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1370-2 Add support for reading templated SECIR models from JSON data #1375

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8e9f700
Add support for reading templated SECIR models from JSON
julianlitz Sep 15, 2025
ccddcd1
Safer FP to int conversion
julianlitz Sep 16, 2025
5641fbd
std::round and static_cast
julianlitz Sep 16, 2025
052e31f
Fix FP metaprogramming madness.
julianlitz Sep 26, 2025
31e299a
FP fixes in Graph_Simulation.h
julianlitz Sep 26, 2025
c20d181
Resolve Issue 1382, 1383, 1384
julianlitz Sep 29, 2025
11bb56c
Implement suggestion to merge round and trunc namespace region
julianlitz Oct 1, 2025
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4 changes: 2 additions & 2 deletions cpp/examples/ode_secir_parameter_study.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,8 @@ write_single_run_result(const size_t run,
return node.id;
});
auto num_groups = (int)(size_t)graph.nodes()[0].property.get_simulation().get_model().parameters.get_num_groups();
BOOST_OUTCOME_TRY(mio::save_result(all_results, ids, num_groups,
mio::path_join(abs_path, ("Results_run" + std::to_string(run) + ".h5"))));
BOOST_OUTCOME_TRY(mio::save_result<ScalarType>(
all_results, ids, num_groups, mio::path_join(abs_path, ("Results_run" + std::to_string(run) + ".h5"))));

return mio::success();
}
Expand Down
9 changes: 5 additions & 4 deletions cpp/examples/ode_secir_parameter_study_graph.cpp
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Expand Up @@ -322,12 +322,13 @@ int main()
mio::log_info("Directory '{:s}' was created.", results_dir.string());
}

auto county_ids = std::vector<int>{1001, 1002, 1003};
auto save_results_status = save_results(ensemble_results, ensemble_params, county_ids, results_dir, false);
auto pairs_edges = std::vector<std::pair<int, int>>{};
auto county_ids = std::vector<int>{1001, 1002, 1003};
auto save_results_status =
save_results<ScalarType>(ensemble_results, ensemble_params, county_ids, results_dir, false);
auto pairs_edges = std::vector<std::pair<int, int>>{};
for (auto& edge : params_graph.edges()) {
pairs_edges.push_back({county_ids[edge.start_node_idx], county_ids[edge.end_node_idx]});
}
auto save_edges_status = save_edges(ensemble_edges, pairs_edges, "test_results", false, true);
auto save_edges_status = save_edges<ScalarType>(ensemble_edges, pairs_edges, "test_results", false, true);
}
}
4 changes: 2 additions & 2 deletions cpp/examples/ode_secir_read_graph.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ int main(int argc, char** argv)
mio::osecir::set_params_distributions_normal(model, t0, tmax, 0.2);

std::cout << "Reading Mobility File..." << std::flush;
auto read_mobility_result = mio::read_mobility_plain(filename);
auto read_mobility_result = mio::read_mobility_plain<ScalarType>(filename);
if (!read_mobility_result) {
std::cout << read_mobility_result.error().formatted_message() << '\n';
std::cout << "Create the mobility file with MEmilio Epidata's getCommuterMobility.py file." << '\n';
Expand All @@ -135,7 +135,7 @@ int main(int argc, char** argv)
std::cout << "Done" << std::endl;

std::cout << "Writing Json Files..." << std::flush;
auto write_status = mio::write_graph(graph, "graph_parameters");
auto write_status = mio::write_graph<ScalarType>(graph, "graph_parameters");
if (!write_status) {
std::cout << "Error: " << write_status.error().formatted_message();
}
Expand Down
3 changes: 2 additions & 1 deletion cpp/examples/ode_secir_save_results.cpp
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Expand Up @@ -83,5 +83,6 @@ int main()
std::vector<mio::TimeSeries<ScalarType>> results_from_sim = {result_from_sim, result_from_sim};
std::vector<int> ids = {1, 2};

auto save_result_status = mio::save_result(results_from_sim, ids, (int)(size_t)nb_groups, "test_result.h5");
auto save_result_status =
mio::save_result<ScalarType>(results_from_sim, ids, (int)(size_t)nb_groups, "test_result.h5");
}
61 changes: 61 additions & 0 deletions cpp/memilio/ad/ad.h
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Expand Up @@ -27,6 +27,67 @@
#include <cmath>
#include <limits>

