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 |
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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
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petab.measurements.
create_measurement_df
() → pandas.core.frame.DataFrame¶ Create empty measurement dataframe
Returns: Created DataFrame
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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
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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
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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
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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 conditioncondition
.
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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).
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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
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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.
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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