Sim casal2 202206

.gitignore

@@ -53,3 +53,4 @@ TestModels/ORH3B/sim/*
 Documentation/UserManual/CASAL2_Age.synctex.gz
 Documentation/UserManual/CASAL2_Length.synctex.gz
 *.txss
+simCASAL2/simCASAL2.exe

BuildSystem/buildtools/classes/ModelRunner.py

@@ -33,7 +33,7 @@ def start(self):
     estimation_betadiff_dir_list = {"TwoSex", "SBW", "Simple","ComplexTag", "SexedLengthBased"}  # requires a config-betadiff.csl2 file
     estimation_gammadiff_dir_list = {"TwoSex", "SBW", "Simple", "SexedLengthBased"} # requires a config-gammadiff.csl2 file
     estimation_adolc_dir_list = {"TwoSex", "SBW", "Simple", "SexedLengthBased"}     # requires a config-adolc.csl2 file
-    simulate_dash_i_dir_list = {"ORH3B"} # if you change this you will need to formulate the report or python code below, not very general.
+    simulate_dash_i_dir_list = {"ORH3B", "SimAllObs"} # if you change this you will need to formulate the report or python code below, not very general.
     run_dash_i_dir_list = {"Complex_input","TwoSex_input"}
     resume_mcmc_from_mpd_dir_list = {"mcmc_start_mpd_mcmc_fixed","mcmc_start_mpd"}
     resume_mcmc_dir_list = {"mcmc_resume"}
@@ -114,7 +114,7 @@ def start(self):
     # test -s functionality 
     for folder in simulate_dash_i_dir_list:
       os.chdir("../TestModels/" + folder)
-	  # create sim directory casal will fail if this doesn't exist
+	    # create sim directory casal will fail if this doesn't exist
       if not os.path.exists("sim"):
         os.mkdir("sim")	  
       ## first delete any previous simulated observations from previous model runners
@@ -131,17 +131,26 @@ def start(self):
         elapsed = time.time() - start
         print('[OK] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
-      # check the correct files were generated
-      if not os.path.exists("sim/CPUEandes.1_01"):
-        print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/CPUEandes.1_01')
-        fail_count += 1
-      if not os.path.exists("sim/CPUEandes.9_10"):
-        print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/CPUEandes.9_10')
-        fail_count += 1		
-      if not os.path.exists("sim/Obs_Andes_LF.3_05"):
-        print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/Obs_Andes_LF.3_05')
-        fail_count += 1			
-      os.chdir(cwd)
+      if folder == "ORH3B":
+        # check the correct files were generated
+        if not os.path.exists("sim/CPUEandes.1_01"):
+          print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/CPUEandes.1_01')
+          fail_count += 1
+        if not os.path.exists("sim/CPUEandes.9_10"):
+          print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/CPUEandes.9_10')
+          fail_count += 1		
+        if not os.path.exists("sim/Obs_Andes_LF.3_05"):
+          print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/Obs_Andes_LF.3_05')
+          fail_count += 1			
+        os.chdir(cwd)
+      else:
+        if not os.path.exists("sim/sim_all_obs.1_01"):
+          print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/sim_all_obs.1_01')
+          fail_count += 1
+        if not os.path.exists("sim/sim_all_obs.1_10"):
+          print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/sim_all_obs.1_10')
+          fail_count += 1			
+        os.chdir(cwd)
     # test -M mpd.log functionality 
     for folder in resume_mcmc_from_mpd_dir_list:
       os.chdir("../TestModels/" + folder)

CASAL2/source/License.h

@@ -11,7 +11,7 @@
 
 const std::string license =
     R"(
-Casal2. Copyright (C) 2017 NIWA
+Casal2. Copyright (C) 2022 NIWA
 
 This program is free software: you can redistribute it and/or 
 modify it under the terms of version 2 of the GNU General 

CASAL2/source/Reports/Common/SimulatedObservation.cpp

@@ -33,21 +33,25 @@ SimulatedObservation::SimulatedObservation() {
  * Validate object
  */
 void SimulatedObservation::DoValidate(shared_ptr<Model> model) {
-  if (observation_label_ == "")
-    observation_label_ = label_;
+
 }
 