// Extend automatic differentiation (AD) library to support std::round and std::trunc.
namespace ad
{
namespace internal
{
using std::round;
template <class AD_TAPE_REAL, class DATA_HANDLER_1>
static inline double round(const ad::internal::active_type<AD_TAPE_REAL, DATA_HANDLER_1>& x)
{
return round(x._value());
}
template <class AD_TAPE_REAL, class A1_T1, class A1_T2, class A1_OP>
static inline double round(const ad::internal::binary_intermediate_aa<AD_TAPE_REAL, A1_T1, A1_T2, A1_OP>& x)
{
return round(x._value());
}
template <class AD_TAPE_REAL, class A1_T1, class A1_OP>
static inline double round(const ad::internal::binary_intermediate_ap<AD_TAPE_REAL, A1_T1, A1_OP>& x)
{
return round(x._value());
}
template <class AD_TAPE_REAL, class A1_T2, class A1_OP>
static inline double round(const ad::internal::binary_intermediate_pa<AD_TAPE_REAL, A1_T2, A1_OP>& x)
{
return round(x._value());
}
template <class AD_TAPE_REAL, class A1_T, class A1_OP>
static inline double round(const ad::internal::unary_intermediate<AD_TAPE_REAL, A1_T, A1_OP>& x)
{
return round(x._value());
}

using std::trunc;
template <class AD_TAPE_REAL, class DATA_HANDLER_1>
static inline double trunc(const ad::internal::active_type<AD_TAPE_REAL, DATA_HANDLER_1>& x)
{
return trunc(x._value());
}
template <class AD_TAPE_REAL, class A1_T1, class A1_T2, class A1_OP>
static inline double trunc(const ad::internal::binary_intermediate_aa<AD_TAPE_REAL, A1_T1, A1_T2, A1_OP>& x)
{
return trunc(x._value());
}
template <class AD_TAPE_REAL, class A1_T1, class A1_OP>
static inline double trunc(const ad::internal::binary_intermediate_ap<AD_TAPE_REAL, A1_T1, A1_OP>& x)
{
return trunc(x._value());
}
template <class AD_TAPE_REAL, class A1_T2, class A1_OP>
static inline double trunc(const ad::internal::binary_intermediate_pa<AD_TAPE_REAL, A1_T2, A1_OP>& x)
{
return trunc(x._value());
}
template <class AD_TAPE_REAL, class A1_T, class A1_OP>
static inline double trunc(const ad::internal::unary_intermediate<AD_TAPE_REAL, A1_T, A1_OP>& x)
{
return trunc(x._value());
}
} // namespace internal
} // namespace ad

// Allow std::numeric_limits to work with AD types.
template <class FP, class DataHandler>
struct std::numeric_limits<ad::internal::active_type<FP, DataHandler>> : public numeric_limits<FP> {
Expand Down
4 changes: 3 additions & 1 deletion cpp/memilio/data/analyze_result.h
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Expand Up @@ -309,6 +309,8 @@ std::vector<TimeSeries<FP>> ensemble_mean(const std::vector<std::vector<TimeSeri
template <typename FP>
std::vector<TimeSeries<FP>> ensemble_percentile(const std::vector<std::vector<TimeSeries<FP>>>& ensemble_result, FP p)
{
using std::floor;

assert(p > 0.0 && p < 1.0 && "Invalid percentile value.");

auto num_runs = ensemble_result.size();
Expand All @@ -328,7 +330,7 @@ std::vector<TimeSeries<FP>> ensemble_percentile(const std::vector<std::vector<Ti
return run[node][time][elem];
});
std::sort(single_element_ensemble.begin(), single_element_ensemble.end());
percentile[node][time][elem] = single_element_ensemble[static_cast<size_t>(num_runs * p)];
percentile[node][time][elem] = single_element_ensemble[static_cast<size_t>(floor(num_runs * p))];
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@julianlitz julianlitz Sep 16, 2025

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To cast a FP to size_t, we need to call either floor, ceil, round or trunc.

}
}
}
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72 changes: 36 additions & 36 deletions cpp/memilio/io/mobility_io.h
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Expand Up @@ -60,13 +60,13 @@ IOResult<int> count_lines(const std::string& filename);
* where N is the number of regions
* @param filename name of file to be read
*/
template <typename FP = ScalarType>
IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename)
template <typename FP>
IOResult<Eigen::MatrixX<FP>> read_mobility_formatted(const std::string& filename)
{
BOOST_OUTCOME_TRY(auto&& num_lines, count_lines(filename));

if (num_lines == 0) {
return success(Eigen::MatrixXd(0, 0));
return success(Eigen::MatrixX<FP>(0, 0));
}

std::fstream file;
Expand All @@ -75,7 +75,7 @@ IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename)
return failure(StatusCode::FileNotFound, filename);
}

Eigen::MatrixXd txt_matrix(num_lines - 1, 3);
Eigen::MatrixX<FP> txt_matrix(num_lines - 1, 3);
std::vector<int> ids;

try {
Expand All @@ -89,9 +89,9 @@ IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename)
filename + ":" + std::to_string(linenumber) + ": Not enough entries in line.");
}
ids.push_back(std::stoi(line[2]));
txt_matrix(linenumber - 1, 0) = std::stoi(line[2]);
txt_matrix(linenumber - 1, 1) = std::stoi(line[3]);
txt_matrix(linenumber - 1, 2) = std::stod(line[4]);
txt_matrix(linenumber - 1, 0) = static_cast<FP>(std::stoi(line[2]));
txt_matrix(linenumber - 1, 1) = static_cast<FP>(std::stoi(line[3]));
txt_matrix(linenumber - 1, 2) = static_cast<FP>(std::stod(line[4]));
}
linenumber++;
}
Expand All @@ -104,7 +104,7 @@ IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename)
std::vector<int>::iterator iter = std::unique(ids.begin(), ids.end());
ids.resize(std::distance(ids.begin(), iter));

Eigen::MatrixXd mobility = Eigen::MatrixXd::Zero(ids.size(), ids.size());
Eigen::MatrixX<FP> mobility = Eigen::MatrixX<FP>::Zero(ids.size(), ids.size());

for (int k = 0; k < num_lines - 1; k++) {
int row_ind = 0;
Expand All @@ -127,13 +127,13 @@ IOResult<Eigen::MatrixXd> read_mobility_formatted(const std::string& filename)
* Matrix, where N is the number of regions
* @param filename name of file to be read
*/
template <typename FP = ScalarType>
IOResult<Eigen::MatrixXd> read_mobility_plain(const std::string& filename)
template <typename FP>
IOResult<Eigen::MatrixX<FP>> read_mobility_plain(const std::string& filename)
{
BOOST_OUTCOME_TRY(auto&& num_lines, count_lines(filename));

if (num_lines == 0) {
return success(Eigen::MatrixXd(0, 0));
return success(Eigen::MatrixX<FP>(0, 0));
}

std::fstream file;
Expand All @@ -142,7 +142,7 @@ IOResult<Eigen::MatrixXd> read_mobility_plain(const std::string& filename)
return failure(StatusCode::FileNotFound, filename);
}

Eigen::MatrixXd mobility(num_lines, num_lines);
Eigen::MatrixX<FP> mobility(num_lines, num_lines);

