fors_detect_spectra.c

00001 /* $Id: fors_detect_spectra.c,v 1.11 2013-10-09 15:59:38 cgarcia Exp $
00002  *
00003  * This file is part of the FORS Data Reduction Pipeline
00004  * Copyright (C) 2002-2010 European Southern Observatory
00005  *
00006  * This program is free software; you can redistribute it and/or modify
00007  * it under the terms of the GNU General Public License as published by
00008  * the Free Software Foundation; either version 2 of the License, or
00009  * (at your option) any later version.
00010  *
00011  * This program is distributed in the hope that it will be useful,
00012  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00013  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00014  * GNU General Public License for more details.
00015  *
00016  * You should have received a copy of the GNU General Public License
00017  * along with this program; if not, write to the Free Software
00018  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
00019  */
00020 
00021 /*
00022  * $Author: cgarcia $
00023  * $Date: 2013-10-09 15:59:38 $
00024  * $Revision: 1.11 $
00025  * $Name: not supported by cvs2svn $
00026  */
00027 
00028 #ifdef HAVE_CONFIG_H
00029 #include <config.h>
00030 #endif
00031 
00032 #include <math.h>
00033 #include <cpl.h>
00034 #include <moses.h>
00035 #include <fors_dfs.h>
00036 
00037 static int fors_detect_spectra_create(cpl_plugin *);
00038 static int fors_detect_spectra_exec(cpl_plugin *);
00039 static int fors_detect_spectra_destroy(cpl_plugin *);
00040 static int fors_detect_spectra(cpl_parameterlist *, cpl_frameset *);
00041 
00042 static char fors_detect_spectra_description[] =
00043 "This recipe is used to detect and locate MOS/MXU slit spectra on the CCD,\n"
00044 "applying a pattern-matching algorithm. The input spectral exposure must\n"
00045 "contain spectra with the dispersion direction approximately horizontal,\n"
00046 "with blue on the left and red on the right. Use recipe fors_wave_calib_lss\n"
00047 "for LSS data, or for MOS/MXU data where all slits have the same offset.\n"
00048 "\n"
00049 "The rows of the input spectral exposure are processed separately, one\n"
00050 "by one. First, the background continuum is removed. Second, a list of\n"
00051 "positions of reference lines candidates is created. Only peaks above a\n"
00052 "given threshold (specified by the parameter --peakdetection) are selected.\n"
00053 "Third, the pattern-matching task selects from the found peaks the ones\n"
00054 "corresponding to the reference lines, listed in the input line catalog,\n"
00055 "associating them to the appropriate wavelengths. The ensuing polynomial\n"
00056 "fit is used to locate the central wavelength of the applied grism along\n"
00057 "each image row. The contributions from all rows form an image of the\n"
00058 "location of all spectra, that can be used as a starting point for the\n"
00059 "proper modeling of the optical and spectral distortions. For more details\n"
00060 "on this reduction strategy please refer to the FORS Pipeline User's Manual.\n"
00061 "\n"
00062 "Note that specifying an input GRISM_TABLE will set some of the recipe\n"
00063 "configuration parameters to default values valid for a particular grism.\n"
00064 "Again, see the pipeline manual for more details.\n"
00065 "\n"
00066 "In the table below the MXU acronym can be alternatively read as MOS.\n\n"
00067 "Input files:\n\n"
00068 "  DO category:               Type:       Explanation:         Required:\n"
00069 "  LAMP_UNBIAS_MXU            Calib       Bias subtracted arc     Y\n"
00070 "  MASTER_LINECAT             Calib       Line catalog            Y\n"
00071 "  GRISM_TABLE                Calib       Grism table             .\n\n"
00072 "Output files:\n\n"
00073 "  DO category:               Data type:  Explanation:\n"
00074 "  SLIT_MAP_MXU               FITS image  Map of central wavelength on CCD\n"
00075 "  SLIT_LOCATION_DETECT_MXU   FITS table  Slits positions on CCD\n"
00076 "  SPECTRA_DETECTION_MXU      FITS image  Check of preliminary detection\n\n";
00077 
00078 #define fors_detect_spectra_exit(message)     \
00079 {                                             \
00080 if ((const char *)message != NULL) cpl_msg_error(recipe, message);  \
