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Commit 90385513 authored by Emmanuel Bertin's avatar Emmanuel Bertin
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Fixed issue with output Check-image headers when reading individual extensions... 

Fixed issue with output Check-image headers when reading individual extensions from MEFs (thanks to user Lantern for the bug report).
parent ec2f0c6f
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man/sex.1
View file @ 90385513
.TH SEXTRACTOR "1" "November 2010" "SExtractor 2.13.1" "User Commands"
.TH SEXTRACTOR "1" "December 2010" "SExtractor 2.13.1" "User Commands"
.SH NAME
sex \- extract a source catalogue from an astronomical FITS image
.SH SYNOPSIS
......
src/check.c
View file @ 90385513
......@@ -22,7 +22,7 @@
* You should have received a copy of the GNU General Public License
* along with SExtractor. If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/10/2010
* Last modified: 12/02/2010
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -155,32 +155,28 @@ initialize check-image.
checkstruct *initcheck(char *filename, checkenum check_type, int next)
{
catstruct *fitscat;
catstruct *cat;
checkstruct *check;
QCALLOC(check, checkstruct, 1);
strcpy(check->filename, filename);
check->type = check_type;
check->next = next;
cat = check->cat = new_cat(1);
strcpy(cat->filename, filename);
if (next>1)
/*-- Create a "pure" primary HDU */
{
fitscat = new_cat(1);
init_cat(fitscat);
strcpy(fitscat->filename, filename);
fitsadd(fitscat->tab->headbuf, "NEXTEND ", "Number of extensions");
fitswrite(fitscat->tab->headbuf, "NEXTEND ", &next, H_INT, T_LONG);
if (open_cat(fitscat, WRITE_ONLY) != RETURN_OK)
init_cat(cat);
addkeywordto_head(cat->tab, "NEXTEND ", "Number of extensions");
fitswrite(cat->tab->headbuf, "NEXTEND ", &next, H_INT, T_LONG);
if (open_cat(cat, WRITE_ONLY) != RETURN_OK)
error(EXIT_FAILURE,"*Error*: cannot open for writing ", filename);
save_tab(fitscat, fitscat->tab);
check->file = fitscat->file;
fitscat->file = NULL;
free_cat(&fitscat, 1);
save_head(cat, cat->tab);
remove_tabs(cat);
}
else
if (!(check->file = fopen(check->filename, "wb")))
error(EXIT_FAILURE, "*Error*: Cannot open for output ", check->filename);
open_cat(cat, WRITE_ONLY);
return check;
}
......@@ -193,25 +189,37 @@ initialize check-image (for subsequent writing).
void reinitcheck(picstruct *field, checkstruct *check)
{
catstruct *cat;
tabstruct *tab;
wcsstruct *wcs;
char *buf;
int i, ival;
size_t padsize;
double dval;
ULONG *ptri;
char *fitshead;
PIXTYPE *ptrf;
double dval;
int i;
cat = check->cat;
/* Inherit the field FITS header */
check->fitsheadsize = field->tab->headnblock*FBSIZE;
QMEMCPY(field->tab->headbuf, check->fitshead, char, check->fitsheadsize);
remove_tabs(cat);
copy_tab_fromptr(field->tab, cat, 0);
tab = cat->tab;
tab->cat = cat;
if (check->next<=1)
prim_head(tab);
check->y = 0;
fitshead = tab->headbuf;
/* Neutralize possible scaling factors */
dval = 1.0;fitswrite(check->fitshead, "BSCALE ", &dval, H_FLOAT, T_DOUBLE);
dval = 0.0;fitswrite(check->fitshead, "BZERO ", &dval, H_FLOAT, T_DOUBLE);
ival = 1;fitswrite(check->fitshead, "BITSGN ", &ival, H_INT, T_LONG);
if (field->tab->compress_type != COMPRESS_NONE)
fitswrite(check->fitshead, "IMAGECOD", "NONE", H_STRING, T_STRING);
fitswrite(check->fitshead, "ORIGIN ", BANNER, H_STRING, T_STRING);
