added utils.field_data_refs(Biomodel) to query biomodel for field data

Author: jcschaff

poetry.lock

@@ -38,6 +38,7 @@ trame-vtk = "^2.8.15"
 trame-vuetify = "^2.8.1"
 pyvista = "^0.44.2"
 trame-server = "^3.4.0"
+sympy = "^1.13.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"

pyproject.toml

@@ -275,6 +275,19 @@ class SpeciesMapping(VcmlNode):
     diff_coef: float | str | None = None
     boundary_values: list[float | str | None] = Field(default_factory=list)
 
+    @property
+    def expressions(self) -> list[str]:
+        exps: list[str] = []
+        if isinstance(self.init_conc, str):
+            exps.append(self.init_conc)
+        if isinstance(self.diff_coef, str):
+            exps.append(self.diff_coef)
+        if self.boundary_values:
+            for value in self.boundary_values:
+                if isinstance(value, str):
+                    exps.append(value)
+        return exps
+
 
 class ReactionMapping(VcmlNode):
     reaction_name: str

pyvcell/vcml/models.py

@@ -1,10 +1,13 @@
 import tempfile
 from pathlib import Path
 
+import sympy  # type: ignore[import-untyped]
 from libvcell import sbml_to_vcml, vcml_to_sbml, vcml_to_vcml
+from sympy.parsing.sympy_parser import parse_expr  # type: ignore[import-untyped]
 
+from pyvcell._internal.simdata.simdata_models import VariableType
 from pyvcell.sbml.sbml_spatial_model import SbmlSpatialModel
-from pyvcell.vcml import VCMLDocument, VcmlReader, VcmlWriter
+from pyvcell.vcml import Application, VCMLDocument, VcmlReader, VcmlWriter
 from pyvcell.vcml.models import Biomodel
 
 
@@ -91,3 +94,55 @@ def to_sbml(bio_model: Biomodel, application_name: str, round_trip_validation: b
             raise ValueError(f"Failed to import SBML: {error_message}")
         sbml_spatial_model = SbmlSpatialModel(filepath=sbml_file_path)
         return sbml_spatial_model
+
+
+def field_data_refs(bio_model: Biomodel, simulation_name: str) -> set[tuple[str, str, VariableType, float]]:
+    """
+    Extract field data references from the VCML model and return them as a list of tuples.
+    Each tuple contains the following elements:
+    - field_data_name: str
+    - field_data_varname: str
+    - field_data_type: VariableType
+    - field_data_time: float
+    """
+    application: Application | None = None
+    for app in bio_model.applications:
+        for sim in app.simulations:
+            if sim.name == simulation_name:
+                application = app
+                break
+
+    if application is None:
+        raise ValueError(f"Simulation name '{simulation_name}' not found in VCML model")
+
+    # Extract field data references from the application (look in species mapping only for now)
+    function_calls: set[sympy.Function] = set()
+    for species_mapping in application.species_mappings:
+        for exp_str in species_mapping.expressions:
+            if "vcField(" in exp_str:
+                func_calls: set[sympy.Function] = parse_expr(exp_str).atoms(sympy.Function)
+                function_calls.update(func_calls)
+
+    field_data_refs: set[tuple[str, str, VariableType, float]] = set()
+    for func_call in function_calls:
+        # e.g. {vcField(test2_lsm_DEMO, species0_cyt, 17.0, Volume), exp(2)}
+        if func_call.func.__name__ == "vcField":
+            from typing import cast
+
+            data_name: sympy.Symbol = cast(sympy.Symbol, func_call.args[0])
+            varname: sympy.Symbol = cast(sympy.Symbol, func_call.args[1])
+            time: sympy.Number = cast(sympy.Number, func_call.args[2])
+            data_type: sympy.Symbol = cast(sympy.Symbol, func_call.args[3])
+            if not isinstance(data_name, sympy.Symbol):
+                raise ValueError(f"Invalid field data name: {data_name}")
+            if not isinstance(varname, sympy.Symbol):
+                raise ValueError(f"Invalid field data varname: {varname}")
+            if not isinstance(data_type, sympy.Symbol):
+                raise ValueError(f"Invalid field data type: {data_type}")
+            if not isinstance(time, sympy.Number):
+                raise ValueError(f"Invalid field data time: {time}")
+            if data_type.name.upper() != VariableType.VOLUME.name:
+                raise ValueError(f"Invalid field data type: {data_type}, expected 'Volume'")
+            field_data_refs.add((data_name.name, varname.name, VariableType.VOLUME, float(time)))
+
+    return field_data_refs

pyvcell/vcml/utils.py

@@ -2,8 +2,10 @@
 import tempfile
 from pathlib import Path
 
+from pyvcell._internal.simdata.simdata_models import VariableType
 from pyvcell.sim_results.result import Result
 from pyvcell.vcml import Biomodel, ModelParameter, VcmlReader
+from pyvcell.vcml.utils import field_data_refs
 from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation
 
 
@@ -44,6 +46,12 @@ def test_vcml_field_data_demo(vcml_field_data_demo_path: Path, vcml_field_data_t
         "species0_cyt",
         "species0_ec",
     ]
+
+    refs = field_data_refs(bio_model=bio_model, simulation_name=sim_name)
+    assert refs == {
+        ("test2_lsm_DEMO", "species0_cyt", VariableType.VOLUME, 0.5),
+        ("test2_lsm_DEMO", "species0_ec", VariableType.VOLUME, 0.5),
+    }
     # assert np.allclose(
     #     results_orig.concentrations[0, 0::10],
     #     np.array(

tests/vcml/test_fielddata.py

@@ -2,9 +2,10 @@
 
 import pytest
 
+from pyvcell._internal.simdata.simdata_models import VariableType
 from pyvcell.sbml.sbml_spatial_model import SbmlSpatialModel
 from pyvcell.vcml import Biomodel, VcmlReader
-from pyvcell.vcml.utils import from_sbml, to_sbml, update_biomodel
+from pyvcell.vcml.utils import field_data_refs, from_sbml, to_sbml, update_biomodel
 
 
 def test_update(vcml_spatial_model_1d_path: Path) -> None:
@@ -85,3 +86,15 @@ def test_from_sbml(sbml_spatial_model_1d_path: Path) -> None:
     sbml_spatial_model = SbmlSpatialModel(sbml_spatial_model_1d_path)
     bio_model: Biomodel = from_sbml(sbml_spatial_model=sbml_spatial_model)
     assert bio_model is not None
+
+
+def test_extract_field_data_refs(vcml_field_data_demo_path: Path) -> None:
+    assert vcml_field_data_demo_path.is_file()
+
+    bio_model: Biomodel = VcmlReader.biomodel_from_file(vcml_source=vcml_field_data_demo_path)
+    assert bio_model.model is not None
+    refs = field_data_refs(bio_model=bio_model, simulation_name="Simulation0")
+    assert refs == {
+        ("test2_lsm_DEMO", "species0_cyt", VariableType.VOLUME, 0.5),
+        ("test2_lsm_DEMO", "species0_ec", VariableType.VOLUME, 0.5),
+    }