Add v2.Problem.{get_output_parameters,get_x_nominal_dict} (PEtab-dev#447)

* Add `v2.Problem.{get_output_parameters,get_x_nominal_dict}`

* Move `get_output_parameters` from v2.lint to v2.Problem
* Add `Problem.get_x_nominal_dict`
* Test

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

Author: dweindl

petab/v1/observables.py

@@ -84,7 +84,7 @@ def get_output_parameters(
 ) -> list[str]:
     """Get output parameters
 
-    Returns IDs of parameters used in observable and noise formulas that are
+    Returns IDs of parameters used in observable or noise formulas that are
     not defined in the model.
 
     Arguments:

petab/v2/core.py

@@ -1693,6 +1693,27 @@ def get_x_nominal(self, free: bool = True, fixed: bool = True) -> list:
 
         return self._apply_mask(v, free=free, fixed=fixed)
 
+    def get_x_nominal_dict(
+        self, free: bool = True, fixed: bool = True
+    ) -> dict[str, float]:
+        """Get parameter nominal values as dict.
+
+        :param free:
+            Whether to return free parameters, i.e. parameters to estimate.
+        :param fixed:
+            Whether to return fixed parameters, i.e. parameters not to
+            estimate.
+        :returns:
+            A dictionary mapping parameter IDs to their nominal values.
+        """
+        return dict(
+            zip(
+                self.get_x_ids(free=free, fixed=fixed),
+                self.get_x_nominal(free=free, fixed=fixed),
+                strict=True,
+            )
+        )
+
     @property
     def x_nominal(self) -> list:
         """Parameter table nominal values"""
@@ -2259,6 +2280,65 @@ def get_measurements_for_experiment(
             if measurement.experiment_id == experiment.id
         ]
 
+    def get_output_parameters(
+        self, observable: bool = True, noise: bool = True
+    ) -> list[str]:
+        """Get output parameters.
+
+        Returns IDs of symbols used in observable and noise formulas that are
+        not observables and that are not defined in the model.
+
+        :param observable:
+            Include parameters from observableFormulas
+        :param noise:
+            Include parameters from noiseFormulas
+        :returns:
+            List of output parameter IDs, including any placeholder parameters.
+        """
+        # collect free symbols from observable and noise formulas,
+        # skipping observable IDs
+        candidates = set()
+        if observable:
+            candidates |= {
+                str_sym
+                for o in self.observables
+                if o.formula is not None
+                for sym in o.formula.free_symbols
+                if (str_sym := str(sym)) != o.id
+            }
+        if noise:
+            candidates |= {
+                str_sym
+                for o in self.observables
+                if o.noise_formula is not None
+                for sym in o.noise_formula.free_symbols
+                if (str_sym := str(sym)) != o.id
+            }
+
+        output_parameters = []
+
+        # filter out symbols that are defined in the model or mapped to
+        #  such symbols
+        for candidate in sorted(candidates):
+            if self.model.symbol_allowed_in_observable_formula(candidate):
+                continue
+
+            # does it map to a model entity?
+            for mapping in self.mappings:
+                if (
+                    mapping.petab_id == candidate
+                    and mapping.model_id is not None
+                ):
+                    if self.model.symbol_allowed_in_observable_formula(
+                        mapping.model_id
+                    ):
+                        break
+            else:
+                # no mapping to a model entity, so it is an output parameter
+                output_parameters.append(candidate)
+
+        return output_parameters
+
 
 class ModelFile(BaseModel):
     """A file in the PEtab problem configuration."""

petab/v2/lint.py

@@ -396,7 +396,7 @@ def run(self, problem: Problem) -> ValidationIssue | None:
             if problem.model
             else set()
         )
-        allowed_targets |= set(get_output_parameters(problem))
+        allowed_targets |= set(problem.get_output_parameters())
         allowed_targets |= {
             m.petab_id for m in problem.mappings if m.model_id is not None
         }
@@ -932,7 +932,7 @@ def get_valid_parameters_for_parameter_table(
             parameter_ids[mapping.petab_id] = None
 
     # add output parameters from observable table
-    output_parameters = get_output_parameters(problem)
+    output_parameters = problem.get_output_parameters()
     for p in output_parameters:
         if p not in invalid:
             parameter_ids[p] = None
@@ -996,19 +996,18 @@ def append_overrides(overrides):
     for formula_type, placeholder_sources in (
         (
             # Observable formulae
-            {"observables": True, "noise": False},
+            {"observable": True, "noise": False},
             # can only contain observable placeholders
-            {"noise": False, "observables": True},
+            {"noise": False, "observable": True},
         ),
         (
             # Noise formulae
-            {"observables": False, "noise": True},
+            {"observable": False, "noise": True},
             # can contain noise and observable placeholders
-            {"noise": True, "observables": True},
+            {"noise": True, "observable": True},
         ),
     ):
-        output_parameters = get_output_parameters(
-            problem,
+        output_parameters = problem.get_output_parameters(
             **formula_type,
         )
         placeholders = get_placeholders(
@@ -1034,77 +1033,17 @@ def append_overrides(overrides):
     return parameter_ids
 
