int anqfits_get_data_start_and_size(const anqfits_t* qf, int ext, off_t* pstart, off_t* psize) { if (pstart) { *pstart = anqfits_data_start(qf, ext); if (*pstart == -1) return -1; } if (psize) { *psize = anqfits_data_size(qf, ext); if (*psize == -1) return -1; } return 0; }
int tabsort(const char* infn, const char* outfn, const char* colname, int descending) { FILE* fin; FILE* fout; int ext, nextens; off_t start, size; void* data = NULL; int* perm = NULL; unsigned char* map = NULL; size_t mapsize = 0; anqfits_t* anq = NULL; 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 \"%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); //logverb("Sorting %i extensions.\n", nextens); for (ext=1; ext<nextens; ext++) { int c; qfits_table* table; qfits_col* col; int mgap; off_t mstart; size_t msize; int atomsize; int (*sort_func)(const void*, const void*); unsigned char* tabledata; unsigned char* tablehdr; off_t hdrstart, hdrsize, datsize, datstart; int i; hdrstart = anqfits_header_start(anq, ext); hdrsize = anqfits_header_size (anq, ext); datstart = anqfits_data_start (anq, ext); datsize = anqfits_data_size (anq, ext); if (!anqfits_is_table(anq, ext)) { ERROR("Extension %i isn't a table. Skipping.\n", ext); continue; } table = anqfits_get_table(anq, ext); if (!table) { ERROR("Failed to open table: file %s, extension %i. Skipping.", infn, ext); continue; } c = fits_find_column(table, colname); if (c == -1) { ERROR("Couldn't find column named \"%s\" in extension %i. Skipping.", colname, ext); continue; } col = table->col + c; switch (col->atom_type) { case TFITS_BIN_TYPE_D: data = realloc(data, table->nr * sizeof(double)); if (descending) sort_func = compare_doubles_desc; else sort_func = compare_doubles_asc; break; case TFITS_BIN_TYPE_E: data = realloc(data, table->nr * sizeof(float)); if (descending) sort_func = compare_floats_desc; else sort_func = compare_floats_asc; break; case TFITS_BIN_TYPE_K: data = realloc(data, table->nr * sizeof(int64_t)); if (descending) sort_func = compare_int64_desc; else sort_func = compare_int64_asc; break; default: ERROR("Column %s is neither FITS type D, E, nor K. Skipping.", colname); continue; } // Grab the sort column. atomsize = fits_get_atom_size(col->atom_type); printf("Reading sort column \"%s\"\n", colname); qfits_query_column_seq_to_array(table, c, 0, table->nr, data, atomsize); // Sort it. printf("Sorting sort column\n"); perm = permuted_sort(data, atomsize, sort_func, NULL, table->nr); // mmap the input file. printf("mmapping input file\n"); start = hdrstart; size = hdrsize + datsize; get_mmap_size(start, size, &mstart, &msize, &mgap); mapsize = msize; map = mmap(NULL, mapsize, PROT_READ, MAP_SHARED, fileno(fin), mstart); if (map == MAP_FAILED) { SYSERROR("Failed to mmap input file %s", infn); map = NULL; goto bailout; } tabledata = map + (off_t)mgap + (datstart - hdrstart); tablehdr = map + (off_t)mgap; // Copy the table header without change. printf("Copying table header.\n"); if (fwrite(tablehdr, 1, hdrsize, fout) != hdrsize) { SYSERROR("Failed to write FITS table header"); goto bailout; } for (i=0; i<table->nr; i++) { unsigned char* rowptr; if (i % 100000 == 0) printf("Writing row %i\n", i); rowptr = tabledata + (off_t)(perm[i]) * (off_t)table->tab_w; if (fwrite(rowptr, 1, table->tab_w, fout) != table->tab_w) { SYSERROR("Failed to write FITS table row"); goto bailout; } } munmap(map, mapsize); map = NULL; free(perm); perm = NULL; if (fits_pad_file(fout)) { ERROR("Failed to add padding to extension %i", ext); goto bailout; } qfits_table_close(table); } free(data); if (fclose(fout)) { SYSERROR("Error closing output file"); fout = NULL; goto bailout; } fclose(fin); anqfits_close(anq); printf("Done\n"); return 0; bailout: free(data); free(perm); if (fout) fclose(fout); fclose(fin); if (map) munmap(map, mapsize); return -1; }
int main(int argc, char *argv[]) { int argchar; char* infn = NULL; char* outfn = NULL; anbool tostdout = FALSE; FILE* fin = NULL; FILE* fout = NULL; il* exts; int i; char* progname = argv[0]; anbool inblocks = FALSE; anbool inmegs = FALSE; int allexts = 0; int Next = -1; anbool dataonly = FALSE; anbool headeronly = FALSE; anqfits_t* anq = NULL; int loglvl = LOG_MSG; exts = il_new(16); while ((argchar = getopt (argc, argv, OPTIONS)) != -1) switch (argchar) { case 'v': loglvl++; break; case 'D': dataonly = TRUE; break; case 'H': headeronly = TRUE; break; case 'a': allexts = 1; break; case 'b': inblocks = TRUE; break; case 'M': inmegs = TRUE; break; case 'e': il_append(exts, atoi(optarg)); break; case 'i': infn = optarg; break; case 'o': outfn = optarg; break; case '?': case 'h': printHelp(progname); return 0; default: return -1; } if (headeronly && dataonly) { fprintf(stderr, "Can't write data blocks only AND header blocks only!\n"); exit(-1); } if (inblocks && inmegs) { fprintf(stderr, "Can't write sizes in FITS blocks and megabytes.\n"); exit(-1); } fits_use_error_system(); log_init(loglvl); log_to(stderr); errors_log_to(stderr); if (infn) { anq = anqfits_open(infn); if (!anq) { ERROR("Failed to open input file \"%s\"", infn); exit(-1); } Next = anqfits_n_ext(anq); fprintf(stderr, "File %s contains %i FITS extensions.\n", infn, Next); } if (infn && !outfn) { for (i=0; i<Next; i++) { off_t hdrstart, hdrlen, datastart, datalen; hdrstart = anqfits_header_start(anq, i); hdrlen = anqfits_header_size(anq, i); datastart = anqfits_data_start(anq, i); datalen = anqfits_data_size(anq, i); if (inblocks) { off_t block = (off_t)FITS_BLOCK_SIZE; fprintf(stderr, "Extension %i : header start %zu , length %zu ; data start %zu , length %zu blocks.\n", i, (size_t)(hdrstart / block), (size_t)(hdrlen / block), (size_t)(datastart / block), (size_t)(datalen / block)); } else if (inmegs) { off_t meg = 1024*1024; fprintf(stderr, "Extension %i : header start %zu , length %zu ; data start %zu , length %zu megabytes.\n", i, (size_t)(hdrstart/meg), (size_t)(hdrlen/meg), (size_t)(datastart/meg), (size_t)(datalen/meg)); } else { fprintf(stderr, "Extension %i : header start %zu , length %zu ; data start %zu , length %zu .\n", i, (size_t)hdrstart, (size_t)hdrlen, (size_t)datastart, (size_t)datalen); } } anqfits_close(anq); exit(0); } if (!infn || !outfn || !(il_size(exts) || allexts)) { printHelp(progname); exit(-1); } if (!strcmp(outfn, "-")) { tostdout = TRUE; if (allexts) { fprintf(stderr, "Specify all extensions (-a) and outputting to stdout (-o -) doesn't make much sense...\n"); exit(-1); } } if (infn) { fin = fopen(infn, "rb"); if (!fin) { fprintf(stderr, "Failed to open input file %s: %s\n", infn, strerror(errno)); exit(-1); } } if (tostdout) fout = stdout; else { if (allexts) for (i=0; i<Next; i++) il_append(exts, i); else { // open the (single) output file. fout = fopen(outfn, "wb"); if (!fout) { fprintf(stderr, "Failed to open output file %s: %s\n", outfn, strerror(errno)); exit(-1); } } } for (i=0; i<il_size(exts); i++) { off_t hdrstart, hdrlen, datastart, datalen; int ext = il_get(exts, i); if (allexts) { char fn[256]; snprintf(fn, sizeof(fn), outfn, ext); fout = fopen(fn, "wb"); if (!fout) { fprintf(stderr, "Failed to open output file %s: %s\n", fn, strerror(errno)); exit(-1); } } hdrstart = anqfits_header_start(anq, ext); hdrlen = anqfits_header_size(anq, ext); datastart = anqfits_data_start(anq, ext); datalen = anqfits_data_size(anq, ext); if (inblocks) { off_t block = (off_t)FITS_BLOCK_SIZE; fprintf(stderr, "Writing extension %i : header start %zu , length %zu ; data start %zu , length %zu blocks.