int nemoinpx(
char *expr,
double *a,
int na)
{
int nret, ncomp;
string *vals, *comp;
vals = burststring(expr,",");
for (nret=0; vals[nret] != NULL; nret++) {
if (nret>=na)
return -23;
comp = burststring(vals[nret],":");
ncomp = xstrlen(comp,sizeof(string))-1;
if (ncomp < 1 || ncomp > 3)
return -13;
a[nret] = atof(comp[0]);
if (ncomp==1) continue;
a[nret] += atof(comp[1])/60.0;
if (ncomp==2) continue;
a[nret] += atof(comp[2])/3600.0;
freestrings(comp);
}
freestrings(vals);
return nret;
}
/*
* return the full path to a filter based on a short name
* or, if the shortname is the full path, return itself
*/
string filtername(string shortname)
{
int nsp;
static char fullname[256];
char line[MAX_LINELEN];
string *sp, fpath;
stream fstr;
if (nemo_file_size(shortname) > 0) return shortname;
fpath = getenv("NEMODAT");
if (fpath == 0) error("NEMODAT does not exist");
sprintf(fullname,"%s/filter/Fnames",fpath);
dprintf(1,"Alias table %s\n",fullname);
fstr = stropen(fullname,"r");
while (fgets(line,MAX_LINELEN,fstr)) {
if (line[0] == '#') continue;
sp = burststring(line," \n");
nsp = xstrlen(sp,sizeof(sp))-1;
if (nsp > 1) {
if (streq(shortname,sp[0])) {
sprintf(fullname,"%s/filter/%s",fpath,sp[1]);
dprintf(1,"Matching %s\n",fullname);
freestrings(sp);
return fullname;
}
}
freestrings(sp);
}
return shortname;
}
int string_index(string options, string s)
{
int i=0;
string *sa = burststring(options,",");
while (sa[i]) {
if (streq(sa[i],s)) {
freestrings(sa);
return i;
}
i++;
}
freestrings(sa);
return -1;
}
static void writesnps(int ncid, int nsnps)
{
size_t start = 0;
size_t count = nsnps;
int snpid, stat;
stat = nc_inq_varid(ncid, "snp", &snpid);
check_err(stat,__LINE__,__FILE__);
stat = nc_put_vara_string(ncid, snpid, &start, &count, (const char **) snps);
check_err(stat,__LINE__,__FILE__);
freestrings(snps, nsnps);
}
convert(stream instr, stream outstr)
{
char line[MAX_LINELEN]; /* input linelength */
double dval;
int nval, i, nlines, sign, decimalval,nhms,ndms;
string *outv, *hms, *dms; /* pointer to vector of strings to write */
string seps=", \t"; /* column separators */
real dd, mm, ss;
nlines=0; /* count lines read so far */
for(;;) { /* loop over all lines in file(s) */
if (get_line(instr, line) < 0)
return 0;
dprintf(3,"LINE: (%s)\n",line);
if(line[0] == '#') continue; /* don't use comment lines */
nlines++;
outv = burststring(line,seps);
i=0;
while (outv[i]) {
if (colmode[i+1] == 0) { /* no special mode: just copy */
if (fromhms[i+1]) {
hms = burststring(outv[i],sep);
nhms = xstrlen(hms,sizeof(string))-1;
dval = atof(hms[0])*3600;
if (nhms > 1) dval += atof(hms[1])*60;
if (nhms > 2) dval += atof(hms[2]);
if (nhms > 3) error("HMS string %s too many %s",outv[i],sep);
fprintf(outstr,fmt,dval/3600.0);
fputs(" ",outstr);
freestrings(hms);
} else if (fromdms[i+1]) {
dms = burststring(outv[i],sep);
ndms = xstrlen(dms,sizeof(string))-1;
dval = atof(dms[0])*3600;
if (ndms > 1) dval += atof(dms[1])*60;
if (ndms > 2) dval += atof(dms[2]);
