A set of Python utilities for reading, merging, and post processing Teledyne Webb Slocum Glider data.

Available through conda. This library requires Python 3.5 or above.

$ conda create -n sgs python=3.5
$ source activate sgs
$ conda install -c axiom-data-science gutils

Example configuration files from the University of South Florida Glider Group can be found in the test resources. Use these files as a basis for your institution, possible datatypes, and gliders. Do not delete any parameters from these files, only adjust their values for your institution. Otherwise, your NetCDF files will not pass the check_glider_netcdf.py script.

A brief overview of each file and folder follows:

• your-glider-name-here/global_attributes.json contains parameters that are specific to the glider institution.
• your-glider-name-here/deployment.json describes the current deployment for a given glider. Includes global attribute details that change between deployments and information about the glider/platform deployed.
• your-glider-name-here/instruments.json provides details about instruments deployed with a single glider. instrument_ctd is the only required instrument in this file.
• your-glider-name-here/datatypes.json maps between glider generated types (e.g., m_depth-m) and types to be output to a NetCDF file (e.g., depth). This file is optional and will fallback to the defaults if not present in the configuration directory. You will only need to edit this file if you need to add datatypes to the NetCDF files. Types in here that are not produced by your glider will NOT cause errors. Hopefully, through collaboration, we will be able to produce a complete mapping of glider types to NetCDF variables and keep the default updated. Please submit a PR if you are using a custom datatypes.json!

$ create_glider_netcdf.py -h

$ create_glider_netcdf.py \
    -f <path to flight file> \
    -s <path to science file> \
    <glider config directory> \
    <NetCDF output directory>

Outputs a set of profiles from a merged flight and science dataset NetCDF files to the output directory. Can also specify only a flight (-f) or science (-s) file without the corresponding file.

For the example above, the glider config directory would be something like this. Point directly at a glider configuration directory.

$ check_glider_netcdf.py -h

$ check_glider_netcdf.py <path to NetCDF file>

Prints errors and returns number of errors. Prints PASS and returns 0 on success.

from gutils.gbdr import (
    GliderBDReader,
    MergedGliderBDReader
)
from gutils.nc import open_glider_netcdf

flightReader = GliderBDReader(
    ['/some/path/to/file.sbd']
)
scienceReader = GliderBDReader(
    ['/some/path/to/file.tbd']
)
reader = MergedGliderBDReader(flightReader, scienceReader)

with open_glider_netcdf(self.test_path, self.mode) as glider_nc:
    for line in reader:
        glider_nc.stream_dict_insert(line)

See a larger example in tests.py

This package is part of the SECOORA Glider System (SGS) and was originally developed by the CMS Ocean Technology Group at the University of South Florida. It is now maintained by SECOORA and Axiom Data Science.

• GUTILS: A set of Python utilities for post processing glider data.
• GSPS: Watches a directory for new *db flight/science files and publishes the data to a ZeroMQ socket.
• GDAM: Watches a directory for new *db flight/science files, inserts the data into a MongoDB instance, and publishes the data to a ZeroMQ socket.