Alternaria
fit cylinders and ellipsoids to fungus
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The best way to do this is by including this header. 00026 * 00027 * Any of the above conditions can be waived if you get permission from the 00028 * copyright holder. 00029 * 00030 * Apart from the remix rights granted under this license, nothing in this 00031 * license impairs or restricts the author's moral rights. 00032 */ 00033 00034 00046 #include <config.h> 00047 00048 #include <cstdlib> 00049 #include <cmath> 00050 #include <cassert> 00051 #include <iostream> 00052 #include <iomanip> 00053 00054 #include <inttypes.h> 00055 00056 #include <jwsc/base/limits.h> 00057 #include <jwsc/prob/pdf.h> 00058 00059 #include <jwsc++/base/exception.h> 00060 00061 #include "sampler.h" 00062 #include "psf_model.h" 00063 #include "psf_moves.h" 00064 00065 00066 using std::isinf; 00067 using std::isnan; 00068 using namespace jwsc; 00069 using jwscxx::base::Exception; 00070 00071 00077 bool PSF_move::run(Sampler_move_parameters* params) throw (Exception) 00078 { 00079 params->init_proposals(); 00080 00081 PSF_model_density* density = params->psf->get_density()->clone(); 00082 00083 float mu = params->psf->get_alpha(); 00084 float sigma = density->get_alpha().get_sigma(); 00085 float min = density->get_alpha().get_min(); 00086 float max = density->get_alpha().get_max(); 00087 density->set_alpha(mu, sigma, min, max); 00088 00089 mu = params->psf->get_beta(); 00090 sigma = density->get_beta().get_sigma(); 00091 min = density->get_beta().get_min(); 00092 max = density->get_beta().get_max(); 00093 density->set_beta(mu, sigma, min, max); 00094 00095 mu = params->psf->get_gamma(); 00096 sigma = density->get_gamma().get_sigma(); 00097 min = density->get_gamma().get_min(); 00098 max = density->get_gamma().get_max(); 00099 density->set_gamma(mu, sigma, min, max); 00100 00101 params->psf_proposal->set(density->sample_alpha(), density->sample_beta(), 00102 density->sample_gamma(), params->imaging_proposal); 00103 00104 delete density; 00105 00106 params->psf_proposal->update_h(params->imaging_proposal); 00107 00108 params->alternaria_proposal->update_scene(params->psf_proposal, 00109 params->imaging_proposal); 00110 00111 params->ll_proposal = params->alternaria_proposal->calc_log_likelihood( 00112 params->psf_proposal, params->imaging_proposal, params->data, 00113 params->data_avg); 00114 00115 double log_alpha = params->ll_proposal; 00116 log_alpha -= params->ll; 00117 log_alpha += params->psf_proposal->get_log_prob(); 00118 log_alpha -= params->psf->get_log_prob(); 00119 00120 #if defined ALTERNARIA_HAVE_ISINF && defined ALTERNARIA_HAVE_ISNAN 00121 assert(!isinf(log_alpha) && !isnan(log_alpha)); 00122 #endif 00123 00124 double log_u = log(sample_uniform_pdf_d(JWSC_MIN_LOG_ARG, 1.0)); 00125 00126 if (log_u <= log_alpha) 00127 { 00128 return true; 00129 } 00130 return false; 00131 } 00132 00133 00140 const std::ostringstream& PSF_move::get_info(Sampler_move_parameters* params) 00141 { 00142 assert(params->psf); 00143 info.str(""); 00144 info << std::left << std::setprecision(4) << std::setw(9) 00145 << params->psf->get_alpha() 00146 << std::left << std::setprecision(4) << std::setw(9) 00147 << params->psf->get_beta() 00148 << std::left << std::setprecision(4) << std::setw(9) 00149 << params->psf->get_gamma(); 00150 return info; 00151 } 00152 00153 00160 const