Glider NetCDF Writer

A library for creating NetCDF files for Teledyne Slocum Glider datasets.

Dependencies

• NumPy and SciPy
• Gibbs Seawater Oceanographic Package
• Glider Binary Data Reader
• Glider Utils

Installation

1. Install dependencies (see above)
2. git clone https://github.com/USF-COT/glider_netcdf_writer
3. cd glider_netcdf_writer
4. sudo python setup.py install

Configuration

Example configuration files from the University of South Florida Glider Group can be found in the example_config directory. Please edit these files 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:

• 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.
• glider_netcdf_writer/config/datatypes.json maps between glider generated types (e.g., m_depth-m) and types to be output to a NetCDF file (e.g., depth). 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.

Usage Examples

Command Line

Create NetCDF File

create_glider_netcdf.py -f <path to flight file> -s <path to science file> <glider name> <base 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, base config directory would be something like the example_config directory in the repository. Do not point directly at a glider configuration directory. That is why you must specify a glider name.

Check NetCDF File

check_glider_netcdf.py <path to NetCDF file>

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

For Help

create_glider_netcdf.py -h

check_glider_netcdf.py -h

In Code

from glider_binary_data_reader import (
    GliderBDReader,
    MergedGliderBDReader
)
from glider_netcdf_writer import (
    open_glider_netcdf
)

flightReader = GliderBDReader(
    ['./test_data/usf-bass/usf-bass-2014-061-1-0.sbd']
)
scienceReader = GliderBDReader(
    ['./test_data/usf-bass/usf-bass-2014-061-1-0.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