argodmqc-owc 0.2.1a1

OWC salinity calibration in Python

	pyowc is a python library for OWC salinity calibration in Python

This software is a python implementation of the "OWC" salinity calibration method used in Argo floats Delayed Mode Quality Control.

Post an issue to get involved if you're interested.

General Guidance

To use this software, you'll need Python, and ideally a virtual environment with the package installed.
A virtual environment is not absolutely essential — you can install the package globally — but it is recommended to avoid issues.

There are two ways of working with this software:

1. Installation and General Usage via PyPI

This method is intended for general usage, without modifying the codebase.
If you intend to use the software this way, follow the documentation from the General Usage section.

2. Installation and Development Work via GitHub

This method is intended for development work and gives access to the codebase, it is intended for those wanting to develop the code. If this is what you intend to do, follow the documentation from the Developer Usage section.

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Overview

To use the app installed via PyPi there are 3 steps to follow.

1. Pip install it

Run pip install argodmqc-owc

2. Setup folder structure The app requires a specific folder structure, and these folders & files are referenced in the config JSON file. The example structure here is reflected in the example config JSON file.

General Usage

To use the app installed via PyPi there are 3 steps to follow.

1. Pip install it

Run pip install argodmqc-owc

2. Setup folder structure

The app requires a specific folder structure, and these folders & files are referenced in the config JSON file. The example structure here is reflected in the example config JSON file. Please note that the data folder is available here

• data
  • climatology
    • historical_argo
    • historical_bot
    • historical_ctd
  • constants
    • bathymetry
    • coastline
    • reefs
  • float_calib
  • float_mapped
  • float_plots
  • float_source

3. Create the config JSON file The JSON file includes all data directory and float configurations and settings.

See the example config JSON file here

4. Run the software

This can be run with the command run-floats --floats 3901960. "3901960" here is the WMO float number to be processed. Multiple floats can be run at once by passing a comma separated list, e.g. ... --floats 1,2,3

Please note that the config JSON is checked before any processing runs, so any errors in the config will be reported back.

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Developer Usage

Using the app as a developer requires git-cloning rather than pip-installing so direct access to the code is possible, and modifying the code is easy. To use the app as a developer it is recommended you follow the sections below in the order prescribed

1. Virtual Environments
2. Installing Poetry
3. Cloning the repository
4. Installing the dependencies
5. Running the linting & tests and docs builder
6. Executing the DMQC code

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Virtual Environments

A virtual environment is recommended to work in as the dependencies wont conflict with any globally installed packages.

To create a virtual environment:

• Mac/Linux

  python3 -m venv .venv

  source .venv/bin/activate

• Windows

  python -m venv .venv

  .\.venv\Scripts\Activate

Installing Poetry

Poetry is a dependency management tool and the software uses a pyproject.toml file to handle the dependencies.

To Install Poetry, run: pip install poetry

If any messages appear with 'poetry not found', try prefixing your command with python or python -m

Cloning the Repository

The repository can be cloned by clicking the green <> Code button near the top of the main page on Github. Follow the prompts to either clone it via the command line, or open with Github Desktop.

It is recommended to clone the repository to a new folder. Make sure you are in this folder with your virtual environment activated and the repository cloned before moving to the next step. You need to make sure you are at the same level as the pyproject.toml file.

Installing the dependencies

Install the dependencies with: poetry install --no-root

This will take a few seconds, and you should see a list of the installed packages in the terminal window.

Running the linting & tests and docs builder

The dependencies for running these utiltiies are also packaged up with Poetry, and they can be ran as follows:

Running the Linter with Poetry

poetry install --no-root --with lint

poetry run ruff check

Running the Docs Builder with Poetry

poetry install --with docs

cd docs

poetry run sphinx-build -M html source build -W

Running the Tests with Poetry

poetry install --with tests

poetry run pytest

Executing the DMQC code

Run the code: poetry run run-floats --floats 3901960.

"3901960" here is the WMO float number to be processed. Multiple floats can be run at once by passing a comma separated list, e.g. ... --floats 1,2,3

A short tutorial is available on the argopy documentation here.

Extra command line arguments

There are several additional options that can be optionally used when running this code

• --headless: Running in headless mode will create the plots but not display them on screen
• -appendRef {suffix}: Appends the provided suffix to the filename of all produced plots (should begin with _)

Parameters for your analysis

Parameters for the analysis are set in a owc_config.json python code. The configuration has the same parameters as the Matlab software (https://github.com/ArgoDMQC/matlab_owc).

• You can change the default directories to locations of your historical data.

  #    Climatology Data Input Paths
  'HISTORICAL_DIRECTORY': "data/climatology/"
  'HISTORICAL_CTD_PREFIX': "/historical_ctd/ctd_"
  'HISTORICAL_BOTTLE_PREFIX': "/historical_bot/bot_"
  'HISTORICAL_ARGO_PREFIX': "/historical_argo/argo_"
  

• To run the analysis,you need to have the float source file in .mat format.

  #    Float Input Path
  'FLOAT_SOURCE_DIRECTORY': "data/float_source/"
  'FLOAT_SOURCE_POSTFIX': ".mat"
  

• The output from the analysis will be saved in default directory of the code.You can change the default directories to locations of your constants.

  #    Constants File Path
  'CONFIG_DIRECTORY': "data/constants/"
  'CONFIG_COASTLINES': "coastdat.mat"
  'CONFIG_WMO_BOXES': "wmo_boxes.mat"
  'CONFIG_SAF': "TypicalProfileAroundSAF.mat"
  

• To set your objective mapping parameters update the following, e.g.

  'MAP_USE_PV': 0
  'MAP_USE_SAF': 0
  
  'MAPSCALE_LONGITUDE_LARGE': 8
  'MAPSCALE_LONGITUDE_SMALL': 4
  'MAPSCALE_LATITUDE_LARGE': 4
  'MAPSCALE_LATITUDE_SMALL': 2
  

• To manually set the calibration values update the following entires below. The calibration contains two additional fields splits and exclusions. The splits field refers to the splitting of profiles, and if left empty will process all the data. If the data is to be split up, then the value needs to be changed to a list of profiles to split into. For example if splits is [5, 10] then splits will be made at profiles 1-4, 5-10, and then 10 until the end. If the exclusions list is empty then all data is processed, but profiles can be added to the exclusions list if they are to be omitted from the program.

  'CALIB_PROFILE_NO': [],
  'BREAKS': [],
  'MAX_BREAKS': 4,
  'SPLITS': [],
  'EXCLUSIONS': [],
  'USE_THETA_LT': [],
  'USE_THETA_GT': [],
  'USE_PRES_LT': [],
  'USE_PRES_GT': [],
  'USE_PERCENT_GT': 0.5,
  

• Optionally you can include bathymetry data on the trajectory plots. Note that turning this on will significantly slow the plot generation speed

  #    Plotting Parameters
  "USE_BATHYMETRY_ON_PLOT": 1
  

Software history

Check out software history at: https://github.com/euroargodev/argodmqc_owc/network