diff --git a/Aforc_CFSR/interp_CFSR.m b/Aforc_CFSR/interp_CFSR.m
index f97ddaa5e389f53b0780840295f8a895909ee2e7..cb2d808450c263943bd6ca2e346bd79c21787f46 100644
--- a/Aforc_CFSR/interp_CFSR.m
+++ b/Aforc_CFSR/interp_CFSR.m
@@ -9,7 +9,7 @@ function interp_CFSR(NCEP_dir,Y,M,Roa,interp_method,...
% 1: Air temperature: Convert from Kelvin to Celsius
%
vname='Temperature_height_above_ground';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
tair=squeeze(nc{vname}(tin,:,:));
close(nc);
tair=get_missing_val(lon1,lat1,mask1.*tair,nan,Roa,nan);
@@ -21,7 +21,7 @@ tair=interp2(lon1,lat1,tair,lon,lat,interp_method);
% Get Specific Humidity [Kg/Kg]
%
vname='Specific_humidity';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
shum=squeeze(nc{vname}(tin,:,:));
close(nc);
shum=get_missing_val(lon1,lat1,mask1.*shum,nan,Roa,nan);
@@ -35,7 +35,7 @@ rhum=shum./qsat(tair);
% 3: Precipitation rate: Convert from [kg/m^2/s] to cm/day
%
vname='Precipitation_rate';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
prate=squeeze(nc{vname}(tin,:,:));
close(nc);
prate=get_missing_val(lon1,lat1,mask1.*prate,nan,Roa,nan);
@@ -49,7 +49,7 @@ prate(abs(prate)<1.e-4)=0;
% Downward solar shortwave
%
vname='Downward_Short-Wave_Rad_Flux_surface';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
dswrf=squeeze(nc{vname}(tin,:,:));
close(nc);
dswrf=get_missing_val(lon1,lat1,mask1.*dswrf,nan,Roa,nan);
@@ -57,7 +57,7 @@ dswrf=get_missing_val(lon1,lat1,mask1.*dswrf,nan,Roa,nan);
% Upward solar shortwave
%
vname='Upward_Short-Wave_Rad_Flux_surface';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
uswrf=squeeze(nc{vname}(tin,:,:));
close(nc);
uswrf=get_missing_val(lon1,lat1,mask1.*uswrf,nan,Roa,nan);
@@ -82,7 +82,7 @@ radsw(radsw<1.e-10)=0;
% 5.1 get the downward longwave flux [W/m^2]
%
vname='Downward_Long-Wave_Rad_Flux';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
dlwrf=squeeze(nc{vname}(tin,:,:));
close(nc);
dlwrf=get_missing_val(lon1,lat1,mask1.*dlwrf,nan,Roa,nan);
@@ -90,7 +90,7 @@ dlwrf=get_missing_val(lon1,lat1,mask1.*dlwrf,nan,Roa,nan);
% 5.2 get the upward longwave flux [W/m^2]
%
vname='Upward_Long-Wave_Rad_Flux_surface';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
ulwrf=squeeze(nc{vname}(tin,:,:));
close(nc);
ulwrf=get_missing_val(lon1,lat1,mask1.*ulwrf,nan,Roa,nan);
@@ -106,14 +106,14 @@ radlw_in=interp2(lon1,lat1,dlwrf,lon,lat,interp_method);
% 6: Wind & Wind stress [m/s]
%
vname='U-component_of_wind';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
uwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
uwnd=get_missing_val(lon1,lat1,mask1.*uwnd,nan,Roa,nan);
uwnd=interp2(lon1,lat1,uwnd,lon,lat,interp_method);
%
vname='V-component_of_wind';
-nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([NCEP_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
vwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
vwnd=get_missing_val(lon1,lat1,mask1.*vwnd,nan,Roa,nan);
diff --git a/Aforc_CFSR/make_CFSR.m b/Aforc_CFSR/make_CFSR.m
index a1dc7e17efab127746be99db314a57c6e6ae3e43..0a9b086cb59b5cbf93119fe1226966641796f4b1 100644
--- a/Aforc_CFSR/make_CFSR.m
+++ b/Aforc_CFSR/make_CFSR.m
@@ -41,6 +41,7 @@ close all
% Common parameters
%
crocotools_param
+isoctave=exist('octave_config_info');
%
frc_prefix=[frc_prefix,'_CFSR_'];
blk_prefix=[blk_prefix,'_CFSR_'];
@@ -60,7 +61,7 @@ end
%
disp(' ')
disp([' Read in the grid ',grdname])
-nc=netcdf(grdname);
+nc=netcdf(grdname,'r');
Lp=length(nc('xi_rho'));
Mp=length(nc('eta_rho'));
lon=nc{'lon_rho'}(:);
