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1379 Add read_graph to python bindings #1380

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Merged
merged 2 commits into from
Sep 29, 2025
Merged

1379 Add read_graph to python bindings #1380

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8d343c1
add read graph and tests
HenrZu Sep 26, 2025
c7f11ea
py arg and doc string
HenrZu Sep 29, 2025
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27 changes: 22 additions & 5 deletions pycode/memilio-simulation/memilio/simulation/bindings/io/mobility_io.h
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

#include "memilio/mobility/metapopulation_mobility_instant.h"
#include "memilio/io/mobility_io.h"
#include "pybind_util.h"

#include "pybind11/pybind11.h"
#include <cstddef>
Expand All @@ -32,11 +33,27 @@ namespace pymio
template <class Model>
void bind_write_graph(pybind11::module_& m)
{
m.def("write_graph",
[&](const mio::Graph<Model, mio::MobilityParameters<double>>& graph, const std::string& directory) {
int ioflags = mio::IOF_None;
auto ioresult = mio::write_graph<double, Model>(graph, directory, ioflags);
});
m.def(
"write_graph",
[&](const mio::Graph<Model, mio::MobilityParameters<double>>& graph, const std::string& directory) {
int ioflags = mio::IOF_None;
auto ioresult = mio::write_graph<double, Model>(graph, directory, ioflags);
},
"Write a graph (nodes and edges) as JSON files to the given directory.", pybind11::arg("graph"),
pybind11::arg("directory"));
}

template <class Model>
void bind_read_graph(pybind11::module_& m)
{
m.def(
"read_graph",
[&](const std::string& directory) {
auto result = mio::read_graph<double, Model>(directory, 0, true);
return pymio::check_and_throw(result);
},
"Read a graph from JSON files in the given directory (see write_graph).", pybind11::arg("directory"),
pybind11::return_value_policy::move);
}

} // namespace pymio
Expand Down
16 changes: 9 additions & 7 deletions pycode/memilio-simulation/memilio/simulation/bindings/models/osecir.cpp
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Expand Up @@ -287,11 +287,11 @@ PYBIND11_MODULE(_simulation_osecir, m)
mio::osecir::InfectionState::InfectedSymptoms, mio::osecir::InfectionState::Recovered};
auto weights = std::vector<ScalarType>{0., 0., 1.0, 1.0, 0.33, 0., 0.};
auto result = mio::set_edges<double, // FP
ContactLocation, mio::osecir::Model<double>, mio::MobilityParameters<double>,
mio::MobilityCoefficientGroup<double>, mio::osecir::InfectionState,
decltype(mio::read_mobility_plain)>(mobility_data_file, params_graph,
mobile_comp, contact_locations_size,
mio::read_mobility_plain, weights);
ContactLocation, mio::osecir::Model<double>, mio::MobilityParameters<double>,
mio::MobilityCoefficientGroup<double>, mio::osecir::InfectionState,
decltype(mio::read_mobility_plain)>(mobility_data_file, params_graph,
mobile_comp, contact_locations_size,
mio::read_mobility_plain, weights);
return pymio::check_and_throw(result);
},
py::return_value_policy::move);
Expand All @@ -302,6 +302,7 @@ PYBIND11_MODULE(_simulation_osecir, m)

#ifdef MEMILIO_HAS_JSONCPP
pymio::bind_write_graph<mio::osecir::Model<double>>(m);
pymio::bind_read_graph<mio::osecir::Model<double>>(m);
m.def(
"read_input_data_county",
[](std::vector<mio::osecir::Model<double>>& model, mio::Date date, const std::vector<int>& county,
Expand All @@ -314,8 +315,9 @@ PYBIND11_MODULE(_simulation_osecir, m)
py::return_value_policy::move);
#endif // MEMILIO_HAS_JSONCPP

m.def("interpolate_simulation_result", py::overload_cast<const MobilityGraph&>(
&mio::interpolate_simulation_result<double, mio::osecir::Simulation<double>>));
m.def("interpolate_simulation_result",
py::overload_cast<const MobilityGraph&>(
&mio::interpolate_simulation_result<double, mio::osecir::Simulation<double>>));

m.def("interpolate_ensemble_results", &mio::interpolate_ensemble_results<MobilityGraph>);

Expand Down
7 changes: 4 additions & 3 deletions pycode/memilio-simulation/memilio/simulation/bindings/models/osecirvvs.cpp
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Expand Up @@ -340,9 +340,9 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)
mio::osecirvvs::InfectionState::InfectedSymptomsImprovedImmunity};
auto weights = std::vector<ScalarType>{0., 0., 1.0, 1.0, 0.33, 0., 0.};
auto result = mio::set_edges<double, // FP,
ContactLocation, mio::osecirvvs::Model<double>,
mio::MobilityParameters<double>, mio::MobilityCoefficientGroup<double>,
mio::osecirvvs::InfectionState, decltype(mio::read_mobility_plain)>(
ContactLocation, mio::osecirvvs::Model<double>,
mio::MobilityParameters<double>, mio::MobilityCoefficientGroup<double>,
mio::osecirvvs::InfectionState, decltype(mio::read_mobility_plain)>(
mobility_data_file, params_graph, mobile_comp, contact_locations_size, mio::read_mobility_plain,
weights);
return pymio::check_and_throw(result);
Expand All @@ -355,6 +355,7 @@ PYBIND11_MODULE(_simulation_osecirvvs, m)

#ifdef MEMILIO_HAS_JSONCPP
pymio::bind_write_graph<mio::osecirvvs::Model<double>>(m);
pymio::bind_read_graph<mio::osecirvvs::Model<double>>(m);
m.def(
"read_input_data_county",
[](std::vector<mio::osecirvvs::Model<double>>& model, mio::Date date, const std::vector<int>& county,
Expand Down
31 changes: 31 additions & 0 deletions pycode/memilio-simulation/memilio/simulation_test/test_mobility.py
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Expand Up @@ -18,6 +18,7 @@
# limitations under the License.
#############################################################################
import unittest
import tempfile

import numpy as np

Expand Down Expand Up @@ -75,6 +76,36 @@ def test_mobility_sim(self):
self.assertGreaterEqual(sim.graph.get_node(
0).property.result.get_num_time_points(), 3)

def test_write_read_graph_simple(self):
# build a simple model graph
model = osecir.Model(1)
model.parameters.TestAndTraceCapacity.value = 42
model.apply_constraints()

graph = osecir.ModelGraph()
graph.add_node(0, model)
graph.add_node(1, model)

num_compartments = 10
graph.add_edge(0, 1, 0.1 * np.ones(num_compartments))
graph.add_edge(1, 0, 0.1 * np.ones(num_compartments))

with tempfile.TemporaryDirectory() as tmpdir:
# save graph
osecir.write_graph(graph, tmpdir)
# read graph back
g_read = osecir.read_graph(tmpdir)

# basic structure
self.assertEqual(graph.num_nodes, g_read.num_nodes)
self.assertEqual(graph.num_edges, g_read.num_edges)

# check one parameter
self.assertEqual(
g_read.get_node(0).property.parameters.TestAndTraceCapacity.value,
42,
)


if __name__ == '__main__':
unittest.main()