Store model entity IDs and names in ReturnData

CHANGELOG.md

@@ -109,6 +109,10 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 * The default directory for model import changed, and a base directory
   can now be specified via the `AMICI_MODELS_ROOT` environment variable.
   See `amici.get_model_dir` for details.
+* IDs and names of model entities are now not only accessible via `Model`, but
+  also via `ReturnData`
+  (`ReturnData.{free_parameter_ids,observable_ids,...}`,
+  `ReturnData.{free_parameter_names,observable_names,...}`).
 
 **Fixes**
 

include/amici/rdata.h

@@ -9,6 +9,8 @@
 #include "amici/vector.h"
 
 #include <vector>
+#include <span>
+#include <string_view>
 
 namespace amici {
 class ReturnData;
@@ -28,7 +30,7 @@ void serialize(Archive& ar, amici::ReturnData& r, unsigned int version);
 namespace amici {
 
 /**
- * @brief Stores all data to be returned by amici::runAmiciSimulation.
+ * @brief Stores all data to be returned by amici::run_simulation.
  *
  * NOTE: multi-dimensional arrays are stored in row-major order (C-style)
  */
@@ -57,14 +59,38 @@ class ReturnData : public ModelDimensions {
      * @param sigma_res_ indicates whether additional residuals are to be added
      * for each sigma
      * @param sigma_offset_ offset to ensure real-valuedness of sigma residuals
+     * @param free_parameter_ids_ IDs of the free parameters
+     * @param free_parameter_names_ Names of the free parameters
+     * @param fixed_parameter_ids_ IDs of the fixed parameters
+     * @param fixed_parameter_names_ Names of the fixed parameters
+     * @param state_ids_ IDs of state variables
+     * @param state_names_ Names of state variables
+     * @param state_ids_solver_ IDs of solver state variables
+     * @param state_names_solver_ Names of solver state variables
+     * @param observable_ids_ IDs of observables
+     * @param observable_names_ Names of observables
+     * @param expression_ids_ IDs of expressions
+     * @param expression_names_ Names of expressions
      */
     ReturnData(
         std::vector<realtype> ts_, ModelDimensions const& model_dimensions_,
         int nmaxevent_, int newton_maxsteps_, std::vector<int> plist_,
         std::vector<ParameterScaling> pscale_, SecondOrderMode o2mode_,
         SensitivityOrder sensi_, SensitivityMethod sensi_meth_,
         RDataReporting rdrm_, bool quadratic_llh_, bool sigma_res_,
-        realtype sigma_offset_
+        realtype sigma_offset_,
+        std::span<std::string_view const> free_parameter_ids_,
+        std::span<std::string_view const> free_parameter_names_,
+        std::span<std::string_view const> fixed_parameter_ids_,
+        std::span<std::string_view const> fixed_parameter_names_,
+        std::span<std::string_view const> state_ids_,
+        std::span<std::string_view const> state_names_,
+        std::span<std::string_view const> state_ids_solver_,
+        std::span<std::string_view const> state_names_solver_,
+        std::span<std::string_view const> observable_ids_,
+        std::span<std::string_view const> observable_names_,
+        std::span<std::string_view const> expression_ids_,
+        std::span<std::string_view const> expression_names_
     );
 
     /**
@@ -112,7 +138,7 @@ class ReturnData : public ModelDimensions {
      * (shape `nx_solver` x `nx_solver`, row-major) evaluated at `t_last`.
      *
      * The corresponding state variable IDs can be obtained from
-     * `Model::getStateIdsSolver()`.
+     * `state_ids_solver()`.
      */
     std::vector<realtype> J;
 
@@ -124,7 +150,7 @@ class ReturnData : public ModelDimensions {
      * at timepoints `ReturnData::ts` (shape `nt` x `nw`, row major).
      *
      * The corresponding expression IDs can be obtained from
-     * `Model::getExpressionIds()`.
+     * `expression_ids`.
      */
     std::vector<realtype> w;
 
@@ -171,7 +197,7 @@ class ReturnData : public ModelDimensions {
      * (shape `nt` x `nx_rdata`, row-major).
      *
      * The corresponding state variable IDs can be obtained from
-     * `Model::getStateIds()`.
+     * `state_ids`.
      */
     std::vector<realtype> x;
 
@@ -184,7 +210,7 @@ class ReturnData : public ModelDimensions {
      * (shape `nt` x `nplist` x `nx_rdata`, row-major).
      *
      * The corresponding state variable IDs can be obtained from
-     * `Model::getStateIds()`.
+     * `state_ids`.
      */
     std::vector<realtype> sx;
 
@@ -195,7 +221,7 @@ class ReturnData : public ModelDimensions {
      * (shape `nt` x `ny`, row-major).
      *
      * The corresponding observable IDs can be obtained from
-     * `Model::getObservableIds()`.
+     * `observable_ids`.
      */
     std::vector<realtype> y;
 
