Python SDK Example Notebooks for The Ocean Data Platform (ODP)

This repo contains examples in Binder for extra functionality in the ODP Python SDK. You can connect to the Ocean Data Platform with Python through the Python SDK, download queried ocean data easily and efficiently into data frames, and use built-in functionality for for easy exploring and processing of data.

For the ODP python SDK please see this repo: odp-sdk

Documentation for python SDK

ODP Python SDK Documentation

Basic python SDK usage

Note: Accessing the Ocean Data Platform requires a personal api-key. Contact ODP to require one.

Import the Ocean Data Platform SDK

from odp_sdk import ODPClient

Connect to the platform

client = ODPClient(api_key='your_personal_api_key_from_ODP')

Get dataframe of ocean data samples (casts) within search criteria

Basic usage:

df=client.casts(longitude=[8,12],
                latitude=[56,60],
                timespan=['2019-06-01','2019-06-07']) 

Basic usage with more options (Specifying the parameters of interest and removing flagged data):

df=client.casts(longitude=[8,12],
                latitude=[56,60],
                timespan=['2018-06-01','2018-08-31'],
                parameters=['date','lon','lat','z','Temperature','Oxygen','Salinity'],
                n_threads=35,
                include_flagged_data=False)

Utility Functions

Examples/UtilityFunctions.py include useful features for interpolating and plotting, and also include functions for plotting aspects of data coverage, distributions, cast breakdowns.

Jupyter Notebook Examples

Example notebooks are found in the Example folder, which includes:

• Basic data retrieaval from ODP
• Download data, plot the casts and create a gridded map of surface temperatures
• Analyzing temperature trends
• Example Notebook Data Coverage shows how functions from DataStatsFunctions.py can help users understand the data they download from the odp_sdk
• Example Notebook Data Exploration shows how users can explore the data they pull from the WOD (i.e. plot temperature over time)
• Example Notebook Marine Regions shows how users can join Marine Regions data to the WOD data

World Ocean Database

The data available through the Python SDK is gathered from the World Ocean Database. The World Ocean Database which is a National Centers for Environmental (NCEI) product and International Oceanographic Data and Information Exchange (IODE) project which provides a composite of publicly available ocean profile data, both historic and recent. It consists of over thousands of datasets consisting of millions of water temperatures, salinity, oxygen, and nutrient profiles (1,2).

Data Organization in WOD and definitions

Cast: A set of one or more profiles taken concurrently or nearly concurrently. All casts from similar instruments with similar resolutions are grouped together. For example, all bathythermograph (BT) data are all part of the same data set (MBT), see below.

Profile: A set of measurements for a single variable (i.e. temperature salinity) along a specific path, which could be vertically in the water column, horizontally along the surface, or discrete areas based on placement of buoys.

Data Description

The data available through the Ocean Data Platform are oceanographic measurements of physical and chemical ocean parameters (temperature, salinity, oxygen, nitrate, ph and chlorophyll), and is based on the data available through NOAA's World Ocean Database. Each cast has a sepcified latitude, longitude and time (lat, lon and datetime), and a depth profile, where each depth has measured physical and chemical parameters. Not all casts have all the the different ocean parameters, missing measurements are populated with nans. Each measurements has a WODflag parameter (i.e Nitrate_WODflag). If flag value is zero, there are no known issues with the measured value.

Parameter	Unit
lon/lat	deg
Z	m
Oxygen	µmol/kg
Temperature	C
Salinity	1e-3
Nitrate	µmol/kg
Chlorophyll	µgram/l
Pressure	dbar

Dataset code	Dataset include
OSD	Ocean Station Data, Low-resolution CTD/XCTD, Plankton data
CTD	High-resolution Conductivity-Temperature-Depth / XCTD data
MBT	Mechanical / Digital / Micro Bathythermograph data
XBT	Expendable Bathythermograph data
SUR	Surface-only data
APB	Autonomous Pinniped data
MRB	Moored buoy data
PFL	Profiling float data
DRB	Drifting buoy data
UOR	Undulating Oceanographic Recorder data
GLD	Glider data

See WORLD OCEAN DATABASE 2018 User’s Manual for more information about the datasets

Data Quality Flag Descriptions

https://www.nodc.noaa.gov/OC5/WOD/CODES/Definition_of_Quality_Flags.html

References:

1. Boyer, T.P., O.K. Baranova, C. Coleman, H. E., Garcia, A. Grodsky, R.A. Locarnini, A. V., Mishonov, C.R. Paver, J.R. Reagan, D. S. & I.V. Smolyar, K.W. Weathers, and M. M. Z. World Ocean Atlas 2018, Volume 1: Temperature. Tech. Ed. NOAA Atlas NESDIS 87 (2018).
2. Boyer, T. P. et al. World Ocean Database 2018. NOAA Atlas NESDIS 87 (2018).