int startree_write_tagalong_table(fitstable_t* intab, fitstable_t* outtab, const char* racol, const char* deccol) { int i, R, NB, N; char* buf; qfits_header* hdr; fitstable_clear_table(intab); fitstable_add_fits_columns_as_struct(intab); fitstable_copy_columns(intab, outtab); if (!racol) racol = "RA"; if (!deccol) deccol = "DEC"; fitstable_remove_column(outtab, racol); fitstable_remove_column(outtab, deccol); fitstable_read_extension(intab, 1); hdr = fitstable_get_header(outtab); qfits_header_add(hdr, "AN_FILE", AN_FILETYPE_TAGALONG, "Extra data for stars", NULL); if (fitstable_write_header(outtab)) { ERROR("Failed to write tag-along data header"); return -1; } R = fitstable_row_size(intab); NB = 1000; logverb("Input row size: %i, output row size: %i\n", R, fitstable_row_size(outtab)); buf = malloc(NB * R); N = fitstable_nrows(intab); for (i=0; i<N; i+=NB) { int nr = NB; if (i+NB > N) nr = N - i; if (fitstable_read_structs(intab, buf, R, i, nr)) { ERROR("Failed to read tag-along data from catalog"); return -1; } if (fitstable_write_structs(outtab, buf, R, nr)) { ERROR("Failed to write tag-along data"); return -1; } } free(buf); if (fitstable_fix_header(outtab)) { ERROR("Failed to fix tag-along data header"); return -1; } return 0; }
matchfile* matchfile_open(const char* fn) { matchfile* mf = NULL; mf = fitstable_open(fn); if (!mf) return NULL; add_columns(mf, FALSE); fitstable_use_buffered_reading(mf, sizeof(MatchObj), 1000); mf->postprocess_read_structs = postprocess_read_structs; if (fitstable_read_extension(mf, 1)) { fprintf(stderr, "matchfile: table in extension 1 didn't contain the required columns.\n"); fprintf(stderr, " missing: "); fitstable_print_missing(mf, stderr); fprintf(stderr, "\n"); matchfile_close(mf); return NULL; } return mf; }
nomad_fits* nomad_fits_open(char* fn) { nomad_fits* cat = NULL; cat = fitstable_open(fn); if (!cat) return NULL; add_columns(cat, FALSE); fitstable_use_buffered_reading(cat, sizeof(nomad_entry), 1000); cat->postprocess_read_structs = postprocess_read_structs; if (fitstable_read_extension(cat, 1)) { fprintf(stderr, "nomad-fits: table in extension 1 didn't contain the required columns.\n"); fprintf(stderr, " missing: "); fitstable_print_missing(cat, stderr); fprintf(stderr, "\n"); nomad_fits_close(cat); return NULL; } return cat; }
int main(int argc, char *argv[]) { int argchar; char* progname = argv[0]; sl* infns = sl_new(16); char* outfnpat = NULL; char* racol = "RA"; char* deccol = "DEC"; char* tempdir = "/tmp"; anbool gzip = FALSE; sl* cols = sl_new(16); int loglvl = LOG_MSG; int nside = 1; double margin = 0.0; int NHP; double md; char* backref = NULL; fitstable_t* intable; fitstable_t** outtables; char** myargs; int nmyargs; int i; while ((argchar = getopt (argc, argv, OPTIONS)) != -1) switch (argchar) { case 'b': backref = optarg; break; case 't': tempdir = optarg; break; case 'c': sl_append(cols, optarg); break; case 'g': gzip = TRUE; break; case 'o': outfnpat = optarg; break; case 'r': racol = optarg; break; case 'd': deccol = optarg; break; case 'n': nside = atoi(optarg); break; case 'm': margin = atof(optarg); break; case 'v': loglvl++; break; case '?': fprintf(stderr, "Unknown option `-%c'.\n", optopt); case 'h': printHelp(progname); return 0; default: return -1; } if (sl_size(cols) == 0) { sl_free2(cols); cols = NULL; } nmyargs = argc - optind; myargs = argv + optind; for (i=0; i<nmyargs; i++) sl_append(infns, myargs[i]); if (!sl_size(infns)) { printHelp(progname); printf("Need input filenames!