\n", ext, (size_t)(hdrstart / block), (size_t)(hdrlen / block), (size_t)(datastart / block), (size_t)(datalen / block)); } else if (inmegs) { off_t meg = 1024*1024; fprintf(stderr, "Writing extension %i : header start %zu , length %zu ; data start %zu , length %zu megabytes.\n", ext, (size_t)(hdrstart/meg), (size_t)(hdrlen/meg), (size_t)(datastart/meg), (size_t)(datalen/meg)); } else { fprintf(stderr, "Writing extension %i : header start %zu , length %zu ; data start %zu , length %zu .\n", ext, (size_t)hdrstart, (size_t)hdrlen, (size_t)datastart, (size_t)datalen); } if (hdrlen && !dataonly) { if (pipe_file_offset(fin, hdrstart, hdrlen, fout)) { fprintf(stderr, "Failed to write header for extension %i: %s\n", ext, strerror(errno)); exit(-1); } } if (datalen && !headeronly) { if (pipe_file_offset(fin, datastart, datalen, fout)) { fprintf(stderr, "Failed to write data for extension %i: %s\n", ext, strerror(errno)); exit(-1); } } if (allexts) if (fclose(fout)) { fprintf(stderr, "Failed to close output file: %s\n", strerror(errno)); exit(-1); } } fclose(fin); if (!allexts && !tostdout) fclose(fout); il_free(exts); anqfits_close(anq); return 0; }
int new_wcs(const char* infn, int extension, const char* wcsfn, const char* outfn, anbool copydata) { FILE* outfid = NULL; int i, N; int e; regex_t re1[NE1]; regex_t re2[NE2]; qfits_header *inhdr=NULL, *outhdr=NULL, *wcshdr=NULL; char key[FITS_LINESZ + 1]; char newkey[FITS_LINESZ + 1]; char val[FITS_LINESZ + 1]; char comment[FITS_LINESZ + 1]; int imatch = -1; // how many REs have successfully been compiled. int n1=0, n2=0; outfid = fopen(outfn, "wb"); if (!outfid) { SYSERROR("Failed to open output file \"%s\"", outfn); goto bailout; } inhdr = anqfits_get_header2(infn, extension); if (!inhdr) { ERROR("Failed to read FITS header from input file \"%s\" ext %i", infn, extension); goto bailout; } wcshdr = anqfits_get_header2(wcsfn, 0); if (!wcshdr) { ERROR("Failed to read FITS header from WCS file \"%s\"", wcsfn); goto bailout; } outhdr = qfits_header_new(); if (!outhdr) { ERROR("Failed to allocate new output FITS header."); goto bailout; } // Compile regular expressions... for (e=0; e<NE1; e++) { int errcode; errcode = regcomp(re1 + e, exclude_input[e], REG_EXTENDED); if (errcode) { char err[256]; regerror(errcode, re1 + e, err, sizeof(err)); ERROR("Failed to compile regular expression \"%s\": %s", exclude_input[e], err); goto bailout; } n1++; } for (e=0; e<NE2; e++) { int errcode; errcode = regcomp(re2 + e, exclude_wcs[e], REG_EXTENDED); if (errcode) { char err[256]; regerror(errcode, re2 + e, err, sizeof(err)); ERROR("Failed to compile regular expression \"%s\": %s", exclude_wcs[e], err); goto bailout; } n2++; } logverb("Reading input file FITS headers...\n"); if (extension) { // Copy the primary header unchanged qfits_header* phdr = anqfits_get_header2(infn, 0); if (!phdr) { ERROR("Failed to read primary FITS header from input file \"%s\n", infn); goto bailout; } if (qfits_header_dump(phdr, outfid) || fits_pad_file(outfid)) { SYSERROR("Failed to write primary header to file %s", outfn); goto bailout; } qfits_header_destroy(phdr); } N = qfits_header_n(inhdr); for (i=0; i<N; i++) { anbool added_newkey = FALSE; char line[FITS_LINESZ + 1]; if (qfits_header_getitem(inhdr, i, key, val, comment, line)) { ERROR("Failed to read FITS header card %i from input file", i); goto bailout; } logverb("Read input header line: \"%s\"\n", line); if (key_matches(key, re1, exclude_input, NE1, &imatch)) { logverb("Regular expression matched: \"%s\", key \"%s\".