@@ -211,7 +237,7 @@ class ReturnData : public ModelDimensions {
      * (shape `nt` x `nplist` x `ny`, row-major).
      *
      * The corresponding observable IDs can be obtained from
-     * `Model::getObservableIds()`.
+     * `observable_ids`.
      */
     std::vector<realtype> sy;
 
@@ -412,7 +438,7 @@ class ReturnData : public ModelDimensions {
      * @brief Initial state of the main simulation (shape `nx_rdata`).
      *
      * The corresponding state variable IDs can be obtained from
-     * `Model::getStateIds()`.
+     * `state_ids`.
      */
     std::vector<realtype> x0;
 
@@ -422,7 +448,7 @@ class ReturnData : public ModelDimensions {
      * The values of the state variables at the pre-equilibration steady state
      * (shape `nx_rdata`).
      * The corresponding state variable IDs can be obtained from
-     * `Model::getStateIds()`.
+     * `state_ids`.
      */
     std::vector<realtype> x_ss;
 
@@ -526,10 +552,46 @@ class ReturnData : public ModelDimensions {
      * @brief Indices of the parameters w.r.t. which sensitivities were
      * computed.
      *
-     * The indices refer to parameter IDs in Model::getParameterIds().
+     * The indices refer to parameter IDs in `free_parameter_ids`.
      */
     std::vector<int> plist;
 
+    /** IDs of the free parameters */
+    std::span<std::string_view const> free_parameter_ids;
+
+    /** Names of the free parameters */
+    std::span<std::string_view const> free_parameter_names;
+
+    /** IDs of the fixed parameters */
+    std::span<std::string_view const> fixed_parameter_ids;
+
+    /** Names of the fixed parameters */
+    std::span<std::string_view const> fixed_parameter_names;
+
+    /** IDs of state variables */
+    std::span<std::string_view const> state_ids;
+
+    /** Names of state variables */
+    std::span<std::string_view const> state_names;
+
+    /** IDs of solver state variables */
+    std::span<std::string_view const> state_ids_solver;
+
+    /** Names of solver state variables */
+    std::span<std::string_view const> state_names_solver;
+
+    /** IDs of observables */
+    std::span<std::string_view const> observable_ids;
+
+    /** Names of observables */
+    std::span<std::string_view const> observable_names;
+
+    /** IDs of expressions */
+    std::span<std::string_view const> expression_ids;
+
+    /** Names of expressions */
+    std::span<std::string_view const> expression_names;
+
   protected:
     /** offset for sigma_residuals */
     realtype sigma_offset{0.0};

python/sdist/amici/sim/sundials/_swig_wrappers.py

@@ -21,7 +21,6 @@
     AmiciExpDataVector,
     AmiciModel,
     AmiciSolver,
-    RDataReporting,
     SensitivityMethod,
     SensitivityOrder,
     Solver,
@@ -82,8 +81,6 @@ def run_simulation(
         _get_ptr(solver), _get_ptr(edata), _get_ptr(model)
     )
     _log_simulation(rdata)
-    if solver.get_return_data_reporting_mode() == RDataReporting.full:
-        _ids_and_names_to_rdata(rdata, model)
     return ReturnDataView(rdata)
 
 
@@ -129,8 +126,6 @@ def run_simulations(
     )
     for rdata in rdata_ptr_list:
         _log_simulation(rdata)
-        if solver.get_return_data_reporting_mode() == RDataReporting.full:
-            _ids_and_names_to_rdata(rdata, model)
 
     return [ReturnDataView(r) for r in rdata_ptr_list]
 
@@ -269,29 +264,6 @@ def _log_simulation(rdata: amici_swig.ReturnData):
         )
 
 
-def _ids_and_names_to_rdata(
-    rdata: amici_swig.ReturnData, model: amici_swig.Model
-):
-    """Copy entity IDs and names from a Model to ReturnData."""
-    for entity_type in (
-        "state",
-        "observable",
-        "expression",
-        "free_parameter",
-        "fixed_parameter",
-    ):
-        for name_or_id in ("ids", "names"):
-            names_or_ids = getattr(model, f"get_{entity_type}_{name_or_id}")()
-            setattr(
-                rdata,
-                f"{entity_type.lower()}_{name_or_id.lower()}",
-                names_or_ids,
-            )
-
-    rdata.state_ids_solver = model.get_state_ids_solver()
-    rdata.state_names_solver = model.get_state_names_solver()
-
-
 @contextlib.contextmanager
 def _solver_settings(solver, sensi_method=None, sensi_order=None):
     """Context manager to temporarily apply solver settings."""

python/tests/test_swig_interface.py

@@ -604,6 +604,23 @@ def test_rdataview(sbml_example_presimulation_module):
                 print(str(e))
 