00081 cpl_image_delete(spectra);                    \
00082 cpl_image_delete(checkwave);                  \
00083 cpl_image_delete(refimage);                   \
00084 cpl_mask_delete(refmask);                     \
00085 cpl_table_delete(grism_table);                \
00086 cpl_table_delete(wavelengths);                \
00087 cpl_table_delete(maskslits);                  \
00088 cpl_table_delete(slits);                      \
00089 cpl_vector_delete(lines);                     \
00090 cpl_propertylist_delete(header);              \
00091 cpl_msg_indent_less();                        \
00092 return -1;                                    \
00093 }
00094 
00095 #define fors_detect_spectra_exit_memcheck(message) \
00096 {                                               \
00097 if ((const char *)message != NULL) cpl_msg_info(recipe, message);     \
00098 printf("free spectra (%p)\n", spectra);         \
00099 cpl_image_delete(spectra);                      \
00100 printf("free checkwave (%p)\n", checkwave);     \
00101 cpl_image_delete(checkwave);                    \
00102 printf("free refimage (%p)\n", refimage);       \
00103 cpl_image_delete(refimage);                     \
00104 printf("free refmask (%p)\n", refmask);         \
00105 cpl_mask_delete(refmask);                       \
00106 printf("free grism_table (%p)\n", grism_table); \
00107 cpl_table_delete(grism_table);                  \
00108 printf("free wavelengths (%p)\n", wavelengths); \
00109 cpl_table_delete(wavelengths);                  \
00110 printf("free maskslits (%p)\n", maskslits);     \
00111 cpl_table_delete(maskslits);                    \
00112 printf("free slits (%p)\n", slits);             \
00113 cpl_table_delete(slits);                        \
00114 printf("free lines (%p)\n", lines);             \
00115 cpl_vector_delete(lines);                       \
00116 printf("free header (%p)\n", header);           \
00117 cpl_propertylist_delete(header);                \
00118 cpl_msg_indent_less();                          \
00119 return 0;                                       \
00120 }
00121 
00122 
00134 int cpl_plugin_get_info(cpl_pluginlist *list)
00135 {
00136     cpl_recipe *recipe = cpl_calloc(1, sizeof *recipe );
00137     cpl_plugin *plugin = &recipe->interface;
00138 
00139     cpl_plugin_init(plugin,
00140                     CPL_PLUGIN_API,
00141                     FORS_BINARY_VERSION,
00142                     CPL_PLUGIN_TYPE_RECIPE,
00143                     "fors_detect_spectra",
00144                     "Detect MOS/MXU spectra on CCD",
00145                     fors_detect_spectra_description,
00146                     "Carlo Izzo",
00147                     PACKAGE_BUGREPORT,
00148     "This file is currently part of the FORS Instrument Pipeline\n"
00149     "Copyright (C) 2002-2010 European Southern Observatory\n\n"
00150     "This program is free software; you can redistribute it and/or modify\n"
00151     "it under the terms of the GNU General Public License as published by\n"
00152     "the Free Software Foundation; either version 2 of the License, or\n"
00153     "(at your option) any later version.\n\n"
00154     "This program is distributed in the hope that it will be useful,\n"
00155     "but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
00156     "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
00157     "GNU General Public License for more details.\n\n"
00158     "You should have received a copy of the GNU General Public License\n"
00159     "along with this program; if not, write to the Free Software Foundation,\n"
00160     "Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA\n",
00161                     fors_detect_spectra_create,
00162                     fors_detect_spectra_exec,
00163                     fors_detect_spectra_destroy);
00164 
00165     cpl_pluginlist_append(list, plugin);
00166     
00167     return 0;
00168 }
00169 
00170 
00181 static int fors_detect_spectra_create(cpl_plugin *plugin)
00182 {
00183     cpl_recipe    *recipe;
00184     cpl_parameter *p;
00185 
00186     /* 
00187      * Check that the plugin is part of a valid recipe 
00188      */
00189 
00190     if (cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE) 
