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Commit880741a

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dweindldilpath
andauthored
Addv2.Problem.{get_output_parameters,get_x_nominal_dict} (#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`* TestCo-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
1 parent1c3b759 commit880741a

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‎petab/v1/observables.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ def get_output_parameters(
8484
)->list[str]:
8585
"""Get output parameters
8686
87-
Returns IDs of parameters used in observableand noise formulas that are
87+
Returns IDs of parameters used in observableor noise formulas that are
8888
not defined in the model.
8989
9090
Arguments:

‎petab/v2/core.py‎

Lines changed: 80 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1693,6 +1693,27 @@ def get_x_nominal(self, free: bool = True, fixed: bool = True) -> list:
16931693

16941694
returnself._apply_mask(v,free=free,fixed=fixed)
16951695

1696+
defget_x_nominal_dict(
1697+
self,free:bool=True,fixed:bool=True
1698+
)->dict[str,float]:
1699+
"""Get parameter nominal values as dict.
1700+
1701+
:param free:
1702+
Whether to return free parameters, i.e. parameters to estimate.
1703+
:param fixed:
1704+
Whether to return fixed parameters, i.e. parameters not to
1705+
estimate.
1706+
:returns:
1707+
A dictionary mapping parameter IDs to their nominal values.
1708+
"""
1709+
returndict(
1710+
zip(
1711+
self.get_x_ids(free=free,fixed=fixed),
1712+
self.get_x_nominal(free=free,fixed=fixed),
1713+
strict=True,
1714+
)
1715+
)
1716+
16961717
@property
16971718
defx_nominal(self)->list:
16981719
"""Parameter table nominal values"""
@@ -2259,6 +2280,65 @@ def get_measurements_for_experiment(
22592280
ifmeasurement.experiment_id==experiment.id
22602281
]
22612282

2283+
defget_output_parameters(
2284+
self,observable:bool=True,noise:bool=True
2285+
)->list[str]:
2286+
"""Get output parameters.
2287+
2288+
Returns IDs of symbols used in observable and noise formulas that are
2289+
not observables and that are not defined in the model.
2290+
2291+
:param observable:
2292+
Include parameters from observableFormulas
2293+
:param noise:
2294+
Include parameters from noiseFormulas
2295+
:returns:
2296+
List of output parameter IDs, including any placeholder parameters.
2297+
"""
2298+
# collect free symbols from observable and noise formulas,
2299+
# skipping observable IDs
2300+
candidates=set()
2301+
ifobservable:
2302+
candidates|= {
2303+
str_sym
2304+
foroinself.observables
2305+
ifo.formulaisnotNone
2306+
forsymino.formula.free_symbols
2307+
if (str_sym:=str(sym))!=o.id
2308+
}
2309+
ifnoise:
2310+
candidates|= {
2311+
str_sym
2312+
foroinself.observables
2313+
ifo.noise_formulaisnotNone
2314+
forsymino.noise_formula.free_symbols
2315+
if (str_sym:=str(sym))!=o.id
2316+
}
2317+
2318+
output_parameters= []
2319+
2320+
# filter out symbols that are defined in the model or mapped to
2321+
# such symbols
2322+
forcandidateinsorted(candidates):
2323+
ifself.model.symbol_allowed_in_observable_formula(candidate):
2324+
continue
2325+
2326+
# does it map to a model entity?
2327+
formappinginself.mappings:
2328+
if (
2329+
mapping.petab_id==candidate
2330+
andmapping.model_idisnotNone
2331+
):
2332+
ifself.model.symbol_allowed_in_observable_formula(
2333+
mapping.model_id
2334+
):
2335+
break
2336+
else:
2337+
# no mapping to a model entity, so it is an output parameter
2338+
output_parameters.append(candidate)
2339+
2340+
returnoutput_parameters
2341+
22622342

22632343
classModelFile(BaseModel):
22642344
"""A file in the PEtab problem configuration."""

