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));
176 for (i = x1; i <= x2; i++) {
178 for (j = y1; j <= y2; j++) {
184 if (ix < 1 || ix > (kMuseOutputXRight + 4*kMusePreOverscanSize) ||
185 iy < 1 || iy > (kMuseOutputYTop + 4*kMusePreOverscanSize)) {
186 fprintf(stderr,
"Excluding bad pixel at given %d,%d %s coordinates, as "
187 "it would be outside the MUSE CCD!\n", i, j,
188 trimmedcoords ?
"trimmed" :
"raw");
191 cpl_table_set_int(table, MUSE_BADPIX_X, irow, ix);
192 cpl_table_set_int(table, MUSE_BADPIX_Y, irow, iy);
193 cpl_table_set_int(table, MUSE_BADPIX_DQ, irow++, dqvalue);
196 cpl_table_set_size(table, irow);
197 printf(
"%"CPL_SIZE_FORMAT
" bad pixel%s created from region %s\n", irow,
198 irow != 1 ?
"s" :
"", region);
199 if (cpl_msg_get_level() == CPL_MSG_DEBUG) {
200 printf(
"first 10 entries of the new table, as converted from region:\n");
201 cpl_table_dump(table, 0, 10, stdout);
208 cpl_propertylist *htest = cpl_propertylist_load(tiname, 0);
210 cpl_propertylist_delete(htest);
212 printf(
"WARNING: could not open input table \"%s\"!\n", tiname);
218 char *chan = cpl_sprintf(
"CHAN%02hhu", nifu);
219 cpl_table *intable = NULL;
222 cpl_errorstate state = cpl_errorstate_get();
225 cpl_errorstate_set(state);
232 cpl_boolean savedsomething = rc == CPL_ERROR_NONE;
235 inext = cpl_fits_find_extension(toname, chan);
237 cpl_propertylist *pheader = NULL,
240 printf(
"WARNING: no pre-existing data, creating minimal header from "
242 pheader = cpl_propertylist_new();
243 cpl_propertylist_append_string(pheader,
"TELESCOP",
"ESO-VLT-U4");
244 cpl_propertylist_append_string(pheader,
"INSTRUME",
"MUSE");
245 cpl_propertylist_append_string(pheader,
"OBJECT",
246 "Bad pixel table for MUSE (BADPIX_TABLE)");
247 header = cpl_propertylist_new();
248 cpl_propertylist_append_string(header,
"EXTNAME", chan);
249 cpl_propertylist_append_string(header,
"ESO DET CHIP NAME", chan);
251 printf(
"Using primary header from \"%s\" as starting point\n", riname);
252 pheader = cpl_propertylist_load_regexp(riname, 0,
"TELESCOP|INSTRUME|"
256 cpl_propertylist_erase_regexp(pheader,
"ESO DET DEV[0-9] (SHUT |EXP )|"
257 "ESO DET (EXP |[DU]IT|NDIT|DKTM)", 0);
258 cpl_propertylist_erase_regexp(pheader,
"ESO DET (CHIP |OUT[1-4])", 0);
259 cpl_propertylist_update_string(pheader,
"OBJECT",
260 "Bad pixel table for MUSE (BADPIX_TABLE)");
261 int refext = cpl_fits_find_extension(riname, extname);
263 printf(
"Using extension header from \"%s[%s]\" (%d)\n", riname, extname,
265 header = cpl_propertylist_load_regexp(riname, refext,
266 "^EXT|ESO DET (CHIP |OUT[1-4])", 0);
268 printf(
"WARNING: no pre-existing extension found, creating minimal "
269 "extension header from scratch!\n");
270 header = cpl_propertylist_new();
271 cpl_propertylist_append_string(header,
"EXTNAME", chan);
272 cpl_propertylist_append_string(header,
"ESO DET CHIP NAME", chan);
275 if (savedsomething) {
277 rc = cpl_table_save(table, NULL, header, toname, CPL_IO_EXTEND);
280 cpl_propertylist_update_string(pheader,
"PIPEFILE", toname);
281 cpl_propertylist_set_comment(pheader,
"PIPEFILE",
282 "pretend to be a pipeline output file");
283 cpl_propertylist_update_string(pheader,
"ESO PRO CATG", MUSE_TAG_BADPIX_TABLE);
284 cpl_propertylist_set_comment(pheader,
"ESO PRO CATG",
285 "MUSE bad pixel table");
286 rc = cpl_table_save(table, pheader, header, toname, CPL_IO_CREATE);
288 if (rc != CPL_ERROR_NONE) {
289 fprintf(stderr,
"Saving to \"%s\" failed (rc=%d): %s\n", toname, rc,
290 cpl_error_get_message());
292 printf(
"Saved to \"%s\" (%s)\n", toname,
293 savedsomething ?
"new extension" :
"new file");
295 cpl_propertylist_delete(pheader);
296 cpl_propertylist_delete(header);
299 cpl_table_delete(table);
301 if (cpl_msg_get_level() == CPL_MSG_DEBUG) {
302 printf(
"Output file \"%s\" has primary header and %"CPL_SIZE_FORMAT
303 " extensions\n", toname, cpl_fits_count_extensions(toname));
304 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.