 /**
  * Build method
  */
 void SimulatedObservation::DoBuild(shared_ptr<Model> model) {
-  observation_ = model->managers()->observation()->GetObservation(observation_label_);
-  if (!observation_) {
-#ifndef TESTMODE
-    LOG_WARNING() << "The report for " << PARAM_OBSERVATION << " with label '" << observation_label_ << "' was requested. This " << PARAM_OBSERVATION
-                  << " was not found in the input configuration file and the report will not be generated";
-#endif
-    is_valid_ = false;
+
+  if (observation_label_ == "") {
+    // print them all in a single file
+    print_all_observations = true;
+  } else {
+    // if users supplied a label check it exists
+    Observation* observation = model->managers()->observation()->GetObservation(observation_label_);
+    if(!observation) {
+      LOG_WARNING() << "The report for " << PARAM_SIMULATED_OBSERVATION << " with label '" << observation_label_ << "' was requested. This " << PARAM_OBSERVATION
+                    << " was not found in the input configuration file and the report will not be generated";
+      is_valid_ = false;
+    }
   }
 }
 
@@ -57,124 +61,136 @@ void SimulatedObservation::DoBuild(shared_ptr<Model> model) {
 void SimulatedObservation::DoExecute(shared_ptr<Model> model) {
   if (!is_valid())
     return;
-
-  cache_ << CONFIG_SECTION_SYMBOL << PARAM_OBSERVATION << " " << label_ << REPORT_EOL;
-  bool                           biomass_abundance_obs = false;
-  bool                           tag_recapture_obs = false;
-  bool                           tag_recapture_for_growth = false;
-
-  ParameterList&                 parameter_list        = observation_->parameters();
-  const map<string, Parameter*>& parameters            = parameter_list.parameters();
-  for (auto iter = parameters.begin(); iter != parameters.end(); ++iter) {
-    if (iter->first == PARAM_LIKELIHOOD) {
-      if (iter->second->values()[0] == PARAM_PSEUDO)
-        cache_ << PARAM_LIKELIHOOD << " " << parameter_list.Get(PARAM_SIMULATED_OBSERVATION)->values()[0] << REPORT_EOL;
-      else
-        cache_ << PARAM_LIKELIHOOD << " " << iter->second->values()[0] << REPORT_EOL;
-
-      continue;
+  observations::Manager& ObservationManager = *model->managers()->observation();
+
+  for(auto observation : ObservationManager.objects()) {
+    // only continue if we have found the observation that 
+    // we are after. Note from CM: I went this route rather than using the manager->getobservation
+    // The code is nasty and I didn't want to duplicate it for the single case vs the multiple case
+    if(!print_all_observations) {
+      if(observation->label() != observation_label_)
+        continue;
     }
+    // start printing out 
+    cache_ << CONFIG_SECTION_SYMBOL << PARAM_OBSERVATION << " " << observation->label() << REPORT_EOL;
+    bool                           biomass_abundance_obs = false;
+    bool                           tag_recapture_obs = false;
+    bool                           tag_recapture_for_growth = false;
+
+    ParameterList&                 parameter_list        = observation->parameters();
+    const map<string, Parameter*>& parameters            = parameter_list.parameters();
+    for (auto iter = parameters.begin(); iter != parameters.end(); ++iter) {
+      if (iter->first == PARAM_LIKELIHOOD) {
+        if (iter->second->values()[0] == PARAM_PSEUDO)
+          cache_ << PARAM_LIKELIHOOD << " " << parameter_list.Get(PARAM_SIMULATED_OBSERVATION)->values()[0] << REPORT_EOL;
+        else
+          cache_ << PARAM_LIKELIHOOD << " " << iter->second->values()[0] << REPORT_EOL;
+
+        continue;
+      }
 