if (ndms > 3) error("DMS string %s too many %s",outv[i],sep);
fprintf(outstr,fmt,dval*15/3600.0);
fputs(" ",outstr);
freestrings(dms);
} else {
fputs(outv[i],outstr);
fputs(" ",outstr);
}
} else {
if (nemoinpd(outv[i],&dval,1)<0)
error("syntax error decoding %s",outv[i]);
if (colmode[i+1] < 0) {
sign = SGN(dval);
dval = ABS(dval); /* do we allow < 0 ??? */
decimalval = (int)floor(dval);
fprintf(outstr,"%d",decimalval*sign);
fprintf(outstr,"%s",sep);
dval -= decimalval;
dval *= ABS(colmode[i+1]);
}
sign = SGN(dval);
dval = ABS(dval);
dd = floor(dval);
dval = (dval-dd)*60.0;
mm = floor(dval);
ss = (dval-mm)*60.0;
fprintf(outstr,"%02d",(int)dd*sign);
fprintf(outstr,"%s",sep);
fprintf(outstr,"%02d",(int)mm);
fprintf(outstr,"%s",sep);
fprintf(outstr,"%06.3f ",ss);
}
i++;
}
fputs("\n",outstr);
freestrings(outv);
} /* for(;;) */
}
void nemo_main(void){
int i,numwritten=0,nummissed=0;
int numimages=0;
stream fp_in,fp,fp2;
string *sp,logic;
int count,n;
int edge_dist; /* exclude sources this many pixels from the edge */
string inFile; /* name of input file */
char line[MAX_LINELEN]; /* a line of text from the inFile */
int racol,deccol,maxcol; /* column numbers for ra/dec in file */
double ra,dec; /* the values of ra/dec for a given line */
int nentries; /* number of valid entries, used for progress tracking */
inFile = getparam("in");
edge_dist = getiparam("edge");
logic = getparam("logic");
sp = burststring(getparam("col"),", \n");
n = xstrlen(sp,sizeof(string)) - 1;
if (n != 2) error("You must specify ra,dec columns for col keyword!");
racol = natoi(sp[0]) - 1;
deccol = natoi(sp[1]) - 1;
freestrings(sp);
if (racol >= deccol)
maxcol = racol;
else
maxcol = deccol;
sp = burststring(getparam("fits"),", \n");
n = xstrlen(sp,sizeof(string))-1;
for (i=0; i<n; i++){
ini_mask(sp[i],i);
numimages++;
}
freestrings(sp);
sp = burststring(getparam("out"),", \n");
n = xstrlen(sp,sizeof(string))-1;
if (n == 1){
fp = stropen(sp[0],"w");
fp2 = stropen("/dev/null","w!");
} else if (n == 2){
fp = stropen(sp[0],"w");
fp2 = stropen(sp[1],"w");
}else
error("You must give one or two output files!\n");
freestrings(sp);
nentries = nemo_file_lines(inFile,0);
progress_init("overlap percent complete:",nentries);
nentries = 0;
fp_in = stropen(inFile,"r");
while (fgets(line,MAX_LINELEN,fp_in)){
progress_update(nentries);
if (line[0] != '#'){
nentries += 1;
sp = burststring(line," \t\n");
n = xstrlen(sp,sizeof(string)) - 2; /* zero based */
if (n < maxcol)
error("Insufficient columns on line!");
ra = natof(sp[racol]);
dec = natof(sp[deccol]);
freestrings(sp);
count = 0;
for (i=0; i< numimages; i++)
count+= is_edge(ra,dec,edge_dist,i);
if(streq(logic,"or") && (count<numimages)){
fprintf(fp,line);
numwritten++;
}
else if(streq(logic,"and") && (count==0) && (numimages > 0)){
fprintf(fp,line);
numwritten++;
}
else {
fprintf(fp2,line);
nummissed++;
}
}
}
strclose(fp_in);
strclose(fp);
strclose(fp2);
progress_finish();
printf("Sources outside regions: %d\n",nummissed);
printf("Sources inside regions: %d\n",numwritten);
