1108 Streamline code for reading in data in model specific IO files

cpp/memilio/CMakeLists.txt

@@ -40,6 +40,8 @@ add_library(memilio
     io/history.h
     io/mobility_io.h
     io/mobility_io.cpp
+    io/parameters_io.h
+    io/parameters_io.cpp
     io/result_io.h
     io/result_io.cpp
     io/epi_data.h

cpp/memilio/io/parameters_io.cpp

@@ -0,0 +1,72 @@
+/* 
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+*     http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*/
+
+#include "memilio/config.h"
+
+#ifdef MEMILIO_HAS_JSONCPP
+
+#include "memilio/io/epi_data.h"
+#include "memilio/io/result_io.h"
+#include "json/value.h"
+#include <string>
+#include <vector>
+
+namespace mio
+{
+IOResult<std::vector<std::vector<double>>> read_population_data(const std::vector<PopulationDataEntry>& population_data,
+                                                                const std::vector<int>& vregion)
+{
+    std::vector<std::vector<double>> vnum_population(
+        vregion.size(), std::vector<double>(ConfirmedCasesDataEntry::age_group_names.size(), 0.0));
+
+    for (auto&& county_entry : population_data) {
+        //accumulate population of states or country from population of counties
+        if (!county_entry.county_id && !county_entry.district_id) {
+            return failure(StatusCode::InvalidFileFormat, "File with county population expected.");
+        }
+        //find region that this county belongs to
+        //all counties belong to the country (id = 0)
+        auto it = std::find_if(vregion.begin(), vregion.end(), [&county_entry](auto r) {
+            return r == 0 ||
+                   (county_entry.county_id &&
+                    regions::StateId(r) == regions::get_state_id(int(*county_entry.county_id))) ||
+                   (county_entry.county_id && regions::CountyId(r) == *county_entry.county_id) ||
+                   (county_entry.district_id && regions::DistrictId(r) == *county_entry.district_id);
+        });
+        if (it != vregion.end()) {
+            auto region_idx      = size_t(it - vregion.begin());
+            auto& num_population = vnum_population[region_idx];
+            for (size_t age = 0; age < num_population.size(); age++) {
+                num_population[age] += county_entry.population[AgeGroup(age)];
+            }
+        }
+    }
+
+    return success(vnum_population);
+}
+
+IOResult<std::vector<std::vector<double>>> 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);
+}
+} // namespace mio
+#endif //MEMILIO_HAS_JSONCPP

cpp/memilio/io/parameters_io.h

@@ -0,0 +1,143 @@
+/* 
+* Copyright (C) 2020-2025 MEmilio
+*
+* Authors: Henrik Zunker
+*
+* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+*     http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*/
+#ifndef MEMILIO_IO_PARAMETER_H
+#define MEMILIO_IO_PARAMETER_H
+
+#include "memilio/config.h"
+
+#ifdef MEMILIO_HAS_JSONCPP
+
+#include "memilio/io/epi_data.h"
+#include "memilio/io/result_io.h"
+#include "json/value.h"
+#include <string>
+#include <vector>
+
+namespace mio
+{
+/**
+ * @brief Gets the region ID (county, state, or district) of an EpiDataEntry. If none are available, 
+ * it defaults to 0 which is representing the whole country.
+ * 
+ * If none are available, it defaults to 0 which is representing the whole country.
+ * 
+ * @tparam EpiDataEntry The type of the data entry.
+ * @param data_entry The (RKI) data entry to extract the region ID from.
+ * @return The region ID as integer, or 0 if no specific region information is available.
+ */
+template <class EpiDataEntry>
+int get_region_id(const EpiDataEntry& data_entry)
+{
+    return data_entry.county_id ? data_entry.county_id->get()
+                                : (data_entry.state_id ? data_entry.state_id->get()
+                                                       : (data_entry.district_id ? data_entry.district_id->get() : 0));
+}
+
+/**
+ * @brief Extracts the number of individuals in critical condition (ICU) for each region 
+ * on a specified date from the provided DIVI data.
+ *
+ * @tparam FP Floating point type (default: double).
+ *
+ * @param[in] divi_data Vector of DIVI data entries containing date, region, and ICU information.
+ * @param[in] vregion Vector of region IDs for which the data is computed.
+ * @param[in] date Date for which the ICU data is computed.
+ * @param[in, out] vnum_icu Output vector containing the number of ICU cases for each region.
+ *
+ * @return An IOResult indicating success or failure.
+ */
+template <typename FP = double>
+IOResult<void> compute_divi_data(const std::vector<DiviEntry>& divi_data, const std::vector<int>& vregion, Date date,
+                                 std::vector<FP>& vnum_icu)
+{
+    auto max_date_entry = std::max_element(divi_data.begin(), divi_data.end(), [](auto&& a, auto&& b) {
+        return a.date < b.date;
+    });
+    if (max_date_entry == divi_data.end()) {
+        log_error("DIVI data is empty.");
+        return failure(StatusCode::InvalidValue, "DIVI data is empty.");
+    }
+    auto max_date = max_date_entry->date;
+    if (max_date < date) {
+        log_error("DIVI data does not contain the specified date.");
+        return failure(StatusCode::OutOfRange, "DIVI data does not contain the specified date.");
+    }
+
+    for (auto&& entry : divi_data) {
+        auto it      = std::find_if(vregion.begin(), vregion.end(), [&entry](auto r) {
+            return r == 0 || r == get_region_id(entry);
+        });
+        auto date_df = entry.date;
+        if (it != vregion.end() && date_df == date) {
+            auto region_idx      = size_t(it - vregion.begin());
+            vnum_icu[region_idx] = entry.num_icu;
+        }
+    }
+
+    return success();
+}
+
+/**
+ * @brief Reads DIVI data from a file and computes the ICU data for specified regions and date.
+ *
+ * @tparam FP Floating point type (default: double).
+ *
+ * @param[in] path Path to the file containing DIVI data.
+ * @param[in] vregion Vector of region IDs for which the data is computed.
+ * @param[in] date Date for which the ICU data is computed.
+ * @param[in, out] vnum_icu Output vector containing the number of ICU cases for each region.
+ *
+ * @return An IOResult indicating success or failure.
+ */
+template <typename FP = double>
+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);
+}
+
+/**
+ * @brief Reads population data from a vector of population data entries.
+ * 
+ * @param[in] population_data Vector of population data entries.
+ * @param[in] vregion Vector of keys representing the regions of interest.
+ * @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.
+ */
+IOResult<std::vector<std::vector<double>>> read_population_data(const std::vector<PopulationDataEntry>& population_data,
+                                                                const std::vector<int>& vregion);
+
+/**
+ * @brief Reads population data from census data.
+ * 
+ * @param[in] path Path to the population data file.
+ * @param[in] vregion Vector of keys representing the regions of interest.
+ * @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.
+ */
+IOResult<std::vector<std::vector<double>>> read_population_data(const std::string& path,
+                                                                const std::vector<int>& vregion);
+
+} // namespace mio
+
+#endif //MEMILIO_HAS_JSONCPP
+
+#endif //MEMILIO_IO_PARAMETER_H

