Oceanarray: Methods and Workflows for Mooring Array Processing

This repository documents and demonstrates the processing steps required to convert raw instrument data from oceanographic mooring arrays into scientifically useful transport and circulation diagnostics such as the meridional overturning circulation (MOC).

It provides methods, example code, and reference documentation for modular, reproducible processing pipelines based on multi-mooring observational arrays.

Warning

Output format is not yet stable. Variable names in Stage 1–3, stack, and grid NetCDF files are being revised for CF and OceanSITES compliance before the 1.0 release. Do not build downstream scripts that depend on specific variable names until the renaming audit is complete. See the Development Roadmap for status.

Contents

Getting started

• Quickstart Guide
  • Prerequisites
  • Organise your files
  • Create the YAML configuration file
  • Validate the YAML
  • Step 1 — run stage 1 and verify raw files are reachable
  • Step 2 — inspect the raw time series and set deployment times
  • Step 3 — run stage 2 and verify trimming
  • Run the full pipeline
  • Open the report
  • Where to go next
• Installation
  • Requirements
  • Install oceanarray
  • Stage 1 and seasenselib
  • RDI ADCP support
  • Verify the installation
• Troubleshooting
  • Installation problems
  • Environment problems
  • Runtime problems
  • Getting help

Processing framework

• OceanArray processing framework
  • Instrument-level processing
  • Mooring-level processing
  • Array-level processing
  • Summary table
• HTML Reports
  • Live example
  • Report pages
  • PDF output
  • Report colour conventions
  • Interpreting processing status pills
• Directory Structure and File Layout
  • Overview
  • Raw directory layout
  • Processed directory layout
  • The YAML configuration file
  • File naming conventions
• File Naming Conventions
  • Raw instrument files
  • Processed output files
  • See also

Stage 1 2 3 - Instrument

• 0. Data Acquisition
• 1. Standardisation
• 2. Clock Offset Analysis (optional)
• 2. Trim to Deployment
• 3. Automatic QC
• 3. Apply Calibration
• 3. Coordinate Transform

Stack & Grid - Moorings

• Stack into one NetCDF
• Grid onto pressure

Caldips

• Calibration dips

Reference

• GitHub Repo
• Python API
• CLI Reference
• YAML Configuration Reference
• OceanArray Project Structure
• OceanArray Data Format Specification
• OceanSITES manual
• Legacy modules

Changelog / Migration

• Migrating from the --basedir Layout

Development

• Development Roadmap
• Project Style Guide
• Convert to OceanSITES (Stage 4)
• Combine Deployments
• Multi-site Merging

Indices and Tables

• Index

• Module Index

• Search Page