00191         recipe = (cpl_recipe *)plugin;
00192     else 
00193         return -1;
00194 
00195     /* 
00196      * Create the (empty) parameters list in the cpl_recipe object 
00197      */
00198 
00199     recipe->parameters = cpl_parameterlist_new(); 
00200 
00201     /*
00202      * Dispersion
00203      */
00204 
00205     p = cpl_parameter_new_value("fors.fors_detect_spectra.dispersion",
00206                                 CPL_TYPE_DOUBLE,
00207                                 "Expected spectral dispersion (Angstrom/pixel)",
00208                                 "fors.fors_detect_spectra",
00209                                 0.0);
00210     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "dispersion");
00211     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00212     cpl_parameterlist_append(recipe->parameters, p);
00213 
00214     /*
00215      * Peak detection level
00216      */
00217 
00218     p = cpl_parameter_new_value("fors.fors_detect_spectra.peakdetection",
00219                                 CPL_TYPE_DOUBLE,
00220                                 "Initial peak detection threshold (ADU)",
00221                                 "fors.fors_detect_spectra",
00222                                 0.0);
00223     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "peakdetection");
00224     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00225     cpl_parameterlist_append(recipe->parameters, p);
00226 
00227     /*
00228      * Degree of wavelength calibration polynomial
00229      */
00230 
00231     p = cpl_parameter_new_value("fors.fors_detect_spectra.wdegree",
00232                                 CPL_TYPE_INT,
00233                                 "Degree of wavelength calibration polynomial",
00234                                 "fors.fors_detect_spectra",
00235                                 0);
00236     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "wdegree");
00237     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00238     cpl_parameterlist_append(recipe->parameters, p);
00239 
00240     /*
00241      * Reference lines search radius
00242      */
00243 
00244     p = cpl_parameter_new_value("fors.fors_detect_spectra.wradius",
00245                                 CPL_TYPE_INT,
00246                                 "Search radius if iterating pattern-matching "
00247                                 "with first-guess method",
00248                                 "fors.fors_detect_spectra",
00249                                 4);
00250     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "wradius");
00251     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00252     cpl_parameterlist_append(recipe->parameters, p);
00253 
00254     /*
00255      * Rejection threshold in dispersion relation polynomial fitting
00256      */
00257 
00258     p = cpl_parameter_new_value("fors.fors_detect_spectra.wreject",
00259                                 CPL_TYPE_DOUBLE,
00260                                 "Rejection threshold in dispersion "
00261                                 "relation fit (pixel)",
00262                                 "fors.fors_detect_spectra",
00263                                 0.7);
00264     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "wreject");
00265     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00266     cpl_parameterlist_append(recipe->parameters, p);
00267 
00268     /*
00269      * Line catalog table column containing the reference wavelengths
00270      */
00271 
00272     p = cpl_parameter_new_value("fors.fors_detect_spectra.wcolumn",
00273                                 CPL_TYPE_STRING,
00274                                 "Name of line catalog table column "
00275                                 "with wavelengths",
00276                                 "fors.fors_detect_spectra",
00277                                 "WLEN");
00278     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "wcolumn");
00279     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00280     cpl_parameterlist_append(recipe->parameters, p);
00281 
00282     /*
00283      * Start wavelength for spectral extraction
00284      */
00285 
00286     p = cpl_parameter_new_value("fors.fors_detect_spectra.startwavelength",
00287                                 CPL_TYPE_DOUBLE,
00288                                 "Start wavelength in spectral extraction",
00289                                 "fors.fors_detect_spectra",
00290                                 0.0);
00291     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "startwavelength");
00292     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00293     cpl_parameterlist_append(recipe->parameters, p);
00294 
00295     /*
00296      * End wavelength for spectral extraction
00297      */
00298 
00299     p = cpl_parameter_new_value("fors.fors_detect_spectra.endwavelength",
00300                                 CPL_TYPE_DOUBLE,
00301                                 "End wavelength in spectral extraction",
00302                                 "fors.fors_detect_spectra",
00303                                 0.0);
00304     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "endwavelength");
00305     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00306     cpl_parameterlist_append(recipe->parameters, p);
00307 
00308     /*
00309      * Try slit identification
00310      */
00311 
00312     p = cpl_parameter_new_value("fors.fors_detect_spectra.slit_ident",
00313                                 CPL_TYPE_BOOL,
00314                                 "Attempt slit identification for MOS or MXU",
00315                                 "fors.fors_detect_spectra",
00316                                 TRUE);
00317     cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "slit_ident");
00318     cpl_parameter_disable(p, CPL_PARAMETER_MODE_ENV);
00319     cpl_parameterlist_append(recipe->parameters, p);
00320 
00321 
00322     return 0;
00323 }
00324 
00325 
00334 static int fors_detect_spectra_exec(cpl_plugin *plugin)
00335 {
00336     cpl_recipe *recipe;
00337     
00338     if (cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE) 
00339         recipe = (cpl_recipe *)plugin;
00340     else 
00341         return -1;
00342 
00343     return fors_detect_spectra(recipe->parameters, recipe->frames);
00344 }
00345 
00346 
00355 static int fors_detect_spectra_destroy(cpl_plugin *plugin)
00356 {
00357     cpl_recipe *recipe;
00358     
00359     if (cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE) 
00360         recipe = (cpl_recipe *)plugin;
00361     else 
00362         return -1;
00363 
00364     cpl_parameterlist_delete(recipe->parameters); 
00365 
00366     return 0;
00367 }
00368 
00369 
00379 static int fors_detect_spectra(cpl_parameterlist *parlist, 
00380                                cpl_frameset *frameset)
00381 {
00382 
00383     const char *recipe = "fors_detect_spectra";
00384 
00385 
00386     /*
00387      * Input parameters
00388      */
00389 
00390     double      dispersion;
00391     double      peakdetection;
00392     int         wdegree;
00393     int         wradius;
00394     double      wreject;
00395     const char *wcolumn;
00396     double      startwavelength;
00397     double      endwavelength;
00398     int         slit_ident;
00399 
00400     /*
00401      * CPL objects
00402      */
00403 
00404     cpl_image        *spectra     = NULL;
00405     cpl_image        *checkwave   = NULL;
00406     cpl_image        *refimage    = NULL;
00407     cpl_mask         *refmask     = NULL;
00408     cpl_table        *grism_table = NULL;
00409     cpl_table        *wavelengths = NULL;
00410     cpl_table        *slits       = NULL;
00411     cpl_table        *positions   = NULL;
00412     cpl_table        *maskslits   = NULL;
00413     cpl_vector       *lines       = NULL;
00414     cpl_propertylist *header      = NULL;
00415 
00416     /*
00417      * Auxiliary variables
00418      */
00419 
00420     char        version[80];
00421     const char *arc_tag;
00422     const char *spectra_detection_tag;
00423     const char *slit_map_tag;
00424     const char *slit_location_tag;
00425     int         lamp_mxu;
00426     int         lamp_mos;
00427     int         lamp_lss;
00428     int         mos;
00429     int         treat_as_lss = 0;
00430     int         nslits;
00431     double      mxpos;
00432     int         narc;
00433     int         nlines;
00434     int         rebin;
00435     double     *line;
00436     int         nx, ny;
00437     double      reference;
00438     int         i;
00439     int         nslits_out_det = 0;
00440 
00441     char       *instrume = NULL;
00442 
00443 
00444     cpl_msg_set_indentation(2);
00445 
00446     /*
00447      * Get configuration parameters
00448      */
00449 
00450     cpl_msg_info(recipe, "Recipe %s configuration parameters:", recipe);
00451     cpl_msg_indent_more();
00452     
00453     if (cpl_frameset_count_tags(frameset, "GRISM_TABLE") > 1)
00454         fors_detect_spectra_exit("Too many in input: GRISM_TABLE"); 
00455 
00456     grism_table = dfs_load_table(frameset, "GRISM_TABLE", 1);
00457 
00458     dispersion = dfs_get_parameter_double(parlist,
00459                     "fors.fors_detect_spectra.dispersion", grism_table);
00460 
00461     if (dispersion <= 0.0)
00462         fors_detect_spectra_exit("Invalid spectral dispersion value");
00463 
00464     peakdetection = dfs_get_parameter_double(parlist,
00465                     "fors.fors_detect_spectra.peakdetection", grism_table);
00466     if (peakdetection <= 0.0)
00467         fors_detect_spectra_exit("Invalid peak detection level");
00468 
00469     wdegree = dfs_get_parameter_int(parlist,
00470                     "fors.fors_detect_spectra.wdegree", grism_table);
00471 
00472     if (wdegree < 1)
00473         fors_detect_spectra_exit("Invalid polynomial degree");
00474 
00475     if (wdegree > 5)
00476         fors_detect_spectra_exit("Max allowed polynomial degree is 5");
00477 
00478     wradius = dfs_get_parameter_int(parlist, 
00479                                     "fors.fors_detect_spectra.wradius", NULL);
00480 
00481     if (wradius < 0)
00482         fors_detect_spectra_exit("Invalid search radius");
00483 
00484     wreject = dfs_get_parameter_double(parlist, 
00485                                     "fors.fors_detect_spectra.wreject", NULL);
00486 
00487     if (wreject <= 0.0)
00488         fors_detect_spectra_exit("Invalid rejection threshold");
00489 
00490     wcolumn = dfs_get_parameter_string(parlist, 
00491                                     "fors.fors_detect_spectra.wcolumn", NULL);
00492 
00493     startwavelength = dfs_get_parameter_double(parlist,
00494                     "fors.fors_detect_spectra.startwavelength", grism_table);
00495     if (startwavelength > 1.0)
00496         if (startwavelength < 3000.0 || startwavelength > 13000.0)
00497             fors_detect_spectra_exit("Invalid wavelength");
00498 
00499     endwavelength = dfs_get_parameter_double(parlist,
00500                     "fors.fors_detect_spectra.endwavelength", grism_table);
00501     if (endwavelength > 1.0) {
00502         if (endwavelength < 3000.0 || endwavelength > 13000.0)
00503             fors_detect_spectra_exit("Invalid wavelength");
00504         if (startwavelength < 1.0)
00505             fors_detect_spectra_exit("Invalid wavelength interval");
00506     }
00507 
00508     if (startwavelength > 1.0)
00509         if (endwavelength - startwavelength <= 0.0)
00510             fors_detect_spectra_exit("Invalid wavelength interval");
00511 
00512     slit_ident = dfs_get_parameter_bool(parlist,
00513                     "fors.fors_detect_spectra.slit_ident", NULL);
00514 
00515     cpl_table_delete(grism_table); grism_table = NULL;
00516 
00517     if (cpl_error_get_code())
00518         fors_detect_spectra_exit("Failure reading the "
00519                                  "configuration parameters");
00520 
00521 
00522     cpl_msg_indent_less();
00523     cpl_msg_info(recipe, "Check input set-of-frames:");
00524     cpl_msg_indent_more();
00525 
00526     narc  = lamp_mxu = cpl_frameset_count_tags(frameset, "LAMP_UNBIAS_MXU");
00527     narc += lamp_mos = cpl_frameset_count_tags(frameset, "LAMP_UNBIAS_MOS");
00528     narc += lamp_lss = cpl_frameset_count_tags(frameset, "LAMP_UNBIAS_LSS");
00529 
00530     if (narc == 0) {
00531         fors_detect_spectra_exit("Missing input arc lamp frame");
00532     }
00533     if (narc > 1) {
00534         cpl_msg_error(recipe, "Too many input arc lamp frames (%d > 1)", narc);
00535         fors_detect_spectra_exit(NULL);
00536     }
00537 
00538     mos = 0;
00539 
00540     if (lamp_mxu) {
00541         arc_tag               = "LAMP_UNBIAS_MXU";
00542         spectra_detection_tag = "SPECTRA_DETECTION_MXU";
00543         slit_map_tag          = "SLIT_MAP_MXU";
00544         slit_location_tag     = "SLIT_LOCATION_DETECT_MXU";
00545     }
00546     else if (lamp_mos) {
00547         mos = 1;
00548         arc_tag               = "LAMP_UNBIAS_MOS";
00549         spectra_detection_tag = "SPECTRA_DETECTION_MOS";
00550         slit_map_tag          = "SLIT_MAP_MOS";
00551         slit_location_tag     = "SLIT_LOCATION_DETECT_MOS";
00552     }
00553     else if (lamp_lss) {
00554         fors_detect_spectra_exit("Use recipe fors_wave_calib_lss "
00555                                  "for LSS data reduction");
00556     }
00557 
00558 
00559     if (cpl_frameset_count_tags(frameset, "MASTER_LINECAT") == 0)
00560         fors_detect_spectra_exit("Missing required input: MASTER_LINECAT");
00561 
00562     if (cpl_frameset_count_tags(frameset, "MASTER_LINECAT") > 1)
00563         fors_detect_spectra_exit("Too many in input: MASTER_LINECAT");
00564 
00565     if (!dfs_equal_keyword(frameset, "ESO INS GRIS1 ID"))
00566         cpl_msg_warning(cpl_func,"Input frames are not from the same grism");
00567 
00568     if (!dfs_equal_keyword(frameset, "ESO INS FILT1 ID"))
00569         cpl_msg_warning(cpl_func,"Input frames are not from the same filter");
00570 
00571     if (!dfs_equal_keyword(frameset, "ESO DET CHIP1 ID"))
00572         cpl_msg_warning(cpl_func,"Input frames are not from the same chip");
00573 
00574 
00575     /*
00576      * Get the reference wavelength and the rebin factor along the
00577      * dispersion direction from the arc lamp exposure
00578      */
00579 
00580     header = dfs_load_header(frameset, arc_tag, 0);
00581 
00582     if (header == NULL)
00583         fors_detect_spectra_exit("Cannot load arc lamp header");
00584 
00585     instrume = (char *)cpl_propertylist_get_string(header, "INSTRUME");
00586     if (instrume == NULL)
00587         fors_detect_spectra_exit("Missing keyword INSTRUME in arc lamp header");
00588 
00589     if (instrume[4] == '1')
00590         snprintf(version, 80, "%s/%s", "fors1", VERSION);
00591     if (instrume[4] == '2')
00592         snprintf(version, 80, "%s/%s", "fors2", VERSION);
00593 
00594     reference = cpl_propertylist_get_double(header, "ESO INS GRIS1 WLEN");
00595 
00596     if (cpl_error_get_code() != CPL_ERROR_NONE)
00597         fors_detect_spectra_exit("Missing keyword ESO INS GRIS1 WLEN "
00598                                  "in arc lamp frame header");
00599 
00600     if (reference < 3000.0)   /* Perhaps in nanometers... */
00601         reference *= 10;
00602 
00603     if (reference < 3000.0 || reference > 13000.0) {
00604         cpl_msg_error(recipe, "Invalid central wavelength %.2f read from "
00605                       "keyword ESO INS GRIS1 WLEN in arc lamp frame header",
00606                       reference);
00607         fors_detect_spectra_exit(NULL);
00608     }
00609 
00610     cpl_msg_info(recipe, "The central wavelength is: %.2f", reference);
00611 
00612     rebin = cpl_propertylist_get_int(header, "ESO DET WIN1 BINX");
00613 
00614     if (cpl_error_get_code() != CPL_ERROR_NONE)
00615         fors_detect_spectra_exit("Missing keyword ESO DET WIN1 BINX "
00616                                  "in arc lamp frame header");
00617 
00618     if (rebin != 1) {
00619         dispersion *= rebin;
00620         cpl_msg_warning(recipe, "The rebin factor is %d, and therefore the "
00621                         "working dispersion used is %f A/pixel", rebin,
00622                         dispersion);
00623     }
00624 
00625 
00626     cpl_msg_info(recipe, "Produce mask slit position table...");
00627 
00628     if (mos)
00629         maskslits = mos_load_slits_fors_mos(header, &nslits_out_det);
00630     else
00631         maskslits = mos_load_slits_fors_mxu(header);
00632 
00633     cpl_propertylist_delete(header); header = NULL;
00634 
00635 
00636     /*
00637      * Check if all slits have the same X offset: in such case,
00638      * treat the observation as a long-slit one!