@@ -103,7 +104,7 @@ if makefrc==1 | makeblk==1
%
% Get the NCEP horizontal grids (it should be the same for every month)
%
- nc=netcdf([NCEP_dir,'Land_cover_1land_2sea.nc']);
+ nc=netcdf([NCEP_dir,'Land_cover_1land_2sea.nc'],'r');
disp(['Use this land file :',char([NCEP_dir,'Land_cover_1land_2sea.nc'])])
lon1=nc{'lon'}(:);
lat1=nc{'lat'}(:);
@@ -141,7 +142,7 @@ if makefrc==1 | makeblk==1
%
% Process time (here in days)
%
- nc=netcdf([NCEP_dir,'Temperature_height_above_ground_Y',num2str(Y),'M',num2str(M),'.nc']);
+ nc=netcdf([NCEP_dir,'Temperature_height_above_ground_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
NCEP_time=nc{'time'}(:);
close(nc);
@@ -231,7 +232,7 @@ if makefrc==1 | makeblk==1
Mm=M;
Ym=Y;
else
- nc=netcdf(fname);
+ nc=netcdf(fname,'r');
tndx=length(nc('time'));
if makefrc==1
for aa=1:itolap_ncep
@@ -300,7 +301,7 @@ if makefrc==1 | makeblk==1
Mp=M;
Yp=Y;
else
- nc=netcdf(fname);
+ nc=netcdf(fname,'r');
if makefrc==1
disp('sms_time')
for tndx=tlen0+itolap_ncep+1:tlen;
@@ -368,8 +369,13 @@ if SPIN_Long>0
frcname=[frc_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
frcname2=[frc_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
disp(['Create ',frcname2])
- eval(['!cp ',frcname,' ',frcname2])
- %
+% eval(['!cp ',frcname,' ',frcname2])
+ if (isoctave == 0)
+ eval(['!cp ',frcname,' ',frcname2])
+ else
+ system(['cp ',frcname,' ',frcname2]
+ end
+ %
% Change the time
%
nc=netcdf(frcname2,'write');
@@ -387,8 +393,13 @@ if SPIN_Long>0
blkname=[blk_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
blkname2=[blk_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
disp(['Create ',blkname2])
- eval(['!cp ',blkname,' ',blkname2])
- %
+ %% eval(['!cp ',blkname,' ',blkname2])
+ if (isoctave == 0)
+ eval(['!cp ',blkname,' ',blkname2])
+ else
+ system(['cp ',blkname,' ',blkname2])
+ end
+ %
% Change the time
%
nc=netcdf(blkname2,'write');
diff --git a/Aforc_CFSR/process_coast_CFSR.m b/Aforc_CFSR/process_coast_CFSR.m
index 00e029734c21820249019e163056c5d95383ea21..fa5841855668289d0bcfd1889ae51873454de928 100644
--- a/Aforc_CFSR/process_coast_CFSR.m
+++ b/Aforc_CFSR/process_coast_CFSR.m
@@ -83,7 +83,7 @@ disp([' Processing mask'])
in_file = [CFSR_dir,char(vnames(k)),'.nc'];
out_file = [CFSR_COAST_dir,char(vnames(k)),'.nc'];
%
-nc=netcdf(in_file);
+nc=netcdf(in_file,'r');
lon=nc{'lon'}(:);
lat=nc{'lat'}(:);
mask=squeeze(nc{'Land_cover_1land_2sea'}(1,:,:));
@@ -192,7 +192,7 @@ for Ye=Ymin:Ymax
in_file = [CFSR_dir,vname,'_Y',num2str(Ye),'M',num2str(Mo),'.nc'];
- nc=netcdf(in_file);
+ nc=netcdf(in_file,'r');
time=nc{'time'}(:);
N=length(time);
diff --git a/Aforc_ERA5/ERA5_parallel_request.py b/Aforc_ERA5/ERA5_parallel_request.py
new file mode 100644
index 0000000000000000000000000000000000000000..62072a922933ee2ac0a9125c8a4d2a4e3af67bfc
--- /dev/null
+++ b/Aforc_ERA5/ERA5_parallel_request.py
@@ -0,0 +1,211 @@
+#!/usr/bin/env python
+
+# Script to download ECMWF ERA5 reanalysis datasets from the Climate Data
+# Store (CDS) of Copernicus https://cds.climate.copernicus.eu
+#
+# This script use the CDS Phyton API[*] to connect and download specific ERA5
+# variables, for a chosen area and monthly date interval, required by CROCO to
+# perform simulations with atmospheric forcing. Furthermore, this script use
+# ERA5 parameter names and not parameter IDs as these did not result in stable
+# downloads.
+#
+# Tested using Python 3.8.6 and Python 3.9.1. This script need the following
+# python libraries pre-installed: "calendar", "datetime", "json" and "os".
