okokyst_toolbox

Toolbox for processing, plotting, and calculating stats of SAIV CTD cast data from stations

Usage:

To make use of this toolbox you also need to install python-ctd package. In the source code for python-ctd localte the folder ctd/read.py and replace the content with the content of file functionSAIV.py. Next, add the new function to the __init__.py file within the ctd directory so that it looks like this:

from .read import from_bl, from_btl, from_cnv, from_edf, from_saiv, from_fsi, rosette_summary

 __all__ = [
    "bindata",
    "despike",
    "from_bl",
    "from_btl",
    "from_cnv",
    "from_edf",
    "from_fsi",
    "from_saiv",
    "lp_filter",
    "movingaverage",
    "plot_cast",
    "press_check",
    "remove_above_water",
    "rosette_summary",
    "smooth",
    "split",
]

Then recompile and install the python-ctd module using: cd python-ctd pip install gsw pip install openpyxl pip install cmocean pip install xlsxwriter python setup.py develop

This adds the possibility to read SAIV files to the toolbox. The python-ctd toolbox is found here: https://github.com/pyoceans/python-ctd

Run this using : python okokyst_processing.py Requires: Data to be located in folders with specific structure:

  =>/Users/trondkr/Dropbox/Sorfjorden_2017_2019/
  ==> 2018-09-07/
  ===> 2018-09-07 CTD data/
  ====> SOE10.txt

To create a time-series contour plot of CTD cast for a specific survey and stations (substations) define these and the datapaths in the 'main' function. Currently supported surveys are:

• MON
• ØKOKYST (Sognefjorden and Hardangerfjorden)
• SØRFJORDEN

if survey == "Hardangerfjorden":
   basepath = "../OKOKYST_NS_Nord_Kvitsoy/"+str(CTDConfig.year)+"/"
   subStations = ["VT70", "VT69", "VT74", "VT53", "VT52", "VT75"]

if survey == "MON":
   basepath = "/Users/trondkr/Dropbox/MON-data/CONVERTED/"
   subStations = ['NORD1','OFOT1','NORD2', 'OFOT2','OKS1','OKS2',
                  'SAG1','SAG2','SJON1','SJON2','TYS1','TYS2']
            
if survey == "Sognefjorden":
   basepath = "../OKOKYST_NS_Nord_Leon/"+str(CTDConfig.year)+"/"
   subStations = ["VT16", "VT179"]

You run the toolbox after having editedt the settings in main with

python okokyst_processing.py

Examples

Below is an example of various contour plots using this toolbox for station VT79 in Hardangerfjorden. Data period is monthly from 2017 to December 2020:

You can also plot timeseries for stations VT53: