EcoFOCI_eofs

This is a wrapper to smoothly analyze EcoFOCI timeseries data via EOF analysis.

Input files are EPIC standard netCDF files. Output files are EPIC standard netCDF files and summary text file.

Tested on python 3.8

Based on python EOF analysis package

eofs V1.3.0

http://ajdawson.github.io/eofs/
https://github.com/ajdawson/eofs
http://doi.org/10.5334/jors.122 - journal article

Many results are not relevant here for these purposes from this package and are available as analysis extensions.

Science Notes

We expect to have the same number of EOF's / PCS's as we have timeseries

Usage

usage: EcoFOCI_eof.py [-h] [-o OUTFILE] [-s START_DATE] [-e END_DATE]
                      [--eof_num EOF_NUM] [--epic]
                      pfile varname config_file_name

Analyze timeseries EOF

positional arguments:
  pfile                 pointer file with full paths on each line
  varname               name of variable, may be EPIC name
  config_file_name      full path to config file - eof_config.yaml

optional arguments:
  -h, --help            show this help message and exit
  -o OUTFILE, --outfile OUTFILE
                        name of output file (run-name)
  -s START_DATE, --start_date START_DATE
                        yyyymmddhhmmss
  -e END_DATE, --end_date END_DATE
                        yyyymmddhhmmss
  --eof_num EOF_NUM     number of eofs. default is all (arbitrarily large
                        number)
  --epic                assume EPIC time format
  --plots               output some basic plots - TODO
  --summary             output summary only

Example

EcoFOCI_eof.py test/14ck9a_curr_brg_subset_f35.point U_320 config/eof_config.yaml -s 20141005000000 -e 20150501000000 --epic

Will run the analysis files listed in: test/14ck9a_curr_brg_subset_f35.point

for the variable: U_320 (which will also select u_1205)
with the EPIC .nc file having properties specified by config/eof_config.yaml

starting at 2014-10-05 00:00:00
ending at 2015-05-01 00:00:00
and expecting EPIC format

EcoFOCI_eof.py test/14ck9a_curr_brg_subset_f35.point U_320 config/eof_config.yaml -s 20141005000000 -e 20150501000000 -eof_num=1 -o=test --epic

is the same as the above but only returning the first EOF and naming the run 'test'

PJS

progdir=/full/path/to/dir/  
pointer=14ck9a_curr_brg_subset_f35.pavlof.point

python ${progdir}EcoFOCI_eof.py ${pointer} U_320 ${progdir}config/eof_config.yaml -s 20141005000000 -e 20150501000000 --epic -o eof_results

Requirements

Found in the ci/requirements.txt - these are kept up-to-date by a dependabot GHAction but are not currently tested against for every upgrade.

The software was initially developed with ci/requirements.orig but is not maintained against them.

Legal Disclaimer

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