+#
+# [*] https://cds.climate.copernicus.eu/api-how-to
+#
+# Copyright (c) DDONOSO February 2021
+# e-mail:ddonoso@dgeo.udec.cl
+#
+
+# You may see all available ERA5 variables at the following website
+# https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation#ERA5:datadocumentation-Parameterlistings
+
+# -------------------------------------------------
+# Getting libraries and utilities
+# -------------------------------------------------
+import cdsapi
+from ERA5_utilities import *
+import calendar
+import datetime
+import json
+import os
+from multiprocessing import Pool
+
+# Importing addmonths4date function from ERA5_utilities
+from ERA5_utilities import addmonths4date
+
+# Function to download data for a single variable
+def download_data(variable, options, product, output):
+ c = cdsapi.Client()
+ c.retrieve(product, options, output)
+
+# Main function to process tasks in parallel
+def process_parallel(tasks):
+ with Pool() as pool:
+ pool.starmap(download_data, tasks)
+
+
+# -------------------------------------------------
+# Import my crocotools_param_python file
+from era5_crocotools_param import *
+print('year_start is '+str(year_start))
+
+# -------------------------------------------------
+dl=2
+if ownArea == 0:
+ lines = [line.rstrip('\n') for line in open(paramFile)]
+ for line in lines:
+ if "lonmin" in line:
+ iStart=line.find('=')+1
+ iEnd=line.find(';')
+ lonmin = line[iStart:iEnd]
+ elif "lonmax" in line:
+ iStart=line.find('=')+1
+ iEnd=line.find(';')
+ lonmax = line[iStart:iEnd]
+ elif "latmin" in line:
+ iStart=line.find('=')+1
+ iEnd=line.find(';')
+ latmin = line[iStart:iEnd]
+ elif "latmax" in line:
+ iStart=line.find('=')+1
+ iEnd=line.find(';')
+ latmax = line[iStart:iEnd]
+
+lonmin = str(float(lonmin)-dl)
+lonmax = str(float(lonmax)+dl)
+latmin = str(float(latmin)-dl)
+latmax = str(float(latmax)+dl)
+print ('lonmin-dl = ', lonmin)
+print ('lonmax+dl =', lonmax)
+print ('latmin-dl =', latmin)
+print ('latmax+dl =', latmax)
+# -------------------------------------------------
+
+area = [latmax, lonmin, latmin, lonmax]
+
+# -------------------------------------------------
+# Setting raw output directory
+# -------------------------------------------------
+# Get the current directory
+os.makedirs(era5_dir_raw,exist_ok=True)
+
+
+# -------------------------------------------------
+# Loading ERA5 variables's information as
+# python Dictionary from JSON file
+# -------------------------------------------------
+with open('ERA5_variables.json', 'r') as jf:
+ era5 = json.load(jf)
+
+
+# -------------------------------------------------
+# Downloading ERA5 datasets
+# -------------------------------------------------
+# Monthly dates limits
+monthly_date_start = datetime.datetime(year_start,month_start,1)
+monthly_date_end = datetime.datetime(year_end,month_end,1)
+
+# Length of monthly dates loop
+len_monthly_dates = (monthly_date_end.year - monthly_date_start.year) * 12 + \
+ (monthly_date_end.month - monthly_date_start.month) + 1
+
+# Initial monthly date
+monthly_date = monthly_date_start
+
+# Construct tasks for parallel processing
+tasks = []
+
+# Monthly dates loop
+for j in range(len_monthly_dates):
+
+ # Year and month
+ year = monthly_date.year
+ month = monthly_date.month
+
+ # Number of days in month
+ days_in_month = calendar.monthrange(year,month)[1]
+
+ # Date limits
+ date_start = datetime.datetime(year,month,1)
+ date_end = datetime.datetime(year,month,days_in_month)
+
+ # Ordinal date limits (days)
+ n_start = datetime.date.toordinal(date_start)
+ n_end = datetime.date.toordinal(date_end)
+
+ # Overlapping date string limits (yyyy-mm-dd)
+ datestr_start_overlap = datetime.date.fromordinal(n_start - n_overlap).strftime('%Y-%m-%d')
+ datestr_end_overlap = datetime.date.fromordinal(n_end + n_overlap).strftime('%Y-%m-%d')
+
+ # Overlapping date string interval
+ vdate = datestr_start_overlap + '/' + datestr_end_overlap
+
+ # Variables/Parameters loop
+ for k in range(len(variables)):
+
+ # Variable's name, long-name and level-type
+ vname = variables[k]
+ vlong = era5[vname][0]
+ vlevt = era5[vname][3]
+
+ # Request options
+ options = {
+ 'product_type': 'reanalysis',
+ 'type': 'an',
+ 'date': vdate,
+ 'variable': vlong,
+ 'levtype': vlevt,
+ 'area': area,
+ 'format': 'netcdf',
+ }
+
+ if vlong == 'sea_surface_temperature':
+ options['time'] = '00'
+ elif vlong == 'land_sea_mask':
+ options['time'] = '00:00'
+ else:
+ options['time'] = time
+
+ if vlong == 'specific_humidity' or vlong == 'relative_humidity':
+ options['pressure_level'] = '1000'
+ product = 'reanalysis-era5-pressure-levels'
+ else:
+ product = 'reanalysis-era5-single-levels'
+
+ # Output filename
