run.process.ECO.batch: Run batch processing to convert ECO meter data in raw format...

View source: R/run.process.ECO.batch.R

run.process.ECO.batchR Documentation

Run batch processing to convert ECO meter data in raw format to backscattering coefficients.

Description

The processing includes the application of the calibration coefficients to convert the raw numerical counts into VSF. The dark offsets may be taken from the calibration file (device file) or from the dark measurements taken on the field. Next, if absorption coefficients are provided, the VSF is corrected for loss of photons due to attenuation along the pathlength. The VSF is finaly converted in to total backscattering and particles backscattering.

Usage

run.process.ECO.batch(log.file = "log.txt", data.path = "./")

Arguments

log.file

is the name of the ASCII file (semicolumn-delimated text) containing the list of samples to process (see details below).

data.path

is the full path where the ECO data are stored

Details

The most important thing to do before runing this programm is to prepare the log.file. This file contains fields (semi-column delimiter) : ECO.filename; dev.file; ECO.type; ECO.bands; Station; Date; UTCTime; Depth; Salinity; dark.file; start; end; process; Anw1;..;AnwX The ASCII files are:

  • ECO.filename: is the file name of an ECO file without the path. It must be put in a sub-folder named raw/ in the data.path;

  • dev.file: is the full path and name of the device file (i.e. the calibration file) of the actual instrument;

  • ECO.type: is a character string for the type of ECO meter: BB9, BB3, VSF3.

  • ECO.bands: is a character string indicating the bands of the VSF3 meter. It could take one of these character: "B", "G", "R" or "BG", or "BGR". It is ignore when the ECO type is a BB meter

  • Station: is the station ID. It will be store in the RData output;

  • Date: is the date in format YYYYMMDD

  • UTCTime: is the is the time and minute in HH:MM format

  • Salinity: is the salinity of the sample.

  • dark.file: is the name of the file containing raw dark measurements made on the field using black tape places on the LED. It must be put in a sub-folder named dark/ in the data.path and be consistent with the ECO.type

  • start: is the begining of the cast in seconds after the instrument warming period. If 999 then the user is prompt to click on the plot of VSF versus Time to choose the start and the end of the cast interactively.

  • end: is the end of the cast in second. If 999 then it takes the end of the cast.

  • process: is a boolean value indicating if the file has to be process (1) or not (0)

  • Anw1..AnwX: is the non-water absorption for each wavelength of the ECO meter. For a BB9, for example, nine columns in expected

The code will process each file one by one and will output a RData file for each raw file processed.

@author Simon Belanger @export


belasi01/Riops documentation built on Sept. 5, 2022, 6:38 p.m.