‎petab/v2/lint.py‎

Lines changed: 10 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -396,7 +396,7 @@ def run(self, problem: Problem) -> ValidationIssue | None:
396396
ifproblem.model
397397
elseset()
398398
)
399-
allowed_targets|=set(get_output_parameters(problem))
399+
allowed_targets|=set(problem.get_output_parameters())
400400
allowed_targets|= {
401401
m.petab_idforminproblem.mappingsifm.model_idisnotNone
402402
}
@@ -932,7 +932,7 @@ def get_valid_parameters_for_parameter_table(
932932
parameter_ids[mapping.petab_id]=None
933933

934934
# add output parameters from observable table
935-
output_parameters=get_output_parameters(problem)
935+
output_parameters=problem.get_output_parameters()
936936
forpinoutput_parameters:
937937
ifpnotininvalid:
938938
parameter_ids[p]=None
@@ -996,19 +996,18 @@ def append_overrides(overrides):
996996
forformula_type,placeholder_sourcesin (
997997
(
998998
# Observable formulae
999-
{"observables":True,"noise":False},
999+
{"observable":True,"noise":False},
10001000
# can only contain observable placeholders
1001-
{"noise":False,"observables":True},
1001+
{"noise":False,"observable":True},
10021002
),
10031003
(
10041004
# Noise formulae
1005-
{"observables":False,"noise":True},
1005+
{"observable":False,"noise":True},
10061006
# can contain noise and observable placeholders
1007-
{"noise":True,"observables":True},
1007+
{"noise":True,"observable":True},
10081008
),
10091009
):
1010-
output_parameters=get_output_parameters(
1011-
problem,
1010+
output_parameters=problem.get_output_parameters(
10121011
**formula_type,
10131012
)
10141013
placeholders=get_placeholders(
@@ -1034,77 +1033,17 @@ def append_overrides(overrides):
10341033
returnparameter_ids
10351034

10361035

1037-
defget_output_parameters(
1038-
problem:Problem,
1039-
observables:bool=True,
1040-
noise:bool=True,
1041-
)->list[str]:
1042-
"""Get output parameters
1043-
1044-
Returns IDs of symbols used in observable and noise formulas that are
1045-
not observables and that are not defined in the model.
1046-
1047-
Arguments:
1048-
problem: The PEtab problem
1049-
observables: Include parameters from observableFormulas
1050-
noise: Include parameters from noiseFormulas
1051-
1052-
Returns:
1053-
List of output parameter IDs, including any placeholder parameters.
1054-
"""
1055-
# collect free symbols from observable and noise formulas,
1056-
# skipping observable IDs
1057-
candidates=set()
1058-
ifobservables:
1059-
candidates|= {
1060-
str_sym
1061-
foroinproblem.observables
1062-
ifo.formulaisnotNone
1063-
forsymino.formula.free_symbols
1064-
if (str_sym:=str(sym))!=o.id
1065-
}
1066-
ifnoise:
1067-
candidates|= {
1068-
str_sym
1069-
foroinproblem.observables
1070-
ifo.noise_formulaisnotNone
1071-
forsymino.noise_formula.free_symbols
1072-
if (str_sym:=str(sym))!=o.id
1073-
}
1074-
1075-
output_parameters=OrderedDict()
1076-
1077-
# filter out symbols that are defined in the model or mapped to
1078-
# such symbols
1079-
forcandidateinsorted(candidates):
1080-
ifproblem.model.symbol_allowed_in_observable_formula(candidate):
1081-
continue
1082-
1083-
# does it map to a model entity?
1084-
formappinginproblem.mappings:
1085-
ifmapping.petab_id==candidateandmapping.model_idisnotNone:
1086-
ifproblem.model.symbol_allowed_in_observable_formula(
1087-
mapping.model_id
1088-
):
1089-
break
1090-
else:
1091-
# no mapping to a model entity, so it is an output parameter
1092-
output_parameters[candidate]=None
1093-
1094-
returnlist(output_parameters.keys())
1095-
1096-
10971036
defget_placeholders(
10981037
problem:Problem,
1099-
observables:bool=True,
1038+
observable:bool=True,
11001039
noise:bool=True,
11011040
)->list[str]:
11021041
"""Get all placeholder parameters from observable table observableFormulas
11031042
and noiseFormulas.
11041043
11051044
Arguments:
11061045
problem: The PEtab problem
1107-
observables: Include parameters from observableFormulas
1046+
observable: Include parameters from observableFormulas
11081047
noise: Include parameters from noiseFormulas
11091048
11101049
Returns:
@@ -1115,7 +1054,7 @@ def get_placeholders(
11151054
# {observable,noise}Parameters
11161055
placeholders= []
11171056
foroinproblem.observables:
1118-
ifobservables:
1057+
ifobservable:
11191058
placeholders.extend(map(str,o.observable_placeholders))
11201059
ifnoise:
11211060
placeholders.extend(map(str,o.noise_placeholders))

‎tests/v2/test_core.py‎

Lines changed: 74 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -762,3 +762,77 @@ def make_yaml(id_line: str) -> str:
762762
f.write(make_yaml(""))
763763
problem=Problem.from_yaml(filepath)
764764
assertproblem.idisNone
765+
766+
767+
deftest_parameter_accessors():# pylint: disable=W0621
768+
"""
769+
Test the petab.Problem functions to get parameter values.
770+
"""
771+
petab_problem=Problem()
772+
petab_problem+=Parameter(
773+
id="par1",lb=0,ub=100,nominal_value=7,estimate=True
774+
)
775+
petab_problem+=Parameter(
776+
id="par2",lb=0.1,ub=100,nominal_value=8,estimate=True
777+
)
778+
petab_problem+=Parameter(
779+
id="par3",lb=0.1,ub=200,nominal_value=9,estimate=False
780+
)
781+
782+
assertpetab_problem.x_ids== ["par1","par2","par3"]
783+
assertpetab_problem.x_free_ids== ["par1","par2"]
784+
assertpetab_problem.x_fixed_ids== ["par3"]
785+
assertpetab_problem.lb== [0,0.1,0.1]
786+
assertpetab_problem.ub== [100,100,200]
787+
assertpetab_problem.x_nominal== [7,8,9]
788+
assertpetab_problem.x_nominal_free== [7,8]
789+
assertpetab_problem.x_nominal_fixed== [9]
790+
791+
assert (
792+
petab_problem.get_x_nominal_dict()
793+
==petab_problem.get_x_nominal_dict(free=True,fixed=True)
794+
== {
795+
"par1":7,
796+
"par2":8,
797+
"par3":9,
798+
}
799+
)
800+
assertpetab_problem.get_x_nominal_dict(free=True,fixed=False)== {
801+
"par1":7,
802+
"par2":8,
803+
}
804+
assertpetab_problem.get_x_nominal_dict(free=False,fixed=True)== {
805+
"par3":9,
806+
}
807+
808+
809+
deftest_get_output_parameters():
810+
"""Test Problem.get_output_parameters"""
811+
petab_problem=Problem()
812+
assertpetab_problem.get_output_parameters()== []
813+
814+
petab_problem+=Parameter(id="p1",lb=0,ub=100,estimate=True)
815+
petab_problem.models.append(SbmlModel.from_antimony("p2 = 1"))
816+
assertpetab_problem.get_output_parameters()== []
817+
818+
petab_problem+=Observable(
819+
id="obs1",formula="p1 + p2",noise_formula="p1 * p2"
820+
)
821+
assertpetab_problem.get_output_parameters()== ["p1"]
822+
823+
petab_problem+=Observable(
824+
id="obs1",
825+
formula="p3 + p4",
826+
noise_formula="p3 * p5",
827+
)
828+
assert (
829+
petab_problem.get_output_parameters()
830+
==petab_problem.get_output_parameters(observable=True,noise=True)
831+
== ["p1","p3","p4","p5"]
832+
)
833+
assertpetab_problem.get_output_parameters(
834+
observable=True,noise=False
835+
)== ["p1","p3","p4"]
836+
assertpetab_problem.get_output_parameters(
837+
observable=False,noise=True
838+
)== ["p1","p3","p5"]

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