SBML import: Allow hardcoding of numerical values

python/sdist/amici/sbml_import.py

@@ -13,7 +13,18 @@
 import warnings
 import xml.etree.ElementTree as ET
 from pathlib import Path
-from typing import Any, Callable, Dict, Iterable, List, Optional, Set, Tuple, Union
+from typing import (
+    Any,
+    Callable,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    Sequence,
+    Set,
+    Tuple,
+    Union,
+)
 
 import libsbml as sbml
 import numpy as np
@@ -281,6 +292,7 @@ def sbml2amici(
         cache_simplify: bool = False,
         log_as_log10: bool = True,
         generate_sensitivity_code: bool = True,
+        hardcode_symbols: Sequence[str] = None,
     ) -> None:
         """
         Generate and compile AMICI C++ files for the model provided to the
@@ -385,6 +397,12 @@ def sbml2amici(
         :param generate_sensitivity_code:
             If ``False``, the code required for sensitivity computation will
             not be generated
+
+        :param hardcode_symbols:
+            List of SBML entitiy IDs that are to be hardcoded in the generated model.
+            Their values cannot be changed anymore after model import.
+            Currently only parameters that are not targets of rules or
+            initial assignments are supported.
         """
         set_log_level(logger, verbose)
 
@@ -401,6 +419,7 @@ def sbml2amici(
             simplify=simplify,
             cache_simplify=cache_simplify,
             log_as_log10=log_as_log10,
+            hardcode_symbols=hardcode_symbols,
         )
 
         exporter = DEExporter(
@@ -437,13 +456,21 @@ def _build_ode_model(
         simplify: Optional[Callable] = _default_simplify,
         cache_simplify: bool = False,
         log_as_log10: bool = True,
+        hardcode_symbols: Sequence[str] = None,
     ) -> DEModel:
         """Generate an ODEModel from this SBML model.
 
         See :py:func:`sbml2amici` for parameters.
         """
         constant_parameters = list(constant_parameters) if constant_parameters else []
 
+        hardcode_symbols = set(hardcode_symbols) if hardcode_symbols else {}
+        if invalid := (set(constant_parameters) & set(hardcode_symbols)):
+            raise ValueError(
+                "The following parameters were selected as both constant "
+                f"and hard-coded which is not allowed: {invalid}"
+            )
+
         if sigmas is None:
             sigmas = {}
 
@@ -460,7 +487,9 @@ def _build_ode_model(
         self.sbml_parser_settings.setParseLog(
             sbml.L3P_PARSE_LOG_AS_LOG10 if log_as_log10 else sbml.L3P_PARSE_LOG_AS_LN
         )
-        self._process_sbml(constant_parameters)
+        self._process_sbml(
+            constant_parameters=constant_parameters, hardcode_symbols=hardcode_symbols
+        )
 
         if (
             self.symbols.get(SymbolId.EVENT, False)
@@ -496,18 +525,26 @@ def _build_ode_model(
         return ode_model
 
     @log_execution_time("importing SBML", logger)
-    def _process_sbml(self, constant_parameters: List[str] = None) -> None:
+    def _process_sbml(
+        self,
+        constant_parameters: List[str] = None,
+        hardcode_symbols: Sequence[str] = None,
+    ) -> None:
         """
         Read parameters, species, reactions, and so on from SBML model
 
         :param constant_parameters:
             SBML Ids identifying constant parameters
+        :param hardcode_parameters:
+            Parameter IDs to be replaced by their values in the generated model.
         """
         if not self._discard_annotations:
             self._process_annotations()
         self.check_support()
-        self._gather_locals()
-        self._process_parameters(constant_parameters)
+        self._gather_locals(hardcode_symbols=hardcode_symbols)
+        self._process_parameters(
+            constant_parameters=constant_parameters, hardcode_symbols=hardcode_symbols
+        )
         self._process_compartments()
         self._process_species()
         self._process_reactions()
@@ -639,18 +676,18 @@ def check_event_support(self) -> None:
                 )
 
     @log_execution_time("gathering local SBML symbols", logger)
-    def _gather_locals(self) -> None:
+    def _gather_locals(self, hardcode_symbols: Sequence[str] = None) -> None:
         """
         Populate self.local_symbols with all model entities.
 