 
+def test_rdata_ids(sbml_example_presimulation_module):
+    """Test that rdata IDs are correctly set."""
+    model_module = sbml_example_presimulation_module
+    model = model_module.get_model()
+
+    model.set_timepoints([0, 1, 2])
+    rdata = model.simulate()
+
+    assert isinstance(rdata.free_parameter_ids, tuple)
+    assert rdata.free_parameter_ids == model.get_free_parameter_ids()
+    assert rdata.fixed_parameter_ids == model.get_fixed_parameter_ids()
+    assert rdata.state_ids == model.get_state_ids()
+    assert rdata.state_ids_solver == model.get_state_ids_solver()
+    assert rdata.observable_ids == model.get_observable_ids()
+    assert rdata.expression_ids == model.get_expression_ids()
+
+
 def test_python_exceptions(sbml_example_presimulation_module):
     """Test that C++ exceptions are correctly caught and re-raised in Python."""
     from amici.sim.sundials import run_simulation

src/rdata.cpp

@@ -25,7 +25,13 @@ ReturnData::ReturnData(Solver const& solver, Model const& model)
           model.get_second_order_mode(), solver.get_sensitivity_order(),
           solver.get_sensitivity_method(),
           solver.get_return_data_reporting_mode(), model.has_quadratic_llh(),
-          model.get_add_sigma_residuals(), model.get_minimum_sigma_residuals()
+          model.get_add_sigma_residuals(), model.get_minimum_sigma_residuals(),
+          model.get_free_parameter_ids(), model.get_free_parameter_names(),
+          model.get_fixed_parameter_ids(), model.get_fixed_parameter_names(),
+          model.get_state_ids(), model.get_state_names(),
+          model.get_state_ids_solver(), model.get_state_names_solver(),
+          model.get_observable_ids(), model.get_observable_names(),
+          model.get_expression_ids(), model.get_expression_names()
       ) {}
 
 ReturnData::ReturnData(
@@ -34,7 +40,19 @@ ReturnData::ReturnData(
     std::vector<ParameterScaling> pscale_, SecondOrderMode o2mode_,
     SensitivityOrder sensi_, SensitivityMethod sensi_meth_,
     RDataReporting rdrm_, bool quadratic_llh_, bool sigma_res_,
-    realtype sigma_offset_
+    realtype sigma_offset_,
+    std::span<std::string_view const> free_parameter_ids_,
+    std::span<std::string_view const> free_parameter_names_,
+    std::span<std::string_view const> fixed_parameter_ids_,
+    std::span<std::string_view const> fixed_parameter_names_,
+    std::span<std::string_view const> state_ids_,
+    std::span<std::string_view const> state_names_,
+    std::span<std::string_view const> state_ids_solver_,
+    std::span<std::string_view const> state_names_solver_,
+    std::span<std::string_view const> observable_ids_,
+    std::span<std::string_view const> observable_names_,
+    std::span<std::string_view const> expression_ids_,
+    std::span<std::string_view const> expression_names_
 )
     : ModelDimensions(model_dimensions_)
     , ts(std::move(ts_))
@@ -49,6 +67,18 @@ ReturnData::ReturnData(
     , rdata_reporting(rdrm_)
     , sigma_res(sigma_res_)
     , plist(plist_)
+    , free_parameter_ids(free_parameter_ids_)
+    , free_parameter_names(free_parameter_names_)
+    , fixed_parameter_ids(fixed_parameter_ids_)
+    , fixed_parameter_names(fixed_parameter_names_)
+    , state_ids(state_ids_)
+    , state_names(state_names_)
+    , state_ids_solver(state_ids_solver_)
+    , state_names_solver(state_names_solver_)
+    , observable_ids(observable_ids_)
+    , observable_names(observable_names_)
+    , expression_ids(expression_ids_)
+    , expression_names(expression_names_)
     , sigma_offset(sigma_offset_)
     , nroots_(ne) {
     model_dimensions_.validate();

tests/cpp/testfunctions.cpp

@@ -24,10 +24,10 @@ extern std::unique_ptr<amici::Model> get_model();
 } // namespace generic_model
 
 std::map<std::string, std::vector<std::string_view>> var_names {
-    {"p", {"p0", "p1", "p2", "p3", "p4"}},
-    {"k", {"k0", "k1", "k2"}},
+    {"p", {"p0", "p1", "p2", "p3", "p4", "p5"}},
+    {"k", {"k0", "k1", "k2", "k3", "k4", "p5"}},
     {"x", {"x0", "x1", "x2", "x3", "x4", "x5"}},
-    {"y", {"y0", "y1", "y2"}}
+    {"y", {"y0", "y1", "y2", "y3", "y4", "y5"}}
 };
 
 std::span<std::string_view const> getVariableNames(std::string const& name, int length) {