+ fname = 'ERA5_ecmwf_' + vname.upper() + '_Y' + str(year) + 'M' + str(month).zfill(2) + '.nc'
+ output = era5_dir_raw + '/' + fname
+
+ # Information strings
+ info_time_clock = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+ info_monthly_date = monthly_date.strftime('%Y-%b')
+ info_n_overlap = ' with ' + str(n_overlap) + ' overlapping day(s) '
+
+ # Printing message on screen
+ print(' ')
+ print('-----------------------------------------------------------')
+ print('',info_time_clock,' ')
+ print(' Performing ERA5 data request, please wait... ')
+ print(' Date [yyyy-mmm] =',info_monthly_date + info_n_overlap,' ')
+ print(' Variable =',vlong,' ')
+ print('-----------------------------------------------------------')
+ print('Request options: ')
+ print(options)
+
+ tasks.append((vname, options, product, output))
+
+ monthly_date = addmonths4date(monthly_date, 1)
+
+# Process tasks in parallel
+process_parallel(tasks)
+
+# Print output message on screen
+print(' ')
+print(' ERA5 data request has been done successfully! ')
+print(' ')
+
+
+
+
diff --git a/Aforc_ERA5/era5_crocotools_param.py b/Aforc_ERA5/era5_crocotools_param.py
index ddc5c9fe7dfff7ba0fbfbd6e277df34b6803ea03..fd3630ea0b6b8ec8467fba1565aee1f29ba3d4aa 100644
--- a/Aforc_ERA5/era5_crocotools_param.py
+++ b/Aforc_ERA5/era5_crocotools_param.py
@@ -8,7 +8,6 @@
#
# General path
#
-##config_dir = '../croco/Run_TEST/' # must be the same than crocotools_param
config_dir = 'path_to_my_run_dir/' # must be the same than crocotools_param
config_name = 'Benguela_LR'
#
diff --git a/Aforc_ERA5/era5_crocotools_param_my.py b/Aforc_ERA5/era5_crocotools_param_my.py
new file mode 100644
index 0000000000000000000000000000000000000000..c293036292ee8a909ded2d6f02ef2b206bd96b3e
--- /dev/null
+++ b/Aforc_ERA5/era5_crocotools_param_my.py
@@ -0,0 +1,86 @@
+#
+# For ERA5 python crocotools parameters list
+#
+# CAUTION IT MUST BE CONSISTENT with your MATLAB CROCOTOOLS_PARAM.m file in Run directory
+# *******************************************************************************
+# U S E R * O P T I O N S
+# *******************************************************************************
+#
+# General path
+#
+config_dir = '/local/tmp/3/gcambon/CONFIGS/RUN_V2.0_cforec_LR_DEV/' # must be the same than crocotools_param
+config_name = 'Benguela_LR'
+#
+# Original ERA5 directory
+#
+era5_dir_raw = config_dir + 'DATA/ERA5_native_' + config_name
+#
+# Output ERA5 directory
+#
+era5_dir_processed = config_dir + 'DATA/ERA5_' + config_name
+#
+# extraction wave variables
+#
+wave_extract=False # True to extract wave variables
+#
+# Dates limits
+#
+year_start = 2005
+month_start = 1
+year_end = 2005
+month_end = 1
+#
+# Year origin of time
+#
+Yorig=2000
+#
+# Overlapping days (at the beginning/end of each month)
+#
+n_overlap = 0
+#
+# Request time (daily hours '00/01/.../23')
+#
+time = '00/01/02/03/04/05/06/07/08/09/10/11/12/13/14/15/16/17/18/19/20/21/22/23'
+#
+# Request variables (see available at ERA5_variables.json)
+variables = ['lsm','tp','strd','ssr','t2m','q','u10','v10'] #note lsm is land_sea_mask
+#
+# Request area ([north, west, south, east])
+#
+ownArea = 0 # 0 if area from a crocotools_param.m file
+ # 1 if own area
+
+if ownArea == 0:
+ # To complete if ownArea==0
+ paramFile = config_dir + 'crocotools_param.m' # path the crocotools_param file of the simulation
+
+else:
+ # To complete if ownArea==1
+ lonmin=7
+ lonmax=23
+ latmin=-45
+ latmax=-20
+#
+# Variable names and conversion coefficients
+# TP: convert from accumlated m in a hour into kg m-2 s-1
+#
+cff_tp=1000./3600. # m in 1 hour -> kg m-2 s-1
+# Heat flux J m-2 in one hour into W m-2
+#
+cff_heat=1./3600. # J m-2 in 1 hour -> W m-2
+# Names, conversion coefficients and new units
+#
+variables = ['lsm' , 'sst' , 'tp' ,'strd' ,'ssr' ,'t2m' ,'q' ,'u10' ,'v10' ]
+conv_cff = [1. , 1. , cff_tp ,cff_heat ,cff_heat ,1. ,1. ,1. ,1. ]
+units = ['(0-1)', 'K' , 'kg m-2 s-1','W m-2' ,'W m-2' ,'K' ,'kg kg-1','m s-1','m s-1']
+
+if wave_extract:
+ ## append waves variables
+ wave_var=['swh', 'mwd', 'pp1d' ,'cdww'];variables.extend(wave_var)
+ wave_conv_cff=[1., 1., 1. , 1.]; conv_cff.extend(wave_conv_cff)
+ wave_units=['m','Degrees true','s', 'dimensionless']; units.extend(wave_units)
+
+
+# *******************************************************************************
+# E N D U S E R * O P T I O N S
+# *******************************************************************************
diff --git a/Aforc_ERA5/interp_ERA5.m b/Aforc_ERA5/interp_ERA5.m
index 5705937cd3fa0a993077b6ebbd64c8264b7a7519..ac371d3e183031dc1d75dd7869ec9ddfa880c385 100644
--- a/Aforc_ERA5/interp_ERA5.m
+++ b/Aforc_ERA5/interp_ERA5.m
@@ -1,5 +1,5 @@
function interp_ERA5(ATMO_dir,Y,M,Roa,interp_method,...
