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vargs.c
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vargs.c
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#include<stdio.h>
#include<string.h>
#include<strings.h>
#include<stdlib.h>
#include<assert.h>
#include "defaults.h"
#include "globals.h"
#include "functions.h"
/*
Set defaults for global variables, parse any command line arguments,
and do some basic insanity checks.
08/20/01 [email protected]
*/
void vargs(int argc, char *argv[]) {
int iarg, i, status=0;
char help[8192], *scrStr;
fitsfile *kPtr;
int kBitpix, kNaxis;
long kNaxes[MAXDIM];
/* set the defaults */
image = NULL;
template = NULL;
outim = NULL;
tNoiseIm = NULL;
iNoiseIm = NULL;
tMaskIm = NULL;
iMaskIm = NULL;
kernelImIn = NULL;
kernelImOut = NULL;
outMask = NULL;
/* nullify arrays of pointers */
mRData = NULL;
check_stack = NULL;
filter_x = NULL;
filter_y = NULL;
temp = NULL;
kernel_vec = NULL;
wxy = NULL;
kernel_coeffs = NULL;
kernel = NULL;
check_mat = NULL;
check_vec = NULL;
ngauss = D_NGAUSS;
deg_fixe = (int *)calloc(ngauss, sizeof(int));
deg_fixe[0] = D_DEG_GAUSS1;
deg_fixe[1] = D_DEG_GAUSS2;
deg_fixe[2] = D_DEG_GAUSS3;
sigma_gauss = (float *)calloc(ngauss, sizeof(float));
sigma_gauss[0] = (1.0/(2.0*D_SIG_GAUSS1*D_SIG_GAUSS1));
sigma_gauss[1] = (1.0/(2.0*D_SIG_GAUSS2*D_SIG_GAUSS2));
sigma_gauss[2] = (1.0/(2.0*D_SIG_GAUSS3*D_SIG_GAUSS3));
/* Things also possibly changed on the command line */
tUThresh = D_UTHRESH;
tUKThresh = tUThresh;
tLThresh = D_LTHRESH;
tGain = D_GAIN;
tRdnoise = D_RDNOISE;
iUThresh = D_UTHRESH;
iUKThresh = iUThresh;
iLThresh = D_LTHRESH;
iGain = D_GAIN;
iRdnoise = D_RDNOISE;
outBzero = D_OUTBZERO;
outBscale = D_OUTBSCALE;
outNiBzero = D_OUTBZERO;
outNiBscale = D_OUTBSCALE;
tPedestal = D_PEDESTAL;
iPedestal = D_PEDESTAL;
hwKernel = D_HWKERNEL;
fwKernelPCA = 2 * D_HWKERNEL + 1;
kerFitThresh = D_KFITTHRESH;
minFracGoodStamps = D_NFITTHRESH;
scaleFitThresh = D_SFITTHRESH;
kfSpreadMask1 = D_INMASKFSPREAD;
kfSpreadMask2 = D_OUMASKFSPREAD;
nRegX = D_NREGIONS;
nRegY = D_NREGIONS;
nStampY = D_NSTAMPS;
nStampX = D_NSTAMPS;
useFullSS = D_USEFULLSS;
cmpFile = D_CMPFILE;
findSSC = D_FINDSSCENTERS;
nKSStamps = D_NKSSTAMPS;
hwKSStamp = D_HWKSSTAMP;
kerOrder = D_KORDER;
bgOrder = D_BGORDER;
statSig = D_STATSIG;
kerSigReject = D_KSIGREJECT;
kerFracMask = D_KFRACMASK;
rescaleOK = D_RESCALEOK;
photNormalize = D_NORMALIZE;
forceConvolve = D_CONVOLVE;
figMerit = D_FIGMERIT;
fillVal = D_FILL;
fillValNoise = D_FILLNOISE;
doSum = D_OUTSUM;
inclNoiseImage = D_NOILAYER;
inclSigmaImage = D_SIGLAYER;
inclConvImage = D_CONVLAYER;
noClobber = D_NOCLOBBER;
doKerInfo = D_KINFO;
outShort = D_OUTSHORT;
outNShort = D_OUTSHORT;
savexyflag = D_SAVEXY;
verbose = D_VERBOSE;
convolveVariance= D_CONVVAR;
usePCA = D_USEPCA;
sprintf(help, "Usage: hotpants [options]\n");
sprintf(help, "%sVersion %s\n", help, version);
sprintf(help, "%sRequired options:\n", help);
sprintf(help, "%s [-inim fitsfile] : comparison image to be differenced\n", help);
sprintf(help, "%s [-tmplim fitsfile]: template image\n", help);
sprintf(help, "%s [-outim fitsfile] : output difference image\n\n", help);
