A package to detect the boundaries of the active mesopelagic zone
Project description
RUBALIZ
RUBALIZ stands for RUpture-Based detection method for the Active mesopeLagIc Zone. It determines the active mesopelagic zone boundaries from CTD casts, using five variables:
- Fluorescence
- 02
- Potential temperature
- Salinity
- Density
RUBALIZ was introduced in Fuchs, Baumas et al. (2022).
Installation
The package can be installed using pip
pip install rubaliz
or alternatively using conda:
conda install rubaliz
Getting started
The metadata have to be filled in a dictionary as shown below:
from rubaliz import rubaliz
# Define CTD files info
info_dict = {'cruise_name': 'DY032',
'station_name': 'PAP',
'ub_range': [280, 320],
'lb_range': [1000, 1300],
'pres_col': 'PRES',
'fluo_col': 'flC',
'oxygen_col': 'oxygen',
'temp_col': 'potemperature',
'density_col': 'sigma-\ufffd00',
'salinity_col': 'PSAL',
'files_format': '.cnv',
'sep': None,
'data_folder': '<your_path_to_data>'}
The cruise and station names are optional. The maximum depth ranges to look for the upper bound and lower boundaries of the active mesopelagic zone, ub_range and lb_range, are set to [280, 320] and [1000, 1300] by default, respectively. The pres_col is the name of the column containing the pressure data in the CTD cast. Similarly, the fluo_col, oxygen_col, temp_col, density_col and salinity_col stand for the column names of the fluorescence, oxygen, potential temperature, density and salinity data, respectively. RUBALIZ can handle '.cnv', '.txt' and '.csv' files. For '.csv' and '.txt' files a separator (sep) has to be set. The data_folder contains all the CTD casts for a given (cruise, station). An example of such a cast is given in the data folder.
The model can be run in the following way:
# Perform the rupture detection
ruba = rubaliz(info_dict)
ruba.fit()
# Access to the estimations
ruba.boundaries
ruba.nb_ctd_ub
ruba.nb_ctd_lb
Project details
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