-    if (iter->first == PARAM_OBS || iter->first == PARAM_ERROR_VALUE || iter->first == PARAM_LABEL || iter->first == PARAM_SIMULATION_LIKELIHOOD)
-      continue;
-
-    if (iter->second->values().size() > 0) {
-      cache_ << iter->first << " ";
-      const vector<string>& values = iter->second->values();
-      for (string value : values) {
-        if (iter->first == PARAM_TYPE)
-          LOG_FINE() << "Type of observation simulating = " << value;
-        if ((iter->first == PARAM_TYPE && value == PARAM_BIOMASS) || (iter->first == PARAM_TYPE && value == PARAM_ABUNDANCE)) {
-          biomass_abundance_obs = true;
-        }
-        if ((iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_AGE) || (iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_LENGTH)) {
-          tag_recapture_obs = true;
-        }
-        if (iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_LENGTH_FOR_GROWTH) {
-          tag_recapture_for_growth = true;
+      if (iter->first == PARAM_OBS || iter->first == PARAM_ERROR_VALUE || iter->first == PARAM_LABEL || iter->first == PARAM_SIMULATION_LIKELIHOOD)
+        continue;
+
+      if (iter->second->values().size() > 0) {
+        cache_ << iter->first << " ";
+        const vector<string>& values = iter->second->values();
+        for (string value : values) {
+          if (iter->first == PARAM_TYPE)
+            LOG_FINE() << "Type of observation simulating = " << value;
+          if ((iter->first == PARAM_TYPE && value == PARAM_BIOMASS) || (iter->first == PARAM_TYPE && value == PARAM_ABUNDANCE)) {
+            biomass_abundance_obs = true;
+          }
+          if ((iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_AGE) || (iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_LENGTH)) {
+            tag_recapture_obs = true;
+          }
+          if (iter->first == PARAM_TYPE && value == PARAM_TAG_RECAPTURE_BY_LENGTH_FOR_GROWTH) {
+            tag_recapture_for_growth = true;
+          }
+          cache_ << value << " ";
         }
-        cache_ << value << " ";
+        cache_ << REPORT_EOL;
       }
-      cache_ << REPORT_EOL;
     }
-  }
 
-  map<unsigned, vector<obs::Comparison> >& comparison = observation_->comparisons();
-  // Print Observations
+    map<unsigned, vector<obs::Comparison> >& comparison = observation->comparisons();
+    // Print Observations
 
-  if (biomass_abundance_obs) {
-    // biomass obs
-    cache_ << PARAM_TABLE << " " << PARAM_OBS << REPORT_EOL;
+    if (biomass_abundance_obs) {
+      // biomass obs
+      cache_ << PARAM_TABLE << " " << PARAM_OBS << REPORT_EOL;
 