- lon1,lat1,lonwave1,latwave1,mask1,maskwave1,tin,...
+ lon1,lat1,lonwave1,latwave1,mask1,maskwave1,maskwave2,tin,...
nc_frc, nc_blk,lon,lat,angle,tout, add_waves)
%
% Read the local ERA5 files and perform the space interpolations
@@ -12,7 +12,7 @@ function interp_ERA5(ATMO_dir,Y,M,Roa,interp_method,...
% 1: Air temperature: Convert from Kelvin to Celsius
%
vname='T2M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
tair=squeeze(nc{vname}(tin,:,:));
close(nc);
tair=get_missing_val(lon1,lat1,mask1.*tair,nan,Roa,nan);
@@ -25,7 +25,7 @@ tair=interp2(lon1,lat1,tair,lon,lat,interp_method);
% Get Specific Humidity [Kg/Kg]
%
vname='Q';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
shum=squeeze(nc{vname}(tin,:,:));
close(nc);
shum=get_missing_val(lon1,lat1,mask1.*shum,nan,Roa,nan);
@@ -40,7 +40,7 @@ rhum=shum./qsat(tair);
% 3: Precipitation rate: Convert from [kg/m^2/s] to cm/day
%
vname='TP';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
prate=squeeze(nc{vname}(tin,:,:));
close(nc);
prate=get_missing_val(lon1,lat1,mask1.*prate,nan,Roa,nan);
@@ -54,7 +54,7 @@ prate(prate<1.e-4)=0;
% Solar shortwave
%
vname='SSR';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
dswrf=squeeze(nc{vname}(tin,:,:));
close(nc);
radsw=get_missing_val(lon1,lat1,mask1.*dswrf,nan,Roa,nan);
@@ -68,7 +68,7 @@ radsw(radsw<1.e-10)=0;
% % 5.1 Get the net longwave flux [W/m^2] ERA5 not downloaded
% %
% vname='STR';
-% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
% dlwrf=squeeze(nc{vname}(tin,:,:));
% close(nc);
% radlw=get_missing_val(lon1,lat1,mask1.*dlwrf,nan,Roa,nan);
@@ -77,7 +77,7 @@ radsw(radsw<1.e-10)=0;
% 5.2 get the downward longwave flux [W/m^2]
%
vname='STRD';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
dlwrf_in=squeeze(nc{vname}(tin,:,:));
close(nc);
radlw_in=get_missing_val(lon1,lat1,mask1.*dlwrf_in,nan,Roa,nan);
@@ -87,7 +87,7 @@ radlw_in=interp2(lon1,lat1,radlw_in,lon,lat,interp_method);
% 6: Wind [m/s]
%
vname='U10M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
uwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
uwnd=get_missing_val(lon1,lat1,mask1.*uwnd,nan,Roa,nan);
@@ -95,7 +95,7 @@ uwnd=interp2(lon1,lat1,uwnd,lon,lat,interp_method);
%
%
vname='V10M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
vwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
vwnd=get_missing_val(lon1,lat1,mask1.*vwnd,nan,Roa,nan);
@@ -107,14 +107,14 @@ wspd=sqrt(uwnd.^2+vwnd.^2);
% % 7: Wind & Wind stress [m/s] => ERA5 not downloaded
% %
% vname='EWSS';
-% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
% tx=squeeze(nc{vname}(tin,:,:));
% close(nc)
% tx=get_missing_val(lon1,lat1,mask1.*tx,nan,0,nan);
% tx=interp2(lon1,lat1,tx,lon,lat,interp_method);
% %
% vname='NSSS';
-% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+% nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
% ty=squeeze(nc{vname}(tin,:,:));
% close(nc)
% ty=get_missing_val(lon1,lat1,mask1.*ty,nan,0,nan);
@@ -149,7 +149,7 @@ if add_waves == 1
% 8: Surface wave amplitude: convert from SWH to Amp
%
vname='SWH';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
awave=1/(2*sqrt(2))*squeeze(nc{vname}(tin,:,:));
close(nc);
%[ATMO_DIR,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']
@@ -159,7 +159,7 @@ if add_waves == 1
% 9: Surface wave direction
%
vname='MWD';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
dwave=squeeze(nc{vname}(tin,:,:));