00639      */
00640 
00641     treat_as_lss = fors_mos_is_lss_like(maskslits, nslits_out_det);
00642 
00643     if (treat_as_lss) {
00644         cpl_msg_error(recipe, "All slits have the same offset: %.2f mm\n"
00645                       "The LSS data reduction strategy must be applied: "
00646                       "please use recipe fors_wave_calib_lss", mxpos);
00647         fors_detect_spectra_exit(NULL);
00648     }
00649 
00650     if (slit_ident == 0) {
00651         cpl_table_delete(maskslits); maskslits = NULL;
00652     }
00653 
00654 
00655     cpl_msg_indent_less();
00656     cpl_msg_info(recipe, "Load arc lamp exposure...");
00657     cpl_msg_indent_more();
00658 
00659     spectra = dfs_load_image(frameset, arc_tag, CPL_TYPE_FLOAT, 0, 0);
00660 
00661     if (spectra == NULL)
00662         fors_detect_spectra_exit("Cannot load arc lamp exposure");
00663 
00664 
00665     cpl_msg_indent_less();
00666     cpl_msg_info(recipe, "Load input line catalog...");
00667     cpl_msg_indent_more();
00668 
00669     wavelengths = dfs_load_table(frameset, "MASTER_LINECAT", 1);
00670 
00671     if (wavelengths == NULL)
00672         fors_detect_spectra_exit("Cannot load line catalog");
00673 
00674 
00675     /*
00676      * Cast the wavelengths into a (double precision) CPL vector
00677      */
00678 
00679     nlines = cpl_table_get_nrow(wavelengths);
00680 
00681     if (nlines == 0)
00682         fors_detect_spectra_exit("Empty input line catalog");
00683 
00684     if (cpl_table_has_column(wavelengths, wcolumn) != 1) {
00685         cpl_msg_error(recipe, "Missing column %s in input line catalog table",
00686                       wcolumn);
00687         fors_detect_spectra_exit(NULL);
00688     }
00689 
00690     line = cpl_malloc(nlines * sizeof(double));
00691 
00692     for (i = 0; i < nlines; i++)
00693         line[i] = cpl_table_get(wavelengths, wcolumn, i, NULL);
00694 
00695     cpl_table_delete(wavelengths); wavelengths = NULL;
00696 
00697     lines = cpl_vector_wrap(nlines, line);
00698 
00699 
00700     cpl_msg_indent_less();
00701     cpl_msg_info(recipe, "Detecting spectra on CCD...");
00702     cpl_msg_indent_more();
00703 
00704     nx = cpl_image_get_size_x(spectra);
00705     ny = cpl_image_get_size_y(spectra);
00706 
00707     refmask = cpl_mask_new(nx, ny);
00708 
00709     if (mos_saturation_process(spectra))
00710     fors_detect_spectra_exit("Cannot process saturation");
00711 
00712     if (mos_subtract_background(spectra))
00713     fors_detect_spectra_exit("Cannot subtract the background");
00714 
00715     checkwave = mos_wavelength_calibration_raw(spectra, lines, dispersion,
00716                                                peakdetection, wradius,
00717                                                wdegree, wreject, reference,
00718                                                &startwavelength, &endwavelength,
00719                                                NULL, NULL, NULL, NULL, NULL,
00720                                                NULL, refmask, NULL);
00721 
00722     cpl_image_delete(spectra); spectra = NULL;
00723     cpl_vector_delete(lines); lines = NULL;
00724 
00725     if (checkwave == NULL)
00726         fors_detect_spectra_exit("Wavelength calibration failure.");
00727 
00728 
00729     /*
00730      * Save check image to disk
00731      */
00732 
00733     header = cpl_propertylist_new();
00734     cpl_propertylist_update_double(header, "CRPIX1", 1.0);
00735     cpl_propertylist_update_double(header, "CRPIX2", 1.0);
00736     cpl_propertylist_update_double(header, "CRVAL1",
00737                                    startwavelength + dispersion/2);
00738     cpl_propertylist_update_double(header, "CRVAL2", 1.0);
00739     /* cpl_propertylist_update_double(header, "CDELT1", dispersion);
00740     cpl_propertylist_update_double(header, "CDELT2", 1.0); */
00741     cpl_propertylist_update_double(header, "CD1_1", dispersion);
00742     cpl_propertylist_update_double(header, "CD1_2", 0.0);