-    for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
-      cache_ << iter->first << " ";
-      for (obs::Comparison comparison : iter->second) 
-        cache_ << comparison.observed_ << " " << comparison.error_value_;
-      cache_ << REPORT_EOL;
-    }
-    cache_ << PARAM_END_TABLE << REPORT_EOL;
-  } else if(tag_recapture_obs)  {
-    // tag recapture 
-    cache_ << PARAM_TABLE << " " << PARAM_RECAPTURED << REPORT_EOL;
-    for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
-      cache_ << iter->first << " ";
-      for (obs::Comparison comparison : iter->second) {
-        cache_ << comparison.observed_ << " ";
-      }
-      cache_ << REPORT_EOL;
-    }
-    cache_ << PARAM_END_TABLE << REPORT_EOL;
-  } else if(tag_recapture_for_growth)  {
-    // tag recapture for growth
-    cache_ << PARAM_TABLE << " " << PARAM_RECAPTURED << REPORT_EOL;
-    for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
-      cache_ << iter->first << " ";
-      for (obs::Comparison comparison : iter->second) {
-        cache_ << comparison.observed_ << " ";
+      for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
+        cache_ << iter->first << " ";
+        for (obs::Comparison comparison : iter->second) 
+          cache_ << comparison.observed_ << " " << comparison.error_value_;
+        cache_ << REPORT_EOL;
       }
-      cache_ << REPORT_EOL;
-    }
-    cache_ << PARAM_END_TABLE << REPORT_EOL;
-  } else {
-    // proportion at age obs
-    cache_ << PARAM_TABLE << " " << PARAM_OBS << REPORT_EOL;
-    for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
-      cache_ << iter->first << " ";
-      for (obs::Comparison comparison : iter->second) {
-        cache_ << comparison.observed_ << " ";
+      cache_ << PARAM_END_TABLE << REPORT_EOL;
+    } else if(tag_recapture_obs)  {
+      // tag recapture 
+      cache_ << PARAM_TABLE << " " << PARAM_RECAPTURED << REPORT_EOL;
+      for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
+        cache_ << iter->first << " ";
+        for (obs::Comparison comparison : iter->second) {
+          cache_ << comparison.observed_ << " ";
+        }
+        cache_ << REPORT_EOL;
       }
-      cache_ << REPORT_EOL;
-    }
-    cache_ << PARAM_END_TABLE << REPORT_EOL;
-  }
-
-  // if not biomass or tag growth print error values
-  if (!biomass_abundance_obs && !tag_recapture_for_growth) {
-    if(tag_recapture_obs) {
-      // tag recpat by length or age
-      cache_ << PARAM_TABLE << " " << PARAM_SCANNED << REPORT_EOL;
+      cache_ << PARAM_END_TABLE << REPORT_EOL;
+    } else if(tag_recapture_for_growth)  {
+      // tag recapture for growth
+      cache_ << PARAM_TABLE << " " << PARAM_RECAPTURED << REPORT_EOL;
       for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
         cache_ << iter->first << " ";
         for (obs::Comparison comparison : iter->second) {
-          cache_ << comparison.error_value_ << " ";
+          cache_ << comparison.observed_ << " ";
         }
         cache_ << REPORT_EOL;
       }
       cache_ << PARAM_END_TABLE << REPORT_EOL;
     } else {
       // proportion at age obs
-      cache_ << PARAM_TABLE << " " << PARAM_ERROR_VALUES << REPORT_EOL;
+      cache_ << PARAM_TABLE << " " << PARAM_OBS << REPORT_EOL;
       for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
         cache_ << iter->first << " ";
         for (obs::Comparison comparison : iter->second) {
-          cache_ << comparison.error_value_ << " ";
+          cache_ << comparison.observed_ << " ";
         }
         cache_ << REPORT_EOL;
       }
       cache_ << PARAM_END_TABLE << REPORT_EOL;
     }
+
+    // if not biomass or tag growth print error values
+    if (!biomass_abundance_obs && !tag_recapture_for_growth) {
+      if(tag_recapture_obs) {
+        // tag recpat by length or age
+        cache_ << PARAM_TABLE << " " << PARAM_SCANNED << REPORT_EOL;
+        for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
+          cache_ << iter->first << " ";
+          for (obs::Comparison comparison : iter->second) {
+            cache_ << comparison.error_value_ << " ";
+          }
+          cache_ << REPORT_EOL;
+        }
+        cache_ << PARAM_END_TABLE << REPORT_EOL;
+      } else {
+        // proportion at age obs
+        cache_ << PARAM_TABLE << " " << PARAM_ERROR_VALUES << REPORT_EOL;
+        for (auto iter = comparison.begin(); iter != comparison.end(); ++iter) {
+          cache_ << iter->first << " ";
+          for (obs::Comparison comparison : iter->second) {
+            cache_ << comparison.error_value_ << " ";
+          }
+          cache_ << REPORT_EOL;
+        }
+        cache_ << PARAM_END_TABLE << REPORT_EOL;
+      }
+    }
+    cache_ << REPORT_EOL;
+    cache_ << REPORT_EOL;
   }
-  cache_ << REPORT_EOL;
   ready_for_writing_ = true;
 }
 

CASAL2/source/Reports/Common/SimulatedObservation.h

@@ -37,7 +37,7 @@ class SimulatedObservation : public Report {
 private:
   // members
   string       observation_label_ = "";
-  Observation* observation_       = nullptr;
+  bool         print_all_observations = false;
 };
 
 } /* namespace reports */

TestModels/ORH3B/Population.csl2

@@ -21,7 +21,6 @@ age_lengths age_len_label*2
 
 @initialisation_phase Equilibrium_phase
 type Derived
-casal_initialisation_switch true
 
 
 # CASAL order of processes in each time step: