25 #include <muse_instrument.h>
26 #include "muse_data_format_z.h"
83 #define PRINT_USAGE(rc) \
84 fprintf(stderr, "Usage: %s [ -i INTABLE ] [ -r REFIMAGE [ -n extname ] ] " \
85 "[ -t ] REGION DQVAL IFUNUM OUTTABLE\n", argv[0]); \
86 cpl_end(); return (rc);
88 int main(
int argc,
char **argv)
94 cpl_init(CPL_INIT_DEFAULT);
95 if (getenv(
"ESOREX_MSG_LEVEL") && !strncmp(getenv(
"ESOREX_MSG_LEVEL"),
97 cpl_msg_set_level(CPL_MSG_DEBUG);
106 unsigned char nifu = 0;
107 cpl_boolean trimmedcoords = CPL_FALSE;
111 for (i = 1; i < argc; i++) {
112 if (strncmp(argv[i],
"-i", 3) == 0) {
120 }
else if (strncmp(argv[i],
"-r", 3) == 0) {
128 }
else if (strncmp(argv[i],
"-n", 3) == 0) {
136 }
else if (strncmp(argv[i],
"-t", 3) == 0) {
138 trimmedcoords = CPL_TRUE;
139 }
else if (strncmp(argv[i],
"-", 1) == 0) {
142 if (region && dqvalue && toname) {
147 }
else if (!dqvalue) {
148 dqvalue = atol(argv[i]);
149 }
else if (nifu == 0) {
150 int ifunum = atoi(argv[i]);
151 if (ifunum < 1 || ifunum > kMuseNumIFUs) {
163 n = sscanf(region,
"[%d:%d,%d:%d]", &x1, &x2, &y1, &y2);
171 printf(
"Converting coordinates from trimmed to raw data dimensions\n");
174 (x2-x1+1) * (y2-y1+1));
175 cpl_size irow = 0, nrow = cpl_table_get_nrow(table);
176 for (i = x1; i <= x2; i++) {
178 for (j = y1; j <= y2; j++) {
184 cpl_table_set_int(table, MUSE_BADPIX_X, irow, ix);
185 cpl_table_set_int(table, MUSE_BADPIX_Y, irow, iy);
186 cpl_table_set_int(table, MUSE_BADPIX_DQ, irow++, dqvalue);
189 printf(
"%"CPL_SIZE_FORMAT
" bad pixel%s created from region %s\n", nrow,
190 nrow != 1 ?
"s" :
"", region);
191 if (cpl_msg_get_level() == CPL_MSG_DEBUG) {
192 printf(
"first 10 entries of the new table, as converted from region:\n");
193 cpl_table_dump(table, 0, 10, stdout);
200 cpl_propertylist *htest = cpl_propertylist_load(tiname, 0);
202 cpl_propertylist_delete(htest);
204 printf(
"WARNING: could not open input table \"%s\"!\n", tiname);
210 char *chan = cpl_sprintf(
"CHAN%02hhu", nifu);
211 cpl_table *intable = NULL;
214 cpl_errorstate state = cpl_errorstate_get();
217 cpl_errorstate_set(state);
224 cpl_boolean savedsomething = rc == CPL_ERROR_NONE;
227 inext = cpl_fits_find_extension(toname, chan);
229 cpl_propertylist *pheader = NULL,
232 printf(
"WARNING: no pre-existing data, creating minimal header from "
234 pheader = cpl_propertylist_new();
235 cpl_propertylist_append_string(pheader,
"TELESCOP",
"ESO-VLT-U4");
236 cpl_propertylist_append_string(pheader,
"INSTRUME",
"MUSE");
237 cpl_propertylist_append_string(pheader,
"OBJECT",
238 "Bad pixel table for MUSE (BADPIX_TABLE)");
239 header = cpl_propertylist_new();
240 cpl_propertylist_append_string(header,
"EXTNAME", chan);
241 cpl_propertylist_append_string(header,
"ESO DET CHIP NAME", chan);
243 printf(
"Using primary header from \"%s\" as starting point\n", riname);
244 pheader = cpl_propertylist_load_regexp(riname, 0,
"TELESCOP|INSTRUME|"
248 cpl_propertylist_erase_regexp(pheader,
"ESO DET DEV[0-9] (SHUT |EXP )|"
249 "ESO DET (EXP |[DU]IT|NDIT|DKTM)", 0);
250 cpl_propertylist_erase_regexp(pheader,
"ESO DET (CHIP |OUT[1-4])", 0);
251 cpl_propertylist_update_string(pheader,
"OBJECT",
252 "Bad pixel table for MUSE (BADPIX_TABLE)");
253 int refext = cpl_fits_find_extension(riname, extname);
255 printf(
"Using extension header from \"%s[%s]\" (%d)\n", riname, extname,
257 header = cpl_propertylist_load_regexp(riname, refext,
258 "^EXT|ESO DET (CHIP |OUT[1-4])", 0);
260 printf(
"WARNING: no pre-existing extension found, creating minimal "
261 "extension header from scratch!\n");
262 header = cpl_propertylist_new();
263 cpl_propertylist_append_string(header,
"EXTNAME", chan);
264 cpl_propertylist_append_string(header,
"ESO DET CHIP NAME", chan);
267 if (savedsomething) {
269 rc = cpl_table_save(table, NULL, header, toname, CPL_IO_EXTEND);
272 cpl_propertylist_update_string(pheader,
"PIPEFILE", toname);
273 cpl_propertylist_set_comment(pheader,
"PIPEFILE",
274 "pretend to be a pipeline output file");
275 cpl_propertylist_update_string(pheader,
"ESO PRO CATG", MUSE_TAG_BADPIX_TABLE);
276 cpl_propertylist_set_comment(pheader,
"ESO PRO CATG",
277 "MUSE bad pixel table");
278 rc = cpl_table_save(table, pheader, header, toname, CPL_IO_CREATE);
280 if (rc != CPL_ERROR_NONE) {
281 fprintf(stderr,
"Saving to \"%s\" failed (rc=%d): %s\n", toname, rc,
282 cpl_error_get_message());
284 printf(
"Saved to \"%s\" (%s)\n", toname,
285 savedsomething ?
"new extension" :
"new file");
287 cpl_propertylist_delete(pheader);
288 cpl_propertylist_delete(header);
291 cpl_table_delete(table);
293 if (cpl_msg_get_level() == CPL_MSG_DEBUG) {
294 printf(
"Output file \"%s\" has primary header and %"CPL_SIZE_FORMAT
295 " extensions\n", toname, cpl_fits_count_extensions(toname));
296 cpl_errorstate_dump(0, CPL_FALSE, NULL);
cpl_error_code muse_quality_copy_badpix_table(const char *aInFile, const char *aOutFile, int aExtension, const cpl_table *aTable)
Copy bad pixel table on disk, replacing the table in one extension.
cpl_table * muse_quality_merge_badpix_from_file(const cpl_table *aTable, const char *aInFile, const char *aExtname, int *aExt)
Merge bad pixel table in memory with table from file on disk.
cpl_table * muse_cpltable_new(const muse_cpltable_def *aDef, cpl_size aLength)
Create an empty table according to the specified definition.
cpl_error_code muse_quadrants_coords_to_raw(cpl_propertylist *aHeader, int *aX, int *aY)
Convert coordinates of a trimmed image to raw-image coordinates.