empalc: For Empa’s LC data

A custom extractor for processing liquid chromatography data exported from the Agilent Online LC in the Materials for Energy Conversion lab at Empa.

yadg.extractors.empalc.csv module

Handles processing of the csv version of the structured format produced by Agilent’s Online LC device at Empa. It contains three sections:

metadata section,

table containing sampling information,

table containing analysed chromatography data.

Usage

Available since yadg-4.2.

pydantic model dgbowl_schemas.yadg.dataschema_6_0.filetype.EmpaLC_csv

Config:

extra: str = forbid

Validators:

field filetype: Literal['empalc.csv'] [Required]

Schema

xarray.DataTree:
  coords:
    uts:            !!float               # Unix timestamp
    species:        !!str                 # Species name
  data_vars:
    height:         (uts, species)        # Peak height
    area:           (uts, species)        # Integrated peak area
    concentration:  (uts, species)        # Peak area with calibration applied
    retention time: (uts, species)        # Position of peak maximum

Metadata

The following metadata is extracted:

sequence: Sample / sequence name.

description: A free-form description of the experiment.

username: User name used to generate the file.

datafile: Original path of the result file.

version: Version of the export function used to generate the file.

Code author: Peter Kraus

yadg.extractors.empalc.csv.extract(*, fn: str, encoding: str, **kwargs: dict) → DataTree

yadg.extractors.empalc.xlsx module

Handles processing of the xlsx version of the structured format produced by Agilent’s Online LC device at Empa. It contains three sections: