int extractAvePlane (char *cubepath, char *impath, int iplane, int nplaneave,
int *splaneave, int *eplaneave, char *errmsg)
{
struct stat buf;
struct FitsHdr hdr;
char str[1024];
char cmd[1024];
int bitpix;
int istatus;
int nhdu, hdutype, hdunum;
int nelements;
int naxis3;
int l;
int j;
int i;
int jj;
int nullcnt;
int splane;
int eplane;
long fpixel[4];
long fpixelo[4];
double *fitsbuf;
double *imbuff;
fitsfile *infptr;
fitsfile *outfptr;
int debugfile = 1;
int debugfile1 = 0;
/*
Make a NaN value to use setting blank pixels
*/
union
{
double d;
char c[8];
}
value;
double nan;
for(i=0; i<8; ++i)
value.c[i] = 255;
nan = value.d;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "\nEnter extractAvePlane: cubepath= [%s]\n",
cubepath);
fprintf (fp_debug, "iplane= [%d]\n", iplane);
fprintf (fp_debug, "nplaneave= [%d]\n", nplaneave);
fprintf (fp_debug, "impath= [%s]\n", impath);
fflush (fp_debug);
}
splane = iplane - nplaneave/2;
eplane = splane + nplaneave - 1;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "splane= [%d] eplane= [%d]\n", splane, eplane);
fflush (fp_debug);
}
istatus = 0;
if (fits_open_file (&infptr, cubepath, READONLY, &istatus)) {
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "istatus= [%d]\n", istatus);
fflush (fp_debug);
}
sprintf (errmsg, "Failed to open FITS file [%s]\n", cubepath);
return (-1);
}
hdunum = 1;
nhdu = 0;
istatus = 0;
istatus = fits_get_num_hdus (infptr, &nhdu, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug,
"returned fits_get_hdu_num: istatus= [%d] nhdu= [%d]\n",
istatus, nhdu);
fflush (fp_debug);
}
if (hdunum > nhdu) {
sprintf (errmsg, "fname [%s] doesn't contain any HDU", cubepath);
return (-1);
}
/*
Read fits keywords from the first HDU
*/
hdutype = 0;
istatus = 0;
istatus = fits_movabs_hdu (infptr, hdunum, &hdutype, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug,
"returned fits_movabs_hdu: istatus= [%d] hdutype= [%d]\n",
istatus, hdutype);
fflush (fp_debug);
}
/*
Read fits keywords
*/
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "simple", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword SIMPLE not found in fits header");
return (-1);
}
if ((strcmp (str, "T") != 0) && (strcmp (str, "F") != 0)) {
sprintf (errmsg, "keyword SIMPLE must be T or F");
return (-1);
}
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "bitpix", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword BITPIX not found in fits header");
return (-1);
}
istatus = str2Integer (str, &bitpix, errmsg);
if (istatus != 0) {
sprintf (errmsg, "keyword BITPIX must be an integer");
return (-1);
}
if ((bitpix != 8) &&
(bitpix != 16) &&
(bitpix != 32) &&
(bitpix != 64) &&
(bitpix != -32) &&
(bitpix != -64)) {
sprintf (errmsg,
"keyword BITPIX value must be 8, 16, 32, 64, -32, -64");
return (-1);
}
hdr.bitpix = bitpix;
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.naxis, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis to integer");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "naxis= [%d]\n", hdr.naxis);
fflush (fp_debug);
}
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis1", str, (char *)NULL,
&istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis1 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.ns, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis1 string to integer");
return (-1);
}
hdr.naxes[0] = hdr.ns;
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis2", str,
(char *)NULL, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis2 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.nl, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis2 string to integer");
return (-1);
}
hdr.naxes[1] = hdr.nl;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "ns= [%d] nl= [%d]\n", hdr.ns, hdr.nl);
fflush (fp_debug);
}
hdr.nplane = 1;
if (hdr.naxis > 2) {
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis3", str,
(char *)NULL, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n",
istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis3 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.naxes[2], errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis3 string to integer");
return (-1);
}
hdr.nplane = hdr.naxes[2];
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "naxes[2]= [%d]\n", hdr.naxes[2]);
fflush (fp_debug);
}
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "nplane= [%d]\n", hdr.nplane);
fflush (fp_debug);
}
istatus = stat (impath, &buf);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "impath exists? : istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus >= 0) {
sprintf (cmd, "unlink %s", impath);
istatus = system (cmd);
}
/*
Create output fits file
*/
istatus = 0;
if (fits_create_file (&outfptr, impath, &istatus)) {
sprintf (errmsg, "Failed to create output fitsfile [%s]\n", impath);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "err: [%s]\n", errmsg);
fflush (fp_debug);
}
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "outptr created\n");
fflush (fp_debug);
}
/*
Copy input fits header to output fitsfile
*/
istatus = 0;
if (fits_copy_header (infptr, outfptr, &istatus)) {
strcpy (errmsg, "Failed to copy fitshdr\n");
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "err: [%s]\n", errmsg);
fflush (fp_debug);
}
return (-1);
}
/*
Update header keyword NAXIS3
*/
naxis3 = 1;
istatus = 0;
if (fits_update_key_lng(outfptr, "NAXIS3", naxis3, (char *)NULL,
&istatus)) {
strcpy (errmsg, "Failed to update keyword NAXIS3\n");
return (-1);
}
istatus = 0;
if (fits_close_file (infptr, &istatus)) {
sprintf (errmsg, "Failed to close cubepath [%s]\n", cubepath);
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "cubepath= [%s]\n", cubepath);
fflush (fp_debug);
}
istatus = 0;
if (fits_open_file (&infptr, cubepath, READONLY, &istatus)) {
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "istatus= [%d]\n", istatus);
fflush (fp_debug);
}
sprintf (errmsg, "Failed to open FITS file [%s]\n", cubepath);
return (-1);
}
/*
Create imbuff for average image
*/
imbuff = (double *)malloc (hdr.ns*hdr.nl*sizeof(double));
for (i=0; i<hdr.nl*hdr.ns; i++) {
imbuff[i] = 0.;
}
/*
Read data from nth plane and write to output fitsfile
*/
nelements = hdr.ns;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "iplane= [%d]\n", iplane);
fflush (fp_debug);
}
fitsbuf = (double *)malloc(hdr.ns*sizeof(double));
if (splane < 1)
splane = 1;
if (eplane > hdr.nplane)
eplane = hdr.nplane;
for (l=splane; l<=eplane; l++) {
fpixel[0] = 1;
fpixel[1] = 1;
fpixel[2] = l;
fpixel[3] = 1;
for (j=0; j<hdr.nl; j++) {
if (j == 0) {
if ((debugfile1) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "l= [%d] fpixel[2]= [%ld]\n",
l, fpixel[2]);
fflush (fp_debug);
}
}
if (fits_read_pix (infptr, TDOUBLE, fpixel, nelements, &nan,
fitsbuf, &nullcnt, &istatus)) {
break;
}
if (j == 10) {
if ((debugfile1) && (fp_debug != (FILE *)NULL)) {
for (i=0; i<hdr.ns; i++) {
fprintf (fp_debug, "j= [%d] i= [%d] fitsbuf= [%lf]\n",
j, i, fitsbuf[i]);
fprintf (fp_debug, "fitsbuf/nplaneave= [%lf]\n",
fitsbuf[i]/nplaneave);
}
fflush (fp_debug);
}
}
/*
Copy data to imbuff for plane averaging
*/
jj = hdr.ns*j;
if ((debugfile1) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "jj= [%d]\n", jj);
fflush (fp_debug);
}
for (i=0; i<hdr.ns; i++) {
imbuff[jj+i] += fitsbuf[i]/nplaneave;
}
if (j == 10) {
if ((debugfile1) && (fp_debug != (FILE *)NULL)) {
for (i=0; i<hdr.ns; i++) {
fprintf (fp_debug, "j= [%d] i= [%d] imbuff= [%lf]\n",
j, i, imbuff[jj+i]);
}
fflush (fp_debug);
}
}
fpixel[1]++;
}
}
/*
Write averaged image to output FITS file
*/
fpixelo[0] = 1;
fpixelo[1] = 1;
fpixelo[2] = 1;
fpixelo[3] = 1;
for (j=0; j<hdr.nl; j++) {
jj = hdr.ns*j;
for (i=0; i<hdr.ns; i++) {
fitsbuf[i] = imbuff[jj+i];
}
if (j == 10) {
if ((debugfile1) && (fp_debug != (FILE *)NULL)) {
for (i=0; i<hdr.ns; i++) {
fprintf (fp_debug, "j= [%d] i= [%d] fitsbuf= [%lf]\n",
j, i, fitsbuf[i]);
}
fflush (fp_debug);
}
}
if (fits_write_pix (outfptr, TDOUBLE, fpixelo, nelements,
(void *)fitsbuf, &istatus)) {
sprintf (errmsg, "fits write error: l= [%d]\n", l);
return (-1);
}
fpixelo[1]++;
}
istatus = 0;
if (fits_close_file (infptr, &istatus)) {
sprintf (errmsg, "Failed to close cubepath [%s]\n", cubepath);
return (-1);
}
istatus = 0;
if (fits_close_file (outfptr, &istatus)) {
sprintf (errmsg, "Failed to close impath [%s]\n", impath);
return (-1);
}
*splaneave = splane;
*eplaneave = eplane;
return (0);
}
int montage_copyHeaderInfo(fitsfile *infptr, fitsfile *outfptr, struct imageParams *params)
{
double tmp;
int naxis2;
int status = 0;
if(fits_copy_header(infptr, outfptr, &status))
montage_printFitsError(status);
/**********************/
/* Update header info */
/**********************/
if(fits_update_key_lng(outfptr, "BITPIX", -64,
(char *)NULL, &status))
montage_printFitsError(status);
if(fits_update_key_lng(outfptr, "NAXIS", 2,
(char *)NULL, &status))
montage_printFitsError(status);
if(fits_update_key_lng(outfptr, "NAXIS1", params->nelements,
(char *)NULL, &status))
montage_printFitsError(status);
naxis2 = params->jend - params->jbegin + 1;
if(fits_update_key_lng(outfptr, "NAXIS2", naxis2,
(char *)NULL, &status))
montage_printFitsError(status);
if(params->isDSS)
{
tmp = params->cnpix[0] + params->ibegin - 1;
if(fits_update_key_dbl(outfptr, "CNPIX1", tmp, -14,
(char *)NULL, &status))
montage_printFitsError(status);
tmp = params->cnpix[1] + params->jbegin - 1;
if(fits_update_key_dbl(outfptr, "CNPIX2", tmp, -14,
(char *)NULL, &status))
montage_printFitsError(status);
}
else
{
tmp = params->crpix[0] - params->ibegin + 1;
if(fits_update_key_dbl(outfptr, "CRPIX1", tmp, -14,
(char *)NULL, &status))
montage_printFitsError(status);
tmp = params->crpix[1] - params->jbegin + 1;
if(fits_update_key_dbl(outfptr, "CRPIX2", tmp, -14,
(char *)NULL, &status))
montage_printFitsError(status);
}
if(debug)
{
printf("naxis1 -> %ld\n", params->nelements);
printf("naxis2 -> %d\n", naxis2);
if(params->isDSS)
{
printf("cnpix1 -> %-g\n", params->cnpix[0]+params->ibegin-1);
printf("cnpix2 -> %-g\n", params->cnpix[1]+params->jbegin-1);
}
else
{
printf("crpix1 -> %-g\n", params->crpix[0]-params->ibegin+1);
printf("crpix2 -> %-g\n", params->crpix[1]-params->jbegin+1);
}
fflush(stdout);
}
return 0;
}
int main(int argc, char *argv[])
{
static struct option long_opts[] = {
{"start", 1, NULL, 's'},
{"end", 1, NULL, 'e'},
{0,0,0,0}
};
fitsfile *infptr, *outfptr; /* FITS file pointers defined in fitsio.h */
int opt, opti;
int i, status = 0, ii = 1, jj=1; /* status must always be initialized = 0 */
int lo_row, hi_row;
unsigned char *buffer = 0;
long nrows;
int ncols;
int tfields;
long pcount;
char extname[FLEN_VALUE];
char *ttype[NFIELDS_I];
char *tform[NFIELDS_I];
char *tunit[NFIELDS_I];
char *tcomm[NFIELDS_I];
float start=0.0, end=1.0;
while ((opt=getopt_long(argc,argv,"s:e:h",long_opts,&opti))!=-1) {
switch (opt) {
case 's':
