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main.c
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#include<stdio.h>
#include<string.h>
#include<math.h>
#include<malloc.h>
#include<stdlib.h>
#include<fitsio.h>
#include<ctype.h>
#include<time.h>
#include<unistd.h>
#include "defaults.h"
#include "globals.h"
#include "functions.h"
#ifdef __MINGW32__
#include <stddef.h>
#endif
int main(int argc,char *argv[]) {
int i,j,k,l,m; /* generic indices */
char scrStr[SCRLEN]; /* scratch string */
double sumKernel; /* photometric normalization */
double meansigSubstamps,scatterSubstamps; /* mean sigma and scatter of substamps, for fits header */
double meansigSubstampsF,scatterSubstampsF; /* mean sigma and scatter of substamps, using final noise */
double meanksumSubstamps,scatterksumSubstamps; /* mean and scatter of ksum */
int NskippedSubstamps; /* Number of skipped substamps, for fits header */
/*
NOTE : The .fits images are 1-indexed, while these arrays contained within are
0 indexed. Thus anything you find below at x,y you will find displayed at
position x+1,y+1.
*/
/* template image */
fitsfile *tPtr;
int tBitpix, tNaxis;
long tNaxes[MAXDIM];
float *tRData = NULL;
double tMerit=0;
double *tKerSol = NULL;
stamp_struct *ctStamps = NULL;
/* comparison image */
fitsfile *iPtr;
int iBitpix, iNaxis;
long iNaxes[MAXDIM];
float *iRData = NULL;
double iMerit=0;
double *iKerSol = NULL;
stamp_struct *ciStamps = NULL;
/* output image */
fitsfile *oPtr;
int oBitpix, oNaxis;
long oNaxes[MAXDIM];
float *oRData = NULL;
/* extraneous image; eRData now defined in globals.h */
fitsfile *ePtr;
float *eRData = NULL;
/* extraneous output regions */
int *misRData = NULL; /* image mask */
int *mtsRData = NULL; /* template mask */
int xMin, yMin, xMax, yMax; /* whole image */
int *rXMins, *rYMins, *rXMaxs, *rYMaxs; /* each region, good data */
int rXMin, rYMin, rXMax, rYMax; /* each region, good data */
int rXBMin, rYBMin, rXBMax, rYBMax; /* each region, including buffer */
int xBufLo, xBufHi, yBufLo, yBufHi; /* buffer */
int nR; /* region counter */
int sXMin, sYMin, sXMax, sYMax; /* each stamp */
int niS, ntS; /* stamp counter */
int convTmpl; /* which way the convolution goes */
/* cfitsio */
long pixMin[2], pixMax[2];
long inc[2] = {1, 1};
int fpixelOutX, fpixelOutY, lpixelOutX, lpixelOutY;
int anynul;
int status = 0, kInfoNum, nx2norm;
char **tform=NULL, **ttype=NULL, **tunit=NULL;
char hKeyword[1024], hInfo[2048];
double sum, mean, median, mode, sd, fwhm, lfwhm, diffrat, x2norm;
double summ, meanm, medianm, modem, sdm, fwhmm, lfwhmm;
double nsum, nmean, nmedian, nmode, nsd, nfwhm, nlfwhm;
double nsumm, nmeanm, nmedianm, nmodem, nsdm, nfwhmm, nlfwhmm;
float iSFrac, tSFrac;
float fitThresh;
int flag;
/* misc */
FILE *rFile;
double inv1;
char *pstr;
int sBorder; /*armin*/
struct tm *tm;
time_t thetime;
/* SET VERSION */
sprintf(version, "5.1.11");
/* set global vars, and grab command line args */
/* return image names in fnames */
vargs(argc, argv);
/******/
/* access input images, create output image shell */
/******/
/* open up, get template bitpix, # dimensions, image size */
if (fits_open_file(&tPtr, template, 0, &status))
printError(status);
if (fits_get_img_param(tPtr, MAXDIM, &tBitpix, &tNaxis, tNaxes, &status))
printError(status);
/* if input noise image, open and check to make sure its the right size */
/* use the ePtr fitsfile temporarily */
if (tNoiseIm) {
if (fits_open_file(&ePtr, tNoiseIm, 0, &status))
printError(status);
if (fits_get_img_param(ePtr, MAXDIM, &oBitpix, &oNaxis, oNaxes, &status))
printError(status);
if ( (oNaxes[0] != tNaxes[0]) || (oNaxes[1] != tNaxes[1]) ) {
fprintf(stderr, "WARNING : Input template noise array not same size as template, ignoring...\n");
tNoiseIm = NULL;
}
