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00020 #ifdef HAVE_CONFIG_H
00021 #include <config.h>
00022 #endif
00023
00024
00025
00026
00027
00028 #include "irplib_ppm.h"
00029 #include "irplib_wlxcorr.h"
00030 #include "irplib_spectrum.h"
00031
00032 #include <math.h>
00033 #include <cpl.h>
00034
00035
00036
00037
00038 #ifdef IRPLIB_PPM_USE_METHOD2
00039 static cpl_vector * irplib_ppm_convolve_line(const cpl_vector *, double,double);
00040 static cpl_vector * irplib_ppm_detect_lines(const cpl_vector *, double) ;
00041 #endif
00042
00043
00047
00048
00051
00068
00069 cpl_polynomial * irplib_ppm_engine(
00070 const cpl_vector * spectrum,
00071 const cpl_bivector * lines_catalog,
00072 const cpl_polynomial * poly_init,
00073 double slitw,
00074 double fwhm,
00075 double thresh,
00076 int degree,
00077 int doplot,
00078 cpl_table ** tab_infos)
00079 {
00080 #ifdef IRPLIB_PPM_USE_METHOD2
00081 cpl_vector * spec_conv ;
00082 #endif
00083 int spec_sz ;
00084 cpl_vector * det_lines ;
00085 cpl_vector * cat_lines ;
00086 double * pcat_lines ;
00087 double wmin, wmax ;
00088 double disp_min, disp_max, disp ;
00089 int nlines_cat, nlines ;
00090 const double * plines_catalog_x ;
00091 const double * plines_catalog_y ;
00092 cpl_bivector * matched ;
00093 cpl_matrix * matchedx;
00094 int match_sz;
00095 cpl_polynomial * fitted ;
00096 cpl_table * spc_table ;
00097 const cpl_vector* vectors_plot[3];
00098 cpl_vector * plot_y ;
00099 int start_ind, stop_ind ;
00100 double fill_val ;
00101 cpl_size deg_loc ;
00102 int i ;
00103 cpl_error_code error;
00104
00105
00106 if (spectrum == NULL) return NULL ;
00107 if (lines_catalog == NULL) return NULL ;
00108 if (poly_init == NULL) return NULL ;
00109
00110
00111 spec_sz = cpl_vector_get_size(spectrum) ;
00112 deg_loc = (cpl_size)degree ;
00113
00114 #ifdef IRPLIB_PPM_USE_METHOD2
00115
00116
00117 if ((spec_conv = irplib_ppm_convolve_line(spectrum, slitw, fwhm)) == NULL) {
00118 cpl_msg_error(cpl_func, "Cannot convolve the signal") ;
00119 return NULL ;
00120 }
00121
00122
00123 if ((det_lines = irplib_ppm_detect_lines(spec_conv, 0.9)) == NULL) {
00124 cpl_msg_error(cpl_func, "Cannot detect lines") ;
00125 cpl_vector_delete(spec_conv) ;
00126 return NULL ;
00127 }
00128 cpl_vector_delete(spec_conv) ;
00129 #else
00130
00131 if ((det_lines = irplib_spectrum_detect_peaks(spectrum, fwhm,
00132 thresh, 0, NULL, NULL)) == NULL) {
00133 cpl_msg_error(cpl_func, "Cannot convolve the signal") ;
00134 return NULL ;
00135 }
00136 #endif
00137 cpl_msg_info(cpl_func, "Detected %"CPL_SIZE_FORMAT" lines",
00138 cpl_vector_get_size(det_lines));
00139
00140
00141 wmin = cpl_polynomial_eval_1d(poly_init, 1.0, NULL) ;
00142 wmax = cpl_polynomial_eval_1d(poly_init, spec_sz, NULL) ;
00143 plines_catalog_x = cpl_bivector_get_x_data_const(lines_catalog) ;
00144 plines_catalog_y = cpl_bivector_get_y_data_const(lines_catalog) ;
00145 nlines = cpl_bivector_get_size(lines_catalog) ;
00146 nlines_cat = 0 ;
00147 start_ind = stop_ind = -1 ;
00148 for (i=0 ; i<nlines ; i++) {
00149 if (plines_catalog_x[i] > wmin && plines_catalog_x[i] < wmax &&