         This is later used during sympifications to avoid sympy builtins
         shadowing model entities as well as to avoid possibly costly
         symbolic substitutions
         """
-        self._gather_base_locals()
+        self._gather_base_locals(hardcode_symbols=hardcode_symbols)
         self._gather_dependent_locals()
 
-    def _gather_base_locals(self):
+    def _gather_base_locals(self, hardcode_symbols: Sequence[str] = None) -> None:
         """
         Populate self.local_symbols with pure symbol definitions that do not
         depend on any other symbol.
@@ -677,8 +714,19 @@ def _gather_base_locals(self):
         ):
             if not c.isSetId():
                 continue
-
-            self.add_local_symbol(c.getId(), _get_identifier_symbol(c))
+            if c.getId() in hardcode_symbols:
+                if self.sbml.getRuleByVariable(c.getId()) is not None:
+                    raise ValueError(
+                        f"Cannot hardcode symbol `{c.getId()}` that is a rule target."
+                    )
+                if self.sbml.getInitialAssignment(c.getId()):
+                    raise NotImplementedError(
+                        f"Cannot hardcode symbol `{c.getId()}` "
+                        "that is an initial assignment target."
+                    )
+                self.add_local_symbol(c.getId(), sp.Float(c.getValue()))
+            else:
+                self.add_local_symbol(c.getId(), _get_identifier_symbol(c))
 
         for x_ref in _get_list_of_species_references(self.sbml):
             if not x_ref.isSetId():
@@ -940,7 +988,11 @@ def _process_annotations(self) -> None:
             self.sbml.removeParameter(parameter_id)
 
     @log_execution_time("processing SBML parameters", logger)
-    def _process_parameters(self, constant_parameters: List[str] = None) -> None:
+    def _process_parameters(
+        self,
+        constant_parameters: List[str] = None,
+        hardcode_symbols: Sequence[str] = None,
+    ) -> None:
         """
         Get parameter information from SBML model.
 
@@ -983,6 +1035,7 @@ def _process_parameters(self, constant_parameters: List[str] = None) -> None:
             if parameter.getId() not in constant_parameters
             and self._get_element_initial_assignment(parameter.getId()) is None
             and not self.is_assignment_rule_target(parameter)
+            and parameter.getId() not in hardcode_symbols
         ]
 
         loop_settings = {

python/tests/test_sbml_import.py

@@ -38,7 +38,7 @@ def simple_sbml_model():
     model.addSpecies(s1)
     p1 = model.createParameter()
     p1.setId("p1")
-    p1.setValue(0.0)
+    p1.setValue(2.0)
     model.addParameter(p1)
 
     return document, model
@@ -662,3 +662,34 @@ def test_code_gen_uses_lhs_symbol_ids():
         )
         dwdx = Path(tmpdir, "dwdx.cpp").read_text()
     assert "dobservable_x1_dx1 = " in dwdx
+
+
+def test_hardcode_parameters(simple_sbml_model):
+    """Test model generation works for model without observables"""
+    sbml_doc, sbml_model = simple_sbml_model
+    sbml_importer = SbmlImporter(sbml_source=sbml_model, from_file=False)
+    r = sbml_model.createRateRule()
+    r.setVariable("S1")
+    r.setFormula("p1")
+    assert sbml_model.getParameter("p1").getValue() != 0
+
+    ode_model = sbml_importer._build_ode_model()
+    assert str(ode_model.parameters()) == "[p1]"
+    assert ode_model.differential_states()[0].get_dt().name == "p1"
+
+    ode_model = sbml_importer._build_ode_model(
+        constant_parameters=[],
+        hardcode_symbols=["p1"],
+    )
+    assert str(ode_model.parameters()) == "[]"
+    assert (
+        ode_model.differential_states()[0].get_dt()
+        == sbml_model.getParameter("p1").getValue()
+    )
+
+    with pytest.raises(ValueError):
+        sbml_importer._build_ode_model(
+            # mutually exclusive
+            constant_parameters=["p1"],
+            hardcode_symbols=["p1"],
+        )