Before starting - Easy Q.C.V BGC

This user manual is accompanied by screenshots to guide you in the Qualification, Calibration, Validation of your BGC dataset measured by Argo Float and by Glider for the moment. If you have any difficulties, or suggestions for improvement, please contact us.

The easy Q.C.V BGC toolkit is organized like this :

Preprocessing of original files
Visualisation tools
Biogeochemical calibration tool

Preprocessing of original files¶

The original files must be pre-processed in order to use the same tools regardless of their origin. This pre-processing is performed by the QCV harmonizer tool.

Visualisation tools¶

The visualisation tools for the qualification, the validation and the extraction or the reporting of the user actions include ODV software, the ODV collection manager and ODV history manager. Read details below.

ODV collection manager details

This tool creates :

Ocean Data View (ODV) spreadsheet collection from the QCV harmonized file(s) based on the ODV user’s guide version 5.7.0 by bringing together as many plastform or reference harmonized datasets are needed
ODV view for Nitrate qualification

This tool is able :

to map the input with expected output QC flag scale if the information is available in the harmonized file and in the odv software
to subset harmonized reference data set used for comparison. subsetting option : 1 (subset), 0 (no subset), -1 (inverse subset for float crossing 180°E/W)

ODV collection manager default parametrization

operator name = anonymmous
QC convention for the output file = ARGO QC flag scale (reference table 2 in argo data management manual)
Subsetting = 1 (yes it is, even there are no “input reference data”)
plt or plot = 0 (no plot showing the subsetting results)

Its outputs are :

odv_collection.txt, an ODV spreadsheet collection merging raw (argo or glider) and reference hamonized file
qualification_startingPoint_nitrate.xview, a ODV view made helping in the Nitrate qualification step
YYYY-MM-DDTHHMM_galaxy_odv-coll-manager_QV.log, a log file summarizing all actions performed by the tool with success or not
other technical /log and .state

ODV history manager details

This tool extracts the QC changes (EDITFLAGS) and edit data (EDITDATA) from the ODV history file and reports them into the QCV harmonized file(s). The tool manages 2 types of ODV history file :

synthetic from the manual export
extended from the automatic export (not available on galaxy for the moment) it is also able to map the QC flag scale used by odv software and asked during the ODV spreadsheet creation (see above) with the output harmonized file if the information is available

Default parametrization

QC convention for the ODV output file = ARGO QC flag scale (reference table 2 in argo data management manual)
ODV convention regarding changes performed on the ODV collection =
- EDITFLAGS (report QC changes from the history to the data collection)
- EDITDATA (report data changes from the history to the data collection).

Its outputs are :

###_harm_qced.nc : extended NetCDF files including changes (as many files as platform have been qualified)
###_harm_history.csv : csv files summarizing user changes (as many files as platform have been qualified)
YYYY-MM-DDTHHMM_galaxy_odv-history-manager_history.log : log file summaring status of the QC & data changes by platform
other technical log and state files

Biogeochemical calibration tool¶

Currently, the Biogegeochemical calibration tool is operational for nitrate and using Method 1 and report DMQC information for the Argo floats. Read below for details

Biogegeochemical calibration details

This tool calibrate :

nitrate using Method 1, with by default
- an automatic evaluation of the reference pressure
- canyonB as method for assess the reference value of nitrate
- a linear regression for evaluating the correction
- the Argo QC flag convention

Default method parametrization

Figure 1:Default parametrization of the Biogegeochemical calibration tool for nitrate

Default QC flag parametrisation

Following ARGO QC flag scale https://archimer.ifremer.fr/doc/00228/33951/32470.pdf - reference table 2)

Bad Data QC = 4
raw QC value to be replaced = 3
QC value of replacement = 1 (for adjusted value)

Several method parametrizations are also possibles as :

a user estimation of the reference pressure
canyon-med or WOA as method for assess the reference value of nitrate
a multi linear regression for evaluating the correction either by a automatic evaluation of the number of break point or a user definition

This tool is able to manage many platforms with many configurations in the same time, useful for comparison.

Its outputs

per platform & per tool parametrization are :
- ###_C{parametrization_number}-nitrate.nc (extended harmonized file with corrected values)
- up to 4 diagnostic figures (according to the success):
  - ###_C{parametrization_number}-nitrateRaw-Ref_Analysis_ref#01_LinearModel.png
  - ###_C{parametrization_number}-nitrateRaw-Ref_Analysis_ref#01_Rsquared.png
  - ###_C{parametrization_number}-nitrateZvar_ref_detailed.png
  - ###_C{parametrization_number}-nitrateZvar_ref_results.png
for the process
- YYYY-MM-DDTHHMM_galaxy_odv-calibration-methods_nitrate_c.log : log file summaring status of correction / adjustment
- other technical log and state files

Easy Q.C.V. BGC workflows

Chlorophyll-a

User manual

How to run Easy Q.C.V BGC on Galaxy