Ocean Sciences 2022

Author: Andrew Reed

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Overview

Welcome. This repo contains the notebooks necessary to recreate the analyses from my Ocean Sciences 2022 talks, as well my walkthrough of OOI Bottle Data processing from the OOI Booth talks:

1. QARTOD in Practice: Two Examples from the Ocean Observatories Initative
2. OOI Carbon System: Data Validation for the Irminger Sea Array
3. Preparing OOI discrete bottle data for comparison with OOI pCO2 and pH timeseries data

Additonally, this repo contains the presentations themselves as well as the necessary input data and metadata when needed.

Setup

0. Make an account on OOINet First, please go to https://ooinet.oceanobservatories.org/ and make an register. Once you have made an account for yourself and logged in, navigate to your account settings by clicking on "User Profile" under your email in the top right corner of your screen. Once at your Profile, record your API Username and API Token. These are necessary if you wish to access and download data from the Ocean Observatories API.

1. Setup python environment Its recommended that miniconda or anaconda3 has been installed. The python environment can be setup with the following commands:

   conda env create -f environment.yaml
   

2. Launch jupyter notebooks Now you are ready to get working with OOI data! Launch a jupyter notebook in your browser and get ready to explore OOI carbon system data.

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Project Files and Structure Description

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Dependencies

The example notebooks in this repo rely heavily on packages, functions, and routines that have been developed over the years by the OOI operators to assist in processing and working with OOI data. There are two principle repos on which the example notebooks lean are:

• OOINet

The modules and tools within this repo are designed to assist in requesting, importing, downloading, and vizualizing data from the Ocean Observatories Initiative API by M2M requests. It can be found at https://github.com/reedan88/OOINet.

• OOI-Data-Explorations

Explorations of Ocean Observatories Initiative Datasets via MATLAB, Python, R, and Julia. It can be found at https://github.com/oceanobservatories/ooi-data-explorations.

These repos are not distributed on either conda or pip, so they will need to be either cloned to your local machine or the files and functions directly downloaded.

Additionally, specific functions written to simplify and streamline the analyses in this repo are stored as modules within the OS2022 subdirectory in this repo.

carbon_system

scripts

• Identify_and_Download_Data.ipynb - The purpose of this notebook is to identify and download the datasets with pH and pCO2 data deployed at the Ocean Observatory Initiative's (OOI) Global Irminger Array (60$^{\circ}$N, 39$^{\circ}$W). OOI deploys the following sensors for measuring the ocean carbon system: Sunburst Sensors, LLC. SAMI-pH (PHSEN) pH, SAMI-pCO$_{2}$ seawater measurements, and the Pro-Oceanus pCO2 sensor measurements. The datasets identified here are used in the Data_Analysis notebook.
• Bottle_Data.ipynb - This notebook provides a quick outline and example of working with OOI Discrete Summary Spreadsheet bottle data. It includes how to load it, how to parse data quality flags, how to derive some important values, and work with the data to make it easy to use for data validation and comparison purposes.
• Data_Analysis.ipynb - The purpose of this notebook is to analyze and validate the performance of the Sunburst Sensors, LLC. SAMI-pH (PHSEN) pH, SAMI-pCO$_{2}$ seawater measurements, and the Pro-Oceanus pCO2 sensor measurements at the Global Irminger Array. This is done on a deployment-by-deployment, site-by-site comparison with the pH measurements from discete water samples collected by Niskin Bottle casts during deployment and recovery of the instrumentation during mooring maintainence.

documents

Folder which contains the presentation titled "**QARTOD in Practice: Two examples from the Ocean Observatories Initative" along with supporting figures and images

• QARTOD.pptx - The presentation for "QARTOD in Practice" given at Ocean Sciences 2022

data

Mostly empty directory except for water sampling data. Setup ready to store intermediate and final datasets generated by the notebooks in this section.

• • water_sampling/ - directory containing the Irminger Sea 1 - 5 discrete summary bottle sheets needed for the notebook Bottle_Data.ipynb

results

An empty directory ready to store figures and output from the analyses performed in this section.

event_detection

scripts

• Argentine_Basin.ipynb - This notebook assess how well the QARTOD climatology test, as implemented by OOI, performs with respect to accurately capturing and flagging the passage of a mid-water-column eddy across the OOI Global Argentine Basin array in July-August of 2016.
• Irminger.ipynb - This notebook assess how well the QARTOD gross range test, as implemented by OOI, performs with respect to accurately flagging practical salinity data from the mid-water-column in the Irminger Sea with respect to a long-term freshening signal.

documents

Folder which contains the presentation titled "**OOI Carbon System Data: Irminger Array" along with supporting figures and images.

• Carbon_Presentation.pptx - The presentation for "OOI Carbon System Data" given at Ocean Sciences 2022

data

An empty directory ready to store intermediate and final datasets generated by the notebooks in this section.

results

An empty directory ready to store figures and output from the analyses performed in this section.

ooi_booth_presentation

scripts

• Presentation.ipynb - This notebook provides a quick outline and example of working with OOI Discrete Summary Spreadsheet bottle data. It includes how to load it, how to parse data quality flags, how to derive some important values, etc.

documents

• Bottle Data.pptx - The presentation from the OOI Booth on March 2nd, 2022.

data

• water_sampling/ - directory containing the Irminger Sea 1 - 5 discrete summary bottle sheets needed for the analysis presented in Presentation.ipynb and shown in Bottle Data.pptx.

OS2022

• utils.py - File containg general functions for the analyses presented above.
• bottle_utils.py - Collection of functions for specifically for processing and interpreting OOI discrete water sampling data.
• plotting.py - Streamlined plotting functions for plotting timeseries of OOI datasets.
• environment.yaml

Files outside this repo

• user_info.yaml - a YAML file which has the user's OOI API username and token. This is not available in the repo; the user should make one for themselves, and place it in the parent directory of their copy of this repo) This file is specifically excluded in the .gitignore.