00150 plines_catalog_y[i] > 0.0) {
00151 nlines_cat++ ;
00152 if (start_ind<0) start_ind = i ;
00153 stop_ind = i ;
00154 }
00155 }
00156 if (nlines_cat == 0) {
00157 cpl_msg_error(cpl_func, "No lines in catalog") ;
00158 cpl_vector_delete(det_lines) ;
00159 return NULL ;
00160 }
00161 cat_lines = cpl_vector_new(nlines_cat) ;
00162 pcat_lines = cpl_vector_get_data(cat_lines) ;
00163 nlines_cat = 0 ;
00164 for (i=0 ; i<nlines ; i++) {
00165 if (plines_catalog_x[i] > wmin && plines_catalog_x[i] < wmax &&
00166 plines_catalog_y[i] > 0.0) {
00167 pcat_lines[nlines_cat] = plines_catalog_x[i] ;
00168 nlines_cat++ ;
00169 }
00170 }
00171
00172
00173 if (doplot) {
00174 double * pdet_lines ;
00175
00176
00177 irplib_wlxcorr_catalog_plot(lines_catalog, wmin, wmax) ;
00178
00179
00180 fill_val = cpl_vector_get_max(spectrum) ;
00181 plot_y = cpl_vector_new(spec_sz);
00182 cpl_vector_fill(plot_y, 0.0) ;
00183 pdet_lines = cpl_vector_get_data(det_lines) ;
00184 for (i=0 ; i<cpl_vector_get_size(det_lines) ; i++) {
00185 cpl_vector_set(plot_y, (int)pdet_lines[i], fill_val) ;
00186 }
00187 vectors_plot[0] = NULL ;
00188 vectors_plot[1] = spectrum ;
00189 vectors_plot[2] = plot_y ;
00190
00191 cpl_plot_vectors("set grid;set xlabel 'Position (Pixel)';set ylabel "
00192 "'Intensity (ADU/sec)';",
00193 "t 'Spectrum with detected lines' w lines", "",
00194 vectors_plot, 3);
00195 cpl_vector_delete(plot_y) ;
00196 }
00197
00198
00199 disp = (wmax-wmin) / spec_sz ;
00200 disp_min = disp - (disp/10) ;
00201 disp_max = disp + (disp/10) ;
00202 matched = cpl_ppm_match_positions(det_lines, cat_lines, disp_min,
00203 disp_max, 0.05, NULL, NULL);
00204 cpl_vector_delete(det_lines) ;
00205 cpl_vector_delete(cat_lines) ;
00206
00207 if (matched == NULL) {
00208 cpl_msg_error(cpl_func, "Cannot apply the point pattern matching") ;
00209 return NULL ;
00210 }
00211
00212 match_sz = cpl_bivector_get_size(matched);
00213
00214 cpl_msg_info(cpl_func, "Matched %d lines", match_sz) ;
00215
00216 if (match_sz <= deg_loc) {
00217 cpl_msg_error(cpl_func, "Not enough match for the fit") ;
00218 cpl_bivector_delete(matched) ;
00219 return NULL ;
00220 }
00221
00222
00223 if (doplot) {
00224 const double * pmatched ;
00225 cpl_bivector * biplot ;
00226 cpl_vector * plot_cat_x ;
00227 cpl_vector * plot_cat_y ;
00228
00229 fill_val = cpl_vector_get_max(spectrum) ;
00230 plot_y = cpl_vector_new(spec_sz);
00231 cpl_vector_fill(plot_y, 0.0) ;
00232 pmatched = cpl_bivector_get_x_data_const(matched) ;
00233 for (i=0 ; i < match_sz; i++) {
00234 cpl_vector_set(plot_y, (int)pmatched[i], fill_val) ;
00235 }
00236 vectors_plot[0] = NULL ;
00237 vectors_plot[1] = spectrum ;
00238 vectors_plot[2] = plot_y ;
00239
00240 cpl_plot_vectors("set grid;set xlabel 'Position (Pixel)';set ylabel "
00241 "'Intensity (ADU/sec)';",
00242 "t 'Spectrum with matched lines' w lines", "",
00243 vectors_plot, 3);
00244 cpl_vector_delete(plot_y) ;
00245
00246
00247 plot_cat_x=cpl_vector_extract(cpl_bivector_get_x_const(lines_catalog),
00248 start_ind, stop_ind, 1) ;
00249 plot_cat_y=cpl_vector_extract(cpl_bivector_get_y_const(lines_catalog),
