static
fitstable_t* _fitstable_open(const char* fn) {
fitstable_t* tab;
tab = fitstable_new();
if (!tab) {
ERROR("Failed to allocate new FITS table structure");
goto bailout;
}
tab->extension = 1;
tab->fn = strdup_safe(fn);
tab->anq = anqfits_open(fn);
if (!tab->anq) {
ERROR("Failed to open FITS file \"%s\"", fn);
goto bailout;
}
tab->primheader = anqfits_get_header(tab->anq, 0);
if (!tab->primheader) {
ERROR("Failed to read primary FITS header from %s", fn);
goto bailout;
}
return tab;
bailout:
if (tab) {
fitstable_close(tab);
}
return NULL;
}
qfits_header* anqfits_get_header_only(const char* fn, int ext) {
qfits_header* hdr;
anqfits_t* anq = anqfits_open_hdu(fn, ext);
if (!anq) {
qfits_error("Failed to read FITS file \"%s\" to extension %i", fn, ext);
return NULL;
}
hdr = anqfits_get_header(anq, ext);
anqfits_close(anq);
return hdr;
}
qfits_header* anqfits_get_header2(const char* fn, int ext) {
qfits_header* hdr;
anqfits_t* anq = anqfits_open(fn);
if (!anq) {
qfits_error("Failed to read FITS file \"%s\"", fn);
return NULL;
}
hdr = anqfits_get_header(anq, ext);
anqfits_close(anq);
return hdr;
}
int fitstable_open_extension(fitstable_t* tab, int ext) {
if (in_memory(tab)) {
fitsext_t* theext;
if (ext > bl_size(tab->extensions)) {
ERROR("Table has only %zu extensions, but you requested #%i",
bl_size(tab->extensions), ext);
return -1;
}
theext = bl_access(tab->extensions, ext-1);
tab->table = theext->table;
tab->header = theext->header;
tab->rows = theext->rows;
tab->extension = ext;
} else {
if (tab->table) {
qfits_table_close(tab->table);
tab->table = NULL;
}
assert(tab->anq);
if (ext >= anqfits_n_ext(tab->anq)) {
ERROR("Requested FITS extension %i in file %s, but there are only %i extensions.\n", ext, tab->fn, anqfits_n_ext(tab->anq));
return -1;
}
tab->table = anqfits_get_table(tab->anq, ext);
if (!tab->table) {
ERROR("FITS extension %i in file %s is not a table (or there was an error opening the file)", ext, tab->fn);
return -1;
}
if (tab->header) {
qfits_header_destroy(tab->header);
}
tab->header = anqfits_get_header(tab->anq, ext);
if (!tab->header) {
ERROR("Couldn't get header for FITS extension %i in file %s", ext, tab->fn);
return -1;
}
tab->extension = ext;
}
return 0;
}
int main(int argc, char *argv[]) {
int argchar;
char* infn = NULL;
char* outfn = NULL;
FILE* fin = NULL;
FILE* fout = NULL;
pl* cols;
char* progname = argv[0];
int nextens;
int ext;
int NC;
int start, size;
anqfits_t* anq = NULL;
qfits_table* outtable;
unsigned char* buffer;
cols = pl_new(16);
while ((argchar = getopt (argc, argv, OPTIONS)) != -1)
switch (argchar) {
case 'c':
pl_append(cols, optarg);
break;
case 'i':
infn = optarg;
break;
case 'o':
outfn = optarg;
break;
case '?':
case 'h':
printHelp(progname);
return 0;
default:
return -1;
}
if (!infn || !outfn || !pl_size(cols)) {
printHelp(progname);
exit(-1);
}
fin = fopen(infn, "rb");
if (!fin) {
ERROR("Failed to open input file %s: %s\n", infn, strerror(errno));
exit(-1);
}
fout = fopen(outfn, "wb");
if (!fout) {
ERROR("Failed to open output file %s: %s\n", outfn, strerror(errno));
exit(-1);
}
// copy the main header exactly.
anq = anqfits_open(infn);
if (!anq) {
ERROR("Failed to read \"%s\"", infn);
exit(-1);
}
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 header.\n");
exit(-1);
}
NC = pl_size(cols);
nextens = anqfits_n_ext(anq);
printf("Translating %i extensions.\n", nextens);
buffer = NULL;
for (ext=1; ext<nextens; ext++) {
int c2, c;
int columns[NC];
int sizes[NC];
int offsets[NC];
int offset = 0;
int off, n;
int totalsize = 0;
const int BLOCK=1000;
qfits_table* table;
qfits_header* header;
qfits_header* tablehdr;
if (ext%100 == 0) {
printf("Extension %i.\n", ext);
fflush(stdout);
}
if (!anqfits_is_table(anq, ext)) {
ERROR("extention %i isn't a table.\n", ext);
// HACK - just copy it.
return -1;
}
table = anqfits_get_table(anq, ext);
if (!table) {
ERROR("failed to open table: file %s, extension %i.\n", infn, ext);
return -1;
}
header = anqfits_get_header(anq, ext);
if (!header) {
ERROR("failed to read header: extension %i\n", ext);
exit(-1);
}
outtable = qfits_table_new(outfn, QFITS_BINTABLE, 0, NC, table->nr);
outtable->tab_w = 0;
for (c=0; c<pl_size(cols); c++) {
columns[c] = -1;
}
for (c=0; c<pl_size(cols); c++) {
char* colname = pl_get(cols, c);
qfits_col* col;
c2 = fits_find_column(table, colname);
if (c2 == -1) {
ERROR("Extension %i: failed to find column named %s\n",
ext, colname);
exit(-1);
}
col = table->col + c2;
columns[c] = c2;
sizes[c] = col->atom_nb * col->atom_size;
offsets[c] = offset;
offset += sizes[c];
qfits_col_fill(outtable->col + c,
col->atom_nb, col->atom_dec_nb,
col->atom_size, col->atom_type,
col->tlabel, col->tunit,
col->nullval, col->tdisp,
col->zero_present,
col->zero,
col->scale_present,
col->scale,
outtable->tab_w);
outtable->tab_w += sizes[c];
}
totalsize = offset;
tablehdr = qfits_table_ext_header_default(outtable);
// add any headers from the original table that aren't part of the BINTABLE extension.
fits_copy_non_table_headers(tablehdr, header);
qfits_header_dump(tablehdr, fout);
qfits_header_destroy(tablehdr);
buffer = realloc(buffer, totalsize * BLOCK);
for (off=0; off<table->nr; off+=n) {
if (off + BLOCK > table->nr)
n = table->nr - off;
else
n = BLOCK;
for (c=0; c<pl_size(cols); c++)
qfits_query_column_seq_to_array_no_endian_swap
(table, columns[c], off, n, buffer + offsets[c], totalsize);
if (fwrite(buffer, totalsize, n, fout) != n) {
ERROR("Error writing a block of data: ext %i: %s\n", ext, strerror(errno));
exit(-1);
}
}
qfits_table_close(outtable);
fits_pad_file(fout);
qfits_header_destroy(header);
qfits_table_close(table);
}
free(buffer);
if (fclose(fout)) {
ERROR("Error closing output file: %s\n", strerror(errno));
}
fclose(fin);
anqfits_close(anq);
pl_free(cols);
return 0;
}