\n"); exit(-1); } log_init(loglvl); fits_use_error_system(); NHP = 12 * nside * nside; logmsg("%i output healpixes\n", NHP); outtables = calloc(NHP, sizeof(fitstable_t*)); assert(outtables); md = deg2dist(margin); /** About the mincaps/maxcaps: These have a center and radius-squared, describing the region inside a small circle on the sphere. The "mincaps" describe the regions that are definitely owned by a single healpix -- ie, more than MARGIN distance from any edge. That is, the mincap is the small circle centered at (0.5, 0.5) in the healpix and with radius = the distance to the closest healpix boundary, MINUS the margin distance. Below, we first check whether a new star is within the "mincap" of any healpix. If so, we stick it in that healpix and continue. Otherwise, we check all the "maxcaps" -- these are the healpixes it could *possibly* be in. We then refine with healpix_within_range_of_xyz. The maxcap distance is the distance to the furthest boundary point, PLUS the margin distance. */ cap_t* mincaps = malloc(NHP * sizeof(cap_t)); cap_t* maxcaps = malloc(NHP * sizeof(cap_t)); for (i=0; i<NHP; i++) { // center double r2; double xyz[3]; double* cxyz; double step = 1e-3; double v; double r2b, r2a; cxyz = mincaps[i].xyz; healpix_to_xyzarr(i, nside, 0.5, 0.5, mincaps[i].xyz); memcpy(maxcaps[i].xyz, cxyz, 3 * sizeof(double)); logverb("Center of HP %i: (%.3f, %.3f, %.3f)\n", i, cxyz[0], cxyz[1], cxyz[2]); // radius-squared: // max is the easy one: max of the four corners (I assume) r2 = 0.0; healpix_to_xyzarr(i, nside, 0.0, 0.0, xyz); logverb(" HP %i corner 1: (%.3f, %.3f, %.3f), distsq %.3f\n", i, xyz[0], xyz[1], xyz[2], distsq(xyz, cxyz, 3)); r2 = MAX(r2, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, 1.0, 0.0, xyz); logverb(" HP %i corner 1: (%.3f, %.3f, %.3f), distsq %.3f\n", i, xyz[0], xyz[1], xyz[2], distsq(xyz, cxyz, 3)); r2 = MAX(r2, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, 0.0, 1.0, xyz); logverb(" HP %i corner 1: (%.3f, %.3f, %.3f), distsq %.3f\n", i, xyz[0], xyz[1], xyz[2], distsq(xyz, cxyz, 3)); r2 = MAX(r2, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, 1.0, 1.0, xyz); logverb(" HP %i corner 1: (%.3f, %.3f, %.3f), distsq %.3f\n", i, xyz[0], xyz[1], xyz[2], distsq(xyz, cxyz, 3)); r2 = MAX(r2, distsq(xyz, cxyz, 3)); logverb(" max distsq: %.3f\n", r2); logverb(" margin dist: %.3f\n", md); maxcaps[i].r2 = square(sqrt(r2) + md); logverb(" max cap distsq: %.3f\n", maxcaps[i].r2); r2a = r2; r2 = 1.0; r2b = 0.0; for (v=0; v<=1.0; v+=step) { healpix_to_xyzarr(i, nside, 0.0, v, xyz); r2 = MIN(r2, distsq(xyz, cxyz, 3)); r2b = MAX(r2b, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, 1.0, v, xyz); r2 = MIN(r2, distsq(xyz, cxyz, 3)); r2b = MAX(r2b, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, v, 0.0, xyz); r2 = MIN(r2, distsq(xyz, cxyz, 3)); r2b = MAX(r2b, distsq(xyz, cxyz, 3)); healpix_to_xyzarr(i, nside, v, 1.0, xyz); r2 = MIN(r2, distsq(xyz, cxyz, 3)); r2b = MAX(r2b, distsq(xyz, cxyz, 3)); } mincaps[i].r2 = square(MAX(0, sqrt(r2) - md)); logverb("\nhealpix %i: min rad %g\n", i, sqrt(r2)); logverb("healpix %i: max rad %g\n", i, sqrt(r2a)); logverb("healpix %i: max rad(b) %g\n", i, sqrt(r2b)); assert(r2a >= r2b); } if (backref) { fitstable_t* tab = fitstable_open_for_writing(backref); int maxlen = 0; char* buf; for (i=0; i<sl_size(infns); i++) { char* infn = sl_get(infns, i); maxlen = MAX(maxlen, strlen(infn)); } fitstable_add_write_column_array(tab, fitscolumn_char_type(), maxlen, "filename", NULL); fitstable_add_write_column(tab, fitscolumn_i16_type(), "index", NULL); if (fitstable_write_primary_header(tab) || fitstable_write_header(tab)) { ERROR("Failed to write header of backref table \"%s\"", backref); exit(-1); } buf = malloc(maxlen+1); assert(buf); for (i=0; i<sl_size(infns); i++) { char* infn = sl_get(infns, i); int16_t ind; memset(buf, 0, maxlen); strcpy(buf, infn); ind = i; if (fitstable_write_row(tab, buf, &ind)) { ERROR("Failed to write row %i of backref table: %s = %i", i, buf, ind); exit(-1); } } if (fitstable_fix_header(tab) || fitstable_close(tab)) { ERROR("Failed to fix header & close backref table"); exit(-1); } logmsg("Wrote backref table %s\n", backref); free(buf); } for (i=0; i<sl_size(infns); i++) { char* infn = sl_get(infns, i); char* originfn = infn; int r, NR; tfits_type any, dubl; il* hps = NULL; bread_t* rowbuf; int R; char* tempfn = NULL; char* padrowdata = NULL; int ii; logmsg("Reading input \"%s\"...\n", infn); if (gzip) { char* cmd; int rtn; tempfn = create_temp_file("hpsplit", tempdir); asprintf_safe(&cmd, "gunzip -cd %s > %s", infn, tempfn); logmsg("Running: \"%s\"\n", cmd); rtn = run_command_get_outputs(cmd, NULL, NULL); if (rtn) { ERROR("Failed to run command: \"%s\"", cmd); exit(-1); } free(cmd); infn = tempfn; } intable = fitstable_open(infn); if (!intable) { ERROR("Couldn't read catalog %s", infn); exit(-1); } NR = fitstable_nrows(intable); logmsg("Got %i rows\n", NR); any = fitscolumn_any_type(); dubl = fitscolumn_double_type(); fitstable_add_read_column_struct(intable, dubl, 1, 0, any, racol, TRUE); fitstable_add_read_column_struct(intable, dubl, 1, sizeof(double), any, deccol, TRUE); fitstable_use_buffered_reading(intable, 2*sizeof(double), 1000); R = fitstable_row_size(intable); rowbuf = buffered_read_new(R, 1000, NR, refill_rowbuffer, intable); if (fitstable_read_extension(intable, 1)) { ERROR("Failed to find RA and DEC columns (called \"%s\" and \"%s\" in the FITS file)", racol, deccol); exit(-1); } for (r=0; r<NR; r++) { int hp = -1; double ra, dec; int j; double* rd; void* rowdata; void* rdata; if (r && ((r % 100000) == 0)) { logmsg("Reading row %i of %i\n", r, NR); } //printf("reading RA,Dec for row %i\n", r); rd = fitstable_next_struct(intable); ra = rd[0]; dec = rd[1]; logverb("row %i: ra,dec %g,%g\n", r, ra, dec); if (margin == 0) { hp = radecdegtohealpix(ra, dec, nside); logverb(" --> healpix %i\n", hp); } else { double xyz[3]; anbool gotit = FALSE; double d2; if (!hps) hps = il_new(4); radecdeg2xyzarr(ra, dec, xyz); for (j=0; j<NHP; j++) { d2 = distsq(xyz, mincaps[j].xyz, 3); if (d2 <= mincaps[j].r2) { logverb(" -> in mincap %i (dist %g vs %g)\n", j, sqrt(d2), sqrt(mincaps[j].r2)); il_append(hps, j); gotit = TRUE; break; } } if (!gotit) { for (j=0; j<NHP; j++) { d2 = distsq(xyz, maxcaps[j].xyz, 3); if (d2 <= maxcaps[j].r2) { logverb(" -> in maxcap %i (dist %g vs %g)\n", j, sqrt(d2), sqrt(maxcaps[j].r2)); if (healpix_within_range_of_xyz(j, nside, xyz, margin)) { logverb(" -> and within range.\n"); il_append(hps, j); } } } } //hps = healpix_rangesearch_radec(ra, dec, margin, nside, hps); logverb(" --> healpixes: ["); for (j=0; j<il_size(hps); j++) logverb(" %i", il_get(hps, j)); logverb(" ]\n"); } //printf("Reading rowdata for row %i\n", r); rowdata = buffered_read(rowbuf); assert(rowdata); j=0; while (1) { if (hps) { if (j >= il_size(hps)) break; hp = il_get(hps, j); j++; } assert(hp < NHP); assert(hp >= 0); if (!outtables[hp]) { char* outfn; fitstable_t* out; // MEMLEAK the output filename. You'll live. asprintf_safe(&outfn, outfnpat, hp); logmsg("Opening output file \"%s\"...\n", outfn); out = fitstable_open_for_writing(outfn); if (!out) { ERROR("Failed to open output table \"%s\"", outfn); exit(-1); } // Set the output table structure. if (cols) { fitstable_add_fits_columns_as_struct3(intable, out, cols, 0); } else fitstable_add_fits_columns_as_struct2(intable, out); if (backref) { tfits_type i16type; tfits_type i32type; // R = fitstable_row_size(intable); int off = R; i16type = fitscolumn_i16_type(); i32type = fitscolumn_i32_type(); fitstable_add_read_column_struct(out, i16type, 1, off, i16type, "backref_file", TRUE); off += sizeof(int16_t); fitstable_add_read_column_struct(out, i32type, 1, off, i32type, "backref_index", TRUE); } //printf("Output table:\n"); //fitstable_print_columns(out); if (fitstable_write_primary_header(out) || fitstable_write_header(out)) { ERROR("Failed to write output file headers for \"%s\"", outfn); exit(-1); } outtables[hp] = out; } if (backref) { int16_t brfile; int32_t brind; if (!padrowdata) { padrowdata = malloc(R + sizeof(int16_t) + sizeof(int32_t)); assert(padrowdata); } // convert to FITS endian brfile = htons(i); brind = htonl(r); // add backref data to rowdata memcpy(padrowdata, rowdata, R); memcpy(padrowdata + R, &brfile, sizeof(int16_t)); memcpy(padrowdata + R + sizeof(int16_t), &brind, sizeof(int32_t)); rdata = padrowdata; } else { rdata = rowdata; } if (cols) { if (fitstable_write_struct_noflip(outtables[hp], rdata)) { ERROR("Failed to copy a row of data from input table \"%s\" to output healpix %i", infn, hp); } } else { if (fitstable_write_row_data(outtables[hp], rdata)) { ERROR("Failed to copy a row of data from input table \"%s\" to output healpix %i", infn, hp); } } if (!hps) break; } if (hps) il_remove_all(hps); } buffered_read_free(rowbuf); // wack... buffered_read_free() just frees its internal buffer, // not the "rowbuf" struct itself. // who wrote this crazy code? Oh, me of 5 years ago. Jerk. free(rowbuf); fitstable_close(intable); il_free(hps); if (tempfn) { logverb("Removing temp file %s\n", tempfn); if (unlink(tempfn)) { SYSERROR("Failed to unlink() temp file \"%s\"", tempfn); } tempfn = NULL; } // fix headers so that the files are valid at this point. for (ii=0; ii<NHP; ii++) { if (!outtables[ii]) continue; off_t offset = ftello(outtables[ii]->fid); if (fitstable_fix_header(outtables[ii])) { ERROR("Failed to fix header for healpix %i after reading input file \"%s\"", ii, originfn); exit(-1); } fseeko(outtables[ii]->fid, offset, SEEK_SET); } if (padrowdata) { free(padrowdata); padrowdata = NULL; } } for (i=0; i<NHP; i++) { if (!outtables[i]) continue; if (fitstable_fix_header(outtables[i]) || fitstable_fix_primary_header(outtables[i]) || fitstable_close(outtables[i])) { ERROR("Failed to close output table for healpix %i", i); exit(-1); } } free(outtables); sl_free2(infns); sl_free2(cols); free(mincaps); free(maxcaps); return 0; }