00250 start_ind, stop_ind, 1) ;
00251 biplot = cpl_bivector_wrap_vectors(plot_cat_x, plot_cat_y) ;
00252 cpl_plot_bivector("set grid;set xlabel 'Wavelength';set ylabel "
00253 "'Emission';", "t 'Catalog' w impulses", "",
00254 biplot);
00255 cpl_bivector_unwrap_vectors(biplot) ;
00256
00257 plot_y = cpl_vector_duplicate(plot_cat_y) ;
00258 cpl_vector_fill(plot_y, 0.0) ;
00259 pmatched = cpl_bivector_get_y_data_const(matched) ;
00260 fill_val=cpl_vector_get_mean(plot_cat_y) ;
00261 for (i=0 ; i < match_sz; i++) {
00262 int wl_ind = 0 ;
00263 while (pmatched[i] > cpl_vector_get(plot_cat_x, wl_ind)
00264 && wl_ind < spec_sz) wl_ind++ ;
00265 if (wl_ind < spec_sz) cpl_vector_set(plot_y, wl_ind, fill_val) ;
00266 }
00267 biplot = cpl_bivector_wrap_vectors(plot_cat_x, plot_y) ;
00268 cpl_plot_bivector("set grid;set xlabel 'Wavelength';set ylabel "
00269 "'Emission';", "t 'Catalog (matched lines)' w "
00270 "impulses", "", biplot) ;
00271 cpl_bivector_unwrap_vectors(biplot) ;
00272 cpl_vector_delete(plot_cat_x) ;
00273 cpl_vector_delete(plot_cat_y) ;
00274 cpl_vector_delete(plot_y) ;
00275 }
00276
00277
00278 matchedx = cpl_matrix_wrap(1, match_sz, cpl_bivector_get_x_data(matched));
00279 fitted = cpl_polynomial_new(1);
00280 error = cpl_polynomial_fit(fitted, matchedx, NULL,
00281 cpl_bivector_get_y_const(matched), NULL,
00282 CPL_FALSE, NULL, °_loc);
00283 cpl_bivector_delete(matched);
00284 (void)cpl_matrix_unwrap(matchedx);
00285 if (error) {
00286 cpl_msg_error(cpl_func, "Cannot fit the polynomial") ;
00287 cpl_polynomial_delete(fitted);
00288 return NULL ;
00289 }
00290
00291
00292 if ((spc_table = irplib_wlxcorr_gen_spc_table(spectrum,
00293 lines_catalog, slitw, fwhm, poly_init, fitted)) == NULL) {
00294 cpl_msg_error(cpl_func, "Cannot generate the infos table") ;
00295 cpl_polynomial_delete(fitted) ;
00296 return NULL ;
00297 }
00298 if (tab_infos != NULL) *tab_infos = spc_table ;
00299 else cpl_table_delete(spc_table) ;
00300 return fitted ;
00301 }
00302
00305 #ifdef IRPLIB_PPM_USE_METHOD2
00306
00317
00318 static cpl_vector * irplib_ppm_convolve_line(
00319 const cpl_vector * spectrum,
00320 double slitw,
00321 double fwhm)
00322 {
00323 cpl_vector * conv_kernel ;
00324 cpl_vector * line_profile ;
00325 cpl_vector * xcorrs ;
00326 cpl_vector * xc_single ;
00327 int hs, line_sz, sp_sz ;
00328 int i ;
00329
00330
00331 if (spectrum == NULL) return NULL ;
00332
00333
00334 if ((conv_kernel = irplib_wlxcorr_convolve_create_kernel(slitw,
00335 fwhm)) == NULL) {
00336 cpl_msg_error(cpl_func, "Cannot create kernel") ;
00337 return NULL ;
00338 }
00339 hs = cpl_vector_get_size(conv_kernel) ;
00340 line_sz = 2 * hs + 1 ;
00341
00342
00343 line_profile = cpl_vector_new(line_sz) ;
00344 cpl_vector_fill(line_profile, 0.0) ;
00345 cpl_vector_set(line_profile, hs, 1.0) ;
00346 if (irplib_wlxcorr_convolve(line_profile, conv_kernel) != 0) {
00347 cpl_msg_error(cpl_func, "Cannot create line profile") ;
00348 cpl_vector_delete(line_profile) ;
00349 cpl_vector_delete(conv_kernel) ;
00350 return NULL ;
00351 }
00352 cpl_vector_delete(conv_kernel) ;