00743     cpl_propertylist_update_double(header, "CD2_1", 0.0);
00744     cpl_propertylist_update_double(header, "CD2_2", 1.0);
00745     cpl_propertylist_update_string(header, "CTYPE1", "LINEAR");
00746     cpl_propertylist_update_string(header, "CTYPE2", "PIXEL");
00747 
00748     if (dfs_save_image(frameset, checkwave, spectra_detection_tag, header,
00749                        parlist, recipe, version))
00750         fors_detect_spectra_exit(NULL);
00751 
00752     cpl_image_delete(checkwave); checkwave = NULL;
00753     cpl_propertylist_delete(header); header = NULL;
00754 
00755 
00756     cpl_msg_info(recipe, "Locate slits at reference wavelength on CCD...");
00757     slits = mos_locate_spectra(refmask);
00758 
00759     if (!slits) {
00760         cpl_msg_error(cpl_error_get_where(), "%s", cpl_error_get_message());
00761         fors_detect_spectra_exit("No slits could be detected!");
00762     }
00763 
00764     refimage = cpl_image_new_from_mask(refmask);
00765     cpl_mask_delete(refmask); refmask = NULL;
00766 
00767     header = dfs_load_header(frameset, arc_tag, 0);
00768     if (dfs_save_image(frameset, refimage, slit_map_tag, header,
00769                        parlist, recipe, version))
00770         fors_detect_spectra_exit(NULL);
00771     cpl_propertylist_delete(header); header = NULL;
00772 
00773     cpl_image_delete(refimage); refimage = NULL;
00774 
00775     if (slit_ident) {
00776 
00777         /*
00778          * Attempt slit identification: this recipe may continue even
00779          * in case of failed identification (i.e., the position table is
00780          * not produced, but an error is not set). In case of failure,
00781          * the spectra would be still extracted, even if they would not
00782          * be associated to slits on the mask.
00783          *
00784          * The reason for making the slit identification an user option
00785          * (via the parameter slit_ident) is to offer the possibility
00786          * to avoid identifications that are only apparently successful,
00787          * as it would happen in the case of an incorrect slit description
00788          * in the data header.
00789          */
00790 
00791         cpl_msg_indent_less();
00792         cpl_msg_info(recipe, "Attempt slit identification (optional)...");
00793         cpl_msg_indent_more();
00794 
00795         positions = mos_identify_slits(slits, maskslits, NULL);
00796         cpl_table_delete(maskslits); maskslits = NULL;
00797 
00798         if (positions) {
00799             cpl_table_delete(slits);
00800             slits = positions;
00801 
00802             /*
00803              * Eliminate slits which are _entirely_ outside the CCD
00804              */
00805 
00806             cpl_table_and_selected_double(slits,
00807                                           "ybottom", CPL_GREATER_THAN, ny-1);
00808             cpl_table_or_selected_double(slits,
00809                                           "ytop", CPL_LESS_THAN, 0);
00810             cpl_table_erase_selected(slits);
00811 
00812             nslits = cpl_table_get_nrow(slits);
00813 
00814             if (nslits == 0)
00815                 fors_detect_spectra_exit("No slits found on the CCD");
00816 
00817             cpl_msg_info(recipe, "%d slits are entirely or partially "
00818                          "contained in CCD", nslits);
00819 
00820         }
00821         else {
00822             slit_ident = 0;
00823             cpl_msg_info(recipe, "Global distortion model cannot be computed");
00824             if (cpl_error_get_code() != CPL_ERROR_NONE) {
00825                 fors_detect_spectra_exit(NULL);
00826             }
00827         }
00828     }
00829 
00830     if (dfs_save_table(frameset, slits, slit_location_tag, NULL,
00831                        parlist, recipe, version))
00832         fors_detect_spectra_exit(NULL);
00833 
00834     cpl_table_delete(slits); slits = NULL;
00835 
00836     return 0;
00837 }

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