tab->bytepix = 4;
tab->bscale = 1.0;
tab->bzero = 0.0;
fitswrite(fitshead, "BSCALE ", &tab->bscale, H_FLOAT, T_DOUBLE);
fitswrite(fitshead, "BZERO ", &tab->bzero, H_FLOAT, T_DOUBLE);
fitswrite(fitshead, "BITSGN ", &tab->bitsgn, H_INT, T_LONG);
if (tab->compress_type != COMPRESS_NONE)
{
tab->compress_type = COMPRESS_NONE;
fitswrite(fitshead, "IMAGECOD", "NONE", H_STRING, T_STRING);
}
fitswrite(fitshead, "ORIGIN ", BANNER, H_STRING, T_STRING);
switch(check->type)
{
......@@ -219,28 +227,25 @@ void reinitcheck(picstruct *field, checkstruct *check)
case CHECK_BACKGROUND:
case CHECK_FILTERED:
case CHECK_SUBTRACTED:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
QMALLOC(ptrf, PIXTYPE, check->width);
check->pix = (void *)ptrf;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
save_head(cat, cat->tab);
break;
case CHECK_BACKRMS:
case CHECK_SUBOBJECTS:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
QMALLOC(ptrf, PIXTYPE, check->width);
check->pix = (void *)ptrf;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
QMALLOC(check->pix, PIXTYPE, check->width);
save_head(cat, cat->tab);
/*---- Allocate memory for replacing the blanked pixels by 0 */
if (!check->line)
QMALLOC(check->line, PIXTYPE, field->width);
......@@ -260,123 +265,97 @@ void reinitcheck(picstruct *field, checkstruct *check)
case CHECK_DISKS:
case CHECK_SUBDISKS:
case CHECK_PATTERNS:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
check->overlay = 30*field->backsig;
QCALLOC(ptrf, PIXTYPE, check->npix);
check->pix = (void *)ptrf;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
QCALLOC(check->pix, PIXTYPE, check->npix);
save_head(cat, cat->tab);
break;
case CHECK_SEGMENTATION:
ival = 32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = 32;
tab->bitsgn = 1;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
QCALLOC(ptri, ULONG, check->npix);
check->pix = (void *)ptri;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
QCALLOC(check->pix, ULONG, check->npix);
save_head(cat, cat->tab);
break;
case CHECK_ASSOC:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
QMALLOC(ptrf, PIXTYPE, check->npix);
check->pix = (void *)ptrf;
QMALLOC(check->pix, PIXTYPE, check->npix);
/*---- Initialize the pixmap to IEEE NaN */
memset(ptrf, 0xFF, check->npix*sizeof(LONG));
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
memset(check->pix, 0xFF, check->npix*sizeof(LONG));
save_head(cat, cat->tab);
break;
case CHECK_MINIBACKGROUND:
case CHECK_MINIBACKRMS:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->nbackx;
fitswrite(check->fitshead, "NAXIS1 ", &check->width, H_INT, T_LONG);
check->height = field->nbacky;
fitswrite(check->fitshead, "NAXIS2 ", &check->height, H_INT, T_LONG);
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->nbackx;
tab->naxisn[1] = check->height = field->nbacky;
/*---- Scale the WCS information if present */
if ((wcs=field->wcs))
{
dval = wcs->cdelt[0]*field->backw;
fitswrite(check->fitshead, "CDELT1 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CDELT1 ", &dval, H_EXPO, T_DOUBLE);
dval = wcs->cdelt[1]*field->backh;
fitswrite(check->fitshead, "CDELT2 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CDELT2 ", &dval, H_EXPO, T_DOUBLE);
dval = (wcs->crpix[0]-0.5)/field->backw + 0.5;
fitswrite(check->fitshead, "CRPIX1 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CRPIX1 ", &dval, H_EXPO, T_DOUBLE);
