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Handle missing nominalValue in Problem.get_x_nominal #223

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Merged
dweindl merged 1 commit into from
Jul 28, 2023
Merged

Handle missing nominalValue in Problem.get_x_nominal #223

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7 changes: 6 additions & 1 deletion petab/problem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

import os
import tempfile
from math import nan
from pathlib import Path, PurePosixPath
from typing import Dict, Iterable, List, Optional, Union, TYPE_CHECKING
from urllib.parse import unquote, urlparse, urlunparse
Expand Down Expand Up @@ -660,7 +661,11 @@ def get_x_nominal(self, free: bool = True, fixed: bool = True,
-------
The parameter nominal values.
"""
v = list(self.parameter_df[NOMINAL_VALUE])
if NOMINAL_VALUE in self.parameter_df:
v = list(self.parameter_df[NOMINAL_VALUE])
else:
v = [nan] * len(self.parameter_df)

if scaled:
v = list(parameters.map_scale(
v, self.parameter_df[PARAMETER_SCALE]))
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5 changes: 5 additions & 0 deletions tests/test_petab.py
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Expand Up @@ -557,6 +557,11 @@ def test_parameter_properties(petab_problem): # pylint: disable=W0621
assert petab_problem.x_nominal_free_scaled == [7, np.log(8)]
assert petab_problem.x_nominal_fixed_scaled == [np.log10(9)]

# Check that a missing nominalValues column is handled correctly
del petab_problem.parameter_df[NOMINAL_VALUE]
assert len(petab_problem.x_nominal) == 3
assert np.isnan(petab_problem.x_nominal).all()


def test_to_float_if_float():
to_float_if_float = petab.core.to_float_if_float
Expand Down