int resort_xylist(const char* infn, const char* outfn, const char* fluxcol, const char* backcol, anbool ascending) { FILE* fin = NULL; FILE* fout = NULL; double *flux = NULL, *back = NULL; int *perm1 = NULL, *perm2 = NULL; anbool *used = NULL; int start, size, nextens, ext; int (*compare)(const void*, const void*); fitstable_t* tab = NULL; anqfits_t* anq = NULL; if (ascending) compare = compare_doubles_asc; else compare = compare_doubles_desc; if (!fluxcol) fluxcol = "FLUX"; if (!backcol) backcol = "BACKGROUND"; fin = fopen(infn, "rb"); if (!fin) { SYSERROR("Failed to open input file %s", infn); return -1; } fout = fopen(outfn, "wb"); if (!fout) { SYSERROR("Failed to open output file %s", outfn); goto bailout; } // copy the main header exactly. anq = anqfits_open(infn); if (!anq) { ERROR("Failed to open file \"%s\"", infn); goto bailout; } start = anqfits_header_start(anq, 0); size = anqfits_header_size (anq, 0); if (pipe_file_offset(fin, start, size, fout)) { ERROR("Failed to copy primary FITS header."); goto bailout; } nextens = anqfits_n_ext(anq); tab = fitstable_open(infn); if (!tab) { ERROR("Failed to open FITS table in file %s", infn); goto bailout; } for (ext=1; ext<nextens; ext++) { int hdrstart, hdrsize, datstart; int i, N; int rowsize; hdrstart = anqfits_header_start(anq, ext); hdrsize = anqfits_header_size (anq, ext); datstart = anqfits_data_start (anq, ext); if (!anqfits_is_table(anq, ext)) { ERROR("Extention %i isn't a table. Skipping", ext); continue; } // Copy the header as-is. if (pipe_file_offset(fin, hdrstart, hdrsize, fout)) { ERROR("Failed to copy the header of extension %i", ext); goto bailout; } if (fitstable_read_extension(tab, ext)) { ERROR("Failed to read FITS table from extension %i", ext); goto bailout; } rowsize = fitstable_row_size(tab); // read FLUX column as doubles. flux = fitstable_read_column(tab, fluxcol, TFITS_BIN_TYPE_D); if (!flux) { ERROR("Failed to read FLUX column from extension %i", ext); goto bailout; } // BACKGROUND back = fitstable_read_column(tab, backcol, TFITS_BIN_TYPE_D); if (!back) { ERROR("Failed to read BACKGROUND column from extension %i", ext); goto bailout; } debug("First 10 rows of input table:\n"); for (i=0; i<10; i++) debug("flux %g, background %g\n", flux[i], back[i]); N = fitstable_nrows(tab); // set back = flux + back (ie, non-background-subtracted flux) for (i=0; i<N; i++) back[i] += flux[i]; // Sort by flux... perm1 = permuted_sort(flux, sizeof(double), compare, NULL, N); // Sort by non-background-subtracted flux... perm2 = permuted_sort(back, sizeof(double), compare, NULL, N); used = malloc(N * sizeof(anbool)); memset(used, 0, N * sizeof(anbool)); // Check sort... for (i=0; i<N-1; i++) { if (ascending) { assert(flux[perm1[i]] <= flux[perm1[i+1]]); assert(back[perm2[i]] <= back[perm2[i+1]]); } else { assert(flux[perm1[i]] >= flux[perm1[i+1]]); assert(back[perm2[i]] >= back[perm2[i+1]]); } } for (i=0; i<N; i++) { int j; int inds[] = { perm1[i], perm2[i] }; for (j=0; j<2; j++) { int index = inds[j]; assert(index < N); if (used[index]) continue; used[index] = TRUE; debug("adding index %i: %s %g\n", index, j==0 ? "flux" : "bgsub", j==0 ? flux[index] : back[index]); if (pipe_file_offset(fin, datstart + index * rowsize, rowsize, fout)) { ERROR("Failed to copy row %i", index); goto bailout; } } } for (i=0; i<N; i++) assert(used[i]); if (fits_pad_file(fout)) { ERROR("Failed to add padding to extension %i", ext); goto bailout; } free(flux); flux = NULL; free(back); back = NULL; free(perm1); perm1 = NULL; free(perm2); perm2 = NULL; free(used); used = NULL; } fitstable_close(tab); tab = NULL; if (fclose(fout)) { SYSERROR("Failed to close output file %s", outfn); return -1; } fclose(fin); return 0; bailout: if (tab) fitstable_close(tab); if (fout) fclose(fout); if (fin) fclose(fin); free(flux); free(back); free(perm1); free(perm2); free(used); return -1; }