close(nc);
dwave=get_missing_val(lonwave1,latwave1,maskwave1.*dwave,nan,Roa,nan);
@@ -168,10 +168,10 @@ if add_waves == 1
% 10: Surface wave peak period
%
vname='PP1D';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']);
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
pwave=squeeze(nc{vname}(tin,:,:));
close(nc);
- pwave=get_missing_val(lonwave1,latwave1,maskwave1.*pwave,nan,Roa,nan);
+ pwave=get_missing_val(lonwave1,latwave1,maskwave2.*pwave,nan,Roa,nan);
pwave=interp2(lonwave1,latwave1,pwave,lon,lat,interp_method);
end
%
diff --git a/Aforc_ERA5/make_ERA5.m b/Aforc_ERA5/make_ERA5.m
index 31d33e21acaa9f03ff6e17987d750777ec59c739..23f548d110912cc0c93ec285a622743ee0e4af00 100644
--- a/Aforc_ERA5/make_ERA5.m
+++ b/Aforc_ERA5/make_ERA5.m
@@ -33,7 +33,8 @@ close all
%
% Common parameters
%
-crocotools_param
+crocotools_param
+isoctave=exist('octave_config_info');
frc_prefix=[frc_prefix,'_ERA5_'];
blk_prefix=[blk_prefix,'_ERA5_'];
%
@@ -52,7 +53,7 @@ end
%
disp(' ')
disp([' Read the grid in ',grdname])
-nc=netcdf(grdname);
+nc=netcdf(grdname,'r');
Lp=length(nc('xi_rho'));
Mp=length(nc('eta_rho'));
lon=nc{'lon_rho'}(:);
@@ -67,7 +68,7 @@ close(nc);
%
% Get the ERA5 horizontal grids (it should be the same for every month)
%
-nc=netcdf([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(Mmin),'.nc']);
+nc=netcdf([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'],'r');
disp(['Use this land file :',char([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'])])
lon1=nc{'lon'}(:);
@@ -88,7 +89,7 @@ if add_waves == 1
% for the atmo variable (0.25° x 0.25° (atmosphere) vs 0.5° x 0.5° (ocean waves))
%
filein=[ERA5_dir,'SWH_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'];
- nc=netcdf(filein);
+ nc=netcdf(filein,'r');
lonwave=nc{'lon'}(:);
latwave=nc{'lat'}(:);
[lon1wave,lat1wave]=meshgrid(lonwave,latwave);
@@ -97,10 +98,21 @@ if add_waves == 1
maskwave(maskwave ~= missvalue_wave ) = 1;
maskwave(maskwave == missvalue_wave ) = NaN ;
close(nc);
+
+ % fix: PP1D doesn t have the same mask than SWH
+ filein2=[ERA5_dir,'PP1D_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'];
+ nc=netcdf(filein2);
+ maskwave2=squeeze(nc{'PP1D'}(1,:,:));
+ missvalue_wave2 = ncreadatt(filein2,'PP1D','missing_value');
+ maskwave2(maskwave2 ~= missvalue_wave2 ) = 1;
+ maskwave2(maskwave2 == missvalue_wave2 ) = NaN ;
+ close(nc);
+ %
else
lon1wave = NaN;
lat1wave = NaN;
maskwave = NaN;
+ maskwave2 = NaN;
end
@@ -134,7 +146,7 @@ for Y=Ymin:Ymax
% Process time (here in days), with SST file (minimum time step)
%
%-------------------------------------------------------------------%
- nc=netcdf([ERA5_dir,'T2M_Y',num2str(Y),'M',num2str(M),'.nc']);
+ nc=netcdf([ERA5_dir,'T2M_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
ERA5_time=nc{'time'}(:);
close(nc);
dt=mean(gradient(ERA5_time));
@@ -190,10 +202,10 @@ for Y=Ymin:Ymax
% %
% % Add the waves
% %
- if makefrc==1 && add_waves==1
- disp(['Add waves data'])
- disp(['=============='])
- end
+ if makefrc==1 && add_waves==1
+ disp(['Add waves data'])
+ disp(['=============='])
+ end
% %
% %
% % Add the tides
@@ -240,7 +252,7 @@ for Y=Ymin:Ymax
Mm=M;
Ym=Y;
else
- nc=netcdf(fname);
+ nc=netcdf(fname,'r');
tndx=length(nc('time'));
if makefrc==1
for aa=1:itolap
@@ -265,7 +277,7 @@ for Y=Ymin:Ymax
aa0=tndx-(itolap-aa);
end
interp_ERA5(ERA5_dir,Ym,Mm,Roa,interp_method,lon1,lat1,lon1wave,lat1wave, ...