if ( fits_close_file(ePtr, &status) )
printError(status);
}
/* open up, get comparison image bitpix, # dimensions, image size */
if (fits_open_file(&iPtr, image, 0, &status))
printError(status);
if (fits_get_img_param(iPtr, MAXDIM, &iBitpix, &iNaxis, iNaxes, &status))
printError(status);
/* if input noise image, open and check to make sure its the right size */
/* use the ePtr fitsfile temporarily */
if (iNoiseIm) {
if (fits_open_file(&ePtr, iNoiseIm, 0, &status))
printError(status);
if (fits_get_img_param(ePtr, MAXDIM, &oBitpix, &oNaxis, oNaxes, &status))
printError(status);
if ( (oNaxes[0] != iNaxes[0]) || (oNaxes[1] != iNaxes[1]) ) {
fprintf(stderr, "WARNING : Input image noise array not same size as image, ignoring...\n");
iNoiseIm = NULL;
}
if ( fits_close_file(ePtr, &status) )
printError(status);
}
if (tNoiseIm) {
if (fits_open_file(&ePtr, tNoiseIm, 0, &status))
printError(status);
if (fits_get_img_param(ePtr, MAXDIM, &oBitpix, &oNaxis, oNaxes, &status))
printError(status);
if ( (oNaxes[0] != iNaxes[0]) || (oNaxes[1] != iNaxes[1]) ) {
fprintf(stderr, "WARNING : Input template noise array not same size as image, ignoring...\n");
tNoiseIm = NULL;
}
if ( fits_close_file(ePtr, &status) )
printError(status);
}
/* same with mask images */
if (iMaskIm) {
if (fits_open_file(&ePtr, iMaskIm, 0, &status))
printError(status);
if (fits_get_img_param(ePtr, MAXDIM, &oBitpix, &oNaxis, oNaxes, &status))
printError(status);
if ( (oNaxes[0] != iNaxes[0]) || (oNaxes[1] != iNaxes[1]) ) {
fprintf(stderr, "WARNING : Input image mask array not same size as image, ignoring...\n");
iMaskIm = NULL;
}
if ( fits_close_file(ePtr, &status) )
printError(status);
}
if (tMaskIm) {
if (fits_open_file(&ePtr, tMaskIm, 0, &status))
printError(status);
if (fits_get_img_param(ePtr, MAXDIM, &oBitpix, &oNaxis, oNaxes, &status))
printError(status);
if ( (oNaxes[0] != iNaxes[0]) || (oNaxes[1] != iNaxes[1]) ) {
fprintf(stderr, "WARNING : Input template mask array not same size as image, ignoring...\n");
tMaskIm = NULL;
}
if ( fits_close_file(ePtr, &status) )
printError(status);
}
/* let em know whats going on... */
fprintf(stderr, "Doing : %s -\n", image);
fprintf(stderr, " %s =\n", template);
fprintf(stderr, " %s\n", outim);
fprintf(stderr, " Good templ data : %.1f -> %.1f\n", tLThresh, tUThresh);
fprintf(stderr, " Good image data : %.1f -> %.1f\n", iLThresh, iUThresh);
/* ADU pedestal? */
tUThresh -= tPedestal;
tUKThresh -= tPedestal;
tLThresh -= tPedestal;
iUThresh -= iPedestal;
iUKThresh -= iPedestal;
iLThresh -= iPedestal;
/* overwrite output image? */
if (!noClobber) { sprintf(scrStr, "!%s", outim); }
else { sprintf(scrStr, "%s", outim); }
oNaxes[0] = imax(tNaxes[0], iNaxes[0]);
oNaxes[1] = imax(tNaxes[1], iNaxes[1]);
oNaxis = 2;
if (outShort)
oBitpix = SHORT_IMG;
else
oBitpix = FLOAT_IMG;
/* create and open new empty output FITS file */
if ( fits_create_file(&oPtr, scrStr, &status) ||
fits_create_img(oPtr, oBitpix, oNaxis, oNaxes, &status) )
printError(status);
/* copy over the fits keywords */
if ( hp_fits_copy_header(iPtr, oPtr, &status) )
printError(status);
/* add info; format taken from SWARP */
fits_write_key_str(oPtr, "COMMENT", "", "", &status);
fits_write_key_str(oPtr, "SOFTNAME", "HOTPanTS", "The software that differenced this image", &status);
fits_write_key_str(oPtr, "SOFTVERS", version, "Version", &status);
fits_write_key_str(oPtr, "SOFTAUTH", "Andrew Becker <becker@astro.washington.edu>", "Maintainer", &status);
fits_write_key_str(oPtr, "SOFTINST", "University of Washington", "Institute", &status);
fits_write_key_str(oPtr, "COMMENT", "", "", &status);
/* user name */
if (!(pstr=getenv("USERNAME"))) /* Cygwin,... */
if ((pstr=getenv("LOGNAME"))) /* Linux,... */
fits_write_key_str(oPtr, "AUTHOR", pstr, "Who ran the software", &status);
if (!pstr)
fits_write_key_str(oPtr, "AUTHOR", "unknown", "Who ran the software", &status);
/* host name */
#ifdef __MINGW32__
strncpy(hInfo, "Unknown", sizeof(hInfo)/sizeof(char));
#else
gethostname(hInfo, 80);
#endif
if (hInfo)
fits_write_key_str(oPtr, "ORIGIN", hInfo, "Where it was done", &status);
/* what was it fired up */
thetime = time(NULL);
tm = gmtime(&thetime);
sprintf(hInfo,"%04d-%02d-%02dT%02d:%02d:%02d",
tm->tm_year+1900, tm->tm_mon+1, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec);
fits_write_key_str(oPtr, "DATE", hInfo, "When it was started (GMT)", &status);
fits_write_key_str(oPtr, "COMMENT", "", "", &status);
/* don't let a failure here kill us */
status = 0;
/* change bscale/bzero AFTER transfering input image header */
if ( fits_update_key_flt(oPtr, "BZERO", outBzero, -5, "", &status) ||
fits_update_key_flt(oPtr, "BSCALE", outBscale, -5, "", &status) )
printError(status);
/* make new image extensions for any extraneous output data */
if (inclConvImage) {
if ( fits_insert_img(oPtr, oBitpix, oNaxis, oNaxes, &status) ||
fits_update_key(oPtr, TSTRING, "OBJECT", "Convolved Image", "", &status) )
printError(status);
}
if (convImage) {
if (!noClobber) { sprintf(scrStr, "!%s", convImage); }
else { sprintf(scrStr, "%s", convImage); }
if (fits_create_file(&ePtr, scrStr, &status) ||
fits_create_img(ePtr, oBitpix, oNaxis, oNaxes, &status) ||
hp_fits_copy_header(iPtr, ePtr, &status) ||
fits_update_key(ePtr, TSTRING, "OBJECT", "Convolved Image", "", &status) ||
fits_close_file(ePtr, &status) )
printError(status);
}
if (inclSigmaImage) {
if ( fits_insert_img(oPtr, oBitpix, 2, oNaxes, &status) ||
fits_update_key(oPtr, TSTRING, "OBJECT", "Noise-scaled (sigma) Difference Image", "", &status) )
printError(status);
}
if (sigmaImage) {
if (!noClobber) { sprintf(scrStr, "!%s", sigmaImage); }
else { sprintf(scrStr, "%s", sigmaImage); }
if (fits_create_file(&ePtr, scrStr, &status) ||
fits_create_img(ePtr, oBitpix, oNaxis, oNaxes, &status) ||
hp_fits_copy_header(iPtr, ePtr, &status) ||
fits_update_key(ePtr, TSTRING, "OBJECT", "Noise-scaled (sigma) Difference Image", "", &status) ||
fits_close_file(ePtr, &status) )
printError(status);
}
if (inclNoiseImage) {
if (outNShort) {
if (fits_insert_img(oPtr, SHORT_IMG, 2, oNaxes, &status))
printError(status);
}
else {
if (fits_insert_img(oPtr, FLOAT_IMG, 2, oNaxes, &status))
printError(status);
}
if (fits_update_key(oPtr, TSTRING, "OBJECT", "HOTPanTS Noise Image", "", &status))
printError(status);
/* manually set bscale and bzero for noise image layer */
if (outNShort) {
if ( fits_update_key_flt(oPtr, "BZERO", outNiBzero, -5, "", &status) ||
fits_update_key_flt(oPtr, "BSCALE", outNiBscale, -5, "", &status) )
printError(status);
}
}
if (noiseImage) {
if (!noClobber) { sprintf(scrStr, "!%s", noiseImage); }
else { sprintf(scrStr, "%s", noiseImage); }
if (fits_create_file(&ePtr, scrStr, &status))
printError(status);
if (outNShort) {
if (fits_create_img(ePtr, SHORT_IMG, oNaxis, oNaxes, &status))
printError(status);
}
else {
if (fits_create_img(ePtr, FLOAT_IMG, oNaxis, oNaxes, &status))
printError(status);
}
if (hp_fits_copy_header(iPtr, ePtr, &status) ||
fits_update_key(ePtr, TSTRING, "OBJECT", "HOTPanTS Noise Image", "", &status) ||
fits_update_key_flt(ePtr, "GAIN", 1., -1, "No gain in noise image", &status) ||
fits_update_key_flt(ePtr, "RDNOISE", 0., -1, "No rdnoise in noise image", &status) ||
fits_write_key_flt(ePtr, "MASKVAL", fillValNoise, -6, "Value of Masked Pixels", &status))
printError(status);
if (outNShort)
if (fits_update_key_flt(ePtr, "BZERO", outNiBzero, -5, "", &status) ||
fits_update_key_flt(ePtr, "BSCALE", outNiBscale, -5, "", &status))
printError(status);
if (fits_close_file(ePtr, &status))
printError(status);
}
if (outMask) {
