/**
* Build any runtime relationships we may have and ensure
* the labels for other objects are valid.
*/
void ProcessRemovalsByLength::DoBuild() {
partition_ = CombinedCategoriesPtr(new niwa::partition::accessors::CombinedCategories(model_, category_labels_));
cached_partition_ = CachedCombinedCategoriesPtr(new niwa::partition::accessors::cached::CombinedCategories(model_, category_labels_));
// if (ageing_error_label_ != "")
// LOG_CODE_ERROR() << "ageing error has not been implemented for the proportions at age observation";
length_results_.resize(number_bins_ * category_labels_.size(), 0.0);
auto time_step = model_->managers().time_step()->GetTimeStep(time_step_label_);
if (!time_step) {
LOG_FATAL_P(PARAM_TIME_STEP)<< time_step_label_ << " could not be found. Have you defined it?";
} else {
auto process = time_step->SubscribeToProcess(this, years_, process_label_);
mortality_instantaneous_ = dynamic_cast<MortalityInstantaneous*>(process);
}
if (!mortality_instantaneous_)
LOG_ERROR_P(PARAM_PROCESS) << "This observation can only be used for Process of type = " << PARAM_MORTALITY_INSTANTANEOUS;
// Need to split the categories if any are combined for checking
vector<string> temp_split_category_labels, split_category_labels;
for (const string& category_label : category_labels_) {
boost::split(temp_split_category_labels, category_label, boost::is_any_of("+"));
for (const string& split_category_label : temp_split_category_labels) {
split_category_labels.push_back(split_category_label);
}
}
// Need to make this a vector so its compatible with the function couldn't be bothered templating sorry
vector<string> methods;
methods.push_back(method_);
// Do some checks so that the observation and process are compatible
if (!mortality_instantaneous_->check_methods_for_removal_obs(methods))
LOG_ERROR_P(PARAM_METHOD_OF_REMOVAL) << "could not find all these methods in the instantaneous_mortality process labeled " << process_label_
<< " please check that the methods are compatible with this process";
if (!mortality_instantaneous_->check_categories_in_methods_for_removal_obs(methods, split_category_labels))
LOG_ERROR_P(PARAM_CATEGORIES) << "could not find all these categories in the instantaneous_mortality process labeled " << process_label_
<< " please check that the categories are compatible with this process";
if (!mortality_instantaneous_->check_years_in_methods_for_removal_obs(years_, methods))
LOG_ERROR_P(PARAM_YEARS) << "could not find catches in all years in the instantaneous_mortality process labeled " << process_label_
<< " please check that the years are compatible with this process";
}
/**
* Build any runtime relationships we may have and ensure
* the labels for other objects are valid.
*/
void ProportionsMigrating::DoBuild() {
partition_ = CombinedCategoriesPtr(new niwa::partition::accessors::CombinedCategories(model_, category_labels_));
cached_partition_ = CachedCombinedCategoriesPtr(new niwa::partition::accessors::cached::CombinedCategories(model_, category_labels_));
// Create a pointer to misclassification matrix
if( ageing_error_label_ != "") {
ageing_error_ = model_->managers().ageing_error()->GetAgeingError(ageing_error_label_);
if (!ageing_error_)
LOG_ERROR_P(PARAM_AGEING_ERROR) << "(" << ageing_error_label_ << ") could not be found. Have you defined it?";
}
age_results_.resize(age_spread_ * category_labels_.size(), 0.0);
TimeStep* time_step = model_->managers().time_step()->GetTimeStep(time_step_label_);
if (!time_step) {
LOG_FATAL_P(PARAM_TIME_STEP) << time_step_label_ << " could not be found. Have you defined it?";
} else
time_step->SubscribeToProcess(this, years_, process_label_);
}
/**
* Build runtime relationships between this object and other objects.
* Build any data objects that need to be built.
*/
void Cinitial::DoBuild() {
LOG_TRACE();
time_steps_ = model_->managers().time_step()->ordered_time_steps();
// Create Category and cached category pointers
partition_ = CombinedCategoriesPtr(new niwa::partition::accessors::CombinedCategories(model_, category_labels_));
cached_partition_ = CachedCombinedCategoriesPtr(new niwa::partition::accessors::cached::CombinedCategories(model_, category_labels_));
// Create derived quantity pointers
unsigned i = 0;
for (auto derived_quantities : derived_quanitity_) {
if (derived_quantities != "") {
derived_ptr_.push_back(model_->managers().derived_quantity()->GetDerivedQuantity(derived_quantities));
if (!derived_ptr_[i]) {
LOG_ERROR() << "Cannot find " << derived_quantities;
}
}
++i;
}
}
