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Roadrunner handling of petab issue 0019 #1419

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Jun 25, 2024
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Roadrunner handling of petab issue 0019 #1419

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Further distinction between initial value override based on parameter…
PaulJonasJost Jun 20, 2024
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PaulJonasJost Jun 25, 2024
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44 changes: 36 additions & 8 deletions pypesto/objective/roadrunner/petab_importer_roadrunner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@
from petab.models.sbml_model import SbmlModel
from petab.parameter_mapping import ParMappingDictQuadruple

import pypesto.C

from ...petab.importer import PetabStartpoints
from ...problem import Problem
from ...startpoint import StartpointMethod
Expand Down Expand Up @@ -211,15 +213,41 @@ def create_parameter_mapping(self):
preeq_id = condition.get(PREEQUILIBRATION_CONDITION_ID)
sim_id = condition.get(SIMULATION_CONDITION_ID)
if preeq_id:
mapping_per_condition[0][
override
] = self.petab_problem.condition_df.loc[preeq_id, override]
mapping_per_condition[2][override] = "lin"
parameter_id_or_value = (
self.petab_problem.condition_df.loc[preeq_id, override]
)
mapping_per_condition[0][override] = parameter_id_or_value
if isinstance(parameter_id_or_value, str):
mapping_per_condition[2][
override
] = self.petab_problem.parameter_df.loc[
parameter_id_or_value, petab.PARAMETER_SCALE
]
elif isinstance(parameter_id_or_value, numbers.Number):
mapping_per_condition[2][override] = pypesto.C.LIN
else:
raise ValueError(
"The parameter value in the condition table "
"is not a number or a parameter ID."
)
if sim_id:
mapping_per_condition[1][
override
] = self.petab_problem.condition_df.loc[sim_id, override]
mapping_per_condition[3][override] = "lin"
parameter_id_or_value = (
self.petab_problem.condition_df.loc[sim_id, override]
)
mapping_per_condition[1][override] = parameter_id_or_value
if isinstance(parameter_id_or_value, str):
mapping_per_condition[3][
override
] = self.petab_problem.parameter_df.loc[
parameter_id_or_value, petab.PARAMETER_SCALE
]
elif isinstance(parameter_id_or_value, numbers.Number):
mapping_per_condition[3][override] = pypesto.C.LIN
else:
raise ValueError(
"The parameter value in the condition table "
"is not a number or a parameter ID."
)
return mapping

def create_objective(
Expand Down
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