cpp/models/ode_secir/parameters_io.cpp

@@ -30,6 +30,7 @@ GCC_CLANG_DIAGNOSTIC(ignored "-Wmaybe-uninitialized")
 
 #include "ode_secir/parameters_io.h"
 #include "memilio/io/epi_data.h"
+#include "memilio/io/parameters_io.h"
 #include "memilio/io/io.h"
 #include "memilio/utils/stl_util.h"
 #include "memilio/utils/date.h"
@@ -42,15 +43,6 @@ namespace osecir
 
 namespace details
 {
-//district, county or state id of a data entry if available, 0 (for whole country) otherwise
-//used to compare data entries to integer ids in STL algorithms
-template <class EpiDataEntry>
-int get_region_id(const EpiDataEntry& entry)
-{
-    return entry.county_id
-               ? entry.county_id->get()
-               : (entry.state_id ? entry.state_id->get() : (entry.district_id ? entry.district_id->get() : 0));
-}
 //overload for integers, so the comparison of data entry to integers is symmetric (required by e.g. equal_range)
 int get_region_id(int id)
 {
@@ -195,76 +187,6 @@ IOResult<void> read_confirmed_cases_data(
     return success();
 }
 
-IOResult<void> read_divi_data(const std::string& path, const std::vector<int>& vregion, Date date,
-                              std::vector<double>& vnum_icu)
-{
-    BOOST_OUTCOME_TRY(auto&& divi_data, mio::read_divi_data(path));
-
-    auto max_date_entry = std::max_element(divi_data.begin(), divi_data.end(), [](auto&& a, auto&& b) {
-        return a.date < b.date;
-    });
-    if (max_date_entry == divi_data.end()) {
-        log_error("DIVI data file is empty.");
-        return failure(StatusCode::InvalidFileFormat, path + ", file is empty.");
-    }
-    auto max_date = max_date_entry->date;
-    if (max_date < date) {
-        log_error("Specified date does not exist in DIVI data.");
-        return failure(StatusCode::OutOfRange, path + ", specified date does not exist in DIVI data.");
-    }
-
-    for (auto&& entry : divi_data) {
-        auto it      = std::find_if(vregion.begin(), vregion.end(), [&entry](auto r) {
-            return r == 0 || r == get_region_id(entry);
-        });
-        auto date_df = entry.date;
-        if (it != vregion.end() && date_df == date) {
-            auto region_idx      = size_t(it - vregion.begin());
-            vnum_icu[region_idx] = entry.num_icu;
-        }
-    }
-
-    return success();
-}
-
-IOResult<std::vector<std::vector<double>>>
-read_population_data(const std::string& path, const std::vector<int>& vregion, bool accumulate_age_groups)
-{
-    BOOST_OUTCOME_TRY(auto&& population_data, mio::read_population_data(path, !accumulate_age_groups));
-    //if we set up the model for one age group, the population data should be read in with the
-    //age groups given in the population data json file and are accumulated later
-    //otherwise the populations are directly saved for the correct model age groups
-    size_t age_group_size = accumulate_age_groups ? PopulationDataEntry::age_group_names.size()
-                                                  : ConfirmedCasesDataEntry::age_group_names.size();
-    std::vector<std::vector<double>> vnum_population(vregion.size(), std::vector<double>(age_group_size, 0.0));
-
-    for (auto&& entry : population_data) {
-        auto it = std::find_if(vregion.begin(), vregion.end(), [&entry](auto r) {
-            return r == 0 || (entry.county_id && regions::StateId(r) == regions::get_state_id(int(*entry.county_id))) ||
-                   (entry.county_id && regions::CountyId(r) == *entry.county_id) ||
-                   (entry.district_id && regions::DistrictId(r) == *entry.district_id);
-        });
-        if (it != vregion.end()) {
-            auto region_idx      = size_t(it - vregion.begin());
-            auto& num_population = vnum_population[region_idx];