dval = (wcs->crpix[1]-0.5)/field->backh + 0.5;
fitswrite(check->fitshead, "CRPIX2 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CRPIX2 ", &dval, H_EXPO, T_DOUBLE);
dval = wcs->cd[0]*field->backw;
fitswrite(check->fitshead, "CD1_1 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CD1_1 ", &dval, H_EXPO, T_DOUBLE);
dval = wcs->cd[1]*field->backh;
fitswrite(check->fitshead, "CD1_2 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CD1_2 ", &dval, H_EXPO, T_DOUBLE);
dval = wcs->cd[wcs->naxis]*field->backw;
fitswrite(check->fitshead, "CD2_1 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CD2_1 ", &dval, H_EXPO, T_DOUBLE);
dval = wcs->cd[wcs->naxis+1]*field->backh;
fitswrite(check->fitshead, "CD2_2 ", &dval, H_EXPO, T_DOUBLE);
fitswrite(fitshead, "CD2_2 ", &dval, H_EXPO, T_DOUBLE);
}
check->npix = check->width*check->height;
QMALLOC(ptrf, PIXTYPE, check->npix);
check->pix = (void *)ptrf;
QMALLOC(check->pix, PIXTYPE, check->npix);
if (check->type==CHECK_MINIBACKRMS)
memcpy(check->pix, field->sigma, check->npix*sizeof(float));
else
memcpy(check->pix, field->back, check->npix*sizeof(float));
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
if (bswapflag)
swapbytes(check->pix, sizeof(float), (int)check->npix);
QFWRITE(check->pix,check->npix*sizeof(float),check->file,
check->filename);
/*---- Put the buffer back to its original state */
if (bswapflag)
swapbytes(check->pix, sizeof(float), (int)check->npix);
save_head(cat, cat->tab);
write_body(cat->tab, check->pix, check->npix);
free(check->pix);
QCALLOC(buf, char, FBSIZE);
padsize = (FBSIZE -((check->npix*sizeof(PIXTYPE))%FBSIZE))% FBSIZE;
if (padsize)
QFWRITE (buf, padsize, check->file, check->filename);
free(buf);
break;
case CHECK_MAPSOM:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
check->width = field->width;
check->height = field->height;
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width = field->width;
tab->naxisn[1] = check->height = field->height;
check->npix = field->npix;
QMALLOC(ptrf, PIXTYPE, check->npix);
check->pix = (void *)ptrf;
for (i=check->npix; i--;)
*(ptrf++) = -10.0;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
save_head(cat, cat->tab);
break;
case CHECK_OTHER:
ival = -32;
fitswrite(check->fitshead, "BITPIX ", &ival, H_INT, T_LONG);
fitswrite(check->fitshead, "NAXIS1 ", &check->width, H_INT, T_LONG);
fitswrite(check->fitshead, "NAXIS2 ", &check->height, H_INT, T_LONG);
tab->bitpix = -32;
tab->bitsgn = 0;
tab->naxisn[0] = check->width;
tab->naxisn[1] = check->height;
check->npix = check->width*check->height;
QMALLOC(ptrf, PIXTYPE, check->npix);
check->pix = (void *)ptrf;
for (i=check->npix; i--;)
*(ptrf++) = 0.0;
QFWRITE(check->fitshead,check->fitsheadsize,check->file,check->filename);
free(check->fitshead);
QCALLOC(check->pix, PIXTYPE, check->npix);
save_head(cat, cat->tab);
break;
default:
......@@ -413,12 +392,7 @@ void writecheck(checkstruct *check, PIXTYPE *data, int w)
data = check->line;
}
if (bswapflag)
swapbytes(data, sizeof(PIXTYPE), w);
QFWRITE(data, w*sizeof(PIXTYPE), check->file, check->filename);
if (bswapflag)
/*-- Put the buffer back to its original state */
swapbytes(data, sizeof(PIXTYPE), w);
write_body(check->cat->tab, data, w);
return;
}
......@@ -430,10 +404,10 @@ Finish current check-image.