sprintf(help, "%sAdditional options:\n", help);
sprintf(help, "%s [-tu tuthresh] : upper valid data count, template (%.0f)\n", help, D_UTHRESH);
sprintf(help, "%s [-tuk tucthresh] : upper valid data count for kernel, template (tuthresh)\n", help);
sprintf(help, "%s [-tl tlthresh] : lower valid data count, template (%.0f)\n", help, D_LTHRESH);
sprintf(help, "%s [-tg tgain] : gain in template (%.0f)\n", help, D_GAIN);
sprintf(help, "%s [-tr trdnoise] : e- readnoise in template (%.0f)\n", help, D_RDNOISE);
sprintf(help, "%s [-tp tpedestal] : ADU pedestal in template (%.0f)\n", help, D_PEDESTAL);
sprintf(help, "%s [-tni fitsfile] : input template noise array (undef)\n", help);
sprintf(help, "%s [-tmi fitsfile] : input template mask image (undef)\n", help);
sprintf(help, "%s [-iu iuthresh] : upper valid data count, image (%.0f)\n", help, D_UTHRESH);
sprintf(help, "%s [-iuk iucthresh] : upper valid data count for kernel, image (iuthresh)\n", help);
sprintf(help, "%s [-il ilthresh] : lower valid data count, image (%.0f)\n", help, D_LTHRESH);
sprintf(help, "%s [-ig igain] : gain in image (%.0f)\n", help, D_GAIN);
sprintf(help, "%s [-ir irdnoise] : e- readnoise in image (%.0f)\n", help, D_RDNOISE);
sprintf(help, "%s [-ip ipedestal] : ADU pedestal in image (%.0f)\n", help, D_PEDESTAL);
sprintf(help, "%s [-ini fitsfile] : input image noise array (undef)\n", help);
sprintf(help, "%s [-imi fitsfile] : input image mask image (undef)\n\n", help);
sprintf(help, "%s [-ki fitsfile] : use kernel table in image header (undef)\n", help);
sprintf(help, "%s [-r rkernel] : convolution kernel half width (%d)\n", help, hwKernel);
sprintf(help, "%s [-kcs step] : size of step for spatial convolution (2*rkernel + 1)\n", help);
sprintf(help, "%s [-ft fitthresh] : RMS threshold for good centroid in kernel fit (%.1f)\n", help, kerFitThresh);
sprintf(help, "%s [-sft scale] : scale fitthresh by this fraction if... (%.1f)\n", help, scaleFitThresh);
sprintf(help, "%s [-nft fraction] : this fraction of stamps are not filled (%.1f)\n", help, minFracGoodStamps);
sprintf(help, "%s [-mins spread] : Fraction of kernel half width to spread input mask (%.1f)\n", help, kfSpreadMask1);
sprintf(help, "%s [-mous spread] : Ditto output mask, negative = no diffim masking (%.1f)\n", help, kfSpreadMask2);
sprintf(help, "%s [-omi fitsfile] : Output bad pixel mask (undef)\n", help);
sprintf(help, "%s [-gd xmin xmax ymin ymax]\n", help);
sprintf(help, "%s : only use subsection of full image (full image)\n\n", help);
sprintf(help, "%s [-nrx xregion] : number of image regions in x dimension (%d)\n", help, nRegX);
sprintf(help, "%s [-nry yregion] : number of image regions in y dimension (%d)\n", help, nRegY);
sprintf(help, "%s -- OR --\n", help);
sprintf(help, "%s [-rf regionfile] : ascii file with image regions 'xmin:xmax,ymin:ymax'\n", help);
sprintf(help, "%s -- OR --\n", help);
sprintf(help, "%s [-rkw keyword num]: header 'keyword[0->(num-1)]' indicates valid regions\n\n", help);
sprintf(help, "%s [-nsx xstamp] : number of each region's stamps in x dimension (%d)\n", help, nStampX);