-            for (size_t age = 0; age < num_population.size(); age++) {
-                num_population[age] += entry.population[AgeGroup(age)];
-            }
-        }
-    }
-    if (accumulate_age_groups) {
-        std::vector<std::vector<double>> vnum_pop_acc(vregion.size(), std::vector<double>(1, 0));
-        for (size_t region = 0; region < vregion.size(); ++region) {
-            vnum_pop_acc[region][0] =
-                std::accumulate(vnum_population[region].begin(), vnum_population[region].end(), 0.0);
-        }
-        return success(vnum_pop_acc);
-    }
-    else {
-        return success(vnum_population);
-    }
-}
-
 } // namespace details
 } // namespace osecir
 } // namespace mio

cpp/models/ode_secir/parameters_io.h

@@ -27,6 +27,7 @@
 
 #include "ode_secir/model.h"
 #include "memilio/io/epi_data.h"
+#include "memilio/io/parameters_io.h"
 #include "memilio/io/result_io.h"
 
 namespace mio
@@ -170,16 +171,6 @@ IOResult<void> set_confirmed_cases_data(std::vector<Model<FP>>& model, const std
     return success();
 }
 
-/**
-     * @brief Reads number of ICU patients from DIVI register into Parameters.
-     * @param[in] path Path to DIVI file.
-     * @param[in] vregion Keys of the region of interest.
-     * @param date Date for which we initialize.
-     * @param vnum_icu Number of ICU patients.
-     */
-IOResult<void> read_divi_data(const std::string& path, const std::vector<int>& vregion, Date date,
-                              std::vector<double>& vnum_icu);
-
 /**
      * @brief Sets populations data from DIVI register into Model.
      * @tparam FP floating point data type, e.g., double.
@@ -225,16 +216,6 @@ IOResult<void> set_divi_data(std::vector<Model<FP>>& model, const std::string& p
     return success();
 }
 
-/**
-     * @brief Reads population data from census data.
-     * @tparam FP floating point data type, e.g., double.
-     * @param[in] path Path to RKI file.
-     * @param[in] vregion Vector of keys of the regions of interest. 
-     * @param[in] accumulate_age_groups Specifies whether population data should be accumulated to one age group.
-     */
-IOResult<std::vector<std::vector<double>>>
-read_population_data(const std::string& path, const std::vector<int>& vregion, bool accumulate_age_groups = false);
-
 /**
 * @brief Sets population data from census data which has been read into num_population.
 * @tparam FP floating point data type, e.g., double.
@@ -270,9 +251,7 @@ template <typename FP = double>
 IOResult<void> set_population_data(std::vector<Model<FP>>& model, const std::string& path,
                                    const std::vector<int>& vregion)
 {
-    // Specifies whether population data should be accumulated to one age group.
-    const bool is_single_age_group = static_cast<size_t>(model[0].parameters.get_num_groups()) == 1;
-    BOOST_OUTCOME_TRY(const auto&& num_population, read_population_data(path, vregion, is_single_age_group));
+    BOOST_OUTCOME_TRY(const auto&& num_population, read_population_data(path, vregion));
     BOOST_OUTCOME_TRY(set_population_data(model, num_population, vregion));
     return success();
 }
@@ -310,7 +289,7 @@ IOResult<void> export_input_data_county_timeseries(
     std::vector<TimeSeries<double>> extrapolated_data(
         region.size(), TimeSeries<double>::zero(num_days + 1, (size_t)InfectionState::Count * num_age_groups));
 
-    BOOST_OUTCOME_TRY(auto&& num_population, details::read_population_data(population_data_path, region));
+    BOOST_OUTCOME_TRY(auto&& num_population, mio::read_population_data(population_data_path, region));
     BOOST_OUTCOME_TRY(auto&& case_data, mio::read_confirmed_cases_data(confirmed_cases_path));
 
     for (int t = 0; t <= num_days; ++t) {