 
-def get_output_parameters(
-    problem: Problem,
-    observables: bool = True,
-    noise: bool = True,
-) -> list[str]:
-    """Get output parameters
-
-    Returns IDs of symbols used in observable and noise formulas that are
-    not observables and that are not defined in the model.
-
-    Arguments:
-        problem: The PEtab problem
-        observables: Include parameters from observableFormulas
-        noise: Include parameters from noiseFormulas
-
-    Returns:
-        List of output parameter IDs, including any placeholder parameters.
-    """
-    # collect free symbols from observable and noise formulas,
-    # skipping observable IDs
-    candidates = set()
-    if observables:
-        candidates |= {
-            str_sym
-            for o in problem.observables
-            if o.formula is not None
-            for sym in o.formula.free_symbols
-            if (str_sym := str(sym)) != o.id
-        }
-    if noise:
-        candidates |= {
-            str_sym
-            for o in problem.observables
-            if o.noise_formula is not None
-            for sym in o.noise_formula.free_symbols
-            if (str_sym := str(sym)) != o.id
-        }
-
-    output_parameters = OrderedDict()
-
-    # filter out symbols that are defined in the model or mapped to
-    #  such symbols
-    for candidate in sorted(candidates):
-        if problem.model.symbol_allowed_in_observable_formula(candidate):
-            continue
-
-        # does it map to a model entity?
-        for mapping in problem.mappings:
-            if mapping.petab_id == candidate and mapping.model_id is not None:
-                if problem.model.symbol_allowed_in_observable_formula(
-                    mapping.model_id
-                ):
-                    break
-        else:
-            # no mapping to a model entity, so it is an output parameter
-            output_parameters[candidate] = None
-
-    return list(output_parameters.keys())
-
-
 def get_placeholders(
     problem: Problem,
-    observables: bool = True,
+    observable: bool = True,
     noise: bool = True,
 ) -> list[str]:
     """Get all placeholder parameters from observable table observableFormulas
     and noiseFormulas.
 
     Arguments:
         problem: The PEtab problem
-        observables: Include parameters from observableFormulas
+        observable: Include parameters from observableFormulas
         noise: Include parameters from noiseFormulas
 
     Returns:
@@ -1115,7 +1054,7 @@ def get_placeholders(
     # {observable,noise}Parameters
     placeholders = []
     for o in problem.observables:
-        if observables:
+        if observable:
             placeholders.extend(map(str, o.observable_placeholders))
         if noise:
             placeholders.extend(map(str, o.noise_placeholders))

tests/v2/test_core.py

@@ -762,3 +762,77 @@ def make_yaml(id_line: str) -> str:
         f.write(make_yaml(""))
     problem = Problem.from_yaml(filepath)
     assert problem.id is None
+
+
+def test_parameter_accessors():  # pylint: disable=W0621
+    """
+    Test the petab.Problem functions to get parameter values.
+    """
+    petab_problem = Problem()
+    petab_problem += Parameter(
+        id="par1", lb=0, ub=100, nominal_value=7, estimate=True
+    )
+    petab_problem += Parameter(
+        id="par2", lb=0.1, ub=100, nominal_value=8, estimate=True
+    )
+    petab_problem += Parameter(
+        id="par3", lb=0.1, ub=200, nominal_value=9, estimate=False
+    )
+
+    assert petab_problem.x_ids == ["par1", "par2", "par3"]
+    assert petab_problem.x_free_ids == ["par1", "par2"]
+    assert petab_problem.x_fixed_ids == ["par3"]
+    assert petab_problem.lb == [0, 0.1, 0.1]
+    assert petab_problem.ub == [100, 100, 200]
+    assert petab_problem.x_nominal == [7, 8, 9]
+    assert petab_problem.x_nominal_free == [7, 8]
+    assert petab_problem.x_nominal_fixed == [9]
+
+    assert (
+        petab_problem.get_x_nominal_dict()
+        == petab_problem.get_x_nominal_dict(free=True, fixed=True)
+        == {
+            "par1": 7,
+            "par2": 8,
+            "par3": 9,
+        }
+    )
+    assert petab_problem.get_x_nominal_dict(free=True, fixed=False) == {
+        "par1": 7,
+        "par2": 8,
+    }
+    assert petab_problem.get_x_nominal_dict(free=False, fixed=True) == {
+        "par3": 9,
+    }
+
+
+def test_get_output_parameters():
+    """Test Problem.get_output_parameters"""
+    petab_problem = Problem()
+    assert petab_problem.get_output_parameters() == []
+
+    petab_problem += Parameter(id="p1", lb=0, ub=100, estimate=True)
+    petab_problem.models.append(SbmlModel.from_antimony("p2 = 1"))
+    assert petab_problem.get_output_parameters() == []
+
+    petab_problem += Observable(
+        id="obs1", formula="p1 + p2", noise_formula="p1 * p2"
+    )
+    assert petab_problem.get_output_parameters() == ["p1"]
+
+    petab_problem += Observable(
+        id="obs1",
+        formula="p3 + p4",
+        noise_formula="p3 * p5",
+    )
+    assert (
+        petab_problem.get_output_parameters()
+        == petab_problem.get_output_parameters(observable=True, noise=True)
+        == ["p1", "p3", "p4", "p5"]
+    )
+    assert petab_problem.get_output_parameters(
+        observable=True, noise=False
+    ) == ["p1", "p3", "p4"]
+    assert petab_problem.get_output_parameters(
+        observable=False, noise=True
+    ) == ["p1", "p3", "p5"]