- mask,maskwave,aa0,nc_frc,nc_blk,lon,lat,angle,aa,add_waves)
+ mask,maskwave,maskwave2,aa0,nc_frc,nc_blk,lon,lat,angle,aa,add_waves)
end
%######################################################################
%
@@ -283,7 +295,7 @@ for Y=Ymin:Ymax
disp(['Step: ',num2str(tndx),' of ',num2str(tlen0)])
end
interp_ERA5(ERA5_dir,Y,M,Roa,interp_method,lon1,lat1,lon1wave,lat1wave,...
- mask,maskwave,tndx,nc_frc,nc_blk,lon,lat,angle,tndx+itolap,add_waves)
+ mask,maskwave,maskwave2,tndx,nc_frc,nc_blk,lon,lat,angle,tndx+itolap,add_waves)
end
disp(' ')
@@ -309,7 +321,7 @@ for Y=Ymin:Ymax
Mp=M;
Yp=Y;
else
- nc=netcdf(fname);
+ nc=netcdf(fname,'r');
if makefrc==1
disp('sms_time')
@@ -343,7 +355,7 @@ for Y=Ymin:Ymax
disp(['tin=',num2str(tin)])
end
interp_ERA5(ERA5_dir,Yp,Mp,Roa,interp_method,lon1,lat1,lon1wave,lat1wave,...
- mask,maskwave,tin,nc_frc,nc_blk,lon,lat,angle,tout,add_waves)
+ mask,maskwave,maskwave2,tin,nc_frc,nc_blk,lon,lat,angle,tout,add_waves)
end;
%
% Close the CROCO forcing files
@@ -380,7 +392,12 @@ disp('Add spin up phase')
blkname=[blk_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
blkname2=[blk_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
disp(['Create ',blkname2])
- eval(['!cp ',blkname,' ',blkname2])
+
+ if (isoctave == 0)
+ eval(['!cp ',blkname,' ',blkname2])
+ else
+ system(['cp ',blkname,' ',blkname2])
+ end
%
% Change the time
%
diff --git a/Aforc_ERA5/make_bry_wkb_ERA5.m b/Aforc_ERA5/make_bry_wkb_ERA5.m
new file mode 100644
index 0000000000000000000000000000000000000000..b9c163c899e4dd9d93833f5b656b65e5be4b51d6
--- /dev/null
+++ b/Aforc_ERA5/make_bry_wkb_ERA5.m
@@ -0,0 +1,190 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Build a CROCO boundary file
+%
+% Extrapole and interpole temperature and salinity from a
+% climatology to get boundary conditions for
+% CROCO (boundary netcdf file) .
+% Get the velocities and sea surface elevation via a
+% geostrophic computation.
+%
+% Data input format (netcdf):
+% temperature(T, Z, Y, X)
+% T : time [Months]
+% Z : Depth [m]
+% Y : Latitude [degree north]
+% X : Longitude [degree east]
+%
+% Data source : IRI/LDEO climate Data Library (World Ocean Atlas 1998)
+% http://ingrid.ldgo.columbia.edu/
+% http://iridl.ldeo.columbia.edu/SOURCES/.NOAA/.NODC/.WOA98/
+%
+% Further Information:
+% http://www.croco-ocean.org
+%
+% This file is part of CROCOTOOLS
+%
+% CROCOTOOLS is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published
+% by the Free Software Foundation; either version 2 of the License,
+% or (at your option) any later version.
+%
+% CROCOTOOLS is distributed in the hope that it will be useful, but
+% WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program; if not, write to the Free Software
+% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
+% MA 02111-1307 USA
+%
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
+%
+% Updated 2016 by Patrick Marchesiello & Rachid Benshila
+% for wave forcing
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+clear all
+close all
+%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Common parameters
+%
+crocotools_param
+%
+%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
+disp(' ')
+disp([' Title: ',CROCO_title])
+%
+% Read in the grid
+%
+disp(' ')
+disp(' Read in the grid...')
+nc=netcdf(grdname);
+h=nc{'h'}(:);
+lon=nc{'lon_rho'}(:);
+lat=nc{'lat_rho'}(:);
+angle=nc{'angle'}(:);
+mask=nc{'mask_rho'}(:);
+Lp=length(nc('xi_rho'));
+Mp=length(nc('eta_rho'));
+hmax=max(max(nc{'h'}(:)));
+result=close(nc);
+grid_angle=mean(mean(angle(mask==1)));
+[M L]=size(h);
+%
+% Loop over monthly files
+%
+for Y=Ymin:Ymax
+ if Y==Ymin
+ mo_min=Mmin;
+ else
+ mo_min=1;
+ end
+ if Y==Ymax
+ mo_max=Mmax;
+ else
+ mo_max=12;
+ end
+ for M=mo_min:mo_max
+%
+% Forcing file name
+%
+ frc_prefix=[frc_prefix,'_ERA5_'];
+ if level==0
+ nc_suffix='.nc';
+ else
+ nc_suffix=['.nc.',num2str(level)];
+ end
+ frcname=[frc_prefix,'Y',num2str(Y),...