*/
void reendcheck(picstruct *field, checkstruct *check)
{
catstruct *cat;
char *buf;
size_t padsize;
padsize = 0; /* To avoid gcc -Wall warnings */
cat = check->cat;
switch(check->type)
{
case CHECK_MINIBACKGROUND:
......@@ -448,7 +422,7 @@ void reendcheck(picstruct *field, checkstruct *check)
free(check->pix);
free(check->line);
check->line = NULL;
padsize = (FBSIZE -((check->npix*sizeof(PIXTYPE))%FBSIZE)) % FBSIZE;
pad_tab(cat, check->npix*sizeof(PIXTYPE));
break;
case CHECK_OBJECTS:
......@@ -468,21 +442,15 @@ void reendcheck(picstruct *field, checkstruct *check)
case CHECK_PATTERNS:
case CHECK_MAPSOM:
case CHECK_OTHER:
if (bswapflag)
swapbytes(check->pix, sizeof(PIXTYPE), (int)check->npix);
QFWRITE(check->pix,check->npix*sizeof(PIXTYPE),
check->file,check->filename);
write_body(cat->tab, check->pix, check->npix);
free(check->pix);
padsize = (FBSIZE-((check->npix*sizeof(PIXTYPE))%FBSIZE)) % FBSIZE;
pad_tab(cat, check->npix*sizeof(PIXTYPE));
break;
case CHECK_SEGMENTATION:
if (bswapflag)
swapbytes(check->pix, sizeof(ULONG), (int)check->npix);
QFWRITE(check->pix,check->npix*sizeof(ULONG),
check->file,check->filename);
write_ibody(cat->tab, check->pix, check->npix);
free(check->pix);
padsize = (FBSIZE -((check->npix*sizeof(ULONG))%FBSIZE)) % FBSIZE;
pad_tab(cat, check->npix*sizeof(FLAGTYPE));
break;
case CHECK_SUBOBJECTS:
......@@ -494,7 +462,7 @@ void reendcheck(picstruct *field, checkstruct *check)
free(check->pix);
free(check->line);
check->line = NULL;
padsize = (FBSIZE -((check->npix*sizeof(PIXTYPE))%FBSIZE)) % FBSIZE;
pad_tab(cat, check->npix*sizeof(PIXTYPE));
break;
}
......@@ -502,11 +470,6 @@ void reendcheck(picstruct *field, checkstruct *check)
error(EXIT_FAILURE, "*Internal Error* in ", "endcheck()!");
}
QCALLOC(buf, char, FBSIZE);
if (padsize)
QFWRITE (buf, padsize, check->file, check->filename);
free(buf);
return;
}
......@@ -516,8 +479,7 @@ close check-image.
*/
void endcheck(checkstruct *check)
{
fclose(check->file);
free_cat(&check->cat,1);
free(check);
return;
......
src/check.h
View file @ 90385513
......@@ -22,18 +22,20 @@
* You should have received a copy of the GNU General Public License
* along with SExtractor. If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/10/2010
* Last modified: 02/12/2010
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
#ifndef _FITSCAT_H_
#include "fits/fitscat.h"
#endif
/*--------------------------------- structures ------------------------------*/
/* Check-image parameters */
typedef struct structcheck
{
char filename[MAXCHAR]; /* ptr to check-image filename */
FILE *file; /* ptr to check-image file structure */
char *fitshead; /* ptr to check-image FITS header */
int fitsheadsize; /* size of check-image FITS header */
int next; /* Number of extensions */
catstruct *cat; /* FITS file structure */
void *pix; /* ptr to check-image pixmap */
int width, height, depth; /* size of check-image */
size_t npix; /* number of pixels in check-image */
......
src/fits/fitsbody.c
View file @ 90385513
......@@ -729,7 +729,7 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
{
unsigned char *bufdata = (unsigned char *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (unsigned char)((*(ptr++)-bz)/bs+0.49999);;
*(bufdata++) = (unsigned char)((*(ptr++)-bz)/bs+0.49999);
}
break;
......@@ -830,6 +830,158 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
}
/******* write_ibody ***********************************************************
PROTO write_ibody(tabstruct *tab, FLAGTYPE *ptr, long size)
PURPOSE Write integer values to a FITS body.
INPUT A pointer to the tab structure,
a pointer to the array in memory,
the number of elements to be written.
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
VERSION 02/12/2010
***/
void write_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
{
static FLAGTYPE bufdata0[DATA_BUFSIZE/sizeof(FLAGTYPE)];
catstruct *cat;
char *cbufdata0;
size_t i, bowl, spoonful;
double bs,bz;
bs = tab->bscale;
bz = tab->bzero;
cat = tab->cat;
if (!cat)
error(EXIT_FAILURE, "*Internal Error*: no parent cat structure for table ",
tab->extname);
cbufdata0 = (char *)bufdata0; /* A trick to remove gcc aliasing warnings */
switch(tab->compress_type)
{
/*-- Uncompressed image */
case COMPRESS_NONE:
bowl = DATA_BUFSIZE/tab->bytepix;
spoonful = size<bowl?size:bowl;
for(; size>0; size -= spoonful)
{
if (spoonful>size)
spoonful = size;
switch(tab->bitpix)
{
case BP_BYTE:
if (tab->bitsgn)
{
char *bufdata = (char *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (char)*(ptr++);
}
else
{
unsigned char *bufdata = (unsigned char *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (unsigned char)*(ptr++);
}
break;
case BP_SHORT:
if (tab->bitsgn)
{
short *bufdata = (short *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (short)*(ptr++);
}
else
{
unsigned short *bufdata = (unsigned short *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (unsigned short)*(ptr++);
}
if (bswapflag)
swapbytes(cbufdata0, 2, spoonful);
break;
case BP_LONG:
if (tab->bitsgn)
{
int *bufdata = (int *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (int)*(ptr++);
}
else
{
unsigned int *bufdata = (unsigned int *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (unsigned int)*(ptr++);
}
if (bswapflag)
swapbytes(cbufdata0, 4, spoonful);
break;
#ifdef HAVE_LONG_LONG_INT
case BP_LONGLONG:
if (tab->bitsgn)
{
LONGLONG *bufdata = (LONGLONG *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (LONGLONG)*(ptr++);
}
else
{
ULONGLONG *bufdata = (ULONGLONG *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (ULONGLONG)*(ptr++);
}
if (bswapflag)
swapbytes(cbufdata0, 8, spoonful);
break;
#endif
case BP_FLOAT:
{
float *bufdata = (float *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = (float)((double)*(ptr++)-bz)/bs;
if (bswapflag)
swapbytes(cbufdata0, 4, spoonful);
}
break;
case BP_DOUBLE:
{
double *bufdata = (double *)cbufdata0;
for (i=spoonful; i--;)
*(bufdata++) = ((double)*(ptr++)-bz)/bs;
if (bswapflag)
swapbytes(cbufdata0, 8, spoonful);
}
break;
default:
error(EXIT_FAILURE,"*FATAL ERROR*: unknown BITPIX type in ",
"read_body()");
break;
}
QFWRITE(cbufdata0, spoonful*tab->bytepix, cat->file, cat->filename);
}
break;
/*-- Compressed image */
case COMPRESS_BASEBYTE:
break;
case COMPRESS_PREVPIX:
break;
default:
error(EXIT_FAILURE,"*Internal Error*: unknown compression mode in ",
"read_body()");
}
return;
}
/******* set_maxram ***********************************************************
PROTO int set_maxram(size_t maxram)
PURPOSE Set the maximum amount of silicon memory that can be allocated for
......
src/fits/fitscat.h
View file @ 90385513
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 09/10/2010
* Last modified: 02/12/2010
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -247,6 +247,7 @@ extern void add_cleanupfilename(char *filename),
voprint_obj(FILE *stream, tabstruct *tab),
warning(char *, char *),
write_body(tabstruct *tab, PIXTYPE *ptr, size_t size),
write_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size),
write_checksum(tabstruct *tab);
extern char *tdisptoprintf(char *tdisp, char *str),
......
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