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, str, …) 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, …) 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(…) 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

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

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

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]

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

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[KT, VT]]) → pandas.core.frame.DataFrame

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

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

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]]

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.write_measurement_df(df: pandas.core.frame.DataFrame, filename: str) → None

Write PEtab measurement table

Parameters:
  • df – PEtab measurement table
  • filename – Destination file name