key(s->fitsfiles[ii], TDOUBLE, "STT_OFFS", &OFFS, comment, &status);
s->start_MJD[ii] += ((long double) SMJD + (long double) OFFS) / SECPERDAY;
// Are we tracking?
fits_read_key(s->fitsfiles[ii], TSTRING, "TRK_MODE", ctmp, comment, &status);
itmp = (strcmp("TRACK", ctmp)==0) ? 1 : 0;
if (ii==0) s->tracking = itmp;
else if (s->tracking != itmp)
printf("Warning!: TRK_MODE values don't match for files 0 and %d!\n", ii);
// Now switch to the SUBINT HDU header
fits_movnam_hdu(s->fitsfiles[ii], BINARY_TBL, "SUBINT", 0, &status);
get_hdr_double("TBIN", s->dt);
get_hdr_int("NCHAN", s->num_channels);
get_hdr_int("NPOL", s->num_polns);
get_hdr_string("POL_TYPE", s->poln_order);
fits_read_key(s->fitsfiles[ii], TINT, "NCHNOFFS", &itmp, comment, &status);
if (itmp > 0)
printf("Warning!: First freq channel is not 0 in file %d!\n", ii);
get_hdr_int("NSBLK", s->spectra_per_subint);
get_hdr_int("NBITS", s->bits_per_sample);
fits_read_key(s->fitsfiles[ii], TINT, "NAXIS2",
&(s->num_subint[ii]), comment, &status);
fits_read_key(s->fitsfiles[ii], TINT, "NSUBOFFS",
&(s->start_subint[ii]), comment, &status);
s->time_per_subint = s->dt * s->spectra_per_subint;
/* This is likely not in earlier versions of PSRFITS so */
/* treat it a bit differently */
fits_read_key(s->fitsfiles[ii], TFLOAT, "ZERO_OFF",
&(s->zero_offset), comment, &status);
if (status==KEY_NO_EXIST) {
status = 0;
s->zero_offset = 0.0;
}
s->zero_offset = fabs(s->zero_offset);
// Get the time offset column info and the offset for the 1st row
{
double offs_sub;
int colnum, anynull, numrows;
// Identify the OFFS_SUB column number
fits_get_colnum(s->fitsfiles[ii], 0, "OFFS_SUB", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the OFFS_SUB column!\n");
status = 0; // Reset status
} else {
if (ii==0) {
s->offs_sub_col = colnum;
} else if (colnum != s->offs_sub_col) {
printf("Warning!: OFFS_SUB column changes between files!\n");
}
}
// Read the OFFS_SUB column value for the 1st row
fits_read_col(s->fitsfiles[ii], TDOUBLE,
s->offs_sub_col, 1L, 1L, 1L,
0, &offs_sub, &anynull, &status);
numrows = (int)((offs_sub - 0.5 * s->time_per_subint) /
s->time_per_subint + 1e-7);
// Check to see if any rows have been deleted or are missing
if (numrows > s->start_subint[ii]) {
printf("Warning: NSUBOFFS reports %d previous rows\n"
" but OFFS_SUB implies %d. Using OFFS_SUB.\n"
" Will likely be able to correct for this.\n",
s->start_subint[ii], numrows);
}
s->start_subint[ii] = numrows;
}
// This is the MJD offset based on the starting subint number
MJDf = (s->time_per_subint * s->start_subint[ii]) / SECPERDAY;
// The start_MJD values should always be correct
s->start_MJD[ii] += MJDf;
// Compute the starting spectra from the times
MJDf = s->start_MJD[ii] - s->start_MJD[0];
if (MJDf < 0.0) {
fprintf(stderr, "Error!: File %d seems to be from before file 0!\n", ii);
exit(1);
}
s->start_spec[ii] = (long long)(MJDf * SECPERDAY / s->dt + 0.5);
// Now pull stuff from the other columns
{
float ftmp;
long repeat, width;
int colnum, anynull;
// Identify the data column and the data type
fits_get_colnum(s->fitsfiles[ii], 0, "DATA", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the DATA column!\n");
status = 0; // Reset status
} else {
if (ii==0) {
s->data_col = colnum;
fits_get_coltype(s->fitsfiles[ii], colnum, &(s->FITS_typecode),
&repeat, &width, &status);
} else if (colnum != s->data_col) {
printf("Warning!: DATA column changes between files!\n");
}
}
// Telescope azimuth
fits_get_colnum(s->fitsfiles[ii], 0, "TEL_AZ", &colnum, &status);
if (status==COL_NOT_FOUND) {
s->azimuth = 0.0;
status = 0; // Reset status
} else {
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum,
1L, 1L, 1L, 0, &ftmp, &anynull, &status);
if (ii==0) s->azimuth = (double) ftmp;
}
// Telescope zenith angle
fits_get_colnum(s->fitsfiles[ii], 0, "TEL_ZEN", &colnum, &status);
if (status==COL_NOT_FOUND) {
s->zenith_ang = 0.0;
status = 0; // Reset status
} else {
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum,
1L, 1L, 1L, 0, &ftmp, &anynull, &status);
if (ii==0) s->zenith_ang = (double) ftmp;
}
// Observing frequencies
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_FREQ", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel freq column!\n");
status = 0; // Reset status
} else {
int jj;
float *freqs = (float *)malloc(sizeof(float) * s->num_channels);
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum, 1L, 1L,
s->num_channels, 0, freqs, &anynull, &status);
if (ii==0) {
s->df = freqs[1]-freqs[0];
s->lo_freq = freqs[0];
s->hi_freq = freqs[s->num_channels-1];
// Now check that the channel spacing is the same throughout
for (jj = 0 ; jj < s->num_channels - 1 ; jj++) {
ftmp = freqs[jj+1] - freqs[jj];
if (fabs(ftmp - s->df) > 1e-7)
printf("Warning!: Channel spacing changes in file %d!\n", ii);
}
} else {
ftmp = fabs(s->df-(freqs[1]-freqs[0]));
if (ftmp > 1e-7)
printf("Warning!: Channel spacing changes between files!\n");
ftmp = fabs(s->lo_freq-freqs[0]);
if (ftmp > 1e-7)
printf("Warning!: Low channel changes between files!\n");
ftmp = fabs(s->hi_freq-freqs[s->num_channels-1]);
if (ftmp > 1e-7)
printf("Warning!: High channel changes between files!\n");
}
free(freqs);
}
// Data weights
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_WTS", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel weights!\n");
status = 0; // Reset status
} else {
if (s->apply_weight < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_wts_col = colnum;
} else if (colnum != s->dat_wts_col) {
printf("Warning!: DAT_WTS column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) * s->num_channels);
fits_read_col(s->fitsfiles[ii], TFLOAT, s->dat_wts_col, 1L, 1L,
s->num_channels, 0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels ; jj++) {
// If the weights are not 1, apply them
if (fvec[jj] != 1.0) {
s->apply_weight = 1;
break;
}
}
free(fvec);
}
if (s->apply_weight < 0) s->apply_weight = 0; // not needed
}
// Data offsets
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_OFFS", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel offsets!\n");
status = 0; // Reset status
} else {
if (s->apply_offset < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_offs_col = colnum;
} else if (colnum != s->dat_offs_col) {
printf("Warning!: DAT_OFFS column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) *
s->num_channels * s->num_polns);
fits_read_col(s->fitsfiles[ii], TFLOAT, s->dat_offs_col, 1L, 1L,
s->num_channels * s->num_polns,
0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels * s->num_polns ; jj++) {
// If the offsets are not 0, apply them
if (fvec[jj] != 0.0) {
s->apply_offset = 1;
break;
}
}
free(fvec);
}
if (s->apply_offset < 0) s->apply_offset = 0; // not needed
}
// Data scalings
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_SCL", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel scalings!\n");
status = 0; // Reset status
} else {
if (s->apply_scale < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_scl_col = colnum;
} else if (colnum != s->dat_scl_col) {
printf("Warning!: DAT_SCL column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) *
s->num_channels * s->num_polns);
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum, 1L, 1L,
s->num_channels * s->num_polns,
0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels * s->num_polns ; jj++) {
// If the scales are not 1, apply them
if (fvec[jj] != 1.0) {
s->apply_scale = 1;
break;
}
}
free(fvec);
}
if (s->apply_scale < 0) s->apply_scale = 0; // not needed
}
}
// Compute the samples per file and the amount of padding
// that the _previous_ file has
s->num_pad[ii] = 0;
s->num_spec[ii] = s->spectra_per_subint * s->num_subint[ii];
if (ii > 0) {
if (s->start_spec[ii] > s->N) { // Need padding
s->num_pad[ii-1] = s->start_spec[ii] - s->N;
s->N += s->num_pad[ii-1];
}
}
s->N += s->num_spec[ii];
}
// Convert the position strings into degrees
{
int d, h, m;
double sec;
ra_dec_from_string(s->ra_str, &h, &m, &sec);
s->ra2000 = hms2rad(h, m, sec) * RADTODEG;
ra_dec_from_string(s->dec_str, &d, &m, &sec);
s->dec2000 = dms2rad(d, m, sec) * RADTODEG;
}
// Are the polarizations summed?
if ((strncmp("AA+BB", s->poln_order, 5)==0) ||
(strncmp("INTEN", s->poln_order, 5)==0))
s->summed_polns = 1;
else
s->summed_polns = 0;
// Calculate some others
s->T = s->N * s->dt;
s->orig_df /= (double) s->orig_num_chan;
s->samples_per_spectra = s->num_polns * s->num_channels;
// Note: the following is the number of bytes that will be in
// the returned array from CFITSIO.
