About seagliderOG1

The seagliderOG1 package converts Seaglider basestation files (*.nc) into OG1 format for standardized oceanographic glider data exchange.

Purpose

Seaglider data is originally produced in a proprietary basestation format that varies between deployments and has evolved over time. The Ocean Gliders community has developed the OG1 (Ocean Gliders 1) format as a standardized, CF-compliant format for sharing glider data.

This package bridges that gap by:

  • Converting individual dive-climb cycle files into mission-level datasets

  • Standardizing variable names, units, and metadata

  • Enriching data with sensor information and calibration metadata

  • Ensuring CF and OG1 compliance for data interoperability

Format Transformation

Major Changes from Basestation to OG1

Data Structure

  • Input: Individual files per dive-climb cycle (pSSSDDDD_YYYYMMDD.nc)

  • Output: Single trajectory file per mission with all cycles concatenated

  • Dimension: sg_data_point → N_MEASUREMENTS (standardized dimension name)

Variable Standardization

The conversion process transforms variable names to follow OG1 conventions:

Basestation → OG1
────────────────────
latitude    → LATITUDE
longitude   → LONGITUDE
ctd_time    → TIME
gps_lat     → LATITUDE_GPS
gps_lon     → LONGITUDE_GPS
eng_pitchAng → PITCH
eng_rollAng → ROLL
ctd_depth   → DEPTH

Metadata Enrichment

  • Sensor Information: Automatically detects and catalogs sensors (CTD, oxygen, fluorometers)

  • Calibration Data: Extracts and preserves sensor calibration coefficients

  • Global Attributes: Adds CF-compliant and OG1-required global metadata

  • QC Variables: Creates quality control flag variables following OG1 standards

GPS Data Integration

GPS fixes are interpolated onto the main measurement time vector to provide:

  • LATITUDE_GPS and LONGITUDE_GPS at measurement times

  • TIME_GPS for GPS fix timestamps

  • Proper handling of surface intervals and data gaps

Units and Standards

  • Unit Conversion: Automatic conversion to OG1 preferred units (e.g., cm/s → m/s)

  • CF Compliance: All variables include standard_name, long_name, and units attributes

  • Vocabulary Control: Uses controlled vocabularies from NERC

Configuration-Driven Approach

The conversion process is highly configurable through YAML files:

  • OG1_var_names.yaml: Variable name mappings

  • OG1_vocab_attrs.yaml: CF-compliant variable attributes

  • OG1_sensor_attrs.yaml: Sensor-specific metadata

  • OG1_global_attrs.yaml: Global attribute templates

This design allows easy adaptation to new Seaglider formats or OG1 specification updates.

OG1 Format Compliance

The output files comply with:

Key OG1 features implemented:

  • Trajectory Format: Each file represents a single glider trajectory

  • Standardized Variables: Core oceanographic variables with controlled vocabularies

  • Sensor Metadata: Detailed sensor information and calibration data

  • Quality Control: QC flag variables for all measurements

  • Global Attributes: Rich metadata for data discovery and citation

Quality Assurance

The package includes extensive validation:

  • Dimension Checking: Ensures proper N_MEASUREMENTS dimension

  • Coordinate Validation: Verifies required coordinates are present

  • Unit Conversion: Validates unit compatibility before conversion

  • Metadata Completeness: Checks for required OG1 attributes

Extended Variables

Beyond standard OG1 variables, the package preserves:

  • Flight Model Variables: Vertical and horizontal velocities from glider flight modeling

  • Engineering Data: Detailed glider state information

  • Derived Variables: Additional oceanographic parameters when available

For more details on the OG1 format, see the Ocean Gliders Community documentation.

Example Workflow

A typical conversion processes multiple basestation files:

from seagliderOG1 import readers, convertOG1, writers

# Load all basestation files from a mission
datasets = readers.load_basestation_files("path/to/mission/files/")

# Convert to OG1 format (concatenates all dives)
og1_dataset, variables = convertOG1.convert_to_OG1(datasets)

# Save standardized trajectory file
writers.save_dataset(og1_dataset, "sg015_mission_001_delayed.nc")

This transforms dozens of individual dive files into a single, standardized trajectory file ready for scientific analysis and data sharing.