std::ostringstream& PSF_move::get_proposal_info 00161 ( 00162 Sampler_move_parameters* params 00163 ) 00164 { 00165 assert(params->psf_proposal); 00166 proposal_info.str(""); 00167 proposal_info << std::left << std::setprecision(4) << std::setw(9) 00168 << params->psf_proposal->get_alpha() 00169 << std::left << std::setprecision(4) << std::setw(9) 00170 << params->psf_proposal->get_beta() 00171 << std::left << std::setprecision(4) << std::setw(9) 00172 << params->psf_proposal->get_gamma(); 00173 return proposal_info; 00174 } 00175 00176 00182 bool PSF_alpha_move::run(Sampler_move_parameters* params) throw (Exception) 00183 { 00184 params->init_proposals(); 00185 00186 PSF_model_density* density = params->psf->get_density()->clone(); 00187 float mu = params->psf->get_alpha(); 00188 float sigma = density->get_alpha().get_sigma(); 00189 float min = density->get_alpha().get_min(); 00190 float max = density->get_alpha().get_max(); 00191 density->set_alpha(mu, sigma, min, max); 00192 00193 params->psf_proposal->set_alpha(density->sample_alpha(), 00194 params->imaging_proposal); 00195 00196 delete density; 00197 00198 params->psf_proposal->update_h(params->imaging_proposal); 00199 00200 params->alternaria_proposal->update_scene(params->psf_proposal, 00201 params->imaging_proposal); 00202 00203 params->ll_proposal = params->alternaria_proposal->calc_log_likelihood( 00204 params->psf_proposal, params->imaging_proposal, params->data, 00205 params->data_avg); 00206 00207 double log_alpha = params->ll_proposal; 00208 log_alpha -= params->ll; 00209 log_alpha += params->psf_proposal->get_log_prob(); 00210 log_alpha -= params->psf->get_log_prob(); 00211 00212 #if defined ALTERNARIA_HAVE_ISINF && defined ALTERNARIA_HAVE_ISNAN 00213 assert(!isinf(log_alpha) && !isnan(log_alpha)); 00214 #endif 00215 00216 double log_u = log(sample_uniform_pdf_d(JWSC_MIN_LOG_ARG, 1.0)); 00217 00218 if (log_u <= log_alpha) 00219 { 00220 return true; 00221 } 00222 return false; 00223 } 00224 00225 00231 const std::ostringstream& PSF_alpha_move::get_info 00232 ( 00233 Sampler_move_parameters* params 00234 ) 00235 { 00236 assert(params->psf); 00237 info.str(""); 00238 info << std::left << std::setprecision(4) << std::setw(9) 00239 << params->psf->get_alpha(); 00240 return info; 00241 } 00242 00243 00249 const std::ostringstream& PSF_alpha_move::get_proposal_info 00250 ( 00251 Sampler_move_parameters* params 00252 ) 00253 { 00254 assert(params->psf_proposal); 00255 proposal_info.str(""); 00256 proposal_info << std::left << std::setprecision(4) << std::setw(9) 00257 << params->psf_proposal->get_alpha(); 00258 return proposal_info; 00259 } 00260 00261 00267 bool PSF_beta_move::run(Sampler_move_parameters* params) throw (Exception) 00268 { 00269 params->init_proposals(); 00270 00271 PSF_model_density* density = params->psf->get_density()->clone(); 00272 float mu = params->psf->get_beta(); 00273 float sigma = density->get_beta().get_sigma(); 00274 float min = density->get_beta().get_min(); 00275 float max = density->get_beta().get_max(); 00276 density->set_beta(mu, sigma, min, max); 00277 00278 params->psf_proposal->set_beta(density->sample_beta(), 00279 params->imaging_proposal); 00280 00281 delete density; 00282 00283 params->psf_proposal->update_h(params->imaging_proposal); 00284 00285 params->alternaria_proposal->update_scene(params->psf_proposal, 00286 params->imaging_proposal); 00287 00288 params->ll_proposal = params->alternaria_proposal->calc_log_likelihood( 00289 params->psf_proposal, params->imaging_proposal, params->data, 00290 params->data_avg); 00291 00292 double log_alpha = params->ll_proposal; 00293 log_alpha -= params->ll; 00294 log_alpha += params->psf_proposal->get_log_prob(); 00295 log_alpha -= params->psf->get_log_prob(); 00296 00297 #if defined ALTERNARIA_HAVE_ISINF && defined ALTERNARIA_HAVE_ISNAN 00298 assert(!isinf(log_alpha) && !isnan(log_alpha)); 00299 #endif 00300 00301 double log_u = log(sample_uniform_pdf_d(JWSC_MIN_LOG_ARG, 1.0)); 00302 00303 if (log_u <= log_alpha) 00304 { 00305 return true; 00306 } 00307 return false; 00308 } 00309 00310 00316 const std::ostringstream& PSF_beta_move::get_info 00317 ( 00318 Sampler_move_parameters* params 00319 ) 00320 { 00321 assert(params->psf); 00322 info.str(""); 00323 info << std::left << std::setprecision(4) << std::setw(9) 00324 << params->psf->get_beta(); 00325 return info; 00326 } 00327 00328 00334 const std::ostringstream& PSF_beta_move::get_proposal_info 00335 ( 00336 Sampler_move_parameters* params 00337 ) 00338 { 00339 assert(params->psf_proposal); 00340 proposal_info.str(""); 00341 proposal_info << std::left << std::setprecision(4) << std::setw(9) 00342 << params->psf_proposal->get_beta(); 00343 return proposal_info; 00344 } 00345 00346 00352 bool PSF_gamma_move::run(Sampler_move_parameters* params) throw (Exception) 00353 { 00354 params->init_proposals(); 00355 00356 PSF_model_density* density = params->psf->get_density()->clone(); 00357 float mu = params->psf->get_gamma(); 00358 float sigma = density->get_gamma().get_sigma(); 00359 float min = density->get_gamma().get_min(); 00360 float max = density->get_gamma().get_max(); 00361 density->set_gamma(mu, sigma, min, max); 00362 00363 params->psf_proposal->set_gamma(density->sample_gamma(), 00364 params->imaging_proposal); 00365 00366 delete density; 00367 00368 params->psf_proposal->update_h(params->imaging_proposal); 00369 00370 params->alternaria_proposal->update_scene(params->psf_proposal, 00371 params->imaging_proposal); 00372 00373 params->ll_proposal = params->alternaria_proposal->calc_log_likelihood( 00374 params->psf_proposal, params->imaging_proposal, params->data, 00375 params->data_avg); 00376 00377 double log_alpha = params->ll_proposal; 00378 log_alpha -= params->ll; 00379 log_alpha += params->psf_proposal->get_log_prob(); 00380 log_alpha -= params->psf->get_log_prob(); 00381 00382 #if defined ALTERNARIA_HAVE_ISINF && defined ALTERNARIA_HAVE_ISNAN 00383 assert(!isinf(log_alpha) && !isnan(log_alpha)); 00384 #endif 00385 00386 double log_u = log(sample_uniform_pdf_d(JWSC_MIN_LOG_ARG, 1.0)); 00387 00388 if (log_u <= log_alpha) 00389 { 00390 return true; 00391 } 00392 return false; 00393 } 00394 00395 00401 const std::ostringstream& PSF_gamma_move::get_info 00402 ( 00403 Sampler_move_parameters* params 00404 ) 00405 { 00406 assert(params->psf); 00407 info.str(""); 00408 info << std::left << std::setprecision(4) << std::setw(9) 00409 << params->psf->get_gamma(); 00410 return info; 00411 } 00412 00413 00419 const std::ostringstream& PSF_gamma_move::get_proposal_info 00420 ( 00421 Sampler_move_parameters* params 00422 ) 00423 { 00424 assert(params->psf_proposal); 00425 proposal_info.str(""); 00426 proposal_info << std::left << std::setprecision(4) << std::setw(9) 00427 << params->psf_proposal->get_gamma(); 00428 return proposal_info; 00429 }