try {
std::string tp;
Expand All @@ -154,7 +154,7 @@ IOResult<Eigen::MatrixXd> read_mobility_plain(const std::string& filename)
}
Eigen::Index i = static_cast<Eigen::Index>(linenumber);
for (Eigen::Index j = 0; j < static_cast<Eigen::Index>(line.size()); j++) {
mobility(i, j) = std::stod(line[j]);
mobility(i, j) = static_cast<FP>(std::stod(line[j]));
}
linenumber++;
}
Expand Down Expand Up @@ -302,9 +302,9 @@ IOResult<Graph<Model, MobilityParameters<FP>>> read_graph(const std::string& dir
* @param[in] filename Name of the file where the results will be saved.
* @return Any io errors that occur during writing of the files.
*/
template <typename FP = ScalarType>
IOResult<void> save_edges(const std::vector<TimeSeries<ScalarType>>& results,
const std::vector<std::pair<int, int>>& ids, const std::string& filename)
template <typename FP>
IOResult<void> save_edges(const std::vector<TimeSeries<FP>>& results, const std::vector<std::pair<int, int>>& ids,
const std::string& filename)
{
const auto num_edges = results.size();
size_t edge_indx = 0;
Expand Down Expand Up @@ -337,18 +337,18 @@ IOResult<void> save_edges(const std::vector<TimeSeries<ScalarType>>& results,
"Failed to create the 'Time' DataSet in group " + h5group_name +
" in the file: " + filename);

auto values_t = std::vector<ScalarType>(result.get_times().begin(), result.get_times().end());
auto values_t = std::vector<FP>(result.get_times().begin(), result.get_times().end());
MEMILIO_H5_CHECK(H5Dwrite(dset_t.id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, values_t.data()),
StatusCode::UnknownError,
"Failed to write 'Time' data in group " + h5group_name + " in the file: " + filename);

int start_id = ids[edge_indx].first;
auto total = Eigen::Matrix<ScalarType, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>::Zero(
num_timepoints, num_elements)
.eval();
auto total =
Eigen::Matrix<FP, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>::Zero(num_timepoints, num_elements)
.eval();
while (edge_indx < num_edges && ids[edge_indx].first == start_id) {
const auto& result_edge = results[edge_indx];
auto edge_result = Eigen::Matrix<ScalarType, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>::Zero(
auto edge_result = Eigen::Matrix<FP, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>::Zero(
num_timepoints, num_elements)
.eval();
for (Eigen::Index t_idx = 0; t_idx < result_edge.get_num_time_points(); ++t_idx) {
Expand Down Expand Up @@ -412,17 +412,17 @@ IOResult<void> save_edges(const std::vector<TimeSeries<ScalarType>>& results,
* @param[in] save_percentiles [Default: true] Defines if percentiles are written.
* @return Any io errors that occur during writing of the files.
*/
template <typename FP = ScalarType>
IOResult<void> save_edges(const std::vector<std::vector<TimeSeries<ScalarType>>>& ensemble_edges,
template <typename FP>
IOResult<void> save_edges(const std::vector<std::vector<TimeSeries<FP>>>& ensemble_edges,
const std::vector<std::pair<int, int>>& pairs_edges, const fs::path& result_dir,
bool save_single_runs = true, bool save_percentiles = true)
{
//save results and sum of results over nodes
auto ensemble_edges_sum = sum_nodes(ensemble_edges);
if (save_single_runs) {
for (size_t i = 0; i < ensemble_edges_sum.size(); ++i) {
BOOST_OUTCOME_TRY(save_edges(ensemble_edges[i], pairs_edges,
(result_dir / ("Edges_run" + std::to_string(i) + ".h5")).string()));
BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges[i], pairs_edges,
(result_dir / ("Edges_run" + std::to_string(i) + ".h5")).string()));
}
}

Expand All @@ -441,17 +441,17 @@ IOResult<void> save_edges(const std::vector<std::vector<TimeSeries<ScalarType>>>

// save percentiles of Edges
{
auto ensemble_edges_p05 = ensemble_percentile(ensemble_edges, 0.05);
auto ensemble_edges_p25 = ensemble_percentile(ensemble_edges, 0.25);
auto ensemble_edges_p50 = ensemble_percentile(ensemble_edges, 0.50);
auto ensemble_edges_p75 = ensemble_percentile(ensemble_edges, 0.75);
auto ensemble_edges_p95 = ensemble_percentile(ensemble_edges, 0.95);

