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keys_sources_CROCO_test.m
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% keys_sources_CROCO.m
%
% keys_sources sets user defined paths and user keys
%
% Paths:
% - path_in: directory containing the input files;
% (default is '..\Data\')
% - path_out: directory for the output files;
% (default is '..\Tracks\')
% - nc_u: full name of the netcdf file with the zonal component of
% velocity (ssu) and the time index (step)
% - nc_v: full name of the netcdf file with the meridional component of
% velocity (ssv) and the time index (step)
% - nc_dim: full name of the netcdf file with the domain coordinates
% (longitude and latitude) and the velocity mask (land-points=0;
% ocean-points=1)
%
% User option keys:
% - type_detection: flag to choose the field use as streamlines
% 1 : using velocity fields
% 2 : using ssh
% 3 : using both velocity fields and ssh for eddy contour,
% and keep the contour of the last one if it existS.
% - extended_diags: flag to have extra diags concerning eddies directly
% computed (like ellipse features or vorticity for each eddy)
% 0 : not computed
% 1 : computed as the same time as eddy detection
% 2 : computed afterward
% - streamlines and daystreamfunction: save streamlines at steps
% 'daystreamfunction' and profils of streamlines scanned as well
% (1:stepF by default )
% - periodic: flag to activate options for East-West periodic
% (e.g. global fields or idealized simulations) domains.
% IMPORTANT: first and last columns of the domain must be
% identical for this to work properly!!!!!
%
%-------------------------
% IMPORTANT - Input file requirements:
%
% All the variables are read from netcdf file.
% The package requires 3 different input files:
% 1) nc_dim with variables x(j,i),y(j,i) and mask(y,x)
% 2) nc_u with variable ssu(t,j,i) in m/s, step(t)
% 3) nc_v with variable ssv(t,j,i) in m/s, step(t)
% you can have also the sea level in an other file
% 4) nc_ssh with variable ssh(t,j,i) in m, step(t)
%
% t is the temporal dimension (number of time steps)
% j is the zonal dimension (number of grid points along y or latitude)
% i is the meridional dimension (number of grid points along x or longitude)
%
% The grid is assumed to be rectangular, with orientation N-S and E-W.
% Grid indices correspond to geography, so that point (1,1) represents the
% south-western corner of the domain.
% Latitudinal and longitudinal grid spacing can vary within the grid domain.
%-------------------------
% Ver Jun 2018 Briac and Romain Pennel
% Ver Apr 2015 Briac Le Vu
% Ver. 2.1 Oct.2012
% Ver. 2.0 Jan.2012
% Ver. 1.3 Apr.2011
% Ver. 1.2 May.2010
% Ver. 1.1 Dec.2009
% Authors: Francesco Nencioli, [email protected]
% Charles Dong, [email protected]
%-------------------------
%
%=========================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% User modification ---------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Experiment setings
%----------------------------------------------
source = 'CROCO';
% name for the experiment
config = 'test';
% postfix name of the data
postname = '';
% use to diferenciate source field of surface height (adt, ssh, psi,...)
sshtype = ''; % ex: adt_, psi_
% use to submit parallel computation
runname = ''; % ex: 1,b2_K5,day10,...
% set the paths
%path_in = ['/bdd/MEDI/workspaces/arsouze/WMED36/'];
%path_in = ['/homedata/rpennel/MEDRYS/EAST/'];
path_in=['/home/blevu/DATA/',source,'/',config,'/'];
%path_out = ['/home/rpennel/CODES/MATLAB/AMEDA_AANORVE/OUT/'];
%path_out = ['/homedata/rpennel/MEDRYS/EAST/AMEDA/MEDRYS_2005_2008/BUGMASK/'];
path_result=['/home/blevu/Resultats/',source,'/',config,'/'];
path_out=[path_result,sshtype,postname,'/',runname,'/'];
path_rossby='/home/blevu/MATLAB/Rossby_radius/';
disp(['Compute from ',path_in])
disp([' to ',path_out])
if exist(path_out,'file')==0
system(['mkdir ',path_result]);
system(['mkdir ',path_result,sshtype,postname,'/']);
system(['mkdir ',path_result,sshtype,postname,'/',runname,'/']);
system(['mkdir ',path_out]);
end
% add path_out path
addpath(path_out)
% input data file absolute name
nc_dim = [path_in,'ameda_croco_sample.nc'];
% nc_u = [path_in,'2_MED108_1d_20120110_20120120_grid_U.nc'];
% nc_v = [path_in,'2_MED108_1d_20120110_20120120_grid_V.nc'];
% nc_ssh = [path_in,'MEDRYS1V1_EAST_2005-2008.nc'];
nc_ssh='';
nc_u = nc_dim;nc_v = nc_dim;
% variable names
y_name = 'nav_lat_rho';
x_name = 'nav_lon_rho';
m_name = 'mask_rho';
u_name = 'u';
v_name = 'v';
s_name= '';
% Rossby deformation radius file
mat_Rd = [path_rossby,'Rossby_radius']; % for Med
name_Rd = 'Rd_baroc1_extra';
% searched eddies typical radius
% eddies smaller than 1/4 this radius will be smoothed
Rd_typ = 4; % km
% minimal size for rmax to be reasonably detected
nRmin = 1/2; % half of the native Dx grid size
% duration experiment
if ~exist('stepF','var')
u0 = squeeze(ncread(nc_u,u_name,[1 1 1 1],[1 1 1 Inf]));
stepF = length(u0);
clear u0
end
disp([' ',num2str(stepF),' time steps'])
disp(' ')
% rotation period (T)
T = 3600*24; % day period in seconds
% the daily time step (dps)
dps = 1/4; % (in days per step) % 1/8 is 3h time step
% depth level analysed during the detection
level = 1; % level to analyse (30=253 m)
% degradation factor to test the algorithm
if ~exist('deg','var')
deg = 1; % from 1 (default) to >10 in some experiment
end
%% Experiment option
%----------------------------------------------
% grid type
grid_ll = 1;
% 0 : spatial grid in cartesian coordinates (x,y)
% 1 : spatial grid in earth coordinates (lon,lat)
% grid regular or not (like arakawa in NEMO)
grid_reg = 1;
% 0 irregular
% 1 regular
% choose the field use as streamlines
type_detection = 1;
% 1 : using velocity fields
% 2 : using ssh
% 3 : using both velocity fields and ssh,
% and keep max velocity along the eddy contour
% if you want extended diags directly computed
extended_diags = 1;
% 0 : not computed
% 1 : computed as the same time as eddy detection
% 2 : computed afterward
% save streamlines at days daystreamfunction and profil as well
streamlines = 0;
daystreamfunction = 1:stepF;
% in case of periodic grid along x boundaries
periodic = 0;
% to keep firts and last detection after the tracking in NRT configuration
nrt = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% End of user modification ---------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%