start = atof(optarg);
break;
case 'e':
end = atof(optarg);
break;
case 'h':
default:
usage();
exit(0);
break;
}
}
if (argc < 3)
{
usage();
return(0);
}
//printf("> %s %s\n", argv[1], argv[2]);
//printf("> %s %s\n", argv[optind], argv[2]);
/* Allocate space for the table parameters and initialize */
for (i=0; i<NFIELDS_I; i++)
{
ttype[i] = (char *) malloc(FLEN_VALUE*sizeof(char));
tform[i] = (char *) malloc(FLEN_VALUE*sizeof(char));
tunit[i] = (char *) malloc(FLEN_VALUE*sizeof(char));
tcomm[i] = (char *) malloc(FLEN_CARD*sizeof(char));
strcpy(ttype[i], " ");
}
/* Open the input file */
if ( !fits_open_file(&infptr, argv[optind], READONLY, &status) )
{
/* Create the output file */
if ( !fits_create_file(&outfptr, argv[optind+1], &status) )
{
/* Copy every HDU until we get an error */
//while( !fits_movabs_hdu(infptr, ii++, NULL, &status) )
/* Copy first HDU */
fits_copy_hdu(infptr, outfptr, 0, &status);
fits_movnam_hdu(infptr, BINARY_TBL, "SUBINT", 0, &status);
fits_get_num_rows(infptr, &nrows, &status);
printf("Number of rows = %ld\n", nrows);
fits_get_num_cols(infptr, &ncols, &status);
printf("Number of cols = %d\n", ncols);
long width;
fits_read_key(infptr, TLONG, "NAXIS1", &width, NULL, &status);
printf("Width = %ld\n", width);
buffer = (unsigned char *) malloc(width);
/* Copy the fits header */
fits_copy_header(infptr, outfptr, &status);
//#if 0
/* Determine low and high row number ot copy */
lo_row = 1 + start * nrows;
hi_row = end * nrows;
printf("lo_row=%d hi_row=%d\n", lo_row, hi_row);
for (ii=lo_row, jj=1; ii<=hi_row; ii++, jj++) {
printf("\rRead %d/%ld", ii, nrows);
fits_read_tblbytes( infptr, ii, 1, width, buffer, &status);
fits_write_tblbytes(outfptr, jj, 1, width, buffer, &status);
}
nrows = (hi_row-lo_row)+1;
fits_update_key(outfptr, TLONG, "NAXIS2", &nrows, 0, &status);
printf("\nDone\n");
//#endif
/* Reset status after normal error */
//if (status == END_OF_FILE) status = 0;
fits_close_file(outfptr, &status);
}
fits_close_file(infptr, &status);
}
/* if error occured, print out error message */
if (status) fits_report_error(stderr, status);
return(status);
}
int main(int argc, char *argv[])
{
fitsfile *afptr, *outfptr; /* FITS file pointers */
int status = 0; /* CFITSIO status value MUST be initialized to zero! */
int anaxis, check = 1, keytype;
long npixels = 1, firstpix[3] = {1,1,1};
long anaxes[3] = {1,1,1};
double *apix;
char card[FLEN_CARD];
if (argc != 3) {
printf("Usage: tofitsbp16 inimage outimage \n");
printf("\n");
printf("Compiled from cfitsio v2.460\n");
printf("\n");
printf("Converts a FITS from BITPIX = -32 to BITPIX = 16\n");
printf("\n");
printf("Example: \n");
printf(" tofitsbp16 in.fit out.fits.\n");
return(0);
}
fits_open_file(&afptr, argv[1], READONLY, &status); /* open input images */
fits_get_img_dim(afptr, &anaxis, &status); /* read dimensions */
fits_get_img_size(afptr, 3, anaxes, &status);
if (status) {
fits_report_error(stderr, status); /* print error message */
return(status);
}
/* create the new empty output file if the above checks are OK */
if (check && !fits_create_file(&outfptr, argv[2], &status) )
{
/* copy all the header keywords from first image to new output file */
fits_copy_header(afptr, outfptr, &status);
/* change to 16 bit integer variable */
fits_modify_key_lng (outfptr, "BITPIX", 16, "&", &status );
npixels = anaxes[0]; /* no. of pixels to read in each row */
apix = (double *) malloc(npixels * sizeof(double)); /* mem for 1 row */
if (apix == NULL) {
printf("Memory allocation error\n");
return(1);
}
/* loop over all planes of the cube (2D images have 1 plane) */
for (firstpix[2] = 1; firstpix[2] <= anaxes[2]; firstpix[2]++)
{
/* loop over all rows of the plane */
for (firstpix[1] = 1; firstpix[1] <= anaxes[1]; firstpix[1]++)
{
/* Read both images as doubles, regardless of actual datatype. */
/* Give starting pixel coordinate and no. of pixels to read. */
/* This version does not support undefined pixels in the image. */
if (fits_read_pix(afptr, TDOUBLE, firstpix, npixels, NULL, apix,
NULL, &status) )
break; /* jump out of loop on error */
fits_write_pix(outfptr, TDOUBLE, firstpix, npixels,
apix, &status); /* write new values to output image */
}
} /* end of loop over planes */
fits_close_file(outfptr, &status);
free(apix);
}
fits_close_file(afptr, &status);
if (status) fits_report_error(stderr, status); /* print any error message */
return(status);
}
struct mShrinkReturn *mShrink(char *input_file, int hduin, char *output_file, double shrinkFactor, int fixedSize, int debug)
{
int i, j, ii, jj, status, bufrow, split;
int ibuffer, jbuffer, ifactor, nbuf, nullcnt, k, l, imin, imax, jmin, jmax;
long fpixel[4], fpixelo[4], nelements, nelementso;
double obegin, oend;
double *colfact, *rowfact;
double *buffer;
double xfactor, flux, area;
double *outdata;
double **indata;
struct mShrinkReturn *returnStruct;
/************************************************/
/* Make a NaN value to use setting blank pixels */
/************************************************/
union
{
double d;
char c[8];
}
value;
double nan;
for(i=0; i<8; ++i)
value.c[i] = 255;
nan = value.d;
/*******************************/
/* Initialize return structure */
/**n****************************/
returnStruct = (struct mShrinkReturn *)malloc(sizeof(struct mShrinkReturn));
bzero((void *)returnStruct, sizeof(returnStruct));
returnStruct->status = 1;
strcpy(returnStruct->msg, "");
/***************************************/
/* Process the command-line parameters */
/***************************************/
time(&currtime);
start = currtime;
hdu = hduin;
xfactor = shrinkFactor;
if(!fixedSize)
{
ifactor = ceil(xfactor);
if((double)ifactor < xfactor)
xfactor += 2;
}
if(xfactor <= 0)
{
if(fixedSize)
mShrink_printError("Requested image size must be positive");
else
mShrink_printError("Shrink factor must be positive");
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(debug >= 1)
{
printf("input_file = [%s]\n", input_file);
printf("output_file = [%s]\n", output_file);
printf("xfactor = %-g\n", xfactor);
printf("ifactor = %d\n", ifactor);
fflush(stdout);
}
/************************/
/* Read the input image */
/************************/
if(mShrink_readFits(input_file))
{
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
// Error if we are trying to shrink to less than one pixel
if(!fixedSize
&& ( shrinkFactor > input.naxes[0]
|| shrinkFactor > input.naxes[1]))
{
mShrink_printError("Trying to shrink image to smaller than one pixel");
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(debug >= 1)
{
printf("\nflux file = %s\n", input_file);
printf("input.bitpix = %ld\n", input.bitpix);
printf("input.naxes[0] = %ld\n", input.naxes[0]);
printf("input.naxes[1] = %ld\n", input.naxes[1]);
if(haveCtype) printf("input.ctype1 = %s\n", input.ctype1);
if(haveCtype) printf("input.typel2 = %s\n", input.ctype2);
if(haveCrval) printf("input.crval1 = %-g\n", input.crval1);
if(haveCrval) printf("input.crval2 = %-g\n", input.crval2);
if(haveCrpix) printf("input.crpix1 = %-g\n", input.crpix1);
if(haveCrpix) printf("input.crpix2 = %-g\n", input.crpix2);
if(haveCnpix) printf("input.cnpix1 = %-g\n", input.cnpix1);
if(haveCnpix) printf("input.cnpix2 = %-g\n", input.cnpix2);
if(havePixelsz) printf("input.xpixelsz = %-g\n", input.xpixelsz);
if(havePixelsz) printf("input.ypixelsz = %-g\n", input.ypixelsz);
if(havePP) printf("input.ppo3 = %-g\n", input.ppo3);
if(havePP) printf("input.ppo6 = %-g\n", input.ppo6);
if(haveCdelt) printf("input.cdelt1 = %-g\n", input.cdelt1);
if(haveCdelt) printf("input.cdelt2 = %-g\n", input.cdelt2);
if(haveCrota2) printf("input.crota2 = %-g\n", input.crota2);
if(haveCD11) printf("input.cd11 = %-g\n", input.cd11);
if(haveCD12) printf("input.cd12 = %-g\n", input.cd12);
if(haveCD21) printf("input.cd21 = %-g\n", input.cd21);
if(haveCD22) printf("input.cd22 = %-g\n", input.cd22);
if(havePC11) printf("input.pc11 = %-g\n", input.pc11);
if(havePC12) printf("input.pc12 = %-g\n", input.pc12);
if(havePC21) printf("input.pc21 = %-g\n", input.pc21);
if(havePC22) printf("input.pc22 = %-g\n", input.pc22);
if(haveEpoch) printf("input.epoch = %-g\n", input.epoch);
if(haveEquinox) printf("input.equinox = %-g\n", input.equinox);
if(haveBunit) printf("input.bunit = %s\n", input.bunit);
if(haveBlank) printf("input.blank = %ld\n", input.blank);
printf("\n");
fflush(stdout);
}
/***********************************************/
/* If we are going for a fixed size, the scale */
/* factor needs to be computed. */
/***********************************************/
if(fixedSize)
{
if(input.naxes[0] > input.naxes[1])
xfactor = (double)input.naxes[0]/(int)xfactor;
else
xfactor = (double)input.naxes[1]/(int)xfactor;
ifactor = ceil(xfactor);
if((double)ifactor < xfactor)
xfactor += 2;
if(debug >= 1)
{
printf("xfactor -> %-g\n", xfactor);
printf("ifactor -> %d\n", ifactor);
fflush(stdout);
}
}
/***********************************************/
/* Compute all the parameters for the shrunken */
/* output file. */
/***********************************************/
output.naxes[0] = floor((double)input.naxes[0]/xfactor);
output.naxes[1] = floor((double)input.naxes[1]/xfactor);
if(debug >= 1)
{
printf("output.naxes[0] = %ld\n", output.naxes[0]);
printf("output.naxes[1] = %ld\n", output.naxes[1]);
fflush(stdout);
}
strcpy(output.ctype1, input.ctype1);
strcpy(output.ctype2, input.ctype2);
output.crval1 = input.crval1;
output.crval2 = input.crval2;
output.crpix1 = (input.crpix1-0.5)/xfactor + 0.5;
output.crpix2 = (input.crpix2-0.5)/xfactor + 0.5;
output.cdelt1 = input.cdelt1*xfactor;
output.cdelt2 = input.cdelt2*xfactor;
output.crota2 = input.crota2;
output.cd11 = input.cd11*xfactor;
output.cd12 = input.cd12*xfactor;
output.cd21 = input.cd21*xfactor;
output.cd22 = input.cd22*xfactor;
output.pc11 = input.pc11;
output.pc12 = input.pc12;
output.pc21 = input.pc21;
output.pc22 = input.pc22;
output.epoch = input.epoch;
output.equinox = input.equinox;
strcpy(output.bunit, input.bunit);
if(haveCnpix)
{
input.crpix1 = input.ppo3 / input.xpixelsz - input.cnpix1 + 0.5;
input.crpix2 = input.ppo6 / input.ypixelsz - input.cnpix2 + 0.5;
output.crpix1 = (input.crpix1-0.5)/xfactor + 0.5;
output.crpix2 = (input.crpix2-0.5)/xfactor + 0.5;
output.xpixelsz = input.xpixelsz * xfactor;
output.ypixelsz = input.ypixelsz * xfactor;
output.cnpix1 = input.ppo3 / output.xpixelsz - output.crpix1 + 0.5;
output.cnpix2 = input.ppo6 / output.ypixelsz - output.crpix2 + 0.5;
}
/********************************/
/* Create the output FITS files */
/********************************/
status = 0;
remove(output_file);
if(fits_create_file(&output.fptr, output_file, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
/******************************************************/
/* Create the FITS image. Copy over the whole header */
/******************************************************/
if(fits_copy_header(input.fptr, output.fptr, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(debug >= 1)
{
printf("\nFITS header copied to output\n");
fflush(stdout);
}
/************************************/
/* Reset all the WCS header kewords */
/************************************/
if(fits_update_key_lng(output.fptr, "NAXIS", 2,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(fits_update_key_lng(output.fptr, "NAXIS1", output.naxes[0],
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(fits_update_key_lng(output.fptr, "NAXIS2", output.naxes[1],
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveBunit && fits_update_key_str(output.fptr, "BUNIT", output.bunit,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveBlank && fits_update_key_lng(output.fptr, "BLANK", output.blank,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCtype && fits_update_key_str(output.fptr, "CTYPE1", output.ctype1,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCtype && fits_update_key_str(output.fptr, "CTYPE2", output.ctype2,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCrval && fits_update_key_dbl(output.fptr, "CRVAL1", output.crval1, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCrval && fits_update_key_dbl(output.fptr, "CRVAL2", output.crval2, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCrpix && fits_update_key_dbl(output.fptr, "CRPIX1", output.crpix1, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCrpix && fits_update_key_dbl(output.fptr, "CRPIX2", output.crpix2, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCnpix && fits_update_key_dbl(output.fptr, "CNPIX1", output.cnpix1, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCnpix && fits_update_key_dbl(output.fptr, "CNPIX2", output.cnpix2, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePixelsz && fits_update_key_dbl(output.fptr, "XPIXELSZ", output.xpixelsz, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePixelsz && fits_update_key_dbl(output.fptr, "YPIXELSZ", output.ypixelsz, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCdelt && fits_update_key_dbl(output.fptr, "CDELT1", output.cdelt1, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCdelt && fits_update_key_dbl(output.fptr, "CDELT2", output.cdelt2, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCrota2 && fits_update_key_dbl(output.fptr, "CROTA2", output.crota2, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCD11 && fits_update_key_dbl(output.fptr, "CD1_1", output.cd11, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCD12 && fits_update_key_dbl(output.fptr, "CD1_2", output.cd12, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCD21 && fits_update_key_dbl(output.fptr, "CD2_1", output.cd21, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveCD22 && fits_update_key_dbl(output.fptr, "CD2_2", output.cd22, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePC11 && fits_update_key_dbl(output.fptr, "PC1_1", output.pc11, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePC12 && fits_update_key_dbl(output.fptr, "PC1_2", output.pc12, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePC21 && fits_update_key_dbl(output.fptr, "PC2_1", output.pc21, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(havePC22 && fits_update_key_dbl(output.fptr, "PC2_2", output.pc22, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveEpoch && fits_update_key_dbl(output.fptr, "EPOCH", output.epoch, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(haveEquinox && fits_update_key_dbl(output.fptr, "EQUINOX", output.equinox, -14,
(char *)NULL, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(debug >= 1)
{
printf("Output header keywords set\n\n");
fflush(stdout);
}
/***********************************************/
/* Allocate memory for a line of output pixels */
/***********************************************/
outdata = (double *)malloc(output.naxes[0] * sizeof(double));
/*************************************************************************/
/* We could probably come up with logic that would work for both scale */
/* factors of less than one and greater than one but the it would be too */
/* hard to follow. Instead, we put in a big switch here to deal with */
/* the two cases separately. */
/*************************************************************************/
if(xfactor < 1.)
{
/************************************************/
/* Allocate memory for "ifactor" lines of input */
/************************************************/
nbuf = 2;
indata = (double **)malloc(nbuf * sizeof(double *));
for(j=0; j<nbuf; ++j)
indata[j] = (double *)malloc((input.naxes[0]+1) * sizeof(double));
/**********************************************************/
/* Create the output array by processing the input pixels */
/**********************************************************/
ibuffer = 0;
buffer = (double *)malloc(input.naxes[0] * sizeof(double));
colfact = (double *)malloc(nbuf * sizeof(double));
rowfact = (double *)malloc(nbuf * sizeof(double));
fpixel[0] = 1;
fpixel[1] = 1;
fpixel[2] = 1;
fpixel[3] = 1;
fpixelo[0] = 1;
fpixelo[1] = 1;
nelements = input.naxes[0];
status = 0;
/******************************/
/* Loop over the output lines */
/******************************/
split = 0;
for(l=0; l<output.naxes[1]; ++l)
{
obegin = (fpixelo[1] - 1.) * xfactor;
oend = fpixelo[1] * xfactor;
if(floor(oend) == oend)
oend = obegin;
if(debug >= 2)
{
printf("OUTPUT row %d: obegin = %.2f -> oend = %.3f\n\n", l, obegin, oend);
fflush(stdout);
}
rowfact[0] = 1.;
rowfact[1] = 0.;
/******************************************/
/* If we have gone over into the next row */
/******************************************/
if(l == 0 || (int)oend > (int)obegin)
{
rowfact[0] = 1.;
rowfact[1] = 0.;
if(l > 0)
{
split = 1;
jbuffer = (ibuffer + 1) % nbuf;
rowfact[1] = (oend - (int)(fpixelo[1] * xfactor))/xfactor;
rowfact[0] = 1. - rowfact[1];
}
else
{
jbuffer = 0;
}
if(debug >= 2)
{
printf("Reading input image row %5ld (ibuffer %d)\n", fpixel[1], jbuffer);
fflush(stdout);
}
if(debug >= 2)
{
printf("Rowfact: %-g %-g\n", rowfact[0], rowfact[1]);
fflush(stdout);
}
/***********************************/
/* Read a line from the input file */
/***********************************/
if(fpixel[1] <= input.naxes[1])
{
if(fits_read_pix(input.fptr, TDOUBLE, fpixel, nelements, &nan,
buffer, &nullcnt, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
}
++fpixel[1];
/************************/
/* For each input pixel */
/************************/
indata[jbuffer][input.naxes[0]] = nan;
for (i=0; i<input.naxes[0]; ++i)
{
indata[jbuffer][i] = buffer[i];
if(debug >= 4)
{
printf("input: line %5ld / pixel %5d: indata[%d][%d] = %10.3e\n",
fpixel[1]-2, i, jbuffer, i, indata[jbuffer][i]);
fflush(stdout);
}
}
if(debug >= 4)
{
printf("---\n");
fflush(stdout);
}
}
/*************************************/
/* Write out the next line of output */
/*************************************/
nelementso = output.naxes[0];
for(k=0; k<nelementso; ++k)
{
/* When "expanding" we never need to use more than two */
/* pixels in more than two rows. The row factors were */
/* computed above and the column factors will be compute */
/* here as we go. */
outdata[k] = nan;
colfact[0] = 1.;
colfact[1] = 0.;
obegin = (double)k * xfactor;
oend = ((double)k+1.) * xfactor;
if(floor(oend) == oend)
oend = obegin;
imin = (int)obegin;
if((int)oend > (int)obegin)
{
colfact[1] = (oend - (int)(((double)k+1.) * xfactor))/xfactor;
colfact[0] = 1. - colfact[1];
}
flux = 0;
area = 0;
for(jj=0; jj<2; ++jj)
{
if(rowfact[jj] == 0.)
continue;
for(ii=0; ii<2; ++ii)
{
bufrow = (ibuffer + jj) % nbuf;
if(!mNaN(indata[bufrow][imin+ii]) && colfact[ii] > 0.)
{
flux += indata[bufrow][imin+ii] * colfact[ii] * rowfact[jj];
area += colfact[ii] * rowfact[jj];
if(debug >= 3)
{
printf("output[%d][%d] -> %10.2e (area: %10.2e) (using indata[%d][%d] = %10.2e, colfact[%d] = %5.3f, rowfact[%d] = %5.3f)\n",
l, k, flux, area,
bufrow, imin+ii, indata[bufrow][imin+ii],
imin+ii, colfact[ii],
jj, rowfact[jj]);
fflush(stdout);
}
}
}
}
if(area > 0.)
outdata[k] = flux/area;
else
outdata[k] = nan;
if(debug >= 3)
{
printf("\nflux[%d] = %-g / area = %-g --> outdata[%d] = %-g\n",
k, flux, area, k, outdata[k]);
printf("---\n");
fflush(stdout);
}
}
if(fpixelo[1] <= output.naxes[1])
{
if(debug >= 2)
{
printf("\nWRITE output image row %5ld\n===========================================\n", fpixelo[1]);
fflush(stdout);
}
if (fits_write_pix(output.fptr, TDOUBLE, fpixelo, nelementso,
(void *)(outdata), &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
}
++fpixelo[1];
if(split)
{
ibuffer = jbuffer;
split = 0;
}
/***************************************************************/
/* Special case: The expansion factor is integral and we have */
/* gotten to the point where we need the next line. */
/***************************************************************/
oend = fpixelo[1] * xfactor;
if(fpixel[1] <= input.naxes[1] && floor(oend) == oend)
{
if(debug >= 2)
{
printf("Reading input image row %5ld (ibuffer %d)\n", fpixel[1], jbuffer);
fflush(stdout);
}
if(fits_read_pix(input.fptr, TDOUBLE, fpixel, nelements, &nan,
buffer, &nullcnt, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
++fpixel[1];
indata[jbuffer][input.naxes[0]] = nan;
for (i=0; i<input.naxes[0]; ++i)
{
indata[jbuffer][i] = buffer[i];
if(debug >= 4)
{
printf("input: line %5ld / pixel %5d: indata[%d][%d] = %10.3e\n",
fpixel[1]-2, i, jbuffer, i, indata[jbuffer][i]);
fflush(stdout);
}
}
if(debug >= 4)
{
printf("---\n");
fflush(stdout);
}
}
}
}
else
{
/************************************************/
/* Allocate memory for "ifactor" lines of input */
/************************************************/
nbuf = ifactor + 1;
indata = (double **)malloc(nbuf * sizeof(double *));
for(j=0; j<nbuf; ++j)
indata[j] = (double *)malloc(input.naxes[0] * sizeof(double));
/**********************************************************/
/* Create the output array by processing the input pixels */
/**********************************************************/
ibuffer = 0;
buffer = (double *)malloc(input.naxes[0] * sizeof(double));
colfact = (double *)malloc(input.naxes[0] * sizeof(double));
rowfact = (double *)malloc(input.naxes[1] * sizeof(double));
fpixel[0] = 1;
fpixel[1] = 1;
fpixel[2] = 1;
fpixel[3] = 1;
fpixelo[0] = 1;
fpixelo[1] = 1;
nelements = input.naxes[0];
status = 0;
/*****************************/
/* Loop over the input lines */
/*****************************/
l = 0;
obegin = (double)l * xfactor;
oend = ((double)l+1.) * xfactor;
jmin = floor(obegin);
jmax = ceil (oend);
for(jj=jmin; jj<=jmax; ++jj)
{
rowfact[jj-jmin] = 1.;
if(jj <= obegin && jj+1 <= oend) rowfact[jj-jmin] = jj+1. - obegin;
else if(jj <= obegin && jj+1 >= oend) rowfact[jj-jmin] = oend - obegin;
else if(jj >= obegin && jj+1 >= oend) rowfact[jj-jmin] = oend - jj;
if(rowfact[jj-jmin] < 0.)
rowfact[jj-jmin] = 0.;
if(debug >= 4)
{
printf("rowfact[%d] %-g\n", jj, rowfact[jj]);
fflush(stdout);
}
}
for (j=0; j<input.naxes[1]; ++j)
{
if(debug >= 2)
{
printf("Reading input image row %5ld (ibuffer %d)\n", fpixel[1], ibuffer);
fflush(stdout);
}
/***********************************/
/* Read a line from the input file */
/***********************************/
if(fits_read_pix(input.fptr, TDOUBLE, fpixel, nelements, &nan,
buffer, &nullcnt, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
++fpixel[1];
/************************/
/* For each input pixel */
/************************/
for (i=0; i<input.naxes[0]; ++i)
{
indata[ibuffer][i] = buffer[i];
if(debug >= 4)
{
printf("input: line %5d / pixel %5d: indata[%d][%d] = %10.2e\n",
j, i, ibuffer, i, indata[ibuffer][i]);
fflush(stdout);
}
}
if(debug >= 4)
{
printf("---\n");
fflush(stdout);
}
/**************************************************/
/* If we have enough for the next line of output, */
/* compute and write it */
/**************************************************/
if(j == jmax || fpixel[1] == input.naxes[1])
{
nelementso = output.naxes[0];
for(k=0; k<nelementso; ++k)
{
/* OK, we are trying to determine the correct flux */
/* for output pixel k in output line l. We have all */
/* the input lines we need (modulo looping back from */
/* indata[ibuffer]) */
outdata[k] = nan;
obegin = (double)k * xfactor;
oend = ((double)k+1.) * xfactor;
imin = floor(obegin);
imax = ceil (oend);
if(debug >= 3)
{
printf("\nimin = %4d, imax = %4d, jmin = %4d, jmax = %4d\n", imin, imax, jmin, jmax);
fflush(stdout);
}
flux = 0;
area = 0;
for(ii=imin; ii<=imax; ++ii)
{
colfact[ii-imin] = 1.;
if(ii <= obegin && ii+1 <= oend) colfact[ii-imin] = ii+1. - obegin;
else if(ii <= obegin && ii+1 >= oend) colfact[ii-imin] = oend - obegin;
else if(ii >= obegin && ii+1 >= oend) colfact[ii-imin] = oend - ii;
if(colfact[ii-imin] < 0.)
colfact[ii-imin] = 0.;
}
for(jj=jmin; jj<=jmax; ++jj)
{
if(rowfact[jj-jmin] == 0.)
continue;
for(ii=imin; ii<=imax; ++ii)
{
bufrow = (ibuffer - jmax + jj + nbuf) % nbuf;
if(!mNaN(indata[bufrow][ii]) && colfact[ii-imin] > 0.)
{
flux += indata[bufrow][ii] * colfact[ii-imin] * rowfact[jj-jmin];
area += colfact[ii-imin] * rowfact[jj-jmin];
if(debug >= 3)
{
printf("output[%d][%d] -> %10.2e (area: %10.2e) (using indata[%d][%d] = %10.2e, colfact[%d-%d] = %5.3f, rowfact[%d-%d] = %5.3f)\n",
l, k, flux, area,
bufrow, ii, indata[bufrow][ii],
ii, imin, colfact[ii-imin],
jj, jmin, rowfact[jj-jmin]);
fflush(stdout);
}
}
}
if(debug >= 3)
{
printf("---\n");
fflush(stdout);
}
}
if(area > 0.)
outdata[k] = flux/area;
else
outdata[k] = nan;
if(debug >= 3)
{
printf("\nflux = %-g / area = %-g --> outdata[%d] = %-g\n",
flux, area, k, outdata[k]);
fflush(stdout);
}
}
if(fpixelo[1] <= output.naxes[1])
{
if(debug >= 2)
{
printf("\nWRITE output image row %5ld\n===========================================\n", fpixelo[1]);
fflush(stdout);
}
if (fits_write_pix(output.fptr, TDOUBLE, fpixelo, nelementso,
(void *)(outdata), &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
}
++fpixelo[1];
++l;
obegin = (double)l * xfactor;
oend = ((double)l+1.) * xfactor;
jmin = floor(obegin);
jmax = ceil (oend);
for(jj=jmin; jj<=jmax; ++jj)
{
rowfact[jj-jmin] = 1.;
if(jj <= obegin && jj+1 <= oend) rowfact[jj-jmin] = jj+1. - obegin;
else if(jj <= obegin && jj+1 >= oend) rowfact[jj-jmin] = oend - obegin;
else if(jj >= obegin && jj+1 >= oend) rowfact[jj-jmin] = oend - jj;
if(rowfact[jj-jmin] < 0.)
rowfact[jj-jmin] = 0.;
if(debug >= 4)
{
printf("rowfact[%d-%d] -> %-g\n", jj, jmin, rowfact[jj-jmin]);
fflush(stdout);
}
}
}
ibuffer = (ibuffer + 1) % nbuf;
}
}
/*******************/
/* Close the files */
/*******************/
if(fits_close_file(input.fptr, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(fits_close_file(output.fptr, &status))
{
mShrink_printFitsError(status);
strcpy(returnStruct->msg, montage_msgstr);
return returnStruct;
}
if(debug >= 1)
{
printf("FITS data image finalized\n");
fflush(stdout);
}
time(&currtime);
returnStruct->status = 0;
sprintf(returnStruct->msg, "time=%.0f", (double)(currtime - start));
sprintf(returnStruct->json, "{\"time\"=%.0f}", (double)(currtime - start));
returnStruct->time = (double)(currtime - start);
return returnStruct;
}
int generateMedianPlane (char *cubepath, char *impath, int iplane,
int nplane_in, int *startplane, int *endplane, char *errmsg)
{
struct stat buf;
struct FitsHdr hdr;
char str[1024];
char cmd[1024];
int bitpix;
int istatus;
int nhdu, hdutype, hdunum;
long nelements;
int naxis3;
int l;
int i;
int j;
int jj;
int nullcnt;
int splane;
int eplane;
int nplane;
int indx;
int indx1;
int indx2;
int npixel;
int midpoint;
long fpixel[4];
long fpixelo[4];
double *fitscubebuf;
double *outbuf;
double *fitsbuf1d;
double *wavebuf;
fitsfile *infptr;
fitsfile *outfptr;
int debugfile = 1;
/*
Make a NaN value to use setting blank pixels
*/
union
{
double d;
char c[8];
}
value;
double nan;
for(i=0; i<8; ++i)
value.c[i] = 255;
nan = value.d;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "\nEnter generateMedianPlane: cubepath= [%s]\n",
cubepath);
fprintf (fp_debug, "impath= [%s]\n", impath);
fprintf (fp_debug, "iplane= [%d]\n", iplane);
fprintf (fp_debug, "nplane_in= [%d]\n", nplane_in);
fflush (fp_debug);
}
nplane = nplane_in;
splane = iplane - nplane/2;
eplane = splane + nplane - 1;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "splane= [%d] eplane= [%d]\n", splane, eplane);
fflush (fp_debug);
}
/*
Open input fits cube
*/
istatus = 0;
if (fits_open_file (&infptr, cubepath, READONLY, &istatus)) {
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "istatus= [%d]\n", istatus);
fflush (fp_debug);
}
sprintf (errmsg, "Failed to open FITS file [%s]\n", cubepath);
return (-1);
}
hdunum = 1;
nhdu = 0;
istatus = 0;
istatus = fits_get_num_hdus (infptr, &nhdu, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug,
"returned fits_get_hdu_num: istatus= [%d] nhdu= [%d]\n",
istatus, nhdu);
fflush (fp_debug);
}
if (hdunum > nhdu) {
sprintf (errmsg, "fname [%s] doesn't contain any HDU", cubepath);
return (-1);
}
/*
Read fits keywords from the first HDU
*/
hdutype = 0;
istatus = 0;
istatus = fits_movabs_hdu (infptr, hdunum, &hdutype, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug,
"returned fits_movabs_hdu: istatus= [%d] hdutype= [%d]\n",
istatus, hdutype);
fflush (fp_debug);
}
/*
Read fits keywords
*/
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "simple", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword SIMPLE not found in fits header");
return (-1);
}
if ((strcmp (str, "T") != 0) && (strcmp (str, "F") != 0)) {
sprintf (errmsg, "keyword SIMPLE must be T or F");
return (-1);
}
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "bitpix", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword BITPIX not found in fits header");
return (-1);
}
istatus = str2Integer (str, &bitpix, errmsg);
if (istatus != 0) {
sprintf (errmsg, "keyword BITPIX must be an integer");
return (-1);
}
if ((bitpix != 8) &&
(bitpix != 16) &&
(bitpix != 32) &&
(bitpix != 64) &&
(bitpix != -32) &&
(bitpix != -64)) {
sprintf (errmsg,
"keyword BITPIX value must be 8, 16, 32, 64, -32, -64");
return (-1);
}
hdr.bitpix = bitpix;
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis", str, (char *)NULL,
&istatus);
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.naxis, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis to integer");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "naxis= [%d]\n", hdr.naxis);
fflush (fp_debug);
}
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis1", str, (char *)NULL,
&istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis1 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.ns, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis1 string to integer");
return (-1);
}
hdr.naxes[0] = hdr.ns;
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis2", str,
(char *)NULL, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis2 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.nl, errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis2 string to integer");
return (-1);
}
hdr.naxes[1] = hdr.nl;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "ns= [%d] nl= [%d]\n", hdr.ns, hdr.nl);
fflush (fp_debug);
}
hdr.nplane = 1;
if (hdr.naxis > 2) {
istatus = 0;
istatus = fits_read_key (infptr, TSTRING, "naxis3", str,
(char *)NULL, &istatus);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "returned fits_read_key: istatus= [%d]\n",
istatus);
fflush (fp_debug);
}
if (istatus == KEY_NO_EXIST) {
sprintf (errmsg, "keyword naxis3 not found in fits header");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "str= [%s]\n", str);
fflush (fp_debug);
}
istatus = str2Integer (str, &hdr.naxes[2], errmsg);
if (istatus < 0) {
sprintf (errmsg, "Failed to convert naxis3 string to integer");
return (-1);
}
hdr.nplane = hdr.naxes[2];
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "naxes[2]= [%d]\n", hdr.naxes[2]);
fflush (fp_debug);
}
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "hdr.nplane= [%d]\n", hdr.nplane);
fflush (fp_debug);
}
if (splane < 1)
splane = 1;
if (eplane > hdr.nplane)
eplane = hdr.nplane;
nplane = eplane - splane + 1;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "hdr.nplane= [%d]\n", hdr.nplane);
fprintf (fp_debug, "splane= [%d] eplane= [%d]\n", splane, eplane);
fprintf (fp_debug, "nplane= [%d]\n", nplane);
fflush (fp_debug);
}
/*
malloc arrays for reading data
*/
fitscubebuf
= (double *)malloc(hdr.ns*hdr.nl*nplane*sizeof(double));
outbuf = (double *)malloc(hdr.ns*hdr.nl*sizeof(double));
wavebuf = (double *)malloc(nplane*sizeof(double));
fitsbuf1d = (double *)malloc(hdr.ns*sizeof(double));
nelements = hdr.ns;
npixel = hdr.ns*hdr.nl;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "npixel= [%d]\n", npixel);
fflush (fp_debug);
}
/*
Read cube data to fitscubebuf
*/
fpixel[0] = 1;
fpixel[3] = 1;
indx = 0;
for (l=splane; l<=eplane; l++)
{
indx2 = hdr.nl*hdr.ns*(l-splane);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "l= [%d]\n", l);
fflush (fp_debug);
}
fpixel[1] = 1;
fpixel[2] = l;
for (j=0; j<hdr.nl; j++)
{
indx1 = hdr.ns*j;
if (fits_read_pix (infptr, TDOUBLE, fpixel, nelements, &nan,
fitsbuf1d, &nullcnt, &istatus)) {
break;
}
for (i=0; i<nelements; i++) {
fitscubebuf[indx2+indx1+i] = fitsbuf1d[i];
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
if ((i == 30) && (j == 25)) {
fprintf (fp_debug, "i=[%d] j=[%d] l=[%d] pixel=[%lf]\n",
i, j, l, fitscubebuf[indx2+indx1+i]);
fflush (fp_debug);
}
}
}
fpixel[1]++;
}
}
/*
istatus = 0;
if (fits_close_file (infptr, &istatus)) {
sprintf (errmsg, "Failed to close cubepath [%s]\n", cubepath);
return (-1);
}
*/
/*
Extract wave axis and compute median values
*/
midpoint = nplane / 2;
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "midpint= [%d]\n", midpoint);
fflush (fp_debug);
}
for (j=0; j<hdr.nl; j++) {
indx1 = hdr.ns*j;
for (i=0; i<hdr.ns; i++) {
for (l=0; l<nplane; l++) {
indx = npixel*l + indx1 + i;
wavebuf[l] = fitscubebuf[indx];
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
if ((i == 30) && (j == 25)) {
fprintf (fp_debug, "i=[%d] j=[%d] l=[%d] pixel=[%lf]\n",
i, j, l, wavebuf[l]);
fflush (fp_debug);
}
}
}
sort (wavebuf, nplane);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
if ((i == 30) && (j == 25)) {
fprintf (fp_debug, "after qsort\n");
for (l=0; l<nplane; l++) {
fprintf (fp_debug, "l=[%d] pixel=[%lf]\n",
l, wavebuf[l]);
}
fflush (fp_debug);
}
}
outbuf[indx1+i] = wavebuf[midpoint];
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
if ((i == 30) && (j == 25)) {
fprintf (fp_debug, "outbuf= [%lf]\n", outbuf[indx1+i]);
fflush (fp_debug);
}
}
}
}
/*
Create output fits file
*/
istatus = stat (impath, &buf);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "impath exists? : istatus= [%d]\n", istatus);
fflush (fp_debug);
}
if (istatus >= 0) {
sprintf (cmd, "unlink %s", impath);
istatus = system (cmd);
}
istatus = 0;
if (fits_create_file (&outfptr, impath, &istatus)) {
sprintf (errmsg, "Failed to create output fitsfile [%s]\n",
impath);
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "err: [%s]\n", errmsg);
fflush (fp_debug);
}
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "outptr created\n");
fflush (fp_debug);
}
/*
Copy input fits header to output fitsfile
*/
istatus = 0;
if (fits_copy_header (infptr, outfptr, &istatus)) {
strcpy (errmsg, "Failed to copy fitshdr\n");
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "err: [%s]\n", errmsg);
fflush (fp_debug);
}
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "header copied\n");
fflush (fp_debug);
}
/*
Update header keyword NAXIS3
*/
naxis3 = 1;
istatus = 0;
if (fits_update_key_lng(outfptr, "NAXIS3", naxis3, (char *)NULL,
&istatus)) {
strcpy (errmsg, "Failed to update keyword NAXIS3\n");
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "naxis3 updated\n");
fflush (fp_debug);
}
/*
Write to output fitsfile
*/
nelements = hdr.ns;
fpixelo[0] = 1;
fpixelo[1] = 1;
fpixelo[2] = 1;
fpixelo[3] = 1;
for (j=0; j<hdr.nl; j++) {
jj = hdr.ns*j;
for (i=0; i<hdr.ns; i++) {
fitsbuf1d[i] = outbuf[jj+i];
}
if (fits_write_pix (outfptr, TDOUBLE, fpixelo, nelements,
(void *)fitsbuf1d, &istatus)) {
sprintf (errmsg, "fits write error: l= [%d] j= [%d]\n", l, j);
return (-1);
}
fpixelo[1]++;
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "here2\n");
fflush (fp_debug);
}
istatus = 0;
if (fits_close_file (infptr, &istatus)) {
sprintf (errmsg, "Failed to close cubepath [%s]\n", cubepath);
return (-1);
}
if ((debugfile) && (fp_debug != (FILE *)NULL)) {
fprintf (fp_debug, "here3\n");
fflush (fp_debug);
}
istatus = 0;
if (fits_close_file (outfptr, &istatus)) {
sprintf (errmsg, "Failed to close impath [%s]\n", impath);
return (-1);
}
*startplane = splane;
*endplane = eplane;
return (0);
}
int main(int argc, char *argv[])
{
fitsfile *afptr, *outfptr; /* FITS file pointers */
int status = 0; /* CFITSIO status value MUST be initialized to zero! */
int anaxis, check = 1, ii, op, keytype;
long npixels = 1, firstpix[3] = {1,1,1}, ntodo;
long anaxes[3] = {1,1,1};
double *apix;
double maxval, minval;
char card[FLEN_CARD];
if (argc != 5) {
printf("Usage: pruneimage image max min outimage \n");
printf("\n");
printf("Compiled from cfitsio v2.460\n");
printf("\n");
printf("Trim off the peaks and valley values of the image.\n");
printf("\n");
printf("outimage is of format BITPIX = -32\n");
printf("\n");
printf("Example: \n");
printf(" pruneimage in.fit 1000 850 out.fits - sets all values above 1000 to 1000\n");
printf(" and all values below 850 to 850.\n");
return(0);
}
fits_open_file(&afptr, argv[1], READONLY, &status); /* open input images */
fits_get_img_dim(afptr, &anaxis, &status); /* read dimensions */
fits_get_img_size(afptr, 3, anaxes, &status);
if (status) {
fits_report_error(stderr, status); /* print error message */
return(status);
}
if (anaxis > 3) {
printf("Error: images with > 3 dimensions are not supported\n");
check = 0;
}
maxval = atof ( argv[2] );
minval = atof ( argv[3] );
/* create the new empty output file if the above checks are OK */
if (check && !fits_create_file(&outfptr, argv[4], &status) )
{
/* copy all the header keywords from first image to new output file */
fits_copy_header(afptr, outfptr, &status);
/* change to floating point variable */
fits_modify_key_lng (outfptr, "BITPIX", -32, "&", &status );
fits_modify_key_flt (outfptr, "DATAMIN", minval, -10, "&", &status );
fits_modify_key_flt (outfptr, "DATAMAX", maxval, -10, "&", &status );
npixels = anaxes[0]; /* no. of pixels to read in each row */
apix = (double *) malloc(npixels * sizeof(double)); /* mem for 1 row */
if (apix == NULL) {
printf("Memory allocation error\n");
return(1);
}
/* loop over all planes of the cube (2D images have 1 plane) */
for (firstpix[2] = 1; firstpix[2] <= anaxes[2]; firstpix[2]++)
{
/* loop over all rows of the plane */
for (firstpix[1] = 1; firstpix[1] <= anaxes[1]; firstpix[1]++)
{
/* Read both images as doubles, regardless of actual datatype. */
/* Give starting pixel coordinate and no. of pixels to read. */
/* This version does not support undefined pixels in the image. */
if (fits_read_pix(afptr, TDOUBLE, firstpix, npixels, NULL, apix,
NULL, &status) )
break; /* jump out of loop on error */
for(ii=0; ii< npixels; ii++) {
if ( apix[ii] > maxval )
apix[ii] = maxval;
else if ( apix[ii] < minval )
apix[ii] = minval;
}
fits_write_pix(outfptr, TDOUBLE, firstpix, npixels,
apix, &status); /* write new values to output image */
}
} /* end of loop over planes */
fits_close_file(outfptr, &status);
free(apix);
}
fits_close_file(afptr, &status);
if (status) fits_report_error(stderr, status); /* print any error message */
return(status);
}
/* Function to write array to FITS file, and copy header info from other file */
void fitswrap_write2file(char *fileout, char *copyhdr, double **array,
long write_size[2], int *status){
/* Variable Declarations & Initializations */
int k,naxis,bitpix;
long fpixel[2],naxes[2],bzero;
char buf_date[FLEN_VALUE],buf_time[FLEN_VALUE],*mod_comm;
fitsfile *fitsfp,*hdrfp;
time_t now;
struct tm *ptr;
*status = 0;
/* Open file from which header will be copied */
hdrfp = fitswrap_open_read(copyhdr, status);
/* Check for output file -- create & open for write */
if(access(fileout,F_OK) == 0) // Check if output file exists
remove(fileout); // If yes, remove it
if(fits_create_file(&fitsfp, fileout, status)){
fitswrap_catcherror(status); // Send pointer not value
}
mod_comm = "Modified by fitswrap routine, TPEB.";
/* Copy header from copyhdr FITS file. */
fits_copy_header(hdrfp, fitsfp, status); // Copy header from input FITS
fits_get_img_param(hdrfp, 2 ,&bitpix, &naxis, naxes, status);
fits_read_key(hdrfp, TLONG, "BZERO", &bzero, NULL, status);
/* Check for needed updates */
// Writing new FITS as double
if(bitpix != DOUBLE_IMG){
bitpix = DOUBLE_IMG;
fits_update_key(fitsfp, TSHORT, "BITPIX", &bitpix, mod_comm, status);
}
// check for 'zero level' (needed for type long FITS headers)
// NOTE: If input header does not contain this keyword (status = 202),
// skip update & reset CFITSIO status to zero.
if(bzero != 0 || *status != 202){
bzero = 0;
fits_update_key(fitsfp, TSHORT, "BZERO", &bzero, mod_comm, status);
}
*status = 0; // Reset Status
// Check new axis lengths are correct
if(naxes[0] != write_size[0])
fits_update_key(fitsfp, TULONG,"NAXIS1",&write_size[0],mod_comm,status);
if(naxes[1] != write_size[1])
fits_update_key(fitsfp, TULONG,"NAXIS2",&write_size[1],mod_comm,status);
/* Write array to file */
fpixel[0] = 1;
for(k=0; k < write_size[1]; k++){ // Loop over size[1] rows (i.e. y)
fpixel[1] = k + 1;
if(fits_write_pix(fitsfp, TDOUBLE, fpixel, write_size[0], array[k],
status)){
fits_report_error(stderr,*status);
break;
}
}
/* Add/modify keyword for date modified 'DATE-MOD' & 'TIME-MOD' */
time(&now);
ptr = localtime(&now);
strftime(buf_date, FLEN_VALUE, "%Y-%m-%d", ptr);
strftime(buf_time, FLEN_VALUE, "%H:%M:%S", ptr);
fits_update_key(fitsfp, TSTRING, "DATE-MOD", buf_date, mod_comm, status);
fits_update_key(fitsfp, TSTRING, "TIME-MOD", buf_time, NULL, status);
/* Clean up */
fits_close_file(fitsfp, status);
fits_close_file(hdrfp, status);
/* Report any CFITSIO errors to stderr */
if(!*status)
fitswrap_catcherror(status); // Send pointer not value
return;
}
int unpermute_quads(quadfile* quadin, codetree* treein,
quadfile* quadout, codetree** p_treeout,
char** args, int argc) {
int i;
qfits_header* codehdr;
qfits_header* hdr;
int healpix;
int hpnside;
int codehp = -1;
qfits_header* qouthdr;
qfits_header* qinhdr;
codetree* treeout;
anbool allsky;
codehdr = codetree_header(treein);
healpix = quadin->healpix;
hpnside = quadin->hpnside;
allsky = qfits_header_getboolean(codehdr, "ALLSKY", 0);
if (allsky)
logverb("Index is all-sky\n");
else {
codehp = qfits_header_getint(codehdr, "HEALPIX", -1);
if (codehp == -1)
ERROR("Warning, input code kdtree didn't have a HEALPIX header");
else if (codehp != healpix) {
ERROR("Quadfile says it's healpix %i, but code kdtree says %i",
healpix, codehp);
return -1;
}
}
quadout->healpix = healpix;
quadout->hpnside = hpnside;
quadout->indexid = quadin->indexid;
quadout->numstars = quadin->numstars;
quadout->dimquads = quadin->dimquads;
quadout->index_scale_upper = quadin->index_scale_upper;
quadout->index_scale_lower = quadin->index_scale_lower;
qouthdr = quadfile_get_header(quadout);
qinhdr = quadfile_get_header(quadin);
boilerplate_add_fits_headers(qouthdr);
qfits_header_add(qouthdr, "HISTORY", "This file was created by the program \"unpermute-quads\".", NULL, NULL);
qfits_header_add(qouthdr, "HISTORY", "unpermute-quads command line:", NULL, NULL);
fits_add_args(qouthdr, args, argc);
qfits_header_add(qouthdr, "HISTORY", "(end of unpermute-quads command line)", NULL, NULL);
qfits_header_add(qouthdr, "HISTORY", "** unpermute-quads: history from input:", NULL, NULL);
fits_copy_all_headers(qinhdr, qouthdr, "HISTORY");
qfits_header_add(qouthdr, "HISTORY", "** unpermute-quads end of history from input.", NULL, NULL);
qfits_header_add(qouthdr, "COMMENT", "** unpermute-quads: comments from input:", NULL, NULL);
fits_copy_all_headers(qinhdr, qouthdr, "COMMENT");
qfits_header_add(qouthdr, "COMMENT", "** unpermute-quads: end of comments from input.", NULL, NULL);
fits_copy_header(qinhdr, qouthdr, "CXDX");
fits_copy_header(qinhdr, qouthdr, "CXDXLT1");
fits_copy_header(qinhdr, qouthdr, "CIRCLE");
fits_copy_header(qinhdr, qouthdr, "ALLSKY");
if (quadfile_write_header(quadout)) {
ERROR("Failed to write quadfile header");
return -1;
}
for (i=0; i<codetree_N(treein); i++) {
unsigned int stars[quadin->dimquads];
int ind = codetree_get_permuted(treein, i);
if (quadfile_get_stars(quadin, ind, stars)) {
ERROR("Failed to read quad entry");
return -1;
}
if (quadfile_write_quad(quadout, stars)) {
ERROR("Failed to write quad entry");
return -1;
}
}
if (quadfile_fix_header(quadout)) {
ERROR("Failed to fix quadfile header");
return -1;
}
treeout = codetree_new();
treeout->tree = malloc(sizeof(kdtree_t));
memcpy(treeout->tree, treein->tree, sizeof(kdtree_t));
treeout->tree->perm = NULL;
hdr = codetree_header(treeout);
fits_copy_header(qinhdr, hdr, "HEALPIX");
fits_copy_header(qinhdr, hdr, "HPNSIDE");
fits_copy_header(qinhdr, hdr, "ALLSKY");
boilerplate_add_fits_headers(hdr);
qfits_header_add(hdr, "HISTORY", "This file was created by the program \"unpermute-quads\".", NULL, NULL);
qfits_header_add(hdr, "HISTORY", "unpermute-quads command line:", NULL, NULL);
fits_add_args(hdr, args, argc);
qfits_header_add(hdr, "HISTORY", "(end of unpermute-quads command line)", NULL, NULL);
qfits_header_add(hdr, "HISTORY", "** unpermute-quads: history from input ckdt:", NULL, NULL);
fits_copy_all_headers(codehdr, hdr, "HISTORY");
qfits_header_add(hdr, "HISTORY", "** unpermute-quads end of history from input ckdt.", NULL, NULL);
qfits_header_add(hdr, "COMMENT", "** unpermute-quads: comments from input ckdt:", NULL, NULL);
fits_copy_all_headers(codehdr, hdr, "COMMENT");
qfits_header_add(hdr, "COMMENT", "** unpermute-quads: end of comments from input ckdt.", NULL, NULL);
fits_copy_header(codehdr, hdr, "CXDX");
fits_copy_header(codehdr, hdr, "CXDXLT1");
fits_copy_header(codehdr, hdr, "CIRCLE");
*p_treeout = treeout;
return 0;
}
int edit_image(char filename[], char newfilename[], double **ppix )
{
fitsfile *fptr, *newfptr;
int status, nfound, day, month, year, timeref;
int naxis = 2; /* 2-dimensional image */
int bitpix = DOUBLE_IMG; /* Output image type is double */
int datatype = TDOUBLE;
long naxes[2]; /* dimensions of the image */
long fpixel, npixels;
char date[FLEN_VALUE], time[FLEN_VALUE];
char *nullcomment;
char outfilename[MAXLENGTH];
nullcomment=0;
/***********************************************************************/
status = 0; /* Initialize status before calling fitsio routines */
/***********************************************************************/
/* Copy newfilename to outfilename. 'newfilename' is passed has a reference,
* therefore any change to it will be passed back to the calling routine
* which is not really what one wants. (as I discovered...)
* The addition of the '!' is meaningful here but not necessarly useful in
* the calling routine. */
if (!strcmp(newfilename,filename)) {
strcpy(outfilename,"!");
strcat(outfilename,filename);
}
else {
strcpy(outfilename,newfilename);
}
printf("Writing %s ... ",newfilename);
fflush(stdout);
/* Open the existing FITS file */
if ( fits_open_file(&fptr, filename, READONLY, &status) )
printerror( status );
/* Create the new FITS file (should I use a template?)*/
if ( fits_create_file(&newfptr, outfilename, &status) )
printerror( status );
/* No need to create an image in the new FITS file because the primary
* array is automatically created when the header is copied */
/* Copy the header from the existing FITS file to the new FITS file */
if ( fits_copy_header(fptr, newfptr, &status) )
printerror( status );
/* Get the length of the axes */
if ( fits_read_keys_lng(newfptr, "NAXIS", 1, 2, naxes, &nfound, &status) )
printerror( status );
/* Write the image (array of pixel values) in the new FITS file */
fpixel = 1; /* first pixel to write */
npixels = naxes[0] * naxes[1]; /* number of pixels to write */
if ( fits_write_img(newfptr, datatype, fpixel, npixels, ppix[0], &status) )
printerror( status );
/* Edit header */
if ( fits_get_system_date(&day, &month, &year, &status) )
printerror( status );
if ( fits_date2str(year, month, day, date, &status) )
printerror( status );
if ( fits_update_key(newfptr, TSTRING, "DATE", date, "", &status) )
printerror( status );
if ( fits_get_system_time(time, &timeref, &status) )
printerror( status );
if ( timeref == 0 ) /* Convert UTC/GMT to Local time */
if ( utc2local(time, FITS_FMT) ) {
printf("Error : Unable to convert time.\n");
exit(1);
}
if ( status = cnvtimefmt(time, FITS_FMT, IRAF_FMT))
printerror( status ); /* Stupid IRAF cannot read the new FITS
* date-time Y2K format */
if ( fits_update_key(newfptr, TSTRING, "IRAF-TLM", time, nullcomment, &status) )
printerror( status );
/* Close the existing FITS file */
if ( fits_close_file(fptr, &status) )
printerror( status );
/* Close the new FITS file */
if ( fits_close_file(newfptr, &status) )
printerror( status );
printf("done\n");
return(0);
}
int main(int argc, char *argv[])
{
int numfiles, ii, numrows, rownum, ichan, itsamp, datidx;
int spec_per_row, status, maxrows;
unsigned long int maxfilesize;
float offset, scale, datum, packdatum, maxval, fulltsubint;
float *datachunk;
FILE **infiles;
struct psrfits pfin, pfout;
Cmdline *cmd;
fitsfile *infits, *outfits;
char outfilename[128], templatename[128], tform[8];
char *pc1, *pc2;
int first = 1, dummy = 0, nclipped;
short int *inrowdata;
unsigned char *outrowdata;
if (argc == 1) {
Program = argv[0];
usage();
exit(1);
}
// Parse the command line using the excellent program Clig
cmd = parseCmdline(argc, argv);
numfiles = cmd->argc;
infiles = (FILE **) malloc(numfiles * sizeof(FILE *));
//Set the max. total size (in bytes) of all rows in an output file,
//leaving some room for PSRFITS header
maxfilesize = (unsigned long int)(cmd->numgb * GB);
maxfilesize = maxfilesize - 1000*KB;
//fprintf(stderr,"cmd->numgb: %f maxfilesize: %ld\n",cmd->numgb,maxfilesize);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n PSRFITS 16-bit to 4-bit Conversion Code\n");
printf(" by J. Deneva, S. Ransom, & S. Chatterjee\n\n");
// Open the input files
status = 0; //fits_close segfaults if this is not initialized
printf("Reading input data from:\n");
for (ii = 0; ii < numfiles; ii++) {
printf(" '%s'\n", cmd->argv[ii]);
//Get the file basename and number from command-line argument
//(code taken from psrfits2fil)
pc2 = strrchr(cmd->argv[ii], '.'); // at .fits
*pc2 = 0; // terminate string
pc1 = pc2 - 1;
while ((pc1 >= cmd->argv[ii]) && isdigit(*pc1))
pc1--;
if (pc1 <= cmd->argv[ii]) { // need at least 1 char before filenum
puts("Illegal input filename. must have chars before the filenumber");
exit(1);
}
pc1++; // we were sitting on "." move to first digit
pfin.filenum = atoi(pc1);
pfin.fnamedigits = pc2 - pc1; // how many digits in filenumbering scheme.
*pc1 = 0; // null terminate the basefilename
strcpy(pfin.basefilename, cmd->argv[ii]);
pfin.initialized = 0; // set to 1 in psrfits_open()
pfin.status = 0;
//(end of code taken from psrfits2fil)
//Open the existing psrfits file
if (psrfits_open(&pfin, READONLY) != 0) {
fprintf(stderr, "error opening file\n");
fits_report_error(stderr, pfin.status);
exit(1);
}
// Create the subint arrays
if (first) {
pfin.sub.dat_freqs = (float *) malloc(sizeof(float) * pfin.hdr.nchan);
pfin.sub.dat_weights = (float *) malloc(sizeof(float) * pfin.hdr.nchan);
pfin.sub.dat_offsets =
(float *) malloc(sizeof(float) * pfin.hdr.nchan * pfin.hdr.npol);
pfin.sub.dat_scales =
(float *) malloc(sizeof(float) * pfin.hdr.nchan * pfin.hdr.npol);
//first is set to 0 after data buffer allocation further below
}
infits = pfin.fptr;
spec_per_row = pfin.hdr.nsblk;
fits_read_key(infits, TINT, "NAXIS2", &dummy, NULL, &status);
pfin.tot_rows = dummy;
numrows = dummy;
//If dealing with 1st input file, create output template
if (ii == 0) {
sprintf(templatename, "%s.template.fits",cmd->outfile);
fits_create_file(&outfits, templatename, &status);
//fprintf(stderr,"pfin.basefilename: %s\n", pfin.basefilename);
//fprintf(stderr,"status: %d\n", status);
//Instead of copying HDUs one by one, can move to the SUBINT
//HDU, and copy all the HDUs preceding it
fits_movnam_hdu(infits, BINARY_TBL, "SUBINT", 0, &status);
fits_copy_file(infits, outfits, 1, 0, 0, &status);
//Copy the SUBINT table header
fits_copy_header(infits, outfits, &status);
fits_flush_buffer(outfits, 0, &status);
//Set NAXIS2 in the output SUBINT table to 0 b/c we haven't
//written any rows yet
dummy = 0;
fits_update_key(outfits, TINT, "NAXIS2", &dummy, NULL, &status);
//Edit the NBITS key
if (DEBUG) {
dummy = 8;
fits_update_key(outfits, TINT, "NBITS", &dummy, NULL, &status);
} else {
fits_update_key(outfits, TINT, "NBITS", &(cmd->numbits), NULL,
&status);
}
//Edit the TFORM17 column: # of data bytes per row
//fits_get_colnum(outfits,1,"DATA",&dummy,&status);
if (DEBUG)
sprintf(tform, "%dB",
pfin.hdr.nsblk * pfin.hdr.nchan * pfin.hdr.npol);
else
sprintf(tform, "%dB", pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * cmd->numbits / 8);
fits_update_key(outfits, TSTRING, "TTYPE17", "DATA", NULL, &status);
fits_update_key(outfits, TSTRING, "TFORM17", tform, NULL, &status);
//Edit NAXIS1: row width in bytes
fits_read_key(outfits, TINT, "NAXIS1", &dummy, NULL, &status);
if (DEBUG) {
dummy = dummy - pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * (pfin.hdr.nbits - 8) / 8;
} else {
dummy = dummy - pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * (pfin.hdr.nbits - cmd->numbits) / 8;
}
fits_update_key(outfits, TINT, "NAXIS1", &dummy, NULL, &status);
//Set the max # of rows per file, based on the requested
//output file size
maxrows = maxfilesize / dummy;
//fprintf(stderr,"maxrows: %d\n",maxrows);
fits_close_file(outfits, &status);
rownum = 0;
}
while (psrfits_read_subint(&pfin, first) == 0) {
fprintf(stderr, "Working on row %d\n", ++rownum);
//If this is the first row, store the length of a full subint
if (ii == 0 && rownum == 1)
fulltsubint = pfin.sub.tsubint;
//If this is the last row and it's partial, drop it.
//(It's pfin.rownum-1 below because the rownum member of the psrfits struct seems to be intended to indicate at the *start* of what row we are, i.e. a row that has not yet been read. In contrast, pfout.rownum indicates how many rows have been written, i.e. at the *end* of what row we are in the output.)
if (pfin.rownum-1 == numrows && fabs(pfin.sub.tsubint - fulltsubint) > pfin.hdr.dt) {
fprintf(stderr,
"Dropping partial row of length %f s (full row is %f s)\n",
pfin.sub.tsubint, fulltsubint);
break;
}
//If we just read in the 1st row, or if we already wrote the last row in the current output file, create a new output file
if ((ii == 0 && rownum == 1) || pfout.rownum == maxrows) {
//Create new output file from the template
pfout.fnamedigits = pfin.fnamedigits;
if(ii == 0)
pfout.filenum = pfin.filenum;
else
pfout.filenum++;
sprintf(outfilename, "%s.%0*d.fits", cmd->outfile, pfout.fnamedigits, pfout.filenum);
fits_create_template(&outfits, outfilename, templatename, &status);
//fprintf(stderr,"After fits_create_template, status: %d\n",status);
fits_close_file(outfits, &status);
//Now reopen the file so that the pfout structure is initialized
pfout.status = 0;
pfout.initialized = 0;
sprintf(pfout.basefilename, "%s.", cmd->outfile);
if (psrfits_open(&pfout, READWRITE) != 0) {
fprintf(stderr, "error opening file\n");
fits_report_error(stderr, pfout.status);
exit(1);
}
outfits = pfout.fptr;
maxval = pow(2, cmd->numbits) - 1;
pfout.rows_per_file = maxrows;
//fprintf(stderr, "maxval: %f\n", maxval);
//fprintf(stderr, "pfout.rows_per_file: %d\n",pfout.rows_per_file);
//These are not initialized in psrfits_open but are needed
//in psrfits_write_subint (not obvious what are the corresponding
//fields in any of the psrfits table headers)
pfout.hdr.ds_freq_fact = 1;
pfout.hdr.ds_time_fact = 1;
}
//Copy the subint struct from pfin to pfout, but correct
//elements that are not the same
pfout.sub = pfin.sub; //this copies array pointers too
pfout.sub.bytes_per_subint =
pfin.sub.bytes_per_subint * pfout.hdr.nbits / pfin.hdr.nbits;
pfout.sub.dataBytesAlloced = pfout.sub.bytes_per_subint;
pfout.sub.FITS_typecode = TBYTE;
if (first) {
//Allocate scaling buffer and output buffer
datachunk = gen_fvect(spec_per_row);
outrowdata = gen_bvect(pfout.sub.bytes_per_subint);
first = 0;
}
pfout.sub.data = outrowdata;
inrowdata = (short int *) pfin.sub.data;
nclipped = 0;
// Loop over all the channels:
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol; ichan++) {
// Populate datachunk[] by picking out all time samples for ichan
for (itsamp = 0; itsamp < spec_per_row; itsamp++)
datachunk[itsamp] = (float) (inrowdata[ichan + itsamp *
pfout.hdr.nchan *
pfout.hdr.npol]);
// Compute the statistics here, and put the offsets and scales in
// pf.sub.dat_offsets[] and pf.sub.dat_scales[]
if (rescale(datachunk, spec_per_row, cmd->numbits, &offset, &scale)
!= 0) {
printf("Rescale routine failed!\n");
return (-1);
}
pfout.sub.dat_offsets[ichan] = offset;
pfout.sub.dat_scales[ichan] = scale;
// Since we have the offset and scale ready, rescale the data:
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datum = (scale == 0.0) ? 0.0 :
roundf((datachunk[itsamp] - offset) / scale);
if (datum < 0.0) {
datum = 0;
nclipped++;
} else if (datum > maxval) {
datum = maxval;
nclipped++;
}
inrowdata[ichan + itsamp * pfout.hdr.nchan * pfout.hdr.npol] =
(short int) datum;
}
// Now inrowdata[ichan] contains rescaled ints.
}
// Then do the conversion and store the
// results in pf.sub.data[]
if (cmd->numbits == 8 || DEBUG) {
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datidx = itsamp * pfout.hdr.nchan * pfout.hdr.npol;
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol;
ichan++, datidx++) {
pfout.sub.data[datidx] = (unsigned char) inrowdata[datidx];
}
}
} else if (cmd->numbits == 4) {
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datidx = itsamp * pfout.hdr.nchan * pfout.hdr.npol;
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol;
ichan += 2, datidx += 2) {
packdatum = inrowdata[datidx] * 16 + inrowdata[datidx + 1];
pfout.sub.data[datidx / 2] = (unsigned char) packdatum;
}
}
} else {
fprintf(stderr, "Only 4 or 8-bit output formats supported.\n");
fprintf(stderr, "Bits per sample requested: %d\n", cmd->numbits);
exit(1);
}
//pfout.sub.offs = (pfout.tot_rows+0.5) * pfout.sub.tsubint;
fprintf(stderr, "nclipped: %d fraction clipped: %f\n", nclipped,
(float) nclipped / (pfout.hdr.nchan * pfout.hdr.npol *
pfout.hdr.nsblk));
// Now write the row.
status = psrfits_write_subint(&pfout);
if (status) {
printf("\nError (%d) writing PSRFITS...\n\n", status);
break;
}
//If current output file has reached the max # of rows, close it
if (pfout.rownum == maxrows)
fits_close_file(outfits, &status);
}
//Close the files
fits_close_file(infits, &status);
}
fits_close_file(outfits, &status);
// Free the structure arrays too...
free(datachunk);
free(infiles);
free(pfin.sub.dat_freqs);
free(pfin.sub.dat_weights);
free(pfin.sub.dat_offsets);
free(pfin.sub.dat_scales);
free(pfin.sub.data);
free(pfout.sub.data);
free(pfin.sub.stat);
return 0;
}
int main(int argc, char **argv)
{
int i, j, countRange, countNaN, status;
int haveMinMax, haveVal, writeOutput;
long fpixel[4], nelements;
double *inbuffer;
double NaNvalue;
double minblank, maxblank;
double *outbuffer;
char *end;
/************************************************/
/* Make a NaN value to use setting blank pixels */
/************************************************/
union
{
double d;
char c[8];
}
value;
double nan;
for(i=0; i<8; ++i)
value.c[i] = 255;
nan = value.d;
/***************************************/
/* Process the command-line parameters */
/***************************************/
fstatus = stdout;
debug = 0;
haveVal = 0;
writeOutput = 1;
for(i=0; i<argc; ++i)
{
if(strcmp(argv[i], "-d") == 0)
{
if(i+1 >= argc)
{
printf("[struct stat=\"ERROR\", msg=\"No debug level given\"]\n");
exit(1);
}
debug = strtol(argv[i+1], &end, 0);
if(end - argv[i+1] < strlen(argv[i+1]))
{
printf("[struct stat=\"ERROR\", msg=\"Debug level string is invalid: '%s'\"]\n", argv[i+1]);
exit(1);
}
if(debug < 0)
{
printf("[struct stat=\"ERROR\", msg=\"Debug level value cannot be negative\"]\n");
exit(1);
}
argv += 2;
argc -= 2;
}
if(strcmp(argv[i], "-v") == 0)
{
if(i+1 >= argc)
{
printf("[struct stat=\"ERROR\", msg=\"No value given for NaN conversion\"]\n");
exit(1);
}
NaNvalue = strtod(argv[i+1], &end);
if(end - argv[i+1] < strlen(argv[i+1]))
{
printf("[struct stat=\"ERROR\", msg=\"NaN conversion value string is invalid: '%s'\"]\n", argv[i+1]);
exit(1);
}
haveVal = 1;
argv += 2;
argc -= 2;
}
}
if (argc < 3)
{
printf ("[struct stat=\"ERROR\", msg=\"Usage: %s [-d level][-v NaN-value] in.fits out.fits [minblank maxblank] (output file name '-' means no file)\"]\n", argv[0]);
exit(1);
}
strcpy(input_file, argv[1]);
if(input_file[0] == '-')
{
printf ("[struct stat=\"ERROR\", msg=\"Invalid input file '%s'\"]\n", input_file);
exit(1);
}
strcpy(output_file, argv[2]);
if(output_file[0] == '-')
writeOutput = 0;
haveMinMax = 0;
minblank = -2;
maxblank = 2;
if(argc > 3)
{
haveMinMax = 1;
minblank = strtod(argv[3], &end);
if(end < argv[3] + strlen(argv[3]))
{
printf ("[struct stat=\"ERROR\", msg=\"min blank value string is not a number\"]\n");
exit(1);
}
maxblank = strtod(argv[4], &end);
if(end < argv[4] + strlen(argv[4]))
{
printf ("[struct stat=\"ERROR\", msg=\"max blank value string is not a number\"]\n");
exit(1);
}
}
if(debug >= 1)
{
printf("input_file = [%s]\n", input_file);
printf("output_file = [%s]\n", output_file);
printf("minblank = %-g\n", minblank);
printf("maxblank = %-g\n", maxblank);
fflush(stdout);
}
/************************/
/* Read the input image */
/************************/
time(&currtime);
start = currtime;
readFits(input_file);
if(debug >= 1)
{
printf("input.naxes[0] = %ld\n", input.naxes[0]);
printf("input.naxes[1] = %ld\n", input.naxes[1]);
printf("input.crpix1 = %-g\n", input.crpix1);
printf("input.crpix2 = %-g\n", input.crpix2);
fflush(stdout);
}
output.naxes[0] = input.naxes[0];
output.naxes[1] = input.naxes[1];
output.crpix1 = input.crpix1;
output.crpix2 = input.crpix2;
if(writeOutput)
{
/********************************/
/* Create the output FITS files */
/********************************/
remove(output_file);
status = 0;
if(fits_create_file(&output.fptr, output_file, &status))
printFitsError(status);
if(debug >= 1)
{
printf("\nFITS output file created (not yet populated)\n");
fflush(stdout);
}
/********************************/
/* Copy all the header keywords */
/* from the input to the output */
/********************************/
if(fits_copy_header(input.fptr, output.fptr, &status))
printFitsError(status);
if(debug >= 1)
{
printf("Header keywords copied to FITS output file\n\n");
fflush(stdout);
}
/***************************/
/* Modify BITPIX to be -64 */
/***************************/
if(fits_update_key_lng(output.fptr, "BITPIX", -64,
(char *)NULL, &status))
printFitsError(status);
}
/*****************************************************/
/* Allocate memory for the input/output image pixels */
/* (same size as the input image) */
/*****************************************************/
outbuffer = (double *)malloc(output.naxes[0] * sizeof(double));
if(debug >= 1)
{
printf("%ld bytes allocated for row of output image pixels\n",
output.naxes[0] * sizeof(double));
fflush(stdout);
}
inbuffer = (double *)malloc(input.naxes[0] * sizeof(double));
if(debug >= 1)
{
printf("%ld bytes allocated for row of input image pixels\n",
input.naxes[0] * sizeof(double));
fflush(stdout);
}
/*****************************/
/* Loop over the input lines */
/*****************************/
fpixel[0] = 1;
fpixel[1] = 1;
fpixel[2] = 1;
fpixel[3] = 1;
nelements = input.naxes[0];
status = 0;
countRange = 0;
countNaN = 0;
for (j=0; j<input.naxes[1]; ++j)
{
if(debug >= 2)
{
if(debug >= 3)
printf("\n");
printf("\rProcessing input row %5d [So far rangeCount=%d, nanCount=%d]",
j, countRange, countNaN);
if(debug >= 3)
printf("\n");
fflush(stdout);
}
for (i=0; i<output.naxes[0]; ++i)
outbuffer[i] = 0.;
/***********************************/
/* Read a line from the input file */
/***********************************/
if(fits_read_pix(input.fptr, TDOUBLE, fpixel, nelements, NULL,
inbuffer, NULL, &status))
printFitsError(status);
/************************/
/* For each input pixel */
/************************/
for (i=0; i<input.naxes[0]; ++i)
{
if(mNaN(inbuffer[i]) && haveVal)
{
++countNaN;
outbuffer[i] = NaNvalue;
if(debug >= 3)
{
printf("pixel[%d][%d] converted to %-g\n", j, i, NaNvalue);
fflush(stdout);
}
}
else if(haveMinMax
&& inbuffer[i] >= minblank
&& inbuffer[i] <= maxblank)
{
++countRange;
if(haveVal)
{
++countNaN;
outbuffer[i] = NaNvalue;
if(debug >= 3)
{
printf("pixel[%d][%d] converted to NaN -> %-g\n", j, i, NaNvalue);
fflush(stdout);
}
}
else
{
outbuffer[i] = nan;
if(debug >= 3)
{
printf("pixel[%d][%d] converted to NaN\n", j, i);
fflush(stdout);
}
}
}
else
outbuffer[i] = inbuffer[i];
}
/***************************/
/* Write the output buffer */
/***************************/
if(writeOutput)
{
if (fits_write_pix(output.fptr, TDOUBLE, fpixel, nelements,
outbuffer, &status))
printFitsError(status);
}
++fpixel[1];
}
if(debug >= 1)
{
time(&currtime);
printf("\nDone copying data (%d seconds)\n",
(int)(currtime - start));
fflush(stdout);
}
/************************/
/* Close the FITS files */
/************************/
if(fits_close_file(input.fptr, &status))
printFitsError(status);
if(writeOutput)
{
if(fits_close_file(output.fptr, &status))
printFitsError(status);
}
if(debug >= 1)
{
time(&currtime);
printf("Done (%d seconds total)\n", (int)(currtime - start));
fflush(stdout);
}
free(inbuffer);
free(outbuffer);
printf("[struct stat=\"OK\", rangeCount=%d, nanCount=%d]\n", countRange, countNaN);
fflush(stdout);
exit(0);
}
/* process this command */
static int ProcessCmd(char *cmd, char **args, int node, int tty)
{
int ip=0;
char tbuf[SZ_LINE];
Finfo finfo, tfinfo;
#if HAVE_CFITSIO
int x0, x1, y0, y1, bin;
int xcolnum, ycolnum, hdunum, hdutype;
int status=0, status2=0;
int dims[2];
double cens[2];
char *cols[2] = {"X", "Y"};
char *ofile=NULL;
char *omode=NULL;
fitsfile *ifptr, *ofptr, *tfptr;
#endif
switch(*cmd){
case 'f':
if( !strcmp(cmd, "fitsFile") ){
if( args && word(args[0], tbuf, &ip) ){
if( !(tfinfo=FinfoLookup(tbuf)) ){
fprintf(stderr, NOIMAGE, tbuf);
return 1;
}
} else if( !(tfinfo=FinfoGetCurrent()) ){
fprintf(stderr, NOFINFO, cmd);
return 1;
}
if( tfinfo->fitsfile ){
if( node ) fprintf(stdout, "fitsFile\r");
fprintf(stdout, "%s %s\n", tfinfo->fname, tfinfo->fitsfile);
fflush(stdout);
}
return 0;
}
break;
break;
case 'i':
if( !strcmp(cmd, "image") ){
if( !args || !word(args[0], tbuf, &ip) ){
fprintf(stderr, WRONGARGS, cmd, 1, 0);
return 1;
}
/* new image */
if( !(finfo = FinfoNew(tbuf)) ){
fprintf(stderr, NONEW, cmd);
return 1;
}
/* make it current */
FinfoSetCurrent(finfo);
if( node ) fprintf(stdout, "image\r");
/* return the FITS file name, if possible */
fprintf(stdout, "%s %s\n",
finfo->fname, finfo->fitsfile ? finfo->fitsfile : "?");
fflush(stdout);
return 0;
} else if( !strcmp(cmd, "image_") ){
if( !args || !word(args[0], tbuf, &ip) ){
fprintf(stderr, WRONGARGS, cmd, 1, 0);
return 1;
}
/* new image */
if( !(finfo = FinfoNew(tbuf)) ){
fprintf(stderr, NONEW, cmd);
return 1;
}
/* make it current */
FinfoSetCurrent(finfo);
/* no output! */
return 0;
} else if( !strcmp(cmd, "imsection") ){
#if HAVE_CFITSIO
if( !(finfo=FinfoGetCurrent()) ){
fprintf(stderr, NOFINFO, cmd);
return 1;
}
ifptr = openFITSFile(finfo->fitsfile, EXTLIST, &hdutype, &status);
if( status ){
fprintf(stderr, "ERROR: can't open FITS file '%s'\n", finfo->fitsfile);
return 1;
}
if( !args || !parseSection(args[0], &x0, &x1, &y0, &y1, &bin) ){
fprintf(stderr,
"ERROR: can't parse section for '%s' [%s]\n",
finfo->fitsfile, (args && args[1]) ? args[1] : "NONE");
return 1;
}
if( args[1] ){
omode = args[1];
} else {
omode = "native";
}
ofile = "stdout";
// create image if ifile is an image or omode is not native
if( (hdutype == IMAGE_HDU) || strcmp(omode, "native") ){
fits_create_file(&ofptr, ofile, &status);
if( status ){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't open output FITS file to section '%s' [%s]\n",
finfo->fitsfile, tbuf);
return 1;
}
switch(hdutype){
case IMAGE_HDU:
if( bin != 1 ){
fprintf(stderr,
"ERROR: imsection of an image must use bin 1 for '%s'\n",
finfo->fitsfile);
return 1;
}
snprintf(tbuf, SZ_LINE-1, "%d:%d,%d:%d", x0, x1, y0, y1);
fits_copy_image_section(ifptr, ofptr, tbuf, &status);
break;
default:
dims[0] = x1 - x0 + 1;
dims[1] = y1 - y0 + 1;
cens[0] = (x0 + x1) / 2;
cens[1] = (y0 + y1) / 2;
tfptr = filterTableToImage(ifptr, NULL, cols, dims, cens, bin,
&status);
if( status ){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't create image from table for '%s' [%s]\n",
finfo->fitsfile, tbuf);
return 1;
}
fits_copy_image_section(tfptr, ofptr, "*,*", &status);
closeFITSFile(tfptr, &status2);
break;
}
if( status ){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't write section FITS file for '%s' [%s]\n",
finfo->fitsfile, tbuf);
closeFITSFile(ofptr, &status);
return 1;
}
closeFITSFile(ofptr, &status);
} else {
// extract (native) table
snprintf(tbuf, SZ_LINE-1,
"x >= %d && x <= %d && y >= %d && y <= %d",
x0, x1, y0, y1);
// ffselect_table(&ifptr, ofile, tbuf, &status);
// copied from cfileio.c/ffselect_table()
/* create new empty file to hold copy of the image */
if (ffinit(&ofptr, ofile, &status) > 0) {
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't init section file for '%s' [%s]\n",
finfo->fitsfile, tbuf);
return 1;
}
/* save current HDU number in input file */
fits_get_hdu_num(ifptr, &hdunum);
/* copy the primary array */
fits_movabs_hdu(ifptr, 1, NULL, &status);
if( fits_copy_hdu(ifptr, ofptr, 0, &status) > 0){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't copy primary for section file '%s' [%s]\n",
finfo->fitsfile, tbuf);
fits_close_file(ofptr, &status);
return 1;
}
/* back to current hdu */
fits_movabs_hdu(ifptr, hdunum, NULL, &status);
/* copy all the header keywords from the input to output file */
if (fits_copy_header(ifptr, ofptr, &status) > 0){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't copy header for section file '%s' [%s]\n",
finfo->fitsfile, tbuf);
fits_close_file(ofptr, &status);
return 1;
}
/* set number of rows = 0 */
/* warning: start of cfitsio black magic */
fits_modify_key_lng(ofptr, "NAXIS2", 0, NULL, &status);
(ofptr->Fptr)->numrows = 0;
(ofptr->Fptr)->origrows = 0;
/* force the header to be scanned */
if (ffrdef(ofptr, &status) > 0){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't rdef for section file '%s' [%s]\n",
finfo->fitsfile, tbuf);
fits_close_file(ofptr, &status);
return 1;
}
/* warning: end of cfitsio black magic */
/* select filtered rows and write to output file */
if (fits_select_rows(ifptr, ofptr, tbuf, &status) > 0){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't select rows for section file '%s' [%s]\n",
finfo->fitsfile, tbuf);
fits_close_file(ofptr, &status);
return 1;
}
/* update params for this section */
if( (fits_get_colnum(ofptr, CASEINSEN, "X", &xcolnum, &status) > 0) ||
(fits_get_colnum(ofptr, CASEINSEN, "Y", &ycolnum, &status) > 0) ){
fits_get_errstatus(status, tbuf);
fprintf(stderr,
"ERROR: can't find X,Y cols for section file '%s' [%s]\n",
finfo->fitsfile, tbuf);
fits_close_file(ofptr, &status);
return 1;
}
/* we can ignore errors here */
status = 0;
snprintf(tbuf, SZ_LINE-1, "TALEN%d", xcolnum);
fits_modify_key_lng(ofptr, tbuf, x1-x0, NULL, &status);
status = 0;
snprintf(tbuf, SZ_LINE-1, "TALEN%d", ycolnum);
fits_modify_key_lng(ofptr, tbuf, y1-y0, NULL, &status);
status = 0;
snprintf(tbuf, SZ_LINE-1, "TLMIN%d", xcolnum);
fits_modify_key_flt(ofptr, tbuf, x0, 6, NULL, &status);
status = 0;
snprintf(tbuf, SZ_LINE-1, "TLMAX%d", xcolnum);
fits_modify_key_flt(ofptr, tbuf, x1, 6, NULL, &status);
status = 0;
snprintf(tbuf, SZ_LINE-1, "TLMIN%d", ycolnum);
fits_modify_key_flt(ofptr, tbuf, y0, 6, NULL, &status);
status = 0;
snprintf(tbuf, SZ_LINE-1, "TLMAX%d", ycolnum);
fits_modify_key_flt(ofptr, tbuf, y1, 6, NULL, &status);
/* close the output file */
status = 0;
fits_close_file(ofptr, &status);
}
closeFITSFile(ifptr, &status);
return 0;
#else
fprintf(stderr,
"ERROR: for section support, build js9helper with cfitsio\n");
return 1;
#endif
} else if( !strcmp(cmd, "info") ){
if( tty ){
if( !(finfo=FinfoGetCurrent()) ){
fprintf(stderr, NOFINFO, cmd);
return 1;
}
/* make sure we have a wcs */
fprintf(stdout, "fname:\t%s\n", finfo->fname);
fprintf(stdout, "fits:\t%s\n", finfo->fitsfile?finfo->fitsfile:"N/A");
fflush(stdout);
}
return 0;
}
break;
case 'l':
/* list all images */
if( !strcmp(cmd, "list") ){
FinfoList(stdout);
return 0;
}
break;
case 's':
if( !strcmp(cmd, "setDataPath") ){
if( args && word(args[0], tbuf, &ip) ){
setenv("JS9_DATAPATH", tbuf, 1);
if( node ) fprintf(stdout, "setDataPath\r");
fprintf(stdout, "%s\n", getenv("JS9_DATAPATH"));
fflush(stdout);
} else {
fprintf(stderr, WRONGARGS, cmd, 1, 0);
return 1;
}
return 0;
}
break;
case 'u':
if( !strcmp(cmd, "unimage") ){
if( !args || !word(args[0], tbuf, &ip) ){
fprintf(stderr, WRONGARGS, cmd, 1, 0);
return 1;
}
/* close this image */
FinfoFree(tbuf);
return 0;
}
break;
case '#':
case '\0':
return 0;
default:
break;
}
/* if we reached here, we did not recognize the command */
fprintf(stderr, "ERROR: unknown command '%s'\n", cmd);
/* return the news */
return 2;
}