sprintf(help, "%s [-nsy ystamp] : number of each region's stamps in y dimension (%d)\n", help, nStampY);
sprintf(help, "%s -- OR --\n", help);
sprintf(help, "%s [-ssf stampfile] : ascii file indicating substamp centers 'x y'\n", help);
sprintf(help, "%s -- OR --\n", help);
sprintf(help, "%s [-cmp cmpfile] : .cmp file indicating substamp centers 'x y'\n\n", help);
sprintf(help, "%s [-afssc find] : autofind stamp centers so #=-nss when -ssf,-cmp (%d)\n", help, findSSC);
sprintf(help, "%s [-nss substamps] : number of centroids to use for each stamp (%d)\n", help, nKSStamps);
sprintf(help, "%s [-rss radius] : half width substamp to extract around each centroid (%d)\n\n", help, hwKSStamp);
sprintf(help, "%s [-savexy file] : save positions of stamps for convolution kernel (undef)\n", help);
sprintf(help, "%s [-c toconvolve] : force convolution on (t)emplate or (i)mage (undef)\n", help);
sprintf(help, "%s [-n normalize] : normalize to (t)emplate, (i)mage, or (u)nconvolved (%s)\n", help, photNormalize);
sprintf(help, "%s [-fom figmerit] : (v)ariance, (s)igma or (h)istogram convolution merit (%s)\n", help, figMerit);
sprintf(help, "%s [-sconv] : all regions convolved in same direction (%d)\n", help, sameConv);
sprintf(help, "%s [-ko kernelorder] : spatial order of kernel variation within region (%d)\n", help, kerOrder);
sprintf(help, "%s [-bgo bgorder] : spatial order of background variation within region (%d)\n", help, bgOrder);
sprintf(help, "%s [-ssig statsig] : threshold for sigma clipping statistics (%.1f)\n", help, statSig);
sprintf(help, "%s [-ks badkernelsig]: high sigma rejection for bad stamps in kernel fit (%.1f)\n", help, kerSigReject);
sprintf(help, "%s [-kfm kerfracmask]: fraction of abs(kernel) sum for ok pixel (%.3f)\n", help, kerFracMask);
sprintf(help, "%s [-okn] : rescale noise for 'ok' pixels (%d)\n", help, rescaleOK);
sprintf(help, "%s [-fi fill] : value for invalid (bad) pixels (%.1e)\n", help, fillVal);
sprintf(help, "%s [-fin fill] : noise image only fillvalue (%.1e)\n", help, fillValNoise);
sprintf(help, "%s [-convvar] : convolve variance not noise (%d)\n\n", help, convolveVariance);
sprintf(help, "%s [-oni fitsfile] : output noise image (undef)\n", help);
sprintf(help, "%s [-ond fitsfile] : output noise scaled difference image (undef)\n", help);
sprintf(help, "%s [-nim] : add noise image as layer to sub image (%d)\n", help, inclNoiseImage);
sprintf(help, "%s [-ndm] : add noise-scaled sub image as layer to sub image (%d)\n\n", help, inclSigmaImage);
sprintf(help, "%s [-oci fitsfile] : output convolved image (undef)\n", help);
sprintf(help, "%s [-cim] : add convolved image as layer to sub image (%d)\n\n", help, inclConvImage);
sprintf(help, "%s [-allm] : output all possible image layers\n\n", help);
sprintf(help, "%s [-nc] : do not clobber output image (%d)\n", help, noClobber);
sprintf(help, "%s [-hki] : print extensive kernel info to output image header (%d)\n\n", help, doKerInfo);
sprintf(help, "%s [-oki fitsfile] : new fitsfile with kernel info (under)\n\n", help);
sprintf(help, "%s [-sht] : output images 16 bitpix int, vs -32 bitpix float (%d)\n", help, outShort);