if (!noClobber) { sprintf(scrStr, "!%s", outMask); }
else { sprintf(scrStr, "%s", outMask); }
if (fits_create_file(&ePtr, scrStr, &status) ||
fits_create_img(ePtr, SHORT_IMG, oNaxis, oNaxes, &status) ||
hp_fits_copy_header(iPtr, ePtr, &status) ||
fits_update_key(ePtr, TSTRING, "OBJECT", "Hotpants output Mask Image", "", &status) ||
fits_update_key_flt(ePtr, "BZERO", 32768, -5, "", &status) ||
fits_update_key_flt(ePtr, "BSCALE", 1, -5, "", &status) ||
fits_close_file(ePtr, &status) )
printError(status);
}
if (kernelImIn) {
/* possibly override defaults with info in kernel image */
getKernelInfo(kernelImIn);
fprintf(stderr, " received kernel info\n");
}
/* determine the size of the data structures */
nCompKer = 0;
for(i = 0; i < ngauss; i++)
nCompKer += ((deg_fixe[i] + 1) * (deg_fixe[i] + 2)) / 2;
nComp = ((kerOrder + 1) * (kerOrder + 2)) / 2;
nC = nCompKer + 2;
nCompBG = (nCompKer - 1) * nComp + 1;
nBGVectors = ((bgOrder + 1) * (bgOrder + 2)) / 2;
nCompTotal = nCompKer * nComp + nBGVectors;
fwKernel = hwKernel * 2 + 1; /* kernel size */
if (useFullSS) {
fwKSStamp = fwKernel; /* substamp size */
fwStamp = fwKernel;
nStampX = (int)(imin(tNaxes[0], iNaxes[0]) / nRegX / fwStamp);
nStampY = (int)(imin(tNaxes[1], iNaxes[1]) / nRegY / fwStamp);
fprintf(stderr, "Using maximial number of stamps : %d x %d\n", nStampX, nStampY);
}
else {
fwKSStamp = hwKSStamp * 2 + 1; /* substamp size */
/* estimate of fwStamp for all these mallocs... */
/* smallest dimension, minus kernel width */
fwStamp = imin( imin(tNaxes[0], iNaxes[0]) / nRegX / nStampX,
imin(tNaxes[1], iNaxes[1]) / nRegY / nStampY );
fwStamp -= fwKernel;
fwStamp -= fwStamp % 2 == 0 ? 1 : 0; /* hmmm, an odd shape... */
/* insanity checking */
if (fwStamp < fwKSStamp) {
fwStamp = fwKSStamp+fwKernel;
fwStamp -= fwStamp % 2 == 0 ? 1 : 0;
nStampX = imin(tNaxes[0], iNaxes[0]) / nRegX / fwStamp;
nStampY = imin(tNaxes[1], iNaxes[1]) / nRegY / fwStamp;
fprintf(stderr, "WARNING : too many stamps requested\n");
fprintf(stderr, " using nsx = %d, nsy = %d\n", nStampX, nStampY);
}
}
kcStep = kcStep ? kcStep : fwKernel; /* size of step in spatial_convolve */
nStamps = nStampX * nStampY;
sBorder = hwKSStamp + hwKernel;
fprintf(stderr, "Mallocing massive amounts of memory...\n");
/* malloc data structures */
if ( !(temp = (float *)calloc((fwKSStamp+fwKernel)*fwKSStamp, sizeof(float))) ||
!(indx = (int *)calloc((nCompTotal+1+100), sizeof(int))) ||
!(kernel = (double *)calloc(fwKernel*fwKernel, sizeof(double))) ||
!(kernel_coeffs = (double *)calloc(nCompKer, sizeof(double))) ||
!(kernel_vec = (double **)calloc(nCompKer, sizeof(double *))) ||
!(filter_x = (double *)calloc(nCompKer*fwKernel, sizeof(double))) ||
!(filter_y = (double *)calloc(nCompKer*fwKernel, sizeof(double))) ||
!(check_mat = (double **)calloc(nC, sizeof(double *))) ||
!(check_vec = (double *)calloc(nC, sizeof(double))) ||
!(check_stack = (double *)calloc(nStamps, sizeof(double))) ) {
exit(1);
}
for (i = 0; i < nC; i++)
if ( !(check_mat[i] = (double *)calloc(nC, sizeof(double))) ) {
exit (1);
}
/******/
/* determine pixel limits of regions, and of stamps in region */
/******/
/* maximum limit of overlap between images */
/* to be used in newest version, which deals with borders later... */
xMin = (gdXmin ? imax(0, gdXmin) : 0);
yMin = (gdYmin ? imax(0, gdYmin) : 0);
xMax = -1 + (gdXmax ? imin(imin(tNaxes[0], iNaxes[0]), gdXmax) : imin(tNaxes[0], iNaxes[0]));
yMax = -1 + (gdYmax ? imin(imin(tNaxes[1], iNaxes[1]), gdYmax) : imin(tNaxes[1], iNaxes[1]));
nR = 0;
if (regFile) {
rFile = fopen(regFile, "r");
while (fscanf(rFile, "%s\n", scrStr) != EOF)
nR++;
rewind(rFile);
if ( !(rXMins = (int *)calloc(nR, sizeof(int))) ||
!(rXMaxs = (int *)calloc(nR, sizeof(int))) ||
!(rYMins = (int *)calloc(nR, sizeof(int))) ||
!(rYMaxs = (int *)calloc(nR, sizeof(int))) )
