oceano2python
This program read ASCII file(s) from oceanographic instruments (Seabird CTD, Sippican XBT, RDI LADCP, etc), extract data from header files and write result into one ASCII and NetCDF OceanSITES file.
The last version use an embedded Sqlite3 database to save and retreive data from memory.
Prequisites for Windows
You must install the following tools:
- Visual Studio Code (https://code.visualstudio.com/)
- Git (https://git-scm.com/downloads)
- miniconda3 (https://docs.conda.io/en/latest/miniconda.html)
- chocolatey (https://chocolatey.org/install) and install GNU Make package (https://community.chocolatey.org/packages/make)
Installation based on an YAML environment file
conda env create -f environment.yml -n <new_env_name>example:
conda env create -f environment-windows.yml -n oceano2pythonInstallation from scratch with conda
The program works under Windows (terminal) or Git bash as well as under Linux. It is recommended to install miniconda and to create a virtual environment oceano2python.
conda create -n oceano2python python=3.9
conda activate oceano2python
conda install -c conda-forge netCDF4 toml matplotlib xarray seawater PyInstaller pysimplegui
pip install julian notanormExport your environment
Duplicate your environment on another machine, just export it to a YAML file, replace "OS" with linux or windows:
conda env export --no-builds > environment-<OS>.ymlBuild and run
To build, run tests, build (compiled version), test examples (CTD/XBT), with GUI, you can use make:
make test
make build
make ctd
make xbt
make ladcp
make btl
make ctd OPT=-g
make ctd OPT=-dConfiguration
As the project consists of several files (modules), it is necessary to define the access path to the program in the environment variables PYTHONPATH and PATH. For example, under Linux:
**Update your PATH in your ~/.profile as:
if [ -d "/mnt/c/git/Python/oceano2python" ] ; then
PATH="/mnt/c/git/Python/oceano2python:$PATH"
fi**Add this line in your ~/.bashrc
export $PYTHONPATH = /mnt/c/git/Python/oceano2python
Usage
By default, the program uses the configuration file under: tests/test.toml, should change in future versions.
cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/CTD
oceano.py data/cnv/dfr320*.cnv -c ../config.toml -r ../../local/code_roscop.csv -i CTD -k PRES DEPTH ETDD TEMP PSAL DENS SVEL DOX2 FLU2 FLU3 TUR3 NAVG
oceano.py data/btl/fr320*.btl -c ../config.toml -r ../../local/code_roscop.csv -i BTL -k PRES DEPTH ETDD TE01 TE02 PSA1 PSA2 DO11 DO12 DO21 DO22 FLU2
cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/CELERITE
oceano.py data/XBT*.edf -c ../config.toml -r ../../local/code_roscop.csv -i XBT -k DEPTH TEMP SVEL
cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/LADCP
oceano.py profiles/*.lad -c ../config.toml -r ../../local/code_roscop.csv -i LADCP -k DEPTH EWCT NSCTThis program read multiple ASCII file, extract physical parameter following ROSCOP codification at the given column, fill arrays, write header file.
positional arguments:
files ASCII file(s) to parse
optional arguments:
-h, --help show this help message and exit
-d, --debug display debug informations
--demo [{CTD,XBT,LADCP,TSG}]
specify the commande line for instrument, eg CTD, XBT,
TSG, LADCP
-c CONFIG, --config CONFIG
toml configuration file, (default: tests/test.toml)
-i [{CTD,XBT,LADCP,TSG}], --instrument [{CTD,XBT,LADCP,TSG}]
specify the instrument that produce files, eg CTD,
XBT, TSG, LADCP
-k KEYS [KEYS ...], --keys KEYS [KEYS ...]
display dictionary for key(s), (default: ['PRES',
'TEMP', 'PSAL'])
-g, --gui use GUI interfaceThe user must describe in the TOML configuration file the metadata and the structure of the files to be read, see tests/test.toml
Developpment tools
We use Visual Studio Code (VSC) with Python, better TOML, markdownlint and makefile extensions
GUI
If you want use QT instead of Tk, replace in oceano.py:
import PySimpleGUI as gswith
import PySimpleGUIQt as gs