sprintf(help, "%s [-obs bscale] : if -sht, output image BSCALE, overrides -inim (%.1f)\n", help, D_OUTBSCALE);
sprintf(help, "%s [-obz bzero] : if -sht, output image BZERO , overrides -inim (%.1f)\n", help, D_OUTBZERO);
sprintf(help, "%s [-nsht] : output noise image 16 bitpix int, vs -32 bitpix float (%d)\n", help, outNShort);
sprintf(help, "%s [-nbs bscale] : noise image only BSCALE, overrides -obs (%.1f)\n", help, D_OUTBSCALE);
sprintf(help, "%s [-nbz bzero] : noise image only BZERO, overrides -obz (%.1f)\n\n", help, D_OUTBZERO);
sprintf(help, "%s [-ng ngauss degree0 sigma0 .. degreeN sigmaN]\n", help);
sprintf(help, "%s : ngauss = number of gaussians which compose kernel (%d)\n", help, ngauss);
sprintf(help, "%s : degree = degree of polynomial associated with gaussian #\n", help);
sprintf(help, "%s (%d %d %d)\n", help, D_DEG_GAUSS1, D_DEG_GAUSS2, D_DEG_GAUSS3);
sprintf(help, "%s : sigma = width of gaussian #\n", help);
sprintf(help, "%s (%.2f %.2f %.2f)\n", help, D_SIG_GAUSS1, D_SIG_GAUSS2, D_SIG_GAUSS3);
sprintf(help, "%s : N = 0 .. ngauss - 1\n\n", help);
sprintf(help, "%s : (%d %d %.2f %d %.2f %d %.2f\n", help, ngauss, D_DEG_GAUSS1, D_SIG_GAUSS1, D_DEG_GAUSS2, D_SIG_GAUSS2, D_DEG_GAUSS3, D_SIG_GAUSS3);
sprintf(help, "%s [-pca nk k0.fits ... n(k-1).fits]\n", help);
sprintf(help, "%s : nk = number of input basis functions\n", help);
sprintf(help, "%s : k?.fits = name of fitsfile holding basis function\n", help);
sprintf(help, "%s : Since this uses input basis functions, it will fix :\n", help);
sprintf(help, "%s : hwKernel \n", help);
sprintf(help, "%s : \n", help);
sprintf(help, "%s [-v] verbosity : level of verbosity, 0-2 (%d)\n", help, verbose);
sprintf(help, "%s NOTE: Fits header params will be added to the difference image\n", help);
sprintf(help, "%s COMMAND (what was called on the command line)\n", help);
sprintf(help, "%s NREGION (number of regions in image)\n", help);
sprintf(help, "%s PHOTNORM (to which system the difference image is normalized)\n", help);
sprintf(help, "%s TARGET (image which was differenced)\n", help);
sprintf(help, "%s TEMPLATE (template for the difference imaging)\n", help);
sprintf(help, "%s DIFFIM (output difference image)\n", help);
sprintf(help, "%s MASKVAL (value for masked pixels)\n", help);
sprintf(help, "%s REGION\?\? (IRAF-format limits for each region in the image)\n", help);
sprintf(help, "%s CONVOL\?\? (which image was convolved for each region)\n", help);
sprintf(help, "%s KSUM\?\? (sum of the convolution kernel for each region)", help);
/* read in command options */
if (argc < 2) {
fprintf(stderr, "%s\n", help);
exit(1);
}
for (iarg=1; iarg < argc; iarg++) {
if (argv[iarg][0]=='-') {
if (strcasecmp(argv[iarg]+1,"inim")==0) {
image = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"tmplim")==0) {
template = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"outim")==0) {
outim = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"tu")==0) {
sscanf(argv[++iarg], "%f", &tUThresh);
} else if (strcasecmp(argv[iarg]+1,"tuk")==0) {
sscanf(argv[++iarg], "%f", &tUKThresh);
