GCWerks Bindings

GCwerks is a software use in chromatography. It is used to process chromatography data.

https://gcwerks.com/

API

Module to handle data of the format required by ebas.

class avoca.bindings.ebas.DataLevel(*values)

Values for different type of data used by ebas.

avoca.bindings.ebas.data_level_after_qa(data_level: DataLevel) → DataLevel

Return the data level after the QA.

avoca.bindings.ebas.extract_concentration_field(text: str) → dict[str, float]

Extract the concentrations from the text.

This is a temporary solution that we found to communicate the concentrations of the standards thgrough the nas files.

avoca.bindings.ebas.get_data_level(nas: EbasNasaAmes) → DataLevel

Get the data level of the nas file.

avoca.bindings.ebas.get_last_written_nas_file(directory: Path) → Path | None

Return path to the last nas file.

avoca.bindings.ebas.nas_to_avoca(nas: EbasNasaAmes) → DataFrame

Convert the ebas file to a pandas dataframe for @voc@.

To read the nas file, you can do:

from ebas.io.file.nasa_ames import EbasNasaAmes

file = "path/to/file.nas"
nas = EbasNasaAmes()
nas.read(file)
df = nas_to_avoca(nas)

Doing this will remove some specific flag information. In particular, @voc@ only accepts flags per compound and not per variable as in ebas.

This for each compound, the flag collects all the compounds of the variables.

@voc@ also requires a runtype for each run. We use for that the calibration flag suggested by ebas. We have to assume that this flag is the same for all compounds.

avoca.bindings.ebas.read_ebas_csv(file: PathLike) → DataFrame

Read the EBAS csv file and return a DataFrame.

This format comes from other EBAS tools.

avoca.bindings.ebas.set_dataframe(nas, df_export: DataFrame, compounds: dict[str, str] | None = None, data_level: DataLevel = DataLevel.CONCS, start_offset: timedelta | None = None, end_offset: timedelta | None = None, flag_all: list[int] = [], invalidate_conc_calib: bool = True)

Put the data from the export dataframe into the nas object.

Parameters:

  • nas – The nas object to fill

  • df_export – The dataframe with the data to export. Format follows the other avoca format.

  • compounds – The dictionary with the compounds. The keys are the the names in df_export. Values are the names in ebas.

  • data_level – The level of the data to export.

  • start_offset – The offset to add to the start time

  • end_offset – The offset to add to the end time

  • flag_all – List of flags to add to all the data

  • invalidate_conc_calib – If True, the concentration calibration will be invalidated (flag 980) for all calib samples.

Returns:

A dictionary with the metadata of the compounds exported.