00353
00354
00355 sp_sz = cpl_vector_get_size(spectrum) ;
00356 xcorrs = cpl_vector_new(sp_sz) ;
00357 cpl_vector_fill(xcorrs, 0.0) ;
00358 xc_single = cpl_vector_new(1) ;
00359
00360
00361 for (i=hs ; i<sp_sz-hs ; i++) {
00362 cpl_vector * spec_ext ;
00363
00364 if ((spec_ext = cpl_vector_extract(spectrum, i-hs, i+hs, 1)) == NULL) {
00365 cpl_msg_error(cpl_func, "Cannot extract spectrum") ;
00366 cpl_vector_delete(xc_single) ;
00367 cpl_vector_delete(line_profile) ;
00368 return NULL ;
00369 }
00370 if (cpl_vector_correlate(xc_single, spec_ext, line_profile) < 0) {
00371 cpl_msg_error(cpl_func, "Cannot correlate") ;
00372 cpl_vector_delete(xc_single) ;
00373 cpl_vector_delete(line_profile) ;
00374 cpl_vector_delete(spec_ext) ;
00375 return NULL ;
00376 }
00377 cpl_vector_set(xcorrs, i, cpl_vector_get(xc_single, 0)) ;
00378 cpl_vector_delete(spec_ext) ;
00379 }
00380 cpl_vector_delete(xc_single) ;
00381 cpl_vector_delete(line_profile) ;
00382
00383 return xcorrs ;
00384 }
00385
00386
00395
00396 static cpl_vector * irplib_ppm_detect_lines(
00397 const cpl_vector * spec,
00398 double threshold)
00399 {
00400 cpl_vector * spec_loc ;
00401 double * pspec_loc ;
00402 cpl_vector * lines ;
00403 double * plines ;
00404 int spec_loc_sz, nlines ;
00405 double max ;
00406 int i ;
00407
00408
00409 if (spec == NULL) return NULL ;
00410
00411
00412 spec_loc = cpl_vector_duplicate(spec) ;
00413 pspec_loc = cpl_vector_get_data(spec_loc) ;
00414 spec_loc_sz = cpl_vector_get_size(spec_loc) ;
00415
00416
00417 for (i=0 ; i<spec_loc_sz ; i++)
00418 if (pspec_loc[i] < threshold) pspec_loc[i] = 0.0 ;
00419
00420
00421 lines = cpl_vector_new(spec_loc_sz) ;
00422 plines = cpl_vector_get_data(lines) ;
00423 nlines = 0 ;
00424
00425
00426 while ((max = cpl_vector_get_max(spec_loc)) > threshold) {
00427
00428 int max_ind = 0 ;
00429 while (max_ind < spec_loc_sz && pspec_loc[max_ind] < max) max_ind++ ;
00430 if (max_ind == spec_loc_sz) {
00431 cpl_msg_error(cpl_func, "Cannot find maximum") ;
00432 cpl_vector_delete(spec_loc) ;
00433 cpl_vector_delete(lines) ;
00434 return NULL ;
00435 }
00436 if (max_ind == 0 || max_ind == spec_loc_sz-1) {
00437 pspec_loc[max_ind] = 0 ;
00438 continue ;
00439 }
00440
00441
00442 plines[nlines] = pspec_loc[max_ind] * max_ind +
00443 pspec_loc[max_ind-1] * (max_ind-1) +
00444 pspec_loc[max_ind+1] * (max_ind+1) ;
00445 plines[nlines] /= pspec_loc[max_ind] + pspec_loc[max_ind+1] +
00446 pspec_loc[max_ind-1] ;
00447 plines[nlines] ++ ;
00448 nlines ++ ;
00449
00450
00451 i = max_ind ;
00452 while (i>=0 && pspec_loc[i] > threshold) {
00453 pspec_loc[i] = 0.0 ;
00454 i-- ;
00455 }
00456 i = max_ind+1 ;
00457 while (i<spec_loc_sz && pspec_loc[i] > threshold) {
00458 pspec_loc[i] = 0.0 ;
00459 i++ ;
00460 }
00461 }
00462 cpl_vector_delete(spec_loc) ;
00463
00464
00465 if (nlines == 0) {
00466 cpl_msg_error(cpl_func, "Cannot detect any line") ;
00467 cpl_vector_delete(lines) ;
00468 return NULL ;
00469 }
00470
00471
00472 cpl_vector_set_size(lines, nlines) ;
00473
00474
00475 cpl_vector_sort(lines, 1) ;
00476
00477 return lines ;
00478 }
00479
00480 #endif