} else if (strcasecmp(argv[iarg]+1,"tl")==0) {
sscanf(argv[++iarg], "%f", &tLThresh);
} else if (strcasecmp(argv[iarg]+1,"tg")==0) {
sscanf(argv[++iarg], "%f", &tGain);
} else if (strcasecmp(argv[iarg]+1,"tr")==0) {
sscanf(argv[++iarg], "%f", &tRdnoise);
} else if (strcasecmp(argv[iarg]+1,"tp")==0) {
sscanf(argv[++iarg], "%f", &tPedestal);
} else if (strcasecmp(argv[iarg]+1,"tni")==0) {
tNoiseIm = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"tmi")==0) {
tMaskIm = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"iu")==0) {
sscanf(argv[++iarg], "%f", &iUThresh);
} else if (strcasecmp(argv[iarg]+1,"iuk")==0) {
sscanf(argv[++iarg], "%f", &iUKThresh);
} else if (strcasecmp(argv[iarg]+1,"il")==0) {
sscanf(argv[++iarg], "%f", &iLThresh);
} else if (strcasecmp(argv[iarg]+1,"ig")==0) {
sscanf(argv[++iarg], "%f", &iGain);
} else if (strcasecmp(argv[iarg]+1,"ir")==0) {
sscanf(argv[++iarg], "%f", &iRdnoise);
} else if (strcasecmp(argv[iarg]+1,"ip")==0) {
sscanf(argv[++iarg], "%f", &iPedestal);
} else if (strcasecmp(argv[iarg]+1,"ini")==0) {
iNoiseIm = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"imi")==0) {
iMaskIm = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"ki")==0) {
kernelImIn = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"r")==0) {
sscanf(argv[++iarg], "%d", &hwKernel);
} else if (strcasecmp(argv[iarg]+1,"kcs")==0) {
sscanf(argv[++iarg], "%d", &kcStep);
} else if (strcasecmp(argv[iarg]+1,"ft")==0) {
sscanf(argv[++iarg], "%f", &kerFitThresh);
} else if (strcasecmp(argv[iarg]+1,"sft")==0) {
sscanf(argv[++iarg], "%f", &scaleFitThresh);
} else if (strcasecmp(argv[iarg]+1,"nft")==0) {
sscanf(argv[++iarg], "%f", &minFracGoodStamps);
} else if (strcasecmp(argv[iarg]+1,"mins")==0) {
sscanf(argv[++iarg], "%f", &kfSpreadMask1);
} else if (strcasecmp(argv[iarg]+1,"mous")==0) {
sscanf(argv[++iarg], "%f", &kfSpreadMask2);
} else if (strcasecmp(argv[iarg]+1,"omi")==0) {
outMask = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"gd")==0) {
sscanf(argv[++iarg], "%d", &gdXmin);
sscanf(argv[++iarg], "%d", &gdXmax);
sscanf(argv[++iarg], "%d", &gdYmin);
sscanf(argv[++iarg], "%d", &gdYmax);
} else if (strcasecmp(argv[iarg]+1,"nrx")==0) {
sscanf(argv[++iarg], "%d", &nRegX);
} else if (strcasecmp(argv[iarg]+1,"nry")==0) {
sscanf(argv[++iarg], "%d", &nRegY);
} else if (strcasecmp(argv[iarg]+1,"rf")==0) {
regFile = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"rkw")==0) {
regKeyWord = argv[++iarg];
sscanf(argv[++iarg], "%d", &numRegKeyWord);
} else if (strcasecmp(argv[iarg]+1,"nsx")==0) {
sscanf(argv[++iarg], "%d", &nStampX);
} else if (strcasecmp(argv[iarg]+1,"nsy")==0) {
sscanf(argv[++iarg], "%d", &nStampY);
} else if (strcasecmp(argv[iarg]+1,"ssf")==0) {
sstampFile = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"cmp")==0) {
sstampFile = argv[++iarg];
cmpFile = 1;
} else if (strcasecmp(argv[iarg]+1,"afssc")==0) {
sscanf(argv[++iarg], "%d", &findSSC);
} else if (strcasecmp(argv[iarg]+1,"nss")==0) {
sscanf(argv[++iarg], "%d", &nKSStamps);
} else if (strcasecmp(argv[iarg]+1,"rss")==0) {
sscanf(argv[++iarg], "%d", &hwKSStamp);
} else if (strcasecmp(argv[iarg]+1,"ko")==0) {