printf("Number of images: %d\n",numimages);
}
void nemo_main() {
int i,j,nentries,ncol,nsp;
FILE *fp; /* File pointer for output file */
string outfile; /* name of output file */
string *sp; /* used to read the command line argument "col" */
string wcs_type; /* WCS projection type (can be XXX or -XXX) */
char type[5]; /* the real WCS for worldpos() ; needs to be '-XXX' */
int nx,ny; /* size of map in pixels for x,y directions */
double index,rzero; /* parameters for powerlaw */
double crval1,crval2; /* center RA and DEC */
double cdelt1,cdelt2; /* delta RA and delta DEC for pixels */
double crpix1,crpix2; /* reference pixel */
double xpix, ypix; /* current x and y pixel position in map */
double ra,dec; /* ra,dec of current pixel position in map */
double flux; /* computed flux for each pixel */
double radius; /* radius, in pixels */
/* Read command line */
index = getdparam("index");
rzero = getdparam("rzero");
outfile = getparam("out");
wcs_type = getparam("type");
if (strlen(wcs_type)==3) { /* make sure type is '-XXX' */
type[0] = '-';
strcpy(&type[1],wcs_type);
} else if (strlen(wcs_type)==4) {
if (*wcs_type == '-')
strcpy(type,wcs_type);
else
error("type=%s probably not legal, should be -XXX",wcs_type);
} else
error("type=%s must be a valid -XXX or XXX WCS descriptor",wcs_type);
sp = burststring(getparam("crval")," ,");
nsp = xstrlen(sp,sizeof(string))-1;
if (nsp != 2)
error("You must specify two values for the crval keyword!");
crval1 = natof(sp[0]);
crval2 = natof(sp[1]);
freestrings(sp);
sp = burststring(getparam("naxis")," ,");
nsp = xstrlen(sp,sizeof(string))-1;
if (nsp != 2)
error("You must specify two values for the naxis keyword!");
nx = natoi(sp[0]);
ny = natoi(sp[1]);
freestrings(sp);
crpix1 = nx/2.0+1;
crpix2 = ny/2.0+1;
cdelt2 = getdparam("cdelt")/3600.;
cdelt1 = -cdelt2;
/* Test to make sure we can write to output file */
fp = stropen(outfile,"w");
strclose(fp);
fprintf(stderr,"nx,ny = %d,%d\n",nx,ny);
fprintf(stderr,"crval1,crval2=%lf,%lf\n",crval1,crval2);
fprintf(stderr,"crpix1,crpix2=%lf,%lf\n",crpix1,crpix2);
fprintf(stderr,"wcs: %s\n",type);
xpix=1.0;
ypix=1.0;
worldpos(xpix,ypix,crval1,crval2,crpix1,crpix2,cdelt1,cdelt2,0.0,type,&ra,&dec);
dprintf(1,"LL corner: %g %g\n",ra,dec);
xpix=nx;
worldpos(xpix,ypix,crval1,crval2,crpix1,crpix2,cdelt1,cdelt2,0.0,type,&ra,&dec);
dprintf(1,"LR corner: %g %g\n",ra,dec);
ypix=ny;
worldpos(xpix,ypix,crval1,crval2,crpix1,crpix2,cdelt1,cdelt2,0.0,type,&ra,&dec);
dprintf(1,"UR corner: %g %g\n",ra,dec);
xpix=1.0;
worldpos(xpix,ypix,crval1,crval2,crpix1,crpix2,cdelt1,cdelt2,0.0,type,&ra,&dec);
dprintf(1,"UL corner: %g %g\n",ra,dec);
/* Write header for TABFITS to file */
fp = stropen(getparam("out"),"w!");
fprintf(fp,"# NAXIS1 = %d\n",nx);
fprintf(fp,"# NAXIS2 = %d\n",ny);
fprintf(fp,"# NAXIS3 = 1\n");
fprintf(fp,"# CDELT1 = %lf\n",cdelt1);
fprintf(fp,"# CDELT2 = %lf\n",cdelt2);
fprintf(fp,"# CRVAL1 = %lf\n",crval1);
fprintf(fp,"# CRVAL2 = %lf\n",crval2);
