CBIOMES-Processing.m

This repository contains prototype workflows, written in Matlab, having to do with CBIOMES model inputs and outputs. A listing, hopefully up to date, of the scripts and their respective purposes is provided below.

standard diagnostics

• README_set_gudA.md documents method to systematically depict model output, including diags_set_drwn3.m and diags_set_gudA.m.
• diags_set_drwn3.m is a standard set of biomass and plankton distribution diagnostics.
• diags_set_gudA.m is a standard set of biochemistry diagnostics with relevance to primary production.
• diags_plot_lightfields.m is a standard set of irradiance reflectance diagnostics.
• diags_plot_planktongroups.m is a standard set of plnakton group diagnostics.

155W section diagnostics

• read_slice_155W.m is a Matlab / Octave function that reads in a variable once it has been interpolated to 155W using interp_to_155W.m
• interp_to_155W.m interpolates from model grid to 155W.
• interp_to_155W_uv.m interpolates velocity to 155W (see C-grid docs).
• read_surf_maps.m, interp_surf_maps.m, and interp_surf_maps_uv.m generate maps of top layer fields (e.g., 0-10m or 5m depth average).

OC-CCI processing, model-data comparison, etc.

• cci_Rrs_tests.m converts irradiance reflectance output to remotely sensed reflectances and interpolate to CCI wavelengths (0D and 2D tests).
• cci_Rrs_remap.m reads in OC-CCI data (netcdf files, sinusoidal grid), remaps it to llc90 grid (using bin-average, binary file).
• cci_Rrs_vs_model.m compares regridded OC-CCI data from cci_Rrs_remap.m with model as in cci_Rrs_tests.m.
• cci_PostProcessModelOutput.m converts monthly model output to daily OC-CCI Rrs (6 wavebands).
• cci_CompareModelData.m plot maps of model and CCI sample averages, model-data difference maps, and time series of model vs dara stats.

other basic diagnostics

• eccov4_climplot.m generates maps and sections of the physical ocean state variables (MLD, T, S, U, V,...).
• llc90drwn3_ptravrg.m time averages tracer model output.
• llc90drwn3_ptrplot.m plots time-averaged tracer output.
• Top50mAveBiomass.m sums biomass and chlorophyll over all plankton types and average over top 50m.

utilities

• PTRACERS_names.m lookup table for tracer actual names.
• PTRACERS_varnames.m lookup table for tracer internal code names.
• PTRACERS_units.m lookup table for tracer variable units.
• PTRACERS_ranges.m lookup table for tracer variable ranges.
• cs510readsample.m reads cs510 grid and sample output.
• cs510readmeta.m reads cs510 sample output format.
• cs510readtiles.m reads cs510 tiled output format.
• runSamples.m demo script to interpolate and create NetCDF files for different types of output formats.
• runCalAveBiomass.m script to calculate Average Biomass for cs510 data, interpolate, and output as NetCDF.
• addLineAvailDiag.m adds line to available_diagnostics.log file.
• calcShannon.m calculates Shannon Index.
• calcSum.m calculates a sum of given fields.
• calcIntegralFull.m calculate full depth integral of a field.

CMAP2019

These are the scripts used to interpolate the data added to CMAP in Spring 2019

• runGroups_cs510.m driver script for calculating new fields, interpolating, and saving to group directories
• setup_pathsflds_cs510.m script that defines which fields to calculate, interpolate, and group