sscanf(argv[++iarg], "%d", &kerOrder);
} else if (strcasecmp(argv[iarg]+1,"bgo")==0) {
sscanf(argv[++iarg], "%d", &bgOrder);
} else if (strcasecmp(argv[iarg]+1,"ssig")==0) {
sscanf(argv[++iarg], "%f", &statSig);
} else if (strcasecmp(argv[iarg]+1,"ks")==0) {
sscanf(argv[++iarg], "%f", &kerSigReject);
} else if (strcasecmp(argv[iarg]+1,"kfm")==0) {
sscanf(argv[++iarg], "%f", &kerFracMask);
} else if (strcasecmp(argv[iarg]+1,"okn")==0) {
rescaleOK = 1;
} else if (strcasecmp(argv[iarg]+1,"c")==0) {
forceConvolve = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"n")==0) {
photNormalize = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"fom")==0) {
figMerit = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"sconv")==0) {
sameConv = 1;
} else if (strcasecmp(argv[iarg]+1,"fi")==0) {
sscanf(argv[++iarg], "%f", &fillVal);
} else if (strcasecmp(argv[iarg]+1,"ef")==0) {
effFile = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"sum")==0) {
doSum = 1;
} else if (strcasecmp(argv[iarg]+1,"oni")==0) {
noiseImage = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"ond")==0) {
sigmaImage = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"nim")==0) {
inclNoiseImage = 1;
} else if (strcasecmp(argv[iarg]+1,"ndm")==0) {
inclSigmaImage = 1;
} else if (strcasecmp(argv[iarg]+1,"oci")==0) {
convImage = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"cim")==0) {
inclConvImage = 1;
} else if (strcasecmp(argv[iarg]+1,"nc")==0) {
noClobber = 1;
} else if (strcasecmp(argv[iarg]+1,"hki")==0) {
doKerInfo = 1;
} else if (strcasecmp(argv[iarg]+1,"oki")==0) {
kernelImOut = argv[++iarg];
} else if (strcasecmp(argv[iarg]+1,"sht")==0) {
outShort = 1;
} else if (strcasecmp(argv[iarg]+1,"obs")==0) {
sscanf(argv[++iarg], "%f", &outBscale);
} else if (strcasecmp(argv[iarg]+1,"obz")==0) {
sscanf(argv[++iarg], "%f", &outBzero);
} else if (strcasecmp(argv[iarg]+1,"nsht")==0) {
outNShort = 1;
} else if (strcasecmp(argv[iarg]+1,"nbs")==0) {
sscanf(argv[++iarg], "%f", &outNiBscale);
} else if (strcasecmp(argv[iarg]+1,"nbz")==0) {
sscanf(argv[++iarg], "%f", &outNiBzero);
} else if (strcasecmp(argv[iarg]+1,"fin")==0) {
sscanf(argv[++iarg], "%f", &fillValNoise);
} else if (strcasecmp(argv[iarg]+1,"convvar")==0) {
convolveVariance = 1;
} else if (strcasecmp(argv[iarg]+1,"allm")==0) {
inclConvImage = 1;
inclSigmaImage = 1;
inclNoiseImage = 1;
} else if (strcasecmp(argv[iarg]+1,"v")==0) {
sscanf(argv[++iarg], "%d", &verbose);
} else if (strcasecmp(argv[iarg]+1,"savexy")==0) {
savexyflag = 1;
strcpy(xyfilename,argv[++iarg]);
} else if (strcasecmp(argv[iarg]+1,"ng")==0) {
sscanf(argv[++iarg], "%d", &ngauss);
deg_fixe = (int *)realloc(deg_fixe, ngauss*sizeof(int));
sigma_gauss = (float *)realloc(sigma_gauss, ngauss*sizeof(float));
for (i = 0; i < ngauss; i++) {
sscanf(argv[++iarg], "%d", °_fixe[i]);
sscanf(argv[++iarg], "%f", &sigma_gauss[i]);
sigma_gauss[i] = (1.0/(2.0*sigma_gauss[i]*sigma_gauss[i]));
}
} else if (strcasecmp(argv[iarg]+1,"pca")==0) {
usePCA = 1;
sscanf(argv[++iarg], "%d", &ngauss); /* effectively ngauss... */
PCA = (float **)malloc(ngauss*sizeof(float *));