exit(1);
nR = 0;
while (fscanf(rFile, "%d:%d,%d:%d", &rXMin, &rXMax, &rYMin, &rYMax) != EOF) {
/* range of good data for the region */
rXMins[nR] = imax(rXMin, xMin);
rYMins[nR] = imax(rYMin, yMin);
rXMaxs[nR] = imin(rXMax, xMax);
rYMaxs[nR] = imin(rYMax, yMax);
nR++;
}
fclose(rFile);
}
else if (regKeyWord) {
if ( !(rXMins = (int *)calloc(numRegKeyWord, sizeof(int))) ||
!(rXMaxs = (int *)calloc(numRegKeyWord, sizeof(int))) ||
!(rYMins = (int *)calloc(numRegKeyWord, sizeof(int))) ||
!(rYMaxs = (int *)calloc(numRegKeyWord, sizeof(int))) )
exit(1);
for (nR = 0; nR < numRegKeyWord; nR++){
sprintf(hKeyword, "%s%d", regKeyWord, nR);
if (fits_read_key_str(tPtr, hKeyword, hInfo, scrStr, &status)) {
rXMins[nR] = xMin;
rXMaxs[nR] = xMax;
rYMins[nR] = yMin;
rYMaxs[nR] = yMax;
status = 0;
}
else
sscanf(hInfo, "[%d:%d,%d:%d]", &rXMins[nR], &rXMaxs[nR], &rYMins[nR], &rYMaxs[nR]);
if (fits_read_key_str(iPtr, hKeyword, hInfo, scrStr, &status)) {
rXMin = xMin;
rXMax = xMax;
rYMin = yMin;
rYMax = yMax;
status = 0;
}
else
sscanf(hInfo, "[%d:%d,%d:%d]", &rXMin, &rXMax, &rYMin, &rYMax);
rXMins[nR] = imax(rXMin, rXMins[nR]);
rYMins[nR] = imax(rYMin, rYMins[nR]);
rXMaxs[nR] = imin(rXMax, rXMaxs[nR]);
rYMaxs[nR] = imin(rYMax, rYMaxs[nR]);
rXMins[nR] = imax(xMin, rXMins[nR]);
rYMins[nR] = imax(yMin, rYMins[nR]);
rXMaxs[nR] = imin(xMax, rXMaxs[nR]);
rYMaxs[nR] = imin(yMax, rYMaxs[nR]);
/* fprintf(stderr, "%d %d %d %d\n", rXMins[nR], rYMins[nR], rXMaxs[nR], rYMaxs[nR]); */
}
}
else {
if ( !(rXMins = (int *)calloc(nRegX*nRegY, sizeof(int))) ||
!(rXMaxs = (int *)calloc(nRegX*nRegY, sizeof(int))) ||
!(rYMins = (int *)calloc(nRegX*nRegY, sizeof(int))) ||
!(rYMaxs = (int *)calloc(nRegX*nRegY, sizeof(int))) )
exit(1);
/* in cfitsio, data are striped along x dimen, thus all loops
are y outer, x inner. or at least they should be... */
for (j = 0; j < nRegY; j++) {
for (i = 0; i < nRegX; i++) {
/* range of good data for the region */
rXMins[nR] = xMin + i * xMax / nRegX;
rYMins[nR] = yMin + j * yMax / nRegY;
rXMaxs[nR] = imin( (i+1) * xMax / nRegX, xMax );
rYMaxs[nR] = imin( (j+1) * yMax / nRegY, yMax );
nR++;
}
}
}
/* now that we know the number of regions, if we want a fits
binary table for the kernel info, create it here */
if ((doKerInfo) || (kernelImOut)){
tform = (char **)calloc(nR, sizeof(char *));
ttype = (char **)calloc(nR, sizeof(char *));
tunit = (char **)calloc(nR, sizeof(char *));
for (k = 0; k < nR; k++) {
tform[k] = (char *)malloc(10*sizeof(char));
ttype[k] = (char *)malloc(10*sizeof(char));
tunit[k] = (char *)malloc(sizeof(char));
strcpy(tform[k], "D10.8");
sprintf(ttype[k], "Region%d", k);
strcpy(tunit[k], "");
}
if (doKerInfo) {
/* lets try it as a layer at the **bottom** of the output difference image */
if ( fits_insert_btbl(oPtr, (nCompTotal+1), nR, ttype, tform, tunit, "Convolution Kernel Information", 0L, &status) ||
fits_update_key(oPtr, TSTRING, "OBJECT", "Convolution Kernel Information", "", &status) ||
fits_get_hdu_num(oPtr, &kInfoNum) )
printError(status);
}
if (kernelImOut) {
if (!noClobber) { sprintf(scrStr, "!%s", kernelImOut); }
else { sprintf(scrStr, "%s", kernelImOut); }
if (fits_create_file(&ePtr, scrStr, &status) ||
fits_insert_btbl(ePtr, (nCompTotal+1), nR, ttype, tform, tunit, "Convolution Kernel Information", 0L, &status) ||
fits_update_key(ePtr, TSTRING, "OBJECT", "Convolution Kernel Information", "", &status) ||
fits_get_hdu_num(ePtr, &kInfoNum) ||
fits_close_file(ePtr, &status))
printError(status);
}
}
xcmp = ycmp = 0;
if (sstampFile) {
/* downsize for speed */
/* armin: this screws things up! */
/*fwStamp = fwKSStamp + fwKernel;*/
/* armin: call function to load x,y from file */
loadxyfile(sstampFile, cmpFile);
}
/* initialize to requested value in case things change later on */