\n", exclude_input[imatch], key); snprintf(newkey, FITS_LINESZ+1, "Original key: \"%s\"", key); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); // Completely skip the END card, since _ND is not a valid line. if (streq(key, "END")) continue; snprintf(newkey, FITS_LINESZ+1, "_%.7s", key+1); logverb("New key: \"%s\"\n", newkey); strcpy(key, newkey); line[0] = '_'; added_newkey = TRUE; } // If the header already contains this new (starting-with-"_") // key, add three comment cards instead. if (starts_with(key, "_") && (qfits_header_getstr(inhdr, key) || qfits_header_getstr(outhdr, key))) { logverb("Key \"%s\" already exists; adding COMMENT cards for value and comment instead\n", key); if (!added_newkey) { snprintf(newkey, FITS_LINESZ+1, "Original key: \"%s\"", key); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); } snprintf(newkey, FITS_LINESZ+1, " = %s", val); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); snprintf(newkey, FITS_LINESZ+1, " / %s", comment); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); continue; } qfits_header_append(outhdr, key, val, comment, line); } qfits_header_destroy(inhdr); inhdr = NULL; logverb("Reading WCS file FITS headers...\n"); qfits_header_append(outhdr, "COMMENT", "", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "--Start of Astrometry.net WCS solution--", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "--Put in by the new-wcs program--", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "", NULL, NULL); N = qfits_header_n(wcshdr); for (i=0; i<N; i++) { char line[FITS_LINESZ + 1]; if (qfits_header_getitem(wcshdr, i, key, val, comment, line)) { ERROR("Failed to read FITS header card %i from WCS file.", i); goto bailout; } if (key_matches(key, re2, exclude_wcs, NE2, &imatch)) { logverb("Regular expression matched: \"%s\", key \"%s\".\n", exclude_wcs[imatch], key); // These don't really need to appear in the output file... /* snprintf(newkey, FITS_LINESZ+1, "Original WCS key: \"%s\"", key); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); snprintf(newkey, FITS_LINESZ+1, "_%.7s", key); strcpy(key, newkey); */ continue; } if (streq(key, "DATE") && qfits_header_getstr(outhdr, key)) { // If the input header already had a DATE card, snprintf(newkey, FITS_LINESZ+1, "Original WCS key: \"%s\"", key); qfits_header_append(outhdr, "COMMENT", newkey, NULL, NULL); snprintf(newkey, FITS_LINESZ+1, "_%.7s", key); strcpy(key, newkey); line[0] = '_'; } qfits_header_append(outhdr, key, val, comment, line); } qfits_header_destroy(wcshdr); wcshdr = NULL; qfits_header_append(outhdr, "COMMENT", "", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "--End of Astrometry.net WCS--", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "--(Put in by the new-wcs program)--", NULL, NULL); qfits_header_append(outhdr, "COMMENT", "", NULL, NULL); qfits_header_append(outhdr, "END", NULL, NULL, NULL); if (qfits_header_dump(outhdr, outfid) || fits_pad_file(outfid)) { SYSERROR("Failed to write output header to file %s", outfn); goto bailout; } qfits_header_destroy(outhdr); outhdr = NULL; if (copydata) { int datsize, datstart; FILE* infid = NULL; anqfits_t* anq = NULL; anq = anqfits_open(infn); if (!anq) { ERROR("Failed to open file \"%s\"", infn); goto bailout; } datstart = anqfits_data_start(anq, extension); datsize = anqfits_data_size (anq, extension); infid = fopen(infn, "rb"); if (!infid) { SYSERROR("Failed to open input file \"%s\"", infn); anqfits_close(anq); goto bailout; } logverb("Copying from offset %i to offset %i (length %i) of the input file to the output.