for (i = 0; i < ngauss; i++) {
scrStr = argv[++iarg];
if (fits_open_file(&kPtr, scrStr, 0, &status) ||
fits_get_img_param(kPtr, MAXDIM, &kBitpix, &kNaxis, kNaxes, &status))
printError(status);
assert (kNaxes[0] == kNaxes[1]); /* square */
if (fwKernelPCA == (2*D_HWKERNEL+1))
fwKernelPCA = kNaxes[0];
else
assert(fwKernelPCA == kNaxes[0]);
fprintf(stderr, " Reading in basis image %s\n", scrStr);
PCA[i] = (float *)malloc(kNaxes[0]*kNaxes[1]*sizeof(float));
if (fits_read_img_flt(kPtr, 0, 1, kNaxes[0]*kNaxes[1], 0, PCA[i], 0, &status) ||
fits_close_file(kPtr, &status))
printError(status);
}
/* hack to not break other parts of the code */
deg_fixe = (int *)realloc(deg_fixe, ngauss*sizeof(int));
sigma_gauss = (float *)realloc(sigma_gauss, ngauss*sizeof(float));
for (i = 0; i < ngauss; i++) {
deg_fixe[i] = 0;
sigma_gauss[i] = -1;
}
} else {
fprintf(stderr, "Unknown option : %s\n", argv[iarg]);
exit(1);
}
} else {
fprintf(stderr, "Unexpected string encountered on command line : %s\n", argv[iarg]);
exit(1);
}
}
/* ngauss */
/*
for (i = 0; i < ngauss; i++) {
fprintf(stderr, "%d %d %f\n", i, deg_fixe[i], sigma_gauss[i]);
}
*/
/* check that the requested options make sense */
if ( !(image) ) {
fprintf(stderr, "FATAL ERROR inim : required command line option\n");
exit(1);
}
if ( !(template) ) {
fprintf(stderr, "FATAL ERROR tmplim : required command line option\n");
exit(1);
}
if ( !(outim) ) {
fprintf(stderr, "FATAL ERROR outim : required command line option\n");
exit(1);
}
/* template thresholds and gain */
if (tUThresh && (tUThresh <= 0)) {
fprintf(stderr, "FATAL ERROR tu (%f) : cannot be negative (or zero)\n", tUThresh);
exit(1);
}
if (tUThresh && tLThresh && (tUThresh < tLThresh)) {
fprintf(stderr, "FATAL ERROR tu (%f) : cannot be smaller than tl (%f)\n", tUThresh, tLThresh);
exit(1);
}
if (tGain && (tGain <= 0)) {
fprintf(stderr, "FATAL ERROR tg (%f) : cannot be negative (or zero)\n", tGain);
exit(1);
}
if (tRdnoise && (tRdnoise <= 0)) {
fprintf(stderr, "FATAL ERROR tr (%f) : cannot be negative (or zero)\n", tRdnoise);
exit(1);
}
/* image thresholds and gain */
if (iUThresh && (iUThresh <= 0)) {
fprintf(stderr, "FATAL ERROR iu (%f) : cannot be negative (or zero)\n", iUThresh);
exit(1);
}
if (iUThresh && iLThresh && (iUThresh < iLThresh)) {
fprintf(stderr, "FATAL ERROR iu (%f) : cannot be smaller than il (%f)\n", iUThresh, iLThresh);
exit(1);
}
if (iGain && (iGain <= 0)) {
fprintf(stderr, "FATAL ERROR ig (%f) : cannot be negative (or zero)\n", iGain);
exit(1);
}
if (iRdnoise && (iRdnoise <= 0)) {
fprintf(stderr, "FATAL ERROR ir (%f) : cannot be negative (or zero)\n", iRdnoise);
exit(1);
}
/* kernel fit pars */
if (hwKernel <= 0) {
fprintf(stderr, "FATAL ERROR r (%d) : cannot be negative (or zero)\n", hwKernel);
exit(1);
}
if (hwKernel == 1) {
fprintf(stderr, "WARNING r (%d) : r = 1 is unstable\n", hwKernel);
}
if (kcStep && (kcStep <= 0)) {
fprintf(stderr, "FATAL ERROR kcs (%d) : cannot be negative (or zero)\n", kcStep);
exit(1);
}
if (kerFitThresh < 0) {
fprintf(stderr, "FATAL ERROR ft (%f) : cannot be negative\n", kerFitThresh);
exit(1);
}