+ 'M',num2str(M),nc_suffix];
+%
+% WKB file name
+%
+ wkb_prefix=[wkb_prefix,'_ERA5_'];
+ brywkbname=[wkb_prefix,'Y',num2str(Y),...
+ 'M',num2str(M),nc_suffix];
+ disp(' ')
+ disp([' Making file: ',brywkbname])
+ disp([' from: ',frcname])
+%
+% Read wave fields data
+%
+ nc=netcdf(frcname);
+ Awave=nc{'Awave'}(:);
+ Dwave=nc{'Dwave'}(:);
+ Pwave=nc{'Pwave'}(:);
+ time =nc{'wwv_time'}(:);
+ close(nc)
+
+ wkb_time=time;
+ wkb_cycle=wkb_time(end);
+%
+% Create the boundary file
+%
+ create_bryfile_wkb(brywkbname,grdname,CROCO_title,wkb_obc,...
+ wkb_time,wkb_cycle,'clobber');
+ disp(' ')
+%
+%
+% Extract boundary data: loop on time and boundaries
+% note: in ERA5, meteo convention for wave direction:
+% --> zero means "coming from north" and 90 "coming from east"
+%
+ disp(' Extracting and writing file ...')
+ nc=netcdf(brywkbname,'write');
+ g=9.81;
+ for l=1:length(time)
+ for obcndx=1:4
+ if obcndx==1
+ suffix='_south'; % SOUTH
+ Dstp=squeeze(h(1,:));
+ hrm=2*squeeze(Awave(l,1,:));
+ cdir=3*pi/2-deg2rad(squeeze(Dwave(l,1,:)))-grid_angle;
+ cfrq=2*pi./squeeze(Pwave(l,1,:));
+ elseif obcndx==2
+ suffix='_east'; % EAST
+ Dstp=squeeze(h(:,L));
+ hrm=2*squeeze(Awave(l,:,L));
+ cdir=3*pi/2-deg2rad(squeeze(Dwave(l,:,L)))-grid_angle;
+ cfrq=2*pi./squeeze(Pwave(l,:,L));
+ elseif obcndx==3
+ suffix='_north'; % NORTH
+ Dstp=squeeze(h(M,:));
+ hrm=2*squeeze(Awave(l,M,:));
+ cdir=3*pi/2-deg2rad(squeeze(Dwave(l,M,:)))-grid_angle;
+ cfrq=2*pi./squeeze(Pwave(l,M,:));
+ elseif obcndx==4
+ suffix='_west'; % WEST
+ Dstp=squeeze(h(:,1));
+ hrm=2*squeeze(Awave(l,:,1));
+ cdir=3*pi/2-deg2rad(squeeze(Dwave(l,:,1)))-grid_angle;
+ cfrq=2*pi./squeeze(Pwave(l,:,1));
+ end
+ dd = Dstp'; %+Tide(l)
+ khd = dd.*cfrq.*cfrq./g;
+ kh = sqrt( khd.*khd + khd./(1.0 + khd.*(0.6666666666 ...
+ +khd.*(0.3555555555 + khd.*(0.1608465608 ...
+ +khd.*(0.0632098765 + khd.*(0.0217540484 ...
+ +khd.*0.0065407983)))))) );
+ kw=kh./dd;
+ cosw=cos(cdir);
+ sinw=sin(cdir);
+ wac=0.125*g*(hrm.^2)./cfrq;
+ wkx=kw.*cosw;
+ wke=kw.*sinw;
+ nc{['wac' suffix]}(l,:)=wac;
+ nc{['wkx' suffix]}(l,:)=wkx;
+ nc{['wke' suffix]}(l,:)=wke;
+ end
+ end
+ close(nc);
+
+ end % M
+end % Y
+%
+% End
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 591406c98f8034a2eac7d8c27d28848992910eba..4ca32706c2bbf516f46cbfac22f4cf5d0a1a3ef0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,28 +1,43 @@
# Changelog
-## [Unreleased]
+Release changelog are available here : https://gitlab.inria.fr/croco-ocean/croco_tools/-/releases
+
+## [Unreleased] - xxxx-xx-xx
-## [v.1.3.1] - 2023-09-21
### Added
-- Add a CHANGELOG.md file
-### Fixed
-- Nesting_tools : fix problems in the create_crocoin.m for time stepping section
-- Rivers : bug fixes + cosmetics
- - bug fixes in the runoff positionning
- - Some little cleaning in make_runoff.m
+- crocotools_param.m: deal with different mercator datasets, see issue [#23](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/23)
+ - Reