Utility and library to interface with CF-Compliant NetCDF flag variables.
So… you want to inspect CF Compliant NetCDF flag variables?
CF Compliant NetCDF Flag variables are integer flags associated with, or having:
- flag_masks (optionally)
Read the CF Conventions on flags for more information.
Install the utility with with pip:
pip install ncflag
On the command line, use ncflag:
Usage: ncflag [OPTIONS] NCFILE FLAG Options: -v, --version Show the version and exit. --show_flags PATH Print the flags this tool can inspect. --use_time_var TEXT -l [DEBUG|INFO|WARNING|ERROR|CRITICAL] log level --help Show this message and exit.
Use –show_flags to discover what flags in a given file can be inspected.
Limitation: can only inspect flags of at most one dimension. See details below for dealing with multidimensional flags.
The nominal output with –use_time_var specified is shown below. Without use_time_var, the index along the dimension will be printed instead of a iso 8601 timestamp.
2017-11-27T21:07:41.543778: [u'data_quality_error'] 2017-11-27T21:07:42.543812: [u'good_data'] 2017-11-27T21:07:43.543807: [u'good_data'] 2017-11-27T21:07:44.543802: [u'good_data']
Occasionally, by some poor misfortune, you may encounter multidimensional flag variables. These are currently not supported by the Command Line Interface (CLI), however, the FlagWrap class can still be used in code, or through an interactive (IPython) session. The FlagWrap.get_flags_set_at_index can be passed a tuple of indicies to get the flags set in a multidimensional flag variable. Below is an example.
from ncflag import FlagWrap import netCDF4 as nc with nc.Dataset("somenetcdf.nc") as nc_in: v = nc_in.variables["mutidim_variable"] print(v.shape) # --> (2, 10), is multidim. w = FlagWrap.init_from_netcdf(v) print(w.get_flags_set_at_index((0, 0))) # --> ["good_quality_qf"]
API and Documentation
To use the FlagWrap in your own code, see the example above for multidimensional flags.
For documentation, please read flag_wrapper.py. It is one file and is documented with comprehensive docstrings. The functions are named descriptively. A following functions are available from a FlagWrap instance.
- get_flag(self, flag_meaning) - reduce(self, exclude_mask, axis=-1) - get_flag_at_index(self, flag_meaning, i) - get_flags_set_at_index(self, i, exit_on_good=False) - find_flag(self, options) - set_flag(self, flag_meaning, should_be_set, zero_if_unset=True) - set_flag_at_index(self, flag_meaning, i) - get_value_for_meaning(self, flag_meaning) - get_mask_for_meaning(self, flag_meaning)
There are tests, using both synthetic flags, as well as some more serious tests for some fairly complex “in the wild” flags taken from a sample GOES-16 EXIS-L1b-SFXR product file.
test/test_theoretical.py is actually a very thourough read to help anyone really understand what’s possible and what’s going on with these flags.
Deploy to pip, after testing with python2 and python3:
rm -r dist/ python setup.py bdist_wheel --universal twine upload dist/*
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