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;
}
