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1016 use interpolate_simulation_result for timeseries in secirvvs python #1017

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Merged
HenrZu merged 1 commit into from
Apr 29, 2024
Merged

1016 use interpolate_simulation_result for timeseries in secirvvs python #1017

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4 changes: 2 additions & 2 deletions pycode/examples/simulation/osecirvvs_simple.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
import pandas as pd

from memilio.simulation import AgeGroup, Damping, SimulationDay
from memilio.simulation.osecirvvs import InfectionState
from memilio.simulation.osecirvvs import InfectionState, interpolate_simulation_result
from memilio.simulation.osecirvvs import Model, simulate


Expand Down Expand Up @@ -152,7 +152,7 @@ def run_secirvvs_simulation(show_plot=True):
result = simulate(t0, tmax, dt, model)

# # interpolate results
# result = interpolate_simulation_result(result)
result = interpolate_simulation_result(result)

print(result.get_last_value())

Expand Down
84 changes: 53 additions & 31 deletions pycode/memilio-simulation/memilio/simulation/osecirvvs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -79,8 +79,7 @@ void bind_ParameterStudy(py::module_& m, std::string const& name)
py::return_value_policy::reference_internal)
.def_property_readonly("model", py::overload_cast<>(&mio::ParameterStudy<Simulation>::get_model, py::const_),
py::return_value_policy::reference_internal)
.def_property_readonly("model_graph",
py::overload_cast<>(&mio::ParameterStudy<Simulation>::get_model_graph),
.def_property_readonly("model_graph", py::overload_cast<>(&mio::ParameterStudy<Simulation>::get_model_graph),
py::return_value_policy::reference_internal)
.def_property_readonly("model_graph",
py::overload_cast<>(&mio::ParameterStudy<Simulation>::get_model_graph, py::const_),
Expand All @@ -89,7 +88,8 @@ void bind_ParameterStudy(py::module_& m, std::string const& name)
"run",
[](mio::ParameterStudy<Simulation>& self,
std::function<void(mio::Graph<mio::SimulationNode<Simulation>, mio::MigrationEdge>, size_t)>
handle_result, bool variant_high) {
handle_result,
bool variant_high) {
self.run(
[variant_high](auto&& g) {
return draw_sample(g, variant_high);
Expand All @@ -104,16 +104,19 @@ void bind_ParameterStudy(py::module_& m, std::string const& name)
});
},
py::arg("handle_result_func"), py::arg("variant_high"))
.def("run",
[](mio::ParameterStudy<Simulation>& self, bool variant_high) { //default argument doesn't seem to work with functions
.def(
"run",
[](mio::ParameterStudy<Simulation>& self,
bool variant_high) { //default argument doesn't seem to work with functions
return self.run([variant_high](auto&& g) {
return draw_sample(g, variant_high);
});
},
return draw_sample(g, variant_high);
});
},
py::arg("variant_high"))
.def(
"run_single",
[](mio::ParameterStudy<Simulation>& self, std::function<void(Simulation, size_t)> handle_result, bool variant_high) {
[](mio::ParameterStudy<Simulation>& self, std::function<void(Simulation, size_t)> handle_result,
bool variant_high) {
self.run(
[variant_high](auto&& g) {
return draw_sample(g, variant_high);
Expand All @@ -124,12 +127,13 @@ void bind_ParameterStudy(py::module_& m, std::string const& name)
});
},
py::arg("handle_result_func"), py::arg("variant_high"))
.def("run_single",
.def(
"run_single",
[](mio::ParameterStudy<Simulation>& self, bool variant_high) {
return filter_graph_results(self.run([variant_high](auto&& g) {
return draw_sample(g, variant_high);
}));
},
},
py::arg("variant_high"));
}

Expand Down Expand Up @@ -165,6 +169,16 @@ PYBIND11_MAKE_OPAQUE(std::vector<mio::Graph<mio::SimulationNode<mio::osecirvvs::

PYBIND11_MODULE(_simulation_osecirvvs, m)
{
m.def("interpolate_simulation_result",
static_cast<mio::TimeSeries<double> (*)(const mio::TimeSeries<double>&, const double)>(
&mio::interpolate_simulation_result),
py::arg("ts"), py::arg("abs_tol") = 1e-14);

m.def("interpolate_simulation_result",
static_cast<mio::TimeSeries<double> (*)(const mio::TimeSeries<double>&, const std::vector<double>&)>(
&mio::interpolate_simulation_result),
py::arg("ts"), py::arg("interpolation_times"));

pymio::iterable_enum<mio::osecirvvs::InfectionState>(m, "InfectionState")
.value("SusceptibleNaive", mio::osecirvvs::InfectionState::SusceptibleNaive)
.value("SusceptiblePartialImmunity", mio::osecirvvs::InfectionState::SusceptiblePartialImmunity)
Expand Down Expand Up @@ -202,28 +216,32 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)

