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mrc-4339: Add a state saver object to configure returned years #12
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cee810b
Add WIP state saver
r-ash b7e4e8a
Add state saver object and interface
r-ash 0bce467
Update standalone example to save output from every year
r-ash 3f457c2
Fix codefactor blank line complaints
r-ash 47a5d8f
Add TODO note about refactoring inputs to OutputState object
r-ash d0f62af
Return const reference to object instead of object
r-ash 98d53b9
Update function names, remove unused arg
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,118 @@ | ||
| #pragma once | ||
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| #include "types.hpp" | ||
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| namespace leapfrog { | ||
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| template<typename real_type> | ||
| class StateSaver { | ||
| public: | ||
| struct OutputState { | ||
| Tensor3<real_type> total_population; | ||
| Tensor3<real_type> natural_deaths; | ||
| Tensor3<real_type> hiv_population; | ||
| Tensor3<real_type> hiv_natural_deaths; | ||
| Tensor4<real_type> hiv_strat_adult; | ||
| Tensor5<real_type> art_strat_adult; | ||
| Tensor1<real_type> births; | ||
| Tensor4<real_type> aids_deaths_no_art; | ||
| Tensor3<real_type> infections; | ||
| Tensor5<real_type> aids_deaths_art; | ||
| Tensor4<real_type> art_initiation; | ||
| Tensor3<real_type> hiv_deaths; | ||
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| OutputState(int age_groups_pop, | ||
| int num_genders, | ||
| int disease_stages, | ||
| int age_groups_hiv, | ||
| int treatment_stages, | ||
| int no_output_years) | ||
| : total_population(age_groups_pop, num_genders, no_output_years), | ||
| natural_deaths(age_groups_pop, num_genders, no_output_years), | ||
| hiv_population(age_groups_pop, num_genders, no_output_years), | ||
| hiv_natural_deaths(age_groups_pop, num_genders, no_output_years), | ||
| hiv_strat_adult(disease_stages, age_groups_hiv, num_genders, no_output_years), | ||
| art_strat_adult(treatment_stages, | ||
| disease_stages, | ||
| age_groups_hiv, | ||
| num_genders, | ||
| no_output_years), | ||
| births(no_output_years), | ||
| aids_deaths_no_art(disease_stages, age_groups_hiv, num_genders, no_output_years), | ||
| infections(age_groups_pop, num_genders, no_output_years), | ||
| aids_deaths_art(treatment_stages, disease_stages, age_groups_hiv, num_genders, no_output_years), | ||
| art_initiation(disease_stages, age_groups_hiv, num_genders, no_output_years), | ||
| hiv_deaths(age_groups_pop, num_genders, no_output_years) { | ||
| total_population.setZero(); | ||
| natural_deaths.setZero(); | ||
| hiv_population.setZero(); | ||
| hiv_natural_deaths.setZero(); | ||
| hiv_strat_adult.setZero(); | ||
| art_strat_adult.setZero(); | ||
| births.setZero(); | ||
| aids_deaths_no_art.setZero(); | ||
| infections.setZero(); | ||
| aids_deaths_art.setZero(); | ||
| art_initiation.setZero(); | ||
| hiv_deaths.setZero(); | ||
| } | ||
| }; | ||
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| StateSaver(int time_steps, | ||
| std::vector<int> save_steps, | ||
| int age_groups_pop, | ||
| int num_genders, | ||
| int disease_stages, | ||
| int age_groups_hiv, | ||
| int treatment_stages) : | ||
| save_steps(save_steps), | ||
| full_state(age_groups_pop, num_genders, disease_stages, age_groups_hiv, treatment_stages, save_steps.size()) { | ||
| for (int step: save_steps) { | ||
| if (step < 0) { | ||
| std::stringstream ss; | ||
| ss << "Output step must be at least 0, got '" << step << "'." << std::endl; | ||
| throw std::runtime_error(ss.str()); | ||
| } | ||
| if (step > time_steps) { | ||
| std::stringstream ss; | ||
| ss << "Output step can be at most number of time steps run which is '" << time_steps << "', got step '" << step | ||
| << "'." << std::endl; | ||
| throw std::runtime_error(ss.str()); | ||
| } | ||
| } | ||
| } | ||
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| void save_state(const State<real_type> &state, int current_year) { | ||
| for (size_t i = 0; i < save_steps.size(); ++i) { | ||
| if (current_year == save_steps[i]) { | ||
| full_state.total_population.chip(i, full_state.total_population.NumDimensions - 1) = state.total_population; | ||
| full_state.natural_deaths.chip(i, full_state.natural_deaths.NumDimensions - 1) = state.natural_deaths; | ||
| full_state.hiv_population.chip(i, full_state.hiv_population.NumDimensions - 1) = state.hiv_population; | ||
| full_state.hiv_natural_deaths.chip(i, full_state.hiv_natural_deaths.NumDimensions - 1) = | ||
| state.hiv_natural_deaths; | ||
| full_state.hiv_strat_adult.chip(i, full_state.hiv_strat_adult.NumDimensions - 1) = state.hiv_strat_adult; | ||
| full_state.art_strat_adult.chip(i, full_state.art_strat_adult.NumDimensions - 1) = state.art_strat_adult; | ||
| full_state.births(i) = state.births; | ||
| full_state.aids_deaths_no_art.chip(i, full_state.aids_deaths_no_art.NumDimensions - 1) = | ||
| state.aids_deaths_no_art; | ||
| full_state.infections.chip(i, full_state.infections.NumDimensions - 1) = state.infections; | ||
| full_state.aids_deaths_art.chip(i, full_state.aids_deaths_art.NumDimensions - 1) = state.aids_deaths_art; | ||
| full_state.art_initiation.chip(i, full_state.art_initiation.NumDimensions - 1) = state.art_initiation; | ||
| full_state.hiv_deaths.chip(i, full_state.hiv_deaths.NumDimensions - 1) = state.hiv_deaths; | ||
| return; | ||
| } | ||
| } | ||
| } | ||
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| const OutputState &get_full_state() const { | ||
| return full_state; | ||
| } | ||
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| private: | ||
| std::vector<int> save_steps; | ||
| OutputState full_state; | ||
| }; | ||
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| } | ||
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most these values, defining the dimensions, are probably subsets of the model parameters? do you want to pass in the parameters object here, or create some sub-struct within the object so that this call signature does not grow unmanageably, and also that a state saver and its underlying model run are always compatible?
Do we imagine that all of these are always wanted?
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Yes they are, so these are all the dimensions of our state-space. We've started thinking about splitting this out in https://github.com/mrc-ide/frogger/pull/11/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5R51 as part of that PR I will update the names and also create some sub-struct for the parameters. If it looks ok I would wait until that PR is pinned down and use whatever struct comes from that. I'll add a TODO note here into the README