fitThresh = kerFitThresh;
/* cycle through all regions */
for (i = 0; i < nR; i++) {
if (kernelImIn) {
/* grab region info from kernelImIn */
readKernel(kernelImIn, i, &tKerSol, &iKerSol, &rXMin, &rXMax, &rYMin, &rYMax,
&meansigSubstamps, &scatterSubstamps,
&meansigSubstampsF, &scatterSubstampsF,
&diffrat, &NskippedSubstamps);
}
else {
rXMin = rXMins[i];
rXMax = rXMaxs[i];
rYMin = rYMins[i];
rYMax = rYMaxs[i];
meansigSubstamps = scatterSubstamps = 0.0;
NskippedSubstamps = 0;
}
if (nR > 1) {
/* buffered - add an extra half-stamp for merging regions */
rXBMin = imax(xMin, rXMin - fwStamp/2);
rYBMin = imax(yMin, rYMin - fwStamp/2);
rXBMax = imin(xMax, rXMax + fwStamp/2);
rYBMax = imin(yMax, rYMax + fwStamp/2);
}
else {
rXBMin = imax(xMin, rXMin - hwKernel);
rYBMin = imax(yMin, rYMin - hwKernel);
rXBMax = imin(xMax, rXMax + hwKernel);
rYBMax = imin(yMax, rYMax + hwKernel);
}
/* size of the buffering, used when merging output image sections */
xBufLo = rXMin - rXBMin;
xBufHi = rXBMax - rXMax;
yBufLo = rYMin - rYBMin;
yBufHi = rYBMax - rYMax;
/* size of buffered region, in pixels */
rPixX = rXBMax - rXBMin + 1;
rPixY = rYBMax - rYBMin + 1;
/* detemine the limits of the input images */
/* NOTE: cfitsio wants first pixel = 1, not 0 */
pixMin[0] = rXBMin + 1;
pixMin[1] = rYBMin + 1;
pixMax[0] = rXBMax + 1;
pixMax[1] = rYBMax + 1;
/* determine the limits of the output images */
fpixelOutX = rXBMin + xBufLo + 1;
fpixelOutY = rYBMin + yBufLo + 1;
lpixelOutX = fpixelOutX + (rPixX - xBufHi - xBufLo - 1);
lpixelOutY = fpixelOutY + (rPixY - yBufHi - yBufLo - 1);
fprintf(stderr, "Region %d pixels : %ld:%ld,%ld:%ld\n"
, i, pixMin[0], pixMax[0], pixMin[1], pixMax[1]);
fprintf(stderr, " Vector Indices (buffered) : %d:%d,%d:%d\n"
, rXBMin, rXBMax, rYBMin, rYBMax);
fprintf(stderr, " Vector Indices (good data): %d:%d,%d:%d\n"
, rXMin, rXMax, rYMin, rYMax);
/* malloc standard input and output arrays */
tRData = (float *)calloc(rPixX*rPixY, sizeof(float));
iRData = (float *)calloc(rPixX*rPixY, sizeof(float));
oRData = (float *)calloc(rPixX*rPixY, sizeof(float));
eRData = (float *)calloc(rPixX*rPixY, sizeof(float));
if (tRData == NULL || iRData == NULL || oRData == NULL || eRData == NULL) {
fprintf(stderr, "Cannot Allocate Standard Data Arrays\n");
exit (1);
}
/* set them to fillVal */
fset(tRData, fillVal, rPixX, rPixY);
fset(iRData, fillVal, rPixX, rPixY);
/* set eRData and oRData to fillValNoise */
fset(oRData, fillValNoise, rPixX, rPixY);
fset(eRData, fillValNoise, rPixX, rPixY);
/* malloc mask arrays */
mRData = (int *)calloc(rPixX*rPixY, sizeof(int));
misRData = (int *)calloc(rPixX*rPixY, sizeof(int));
mtsRData = (int *)calloc(rPixX*rPixY, sizeof(int));
if (mRData == NULL || misRData == NULL || mtsRData == NULL ) {
fprintf(stderr, "Cannot Allocate Mask Arrays\n");
exit (1);
}
/* dont bother if info already from kernel image */
if (!(kernelImIn)) {
/* ciStamps contains stamp information about convolving image */
/* ctStamps contains stamp information about convolving template */
if (!(strncmp(forceConvolve, "i", 1)==0)) {
if (verbose>=2) fprintf(stderr,"Allocating stamps...\n");
if(!(ctStamps = (stamp_struct *)calloc(nStamps, sizeof(stamp_struct)))) {
printf("Cannot Allocate Stamp List\n");
exit (1);
}
if (allocateStamps(ctStamps, nStamps)) {
fprintf(stderr,"Cannot Allocate Stamp Vector\n");
exit (1);
}
tKerSol = (double *)calloc((nCompTotal+1), sizeof(double));
}
if (!(strncmp(forceConvolve, "t", 1)==0)) {
if(!(ciStamps = (stamp_struct *)calloc(nStamps, sizeof(stamp_struct)))) {
printf("Cannot Allocate Stamp List\n");
exit (1);
}
if (allocateStamps(ciStamps, nStamps)) {
fprintf(stderr,"Cannot Allocate Stamp Vector\n");
exit(1);
}
iKerSol = (double *)calloc((nCompTotal+1), sizeof(double));
}
}
/* read image region from fits files into input arrays */
if (fits_read_subset_flt(tPtr, 0, tNaxis, tNaxes, pixMin, pixMax, inc, 0, tRData, &anynul, &status) ||
fits_read_subset_flt(iPtr, 0, iNaxis, iNaxes, pixMin, pixMax, inc, 0, iRData, &anynul, &status)) {
printError(status);
}
/* take off possible pedestal */
if (tPedestal != 0. || iPedestal != 0.) {
for (l = rPixX*rPixY; l--; ) {
tRData[l] -= tPedestal;
iRData[l] -= iPedestal;
}
}
/* we will use eRData and oRData here to make the APPROXIMATE
noise image - approximate because you don't know which way to
convolve yet */
if (iNoiseIm) {
if (fits_open_file(&ePtr, iNoiseIm, 0, &status))
printError(status);
if (fits_read_subset_flt(ePtr, 0, iNaxis, iNaxes, pixMin, pixMax, inc, 0, oRData, &anynul, &status) ||
fits_close_file(ePtr, &status))
printError(status);
for (l = rPixX*rPixY; l--; )
oRData[l] *= oRData[l];
}
else {
oRData = makeNoiseImage4(iRData, 1./iGain, iRdnoise/iGain);
}
if (tNoiseIm) {
if (fits_open_file(&ePtr, tNoiseIm, 0, &status))
printError(status);
if (fits_read_subset_flt(ePtr, 0, tNaxis, tNaxes, pixMin, pixMax, inc, 0, eRData, &anynul, &status) ||
fits_close_file(ePtr, &status))
printError(status);
for (l = rPixX*rPixY; l--; )
eRData[l] *= eRData[l];
}
else {
eRData = makeNoiseImage4(tRData, 1./tGain, tRdnoise/tGain);
}
/* add noise portions, NOT SQRT HERE
this is only used for getStampSig() */
for (l = rPixX*rPixY; l--; )
oRData[l] += eRData[l];
/* NOTE : oRData is (temporarily) the approximate noise squared per pixel */
/* and eRData gets realloced later */
/*
mask out bad input pixels, spread by hwKernel * kfSpreadMask1
*/
if (iMaskIm) {
if (fits_open_file(&ePtr, iMaskIm, 0, &status))
printError(status);
if (fits_read_subset_int(ePtr, 0, tNaxis, tNaxes, pixMin, pixMax, inc, 0, misRData, &anynul, &status) ||
fits_close_file(ePtr, &status))
printError(status);
/* register as read in from input mask */
for (l = rPixX*rPixY; l--; ) {
misRData[l] |= FLAG_INPUT_MASK * (misRData[l] > 0);
mRData[l] |= misRData[l];
}
}
if (tMaskIm) {
if (fits_open_file(&ePtr, tMaskIm, 0, &status))
printError(status);
if (fits_read_subset_int(ePtr, 0, tNaxis, tNaxes, pixMin, pixMax, inc, 0, mtsRData, &anynul, &status) ||
fits_close_file(ePtr, &status))
printError(status);
/* register as read in from input mask */
for (l = rPixX*rPixY; l--; ) {
mtsRData[l] |= FLAG_INPUT_MASK * (mtsRData[l] > 0);
mRData[l] |= mtsRData[l];
}
}
/* add own bits and spread */
makeInputMask(tRData, iRData, mRData);
/* make sure program can't find a valid stamp center around the edge of the image */
/* mask with 0x100 & 0x400 */
for (l = 0; l < rPixY; l++) {
for (k = 0; k < sBorder; k++) {
mRData[k+rPixX*l] |= (FLAG_T_BAD | FLAG_I_BAD);
}
for (k = rPixX-sBorder; k < rPixX; k++) {
mRData[k+rPixX*l] |= (FLAG_T_BAD | FLAG_I_BAD);
}
}
for (l = 0; l < sBorder; l++)
for (k = sBorder; k < rPixX-sBorder; k++)
mRData[k+rPixX*l] |= (FLAG_T_BAD | FLAG_I_BAD);
for (l = rPixY-sBorder; l < rPixY; l++)
for (k = sBorder; k < rPixX-sBorder; k++)
mRData[k+rPixX*l] |= (FLAG_T_BAD | FLAG_I_BAD);
status = 1;
flag = 1;
kerFitThresh = fitThresh;
if (!(kernelImIn)) {
/* only do a single loop for now... */
while ((status <= 2) && (flag)) {
flag = 0;
niS = 0;
ntS = 0;
for (l = 0; l < nStampY; l++) {
for (k = 0; k < nStampX; k++) {
fprintf(stderr, "Build stamp : t %4d i %4d (grid coord %2d %2d)\n", ntS, niS, k, l);
/* coordinates in the image, not the region */
/* NOTE : we keep float-valued 'rPixX / nStampX' in
here to not exclude a full stamps' width of space on
the right and upper sides of the image. Allows the
stamps to be separated by a little bit but fills the
region more evenly. */
sXMin = rXBMin + k * rPixX / nStampX;
sYMin = rYBMin + l * rPixY / nStampY;
sXMax = imin(sXMin + fwStamp - 1, rXBMax);
sYMax = imin(sYMin + fwStamp - 1, rYBMax);
