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Infrared DIC analysis

koolstof.infrared contains tools for processing infrared absorbance data to determine total dissolved inorganic carbon.

These tools were specifically designed for infrared absorbance data recorded by a LI-COR LI-7000 via its Windows Interface Software v2.0.3 and connected to a Marianda AIRICA.

The examples below all assume the following import convention has been used:

from koolstof import infrared as ksi

Data import

koolstof.infrared.io contains functions to import relevant data.

Under the hood

koolstof.infrared.io.read_dbs and koolstof.infrared.io.read_LI7000 are both very light wrappers around pandas.read_table. Any additional kwargs used with either will be passed on to that pandas function, but none should be required.

AIRICA databases

koolstof.infrared.io.read_dbs imports the databases generated by a Marianda AIRICA as a pandas DataFrame:

dbs = ksi.read_dbs(filename)

A new "datetime" column is added containing the analysis date and time as a pandas Timestamp. It is also calculated as a Matplotlib date number in the column "datenum".

Finally, the original dbs column names are mapped to be more friendly.

dbs column name changes

koolstof.infrared.io.read_dbs renames the dbs columns as follows:

  • "run type" → "run_type"
  • "i.s. temp." → "temperature_insitu"
  • "sample mass" → "mass_sample"
  • "rep#" → "rep"
  • "CT" → "dic"
  • "factor CT" → "dic_factor"
  • "CV (µmol)" → "cv_micromol"
  • "CV (%)" → "cv_percent"
  • "last CRM CT" → "lastcrm_dic_measured"
  • "cert. CRM CT" → "lastcrm_dic_certified"
  • "CRM batch" → "lastcrm_batch"
  • "calc. mode" → "mode_calculation"
  • "integ. mode" → "mode_integration"
  • "Lat." → "latitude"
  • "Long." → "longitude"
  • "area#1" → "area_1"
  • "area#2" → "area_2"
  • "area#3" → "area_3"
  • "area#4" → "area_4"

All other column names are left unchanged.

LI-7000 measurements

koolstof.infrared.io.read_LI7000 imports the text files recorded by a LI-COR LI-7000 via its Windows Interface Software v2.0.3 as a pandas DataFrame:

licor = ksi.read_LI7000(filename)

At least the "Time" column must be present in the text file. This is converted into a pandas Timestamp and the column is renamed as "datetime". It is also calculated as a Matplotlib date number in the column "datenum".

Later processing functions here also expect the "CO2B um/m", "H2OB mm/m", "T C" and "P kPa" columns.

The original column names are mapped to be more friendly.

LI-7000 column name changes

koolstof.infrared.io.read_LI7000 renames the text file's columns as follows:

  • "Time" → "datetime",
  • "CO2B um/m" → "x_CO2",
  • "H2OB mm/m" → "x_H2O",
  • "T C" → "temperature",
  • "P kPa" → "pressure",
  • "RH %" → "humidity_relative",
  • "Flow V" → "flow_voltage",

Any other column names are left unchanged.