petab.measurements¶

Functions operating on the PEtab measurement table

Functions

`assert_overrides_match_parameter_count`(…)	Ensure that number of parameters in the observable definition matches the number of overrides in `measurement_df`
`create_measurement_df`()	Create empty measurement dataframe
`get_measurement_df`(measurement_file)	Read the provided measurement file into a `pandas.Dataframe`.
`get_measurement_parameter_ids`(measurement_df)	Return list of ID of parameters which occur in measurement table as observable or noise parameter overrides.
`get_noise_distributions`(measurement_df)	Returns dictionary of cost definitions per observable, if specified.
`get_rows_for_condition`(measurement_df, condition)	Extract rows in measurement_df for condition according to ‘preequilibrationConditionId’ and ‘simulationConditionId’ in condition.
`get_simulation_conditions`(measurement_df)	Create a table of separate simulation conditions.
`measurements_have_replicates`(measurement_df)	Tests whether the measurements come with replicates
`split_parameter_replacement_list`(list_string)	Split values in observableParameters and noiseParameters in measurement table.
`write_measurement_df`(df, filename)	Write PEtab measurement table

petab.measurements.assert_overrides_match_parameter_count(measurement_df: pandas.core.frame.DataFrame, observable_df: pandas.core.frame.DataFrame) → None [source]¶

Ensure that number of parameters in the observable definition matches the number of overrides in measurement_df

Parameters

measurement_df – PEtab measurement table
observable_df – PEtab observable table

petab.measurements.create_measurement_df() → pandas.core.frame.DataFrame[source]¶

Create empty measurement dataframe

Returns: Created DataFrame

petab.measurements.get_measurement_df(measurement_file: Union[None, str, pandas.core.frame.DataFrame]) → pandas.core.frame.DataFrame[source]¶

Read the provided measurement file into a pandas.Dataframe.

Parameters: measurement_file – Name of file to read from or pandas.Dataframe
Returns: Measurement DataFrame

petab.measurements.get_measurement_parameter_ids(measurement_df: pandas.core.frame.DataFrame) → List[str][source]¶

Return list of ID of parameters which occur in measurement table as observable or noise parameter overrides.

Parameters: measurement_df – PEtab measurement DataFrame
Returns: List of parameter IDs

petab.measurements.get_noise_distributions(measurement_df: pandas.core.frame.DataFrame) → dict [source]¶

Returns dictionary of cost definitions per observable, if specified.

Looks through all parameters satisfying sbml_parameter_is_cost and return as dictionary.

Parameters: measurement_df – PEtab measurement table
Returns: Dictionary with observableId => cost definition

petab.measurements.get_rows_for_condition(measurement_df: pandas.core.frame.DataFrame, condition: Union[pandas.core.series.Series, pandas.core.frame.DataFrame, Dict]) → pandas.core.frame.DataFrame[source]¶

Extract rows in measurement_df for condition according to ‘preequilibrationConditionId’ and ‘simulationConditionId’ in condition.

Parameters

measurement_df – PEtab measurement DataFrame
condition – DataFrame with single row (or Series) and columns ‘preequilibrationConditionId’ and ‘simulationConditionId’. Or dictionary with those keys.

Returns

The subselection of rows in measurement_df for the condition

condition.

petab.measurements.get_simulation_conditions(measurement_df: pandas.core.frame.DataFrame) → pandas.core.frame.DataFrame[source]¶

Create a table of separate simulation conditions. A simulation condition is a specific combination of simulationConditionId and preequilibrationConditionId.

Parameters: measurement_df – PEtab measurement table
Returns: Dataframe with columns ‘simulationConditionId’ and ‘preequilibrationConditionId’. All-null columns will be omitted. Missing ‘preequilibrationConditionId’s will be set to ‘’ (empty string).

petab.measurements.measurements_have_replicates(measurement_df: pandas.core.frame.DataFrame) → bool [source]¶

Tests whether the measurements come with replicates

Parameters: measurement_df – Measurement table
Returns: True if there are replicates, False otherwise

petab.measurements.split_parameter_replacement_list(list_string: Union[str, numbers.Number], delim: str = ';') → List[Union[str, float]][source]¶

Split values in observableParameters and noiseParameters in measurement table.

Parameters

list_string – delim-separated stringified list
delim – delimiter

Returns

List of split values. Numeric values converted to float.

petab.measurements.warn(message, category=None, stacklevel=1, source=None)¶: Issue a warning, or maybe ignore it or raise an exception.

petab.measurements.write_measurement_df(df: pandas.core.frame.DataFrame, filename: str) → None [source]¶

Write PEtab measurement table

Parameters

df – PEtab measurement table
filename – Destination file name