\n", datstart, datstart + datsize, datsize); if (pipe_file_offset(infid, datstart, datsize, outfid)) { ERROR("Failed to copy the data block"); fclose(infid); anqfits_close(anq); goto bailout; } fclose(infid); if (fits_pad_file(outfid)) { ERROR("Failed to pad FITS file \"%s\"", outfn); anqfits_close(anq); goto bailout; } anqfits_close(anq); anq = NULL; } if (fclose(outfid)) { SYSERROR("Failed to close output file \"%s\"", outfn); goto bailout; } // Free regular expressions... for (e=0; e<NE1; e++) regfree(re1 + e); for (e=0; e<NE2; e++) regfree(re2 + e); return 0; bailout: if (outfid) fclose(outfid); if (inhdr) qfits_header_destroy(inhdr); if (outhdr) qfits_header_destroy(outhdr); if (wcshdr) qfits_header_destroy(wcshdr); for (i=0; i<n1; i++) regfree(re1 + i); for (i=0; i<n2; i++) regfree(re2 + i); return -1; }
int main(int argc, char *argv[]) { int argchar; char* infn = NULL; char* outfn = NULL; anbool tostdout = FALSE; FILE* fin = NULL; FILE* fout = NULL; il* exts; il* sizes; int i; char* progname = argv[0]; int Next; anqfits_t* anq; exts = il_new(16); sizes = il_new(16); while ((argchar = getopt (argc, argv, OPTIONS)) != -1) switch (argchar) { case 'e': il_append(exts, atoi(optarg)); break; case 's': il_append(sizes, atoi(optarg)); break; case 'i': infn = optarg; break; case 'o': outfn = optarg; break; case '?': case 'h': printHelp(progname); return 0; default: return -1; } log_init(LOG_MSG); if (!infn || !outfn || !il_size(exts) || (il_size(exts) != il_size(sizes))) { printHelp(progname); exit(-1); } if (infn) { fin = fopen(infn, "rb"); if (!fin) { SYSERROR("Failed to open input file %s", infn); exit(-1); } } anq = anqfits_open(infn); if (!anq) { ERROR("Failed to open input file %s", infn); exit(-1); } Next = anqfits_n_ext(anq); if (Next == -1) { ERROR("Couldn't determine how many extensions are in file %s", infn); exit(-1); } else { logverb("File %s contains %i FITS extensions.\n", infn, Next); } for (i=0; i<il_size(exts); i++) { int e = il_get(exts, i); int s = il_get(sizes, i); if (e < 0 || e >= Next) { logerr("Extension %i is not valid: must be in [%i, %i]\n", e, 0, Next); exit(-1); } if (s != 2 && s != 4 && s != 8) { logerr("Invalid byte size %i: must be 2, 4, or 8.\n", s); exit(-1); } } if (!strcmp(outfn, "-")) tostdout = TRUE; if (tostdout) fout = stdout; else { fout = fopen(outfn, "wb"); if (!fout) { SYSERROR("Failed to open output file %s", outfn); exit(-1); } } for (i=0; i<Next; i++) { int hdrstart, hdrlen, datastart, datalen; int ind; int size; ind = il_index_of(exts, i); if (ind == -1) { size = 0; } else { size = il_get(sizes, ind); } hdrstart = anqfits_header_start(anq, i); hdrlen = anqfits_header_size (anq, i); datastart = anqfits_data_start(anq, i); datalen = anqfits_data_size (anq, i); if (hdrlen) { if (pipe_file_offset(fin, hdrstart, hdrlen, fout)) { ERROR("Failed to write header for extension %i", i); exit(-1); } } if (!datalen) continue; if (size) { int Nitems = datalen / size; int j; char buf[size]; logmsg("Extension %i: flipping words of length %i bytes.\n", i, size); for (j=0; j<Nitems; j++) { if (fread(buf, size, 1, fin) != 1) { SYSERROR("Failed to read data element %i from extension %i", j, i); exit(-1); } endian_swap(buf, size); if (fwrite(buf, size, 1, fout) != 1) { SYSERROR("Failed to write data element %i to extension %i", j, i); exit(-1); } } } else { logmsg("Extension %i: copying verbatim.\n", i); // passthrough if (pipe_file_offset(fin, datastart, datalen, fout)) { ERROR("Failed to write data for extension %i", i); exit(-1); } } } fclose(fin); anqfits_close(anq); if (!tostdout) fclose(fout); il_free(exts); il_free(sizes); return 0; }