// CFITSIO turns bits into bytes when FITS_typecode=1
// and we turn 2-bits or 4-bits into bytes if bits_per_sample < 8
if (s->bits_per_sample < 8)
s->bytes_per_spectra = s->samples_per_spectra;
else
s->bytes_per_spectra = (s->bits_per_sample * s->samples_per_spectra) / 8;
s->samples_per_subint = s->samples_per_spectra * s->spectra_per_subint;
s->bytes_per_subint = s->bytes_per_spectra * s->spectra_per_subint;
// Flip the band?
if (s->hi_freq < s->lo_freq) {
float ftmp = s->hi_freq;
s->hi_freq = s->lo_freq;
s->lo_freq = ftmp;
s->df *= -1.0;
s->apply_flipband = 1;
}
// Compute the bandwidth
s->BW = s->num_channels * s->df;
// Flip the bytes for Parkes FB_1BIT data
if (s->bits_per_sample==1 &&
strcmp(s->telescope, "Parkes")==0 &&
strcmp(s->backend, "FB_1BIT")==0) {
printf("Flipping bit ordering since Parkes FB_1BIT data.\n");
s->flip_bytes = 1;
} else {
s->flip_bytes = 0;
}
// Allocate the buffers
cdatabuffer = gen_bvect(s->bytes_per_subint);
// Following is twice as big because we use it as a ringbuffer too
fdatabuffer = gen_fvect(2 * s->spectra_per_subint * s->num_channels);
s->padvals = gen_fvect(s->num_channels);
for (ii = 0 ; ii < s->num_channels ; ii++)
s->padvals[ii] = 0.0;
offsets = gen_fvect(s->num_channels * s->num_polns);
scales = gen_fvect(s->num_channels * s->num_polns);
weights = gen_fvect(s->num_channels);
// Initialize these if we won't be reading them from the file
if (s->apply_offset==0)
for (ii = 0 ; ii < s->num_channels * s->num_polns ; ii++)
offsets[ii] = 0.0;
if (s->apply_scale==0)
for (ii = 0 ; ii < s->num_channels * s->num_polns ; ii++)
scales[ii] = 1.0;
if (s->apply_weight==0)
for (ii = 0 ; ii < s->num_channels ; ii++)
weights[ii] = 1.0;
}
// Return the number of channels
int readBandpass(fitsfile *fp,float *bpass)
{
int status=0;
int samplesperbyte;
long nrows;
int colnum;
int j,pol,subint;
int initflag=0;
float val=1;
float nval = 0;
long npts;
int start,end;
int i,anynul;
float dat_offs,dat_scl;
float freq,bw,chanbw;
long nchan;
int naxis;
int typecode;
long repeat,width;
// Go to bandpass table
fits_movnam_hdu(fp,BINARY_TBL,"BANDPASS",1,&status);
if (status) {
printf("Unable to move to bandpass table in FITS file\n");
exit(1);
}
fits_get_colnum(fp,CASEINSEN,"DAT_OFFS",&colnum,&status);
fits_read_col(fp,TFLOAT,colnum,1,1,1,&nval,&dat_offs,&anynul,&status);
if (status){
printf("Error in bandpass header 1\n");
fits_report_error(stderr,status);
exit(1);
}
fits_get_colnum(fp,CASEINSEN,"DAT_SCL",&colnum,&status);
fits_read_col(fp,TFLOAT,colnum,1,1,1,&nval,&dat_scl,&anynul,&status);
if (status){
printf("Error in bandpass header\n");
fits_report_error(stderr,status);
exit(1);
}
fits_get_colnum(fp,CASEINSEN,"DATA",&colnum,&status);
if (status){
fits_report_error(stderr,status);
exit(1);
}
fits_get_coltype(fp,colnum,&typecode,&repeat,&width,&status);
nchan = (int)repeat-1; // Don't read the first channel
printf("nc = %d, na = %d\n",(int)nchan,(int)naxis);
for (i=1;i<(int)nchan;i++)
{
fits_read_col(fp,TFLOAT,colnum,1,i+1,1,&nval,&val,&anynul,&status);
bpass[i-1] = val*dat_scl + dat_offs;
if (status){
fits_report_error(stderr,status);
exit(1);
}
}
fits_close_file(fp,&status);
return nchan;
}