if ((scaleFitThresh > 1) || (scaleFitThresh < 0)) {
fprintf(stderr, "FATAL ERROR sft (%f) : cannot be negative or greater than 1\n", scaleFitThresh);
exit(1);
}
if ((minFracGoodStamps > 1) || (minFracGoodStamps < 0) ) {
fprintf(stderr, "FATAL ERROR nft (%f) : cannot be negative or greater than 1\n", minFracGoodStamps);
exit(1);
}
if (kerSigReject < 0) {
fprintf(stderr, "FATAL ERROR ks (%f) : cannot be negative\n", kerSigReject);
exit(1);
}
/* masking pars */
if (kfSpreadMask1 < 0) {
fprintf(stderr, "FATAL ERROR mins (%f) : cannot be negative\n", kfSpreadMask1);
exit(1);
}
/* asking for subsections of image */
if ((gdXmin < 0) || (gdXmax < 0) || (gdXmin > gdXmax) || (gdYmin < 0) || (gdYmax < 0) || (gdYmin > gdYmax)) {
fprintf(stderr, "FATAL ERROR gd : (%d,%d) < x,y < (%d,%d)\n", gdXmin, gdYmin, gdXmax, gdYmax);
exit(1);
}
/* changing default region/stamp size */
if (regFile && sstampFile) {
fprintf(stderr, "FATAL ERROR rf (%s) and ssf (%s) : conflicting requests\n", regFile, sstampFile);
exit(1);
}
/* region keyword */
if (regKeyWord && regFile) {
fprintf(stderr, "FATAL ERROR rkw (%s) and rf (%s) : conflicting requests\n", regKeyWord, regFile);
exit(1);
}
if (regKeyWord) {
if (numRegKeyWord < 1) {
fprintf(stderr, "FATAL ERROR rkw (%s) : number of regions invalid (%d)\n", regKeyWord, numRegKeyWord);
exit(1);
}
}
/* substamp properties */
if (nKSStamps < 0) {
fprintf(stderr, "FATAL ERROR nss (%d) : cannot be negative\n", nKSStamps);
exit(1);
}
if (hwKSStamp < 0) {
fprintf(stderr, "FATAL ERROR nss (%d) : cannot be negative\n", hwKSStamp);
exit(1);
}
if (hwKSStamp < hwKernel) {
fprintf(stderr, "FATAL ERROR rss (%d) < r (%d) : conflicting requests\n", hwKSStamp, hwKernel);
exit(1);
}
/* defining convolution or normalization */
if (forceConvolve &&
( !((strncmp(forceConvolve, "i", 1)==0) || (strncmp(forceConvolve, "t", 1)==0) || (strncmp(forceConvolve, "b", 1)==0)) )) {
fprintf(stderr, "FATAL ERROR c (%s) : invalid char ('i' or 't' or 'b')\n", forceConvolve);
exit(1);
}
if (photNormalize && ( !((strncmp(photNormalize, "i", 1)==0) || (strncmp(photNormalize, "t", 1)==0) || (strncmp(photNormalize, "u", 1)==0)) )) {
fprintf(stderr, "FATAL ERROR n (%s) : invalid char ('i', 't', or 'u')\n", photNormalize);
exit(1);
}
/* good figure of merit request */
if (figMerit && ( !((strncmp(figMerit, "s", 1)==0) || (strncmp(figMerit, "h", 1)==0) || (strncmp(figMerit, "v", 1)==0)) )) {
fprintf(stderr, "FATAL ERROR fom (%s) : invalid char ('v', 's' or 'h')\n", figMerit);
exit(1);
}
/* fit orders */
if (kerOrder < 0) {
fprintf(stderr, "FATAL ERROR ko (%d) : cannot be negative\n", kerOrder);
exit(1);
}
if (bgOrder < 0) {
fprintf(stderr, "FATAL ERROR bgo (%d) : cannot be negative\n", bgOrder);
exit(1);
}
/* bscale, bzero */
if (outBscale && (outBscale == 0.)) {
fprintf(stderr, "FATAL ERROR obs (%f) : cannot be zero\n", outBscale);
exit(1);
}
if (outNiBscale && (outNiBscale == 0.)) {
fprintf(stderr, "FATAL ERROR nbs (%f) : cannot be zero\n", outNiBscale);
exit(1);
}
/* PCA */
if (usePCA) {
hwKernel = fwKernelPCA / 2;
fprintf(stderr, "ATTN : size of input kernel images fixes hwKernel to %d\n", hwKernel);
}
return;
}