BOOST_OUTCOME_TRY(save_edges(ensemble_edges_p05, pairs_edges, (result_dir_p05 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges(ensemble_edges_p25, pairs_edges, (result_dir_p25 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges(ensemble_edges_p50, pairs_edges, (result_dir_p50 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges(ensemble_edges_p75, pairs_edges, (result_dir_p75 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges(ensemble_edges_p95, pairs_edges, (result_dir_p95 / "Edges.h5").string()));
auto ensemble_edges_p05 = ensemble_percentile<FP>(ensemble_edges, 0.05);
auto ensemble_edges_p25 = ensemble_percentile<FP>(ensemble_edges, 0.25);
auto ensemble_edges_p50 = ensemble_percentile<FP>(ensemble_edges, 0.50);
auto ensemble_edges_p75 = ensemble_percentile<FP>(ensemble_edges, 0.75);
auto ensemble_edges_p95 = ensemble_percentile<FP>(ensemble_edges, 0.95);

BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges_p05, pairs_edges, (result_dir_p05 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges_p25, pairs_edges, (result_dir_p25 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges_p50, pairs_edges, (result_dir_p50 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges_p75, pairs_edges, (result_dir_p75 / "Edges.h5").string()));
BOOST_OUTCOME_TRY(save_edges<FP>(ensemble_edges_p95, pairs_edges, (result_dir_p95 / "Edges.h5").string()));
}
}
return success();
Expand Down
23 changes: 11 additions & 12 deletions cpp/memilio/io/parameters_io.h
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ int get_region_id(const EpiDataEntry& data_entry)
*
* @return An IOResult indicating success or failure.
*/
template <typename FP = ScalarType>
template <typename FP>
IOResult<void> compute_divi_data(const std::vector<DiviEntry>& divi_data, const std::vector<int>& vregion, Date date,
std::vector<FP>& vnum_icu)
{
Expand Down Expand Up @@ -106,12 +106,12 @@ IOResult<void> compute_divi_data(const std::vector<DiviEntry>& divi_data, const
*
* @return An IOResult indicating success or failure.
*/
template <typename FP = ScalarType>
template <typename FP>
IOResult<void> read_divi_data(const std::string& path, const std::vector<int>& vregion, Date date,
std::vector<FP>& vnum_icu)
{
BOOST_OUTCOME_TRY(auto&& divi_data, mio::read_divi_data(path));
return compute_divi_data(divi_data, vregion, date, vnum_icu);
return compute_divi_data<FP>(divi_data, vregion, date, vnum_icu);
}

/**
Expand All @@ -122,12 +122,12 @@ IOResult<void> read_divi_data(const std::string& path, const std::vector<int>& v
* @return An IOResult containing a vector of vectors, where each inner vector represents the population
* distribution across age groups for a specific region, or an error if the function fails.
*/
template <typename FP = ScalarType>
IOResult<std::vector<std::vector<ScalarType>>>
read_population_data(const std::vector<PopulationDataEntry>& population_data, const std::vector<int>& vregion)
template <typename FP>
IOResult<std::vector<std::vector<FP>>> read_population_data(const std::vector<PopulationDataEntry>& population_data,
const std::vector<int>& vregion)
{
std::vector<std::vector<ScalarType>> vnum_population(
vregion.size(), std::vector<ScalarType>(ConfirmedCasesDataEntry::age_group_names.size(), 0.0));
std::vector<std::vector<FP>> vnum_population(vregion.size(),
std::vector<FP>(ConfirmedCasesDataEntry::age_group_names.size(), 0.0));

for (auto&& county_entry : population_data) {
//accumulate population of states or country from population of counties
Expand Down Expand Up @@ -163,12 +163,11 @@ read_population_data(const std::vector<PopulationDataEntry>& population_data, co
* @return An IOResult containing a vector of vectors, where each inner vector represents the population
* distribution across age groups for a specific region, or an error if the function fails.
*/
template <typename FP = ScalarType>
IOResult<std::vector<std::vector<ScalarType>>> read_population_data(const std::string& path,
const std::vector<int>& vregion)
template <typename FP>
IOResult<std::vector<std::vector<FP>>> read_population_data(const std::string& path, const std::vector<int>& vregion)
{
BOOST_OUTCOME_TRY(auto&& population_data, mio::read_population_data(path));
return read_population_data(population_data, vregion);
return read_population_data<FP>(population_data, vregion);
}

} // namespace mio
Expand Down
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