/* armin: reinitializing sscnt and nss? */
if (!(strncmp(forceConvolve, "i", 1)==0)) {
ctStamps[ntS].sscnt = ctStamps[ntS].nss = 0;
ctStamps[ntS].chi2 = 0.0;
}
if (!(strncmp(forceConvolve, "t", 1)==0)) {
ciStamps[niS].sscnt = ciStamps[niS].nss = 0;
ciStamps[niS].chi2 = 0.0;
}
if (sstampFile) {
if (verbose >= 2) fprintf(stderr, "Adding centers manually\n");
for (m = 0; m < Ncmp; m++) {
if ((xcmp[m] > sXMin + hwKernel + 1) && (xcmp[m] < sXMax - hwKernel - 1) &&
(ycmp[m] > sYMin + hwKernel + 1) && (ycmp[m] < sYMax - hwKernel - 1)) {
buildStamps(sXMin, sXMax, sYMin, sYMax, &niS, &ntS, 0, rXBMin, rYBMin,
ciStamps, ctStamps, iRData, tRData,
xcmp[m] - rXBMin, ycmp[m] - rYBMin);
}
}
if (findSSC) {
if (verbose >= 2) fprintf(stderr, "Automatically finding additional centers\n");
/* and then choose enough stamps manually to fill the array */
buildStamps(sXMin, sXMax, sYMin, sYMax, &niS, &ntS, 1, rXBMin, rYBMin,
ciStamps, ctStamps, iRData, tRData, 0, 0);
}
}
else {
if (useFullSS) {
/* don't try and find centers, just use center of stamp */
buildStamps(sXMin, sXMax, sYMin, sYMax, &niS, &ntS, 0, rXBMin, rYBMin,
ciStamps, ctStamps, iRData, tRData, 0, 0);
}
else {
buildStamps(sXMin, sXMax, sYMin, sYMax, &niS, &ntS, 1, rXBMin, rYBMin,
ciStamps, ctStamps, iRData, tRData, 0, 0);
}
}
if (!(strncmp(forceConvolve, "i", 1)==0)) {
if (verbose>=2) fprintf(stderr," templ: %d substamps\n",ctStamps[ntS].nss);
if (ctStamps[ntS].nss > 0) ntS += 1;
}
if (!(strncmp(forceConvolve, "t", 1)==0)) {
if (verbose>=2) fprintf(stderr," image: %d substamps\n",ciStamps[niS].nss);
if (ciStamps[niS].nss > 0) niS += 1;
}
}
}
iSFrac = niS / (float) nStamps;
tSFrac = ntS / (float) nStamps;
if (strncmp(forceConvolve, "i", 1)==0) {
fprintf(stderr, "%d stamps built (%.2f%s)\n\n", niS, iSFrac, "%");
if (iSFrac < minFracGoodStamps)
flag = 1;
}
else if (strncmp(forceConvolve, "t", 1)==0) {
fprintf(stderr, "%d stamps built (%.2f%s)\n\n", ntS, tSFrac, "%");
if (tSFrac < minFracGoodStamps)
flag = 1;
}
else if ((iSFrac < minFracGoodStamps) || (tSFrac < minFracGoodStamps)) {
fprintf(stderr, "%d and %d stamps built (%.2f%s, %.2f%s)\n\n", ntS, niS, tSFrac, "%", iSFrac, "%");
flag = 1;
}
else {
fprintf(stderr, "%d and %d stamps built (%.2f%s, %.2f%s)\n\n", ntS, niS, tSFrac, "%", iSFrac, "%");
break;
}
/*
success here requires that you have chosen the number of
stamps such that you expect 1 object at good S/N in each
one. if too few stamps have been chosen, either
A : asking for too many stamps
B : too few objects at high S/N
i think B is the more likely scenario, so we lower the
fitting threshold. do it only once now to be safe,
since this is a new feature brought on by lack on sleep
during Chilean obsreving runs...
*/
if ((flag) && (status <= 1) && (scaleFitThresh < 1.)) {
/* start over... */
kerFitThresh *= scaleFitThresh;
fprintf(stderr, "Too few stamps were fit, scaling down fitting threshold to %.2f\n", kerFitThresh);
if (ctStamps) {
freeStampMem(ctStamps, nStamps);
free(ctStamps);
ctStamps = NULL;
}
if (ciStamps) {
freeStampMem(ciStamps, nStamps);
free(ciStamps);
ciStamps = NULL;
}
/* sheesh, reallocate stamps ... */
if (!(strncmp(forceConvolve, "i", 1)==0)) {
if(!(ctStamps = (stamp_struct *)calloc(nStamps, sizeof(stamp_struct)))) {
printf("Cannot Allocate Stamp List\n");
exit (1);
}
if (allocateStamps(ctStamps, nStamps)) {
fprintf(stderr,"Cannot Allocate Stamp Vector\n");
exit (1);
}
}
if (!(strncmp(forceConvolve, "t", 1)==0)) {
if(!(ciStamps = (stamp_struct *)calloc(nStamps, sizeof(stamp_struct)))) {
printf("Cannot Allocate Stamp List\n");
exit (1);
}
if (allocateStamps(ciStamps, nStamps)) {
fprintf(stderr,"Cannot Allocate Stamp Vector\n");
exit(1);
}
}
/* allow getpsfcenter to use pixels again */
for (l = rPixX*rPixY; l--; )
mRData[l] &= ~0xa00;
}