fprintf(fp,"# CRPIX1 = %f\n",crpix1);
fprintf(fp,"# CRPIX2 = %f\n",crpix2);
fprintf(fp,"# CTYPE1 = 'RA--%s'\n",type);
fprintf(fp,"# CTYPE2 = 'DEC-%s'\n",type);
fprintf(fp,"# COMMENT index=%g / powerlaw index\n",index);
fprintf(fp,"# COMMENT rzero=%g / rzero parameter\n",rzero);
fprintf(fp,"# COMMENT out=%s / output table\n",outfile);
fprintf(fp,"# COMMENT crval=%f,%f / Center WCS coordinates\n",crval1,crval2);
fprintf(fp,"# COMMENT naxis=%d,%d / Image size in pixels\n",nx,ny);
fprintf(fp,"# COMMENT cdelt=%f / pixel size in arcseconds\n",cdelt2*3600);
fprintf(fp,"# COMMENT type=%s / Projection type\n",type);
fprintf(fp,"# COMMENT VERSION=%s / Version number\n",getparam("VERSION"));
for (i=0; i< ny; i++){
ypix = i + 1.0;
for (j=0; j< nx; j++){
xpix = j + 1.0;
worldpos(xpix,ypix,crval1,crval2,crpix1,crpix2,cdelt1,cdelt2,0.0,
type,&ra,&dec);
radius = sqrt((xpix-crpix1)*(xpix-crpix1) + (ypix-crpix2)*(ypix-crpix2));
flux = 1.0/(1.0 + pow(radius/rzero,index));
/* if (radius <= 4)
flux = 1.0;
else
flux = 1.0/(1.0 + pow(radius-4,index)); */
fprintf(fp,"%lf %lf %4.2e\n",ra,dec,flux);
}
}
strclose(fp);
}
void nemo_main() {
string *sp; /* string pointer for output of burststring */
int nsp; /* number of tokens in sp after using burststring */
double magj,magh,magks; /* JHKs magnitudes */
double sigmaj,sigmah,sigmaks; /* JHKs uncertainties in magnitudes */
double sum_jh,sum_jh2; /* Sums for J-H weighted averages */
double sum_hks,sum_hks2; /* Sums for H-Ks weighted averages */
double w_jh,w_hks,w_jhhks; /* sums of weights for J-H,H-Ks, and covariance */
double w_jh2,w_hks2,w_jhhks2; /* sums of square of weights for J-H,H-Ks, and cov. */
double sum_jhhks; /* for covariance matrix */
double sum_jhalt,sum_hksalt; /* for covariance matrix */
double tmp1,tmp2,tmp3; /* temp variables */
double avg_jh,avg_hks; /* average values of J-H,H-Ks */
double std_jh,std_hks; /* Std. deviations of J-H,H-Ks*/
double cov; /* covariance of J-H and H-Ks */
double no_jh,no_hks,no_jhhks; /* unweighted sums */
double no_jh2,no_hks2; /* unweighted sums */
int num; /* number of sources read */
stream fp; /* File pointer */
char line[MAX_LINELEN]; /* Character string for reading from file */
/* Initialize variables */
sum_jh = 0;
sum_jh2 = 0;
sum_hks = 0;
sum_hks2 = 0;
sum_jhhks = 0;
sum_jhalt = 0;
sum_hksalt= 0;
w_jh = 0;
w_hks = 0;
w_jhhks = 0;
w_jh2 = 0;
w_hks2 = 0;
w_jhhks2 = 0;
num = 0;
no_jh = 0;
no_hks = 0;
no_jhhks = 0;
no_jh2 = 0;
no_hks2 = 0;
fp = stropen(getparam("in"),"r");
while (fgets(line,MAX_LINELEN,fp)){
if (line[0] != '#'){ /* lines starting with # are comments */
sp = burststring(line," \t\n");
nsp = xstrlen(sp,sizeof(string))-1;
if (nsp < 8)
warning("Skipping line: %s",line);
magj = natof(sp[2]);
sigmaj = natof(sp[3]);
magh = natof(sp[4]);
sigmah = natof(sp[5]);
magks = natof(sp[6]);
sigmaks = natof(sp[7]);
num += 1;
tmp1 = 1.0/(sigmaj*sigmaj + sigmah*sigmah);
tmp2 = 1.0/(sigmah*sigmah + sigmaks*sigmaks);
tmp3 = sqrt(tmp1*tmp2);
sum_jh += tmp1*(magj - magh);
sum_jh2 += tmp1*(magj - magh)*(magj - magh);
sum_hks += tmp2*(magh - magks);
sum_hks2 += tmp2*(magh - magks)*(magh - magks);
sum_jhhks += tmp3*(magj - magh)*(magh - magks);
sum_jhalt += tmp3*(magj - magh);
sum_hksalt += tmp3*(magh - magks);
no_jh += (magj - magh);
no_jh2 += (magj - magh)*(magj - magh);
no_hks += (magh - magks);
no_hks2 += (magh - magks)*(magh - magks);
no_jhhks += (magj - magh)*(magh - magks);
w_jh += tmp1;
w_hks += tmp2;
w_jhhks += tmp3;
w_jh2 += tmp1*tmp1;
w_hks2 += tmp2*tmp2;
w_jhhks2 += tmp3*tmp3;
freestrings(sp);
}
}
strclose(fp);
avg_jh = sum_jh/w_jh;
avg_hks = sum_hks/w_hks;
std_jh = sqrt(w_jh/(w_jh*w_jh - w_jh2)*(sum_jh2 - avg_jh*avg_jh*w_jh));
std_hks = sqrt(w_hks/(w_hks*w_hks - w_hks2)*(sum_hks2 - avg_hks*avg_hks*w_hks));
cov = sum_jhhks - avg_hks*sum_jhalt - avg_jh*sum_hksalt + avg_jh*avg_hks*w_jhhks;
cov = w_jhhks/(w_jhhks*w_jhhks - w_jhhks2)*cov;
fprintf(stdout,"Weighted:\n");
fprintf(stdout,"Average J-H = %5.3e +- %5.3e\n",avg_jh,std_jh);
fprintf(stdout,"Average H-Ks = %5.3e +- %5.3e\n",avg_hks,std_hks);
fprintf(stdout,"Covariance = %5.3e\n",cov);
avg_jh = no_jh/num;
avg_hks = no_hks/num;
std_jh = sqrt((no_jh2 - avg_jh*avg_jh*num)/(num - 1));
std_hks = sqrt((no_hks2 - avg_hks*avg_hks*num)/(num - 1));
no_jhhks = (no_jhhks- avg_jh*avg_hks*num)/(num - 1);
fprintf(stdout,"Unweighted:\n");
fprintf(stdout,"Average J-H = %5.3e +- %5.3e\n",avg_jh,std_jh);
fprintf(stdout,"Average H-Ks = %5.3e +- %5.3e\n",avg_hks,std_hks);
fprintf(stdout,"Covariance = %5.3e\n",no_jhhks);
}
convert(stream instr, stream outstr)
{
char line[MAX_LINELEN]; /* input linelength */
int nlines, nwords, nskip;
long long nt0, nt;
real dt;
struct tm tm, tm0;
string *bp;
if (time0) {
tm0.tm_sec= tm0.tm_min = tm0.tm_hour = 0;
strptime(time0,format1,&tm0);
strftime(line,MAX_LINELEN,"%s",&tm0);
nt0 = atoll(line);
dprintf(0,"Using time0=%lld sec since 1970.0 using %s on %s \n",
nt0,format1,time0);
}
nlines=0; /* count lines read so far */
nskip=0;
for(;;) { /* loop over all lines in file(s) */
if (get_line(instr, line) < 0)
return 0;
dprintf(3,"LINE: (%s)\n",line);
if(line[0] == '#') continue; /* don't use comment lines */
nlines++;
tm.tm_sec= tm.tm_min = tm.tm_hour = 0;
if (dcol>0) {
bp = burststring(line,", "); /* split line in words */
nwords = xstrlen(bp,sizeof(string))-1;
if (nwords<dcol) {
nskip++;
continue;
}
strcpy(line,bp[dcol-1]); /* only pick out 1 column now */
freestrings(bp);
}
strptime(line,format1,&tm);
if (need_time0) {
dprintf(0,"First line: %s\n",line);
strftime(line,MAX_LINELEN,"%s",&tm);
time0 = strdup(line);
nt0 = atoll(time0);
dprintf(0,"First line uses: time0=%lld sec since 1970.0\n",nt0);
need_time0 = FALSE;
}
strftime(line,MAX_LINELEN,format2,&tm);
if (time0) {
nt = atoll(line);
if (use_scale) {
dt = (nt-nt0)/scale;
sprintf(line,"%g",dt);
} else
sprintf(line,"%lld",nt-nt0);
}
fputs(line,outstr);
fputs("\n",outstr);
} /* for(;;) */
dprintf(1,"Processed %d lines\n",nlines);
if (nskip) warning("%d/%d lines skipped because dcol too large",nskip,nlines);
}