py::class_<mio::osecirvvs::Parameters, mio::osecirvvs::ParametersBase>(m, "Parameters")
.def(py::init<mio::AgeGroup>())
.def_property("commuter_nondetection",
.def_property(
"commuter_nondetection",
[](const mio::osecirvvs::Parameters& self) {
return self.get_commuter_nondetection();
},
[](mio::osecirvvs::Parameters& self, double v) {
self.get_commuter_nondetection() = v;
})
.def_property("start_commuter_detection",
.def_property(
"start_commuter_detection",
[](const mio::osecirvvs::Parameters& self) {
return self.get_start_commuter_detection();
},
[](mio::osecirvvs::Parameters& self, double v) {
self.get_start_commuter_detection() = v;
})
.def_property("end_commuter_detection",
.def_property(
"end_commuter_detection",
[](const mio::osecirvvs::Parameters& self) {
return self.get_end_commuter_detection();
},
[](mio::osecirvvs::Parameters& self, double v) {
self.get_end_commuter_detection() = v;
})
.def_property("end_dynamic_npis",
.def_property(
"end_dynamic_npis",
[](const mio::osecirvvs::Parameters& self) {
return self.get_end_dynamic_npis();
},
Expand Down Expand Up @@ -269,7 +287,8 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
//normally, std::vector is bound to any python iterable, but this doesn't work for move-only elements
//Bound the vector as a custom type that serves as output of ParameterStudy::run and input to
//interpolate_ensemble_results
py::bind_vector<std::vector<mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>>>(m, "EnsembleGraphResults");
py::bind_vector<std::vector<mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>>>(
m, "EnsembleGraphResults");
bind_ParameterStudy<mio::osecirvvs::Simulation<>>(m, "ParameterStudy");

m.def(
Expand All @@ -282,8 +301,8 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
// These functions are in general not secir dependent, only with the current config
m.def(
"set_nodes",
[](const mio::osecirvvs::Parameters& params, mio::Date start_date, mio::Date end_date, const std::string& data_dir,
const std::string& population_data_path, bool is_node_for_county,
[](const mio::osecirvvs::Parameters& params, mio::Date start_date, mio::Date end_date,
const std::string& data_dir, const std::string& population_data_path, bool is_node_for_county,
mio::Graph<mio::osecirvvs::Model, mio::MigrationParameters>& params_graph,
const std::vector<double>& scaling_factor_inf, double scaling_factor_icu, double tnt_capacity_factor,
int num_days = 0, bool export_time_series = false) {
Expand All @@ -303,17 +322,17 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
[](const std::string& data_dir, mio::Graph<mio::osecirvvs::Model, mio::MigrationParameters>& params_graph,
size_t contact_locations_size) {
auto migrating_comp = {mio::osecirvvs::InfectionState::SusceptibleNaive,
mio::osecirvvs::InfectionState::ExposedNaive,
mio::osecirvvs::InfectionState::InfectedNoSymptomsNaive,
mio::osecirvvs::InfectionState::InfectedSymptomsNaive,
mio::osecirvvs::InfectionState::SusceptibleImprovedImmunity,
mio::osecirvvs::InfectionState::SusceptiblePartialImmunity,
mio::osecirvvs::InfectionState::ExposedPartialImmunity,
mio::osecirvvs::InfectionState::InfectedNoSymptomsPartialImmunity,
mio::osecirvvs::InfectionState::InfectedSymptomsPartialImmunity,
mio::osecirvvs::InfectionState::ExposedImprovedImmunity,
mio::osecirvvs::InfectionState::InfectedNoSymptomsImprovedImmunity,
mio::osecirvvs::InfectionState::InfectedSymptomsImprovedImmunity};
mio::osecirvvs::InfectionState::ExposedNaive,
mio::osecirvvs::InfectionState::InfectedNoSymptomsNaive,
mio::osecirvvs::InfectionState::InfectedSymptomsNaive,
mio::osecirvvs::InfectionState::SusceptibleImprovedImmunity,
mio::osecirvvs::InfectionState::SusceptiblePartialImmunity,
mio::osecirvvs::InfectionState::ExposedPartialImmunity,
mio::osecirvvs::InfectionState::InfectedNoSymptomsPartialImmunity,
mio::osecirvvs::InfectionState::InfectedSymptomsPartialImmunity,
mio::osecirvvs::InfectionState::ExposedImprovedImmunity,
mio::osecirvvs::InfectionState::InfectedNoSymptomsImprovedImmunity,
mio::osecirvvs::InfectionState::InfectedSymptomsImprovedImmunity};
auto weights = std::vector<ScalarType>{0., 0., 1.0, 1.0, 0.33, 0., 0.};
auto result = mio::set_edges<ContactLocation, mio::osecirvvs::Model, mio::MigrationParameters,
mio::MigrationCoefficientGroup, mio::osecirvvs::InfectionState,
Expand Down Expand Up @@ -342,9 +361,12 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
#endif // MEMILIO_HAS_JSONCPP

m.def("interpolate_simulation_result",
py::overload_cast<const mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>&>(&mio::interpolate_simulation_result<mio::osecirvvs::Simulation<>>));
py::overload_cast<const mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>&>(
&mio::interpolate_simulation_result<mio::osecirvvs::Simulation<>>));

m.def("interpolate_ensemble_results", &mio::interpolate_ensemble_results<mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>>);
m.def("interpolate_ensemble_results",
&mio::interpolate_ensemble_results<
mio::Graph<mio::SimulationNode<mio::osecirvvs::Simulation<>>, mio::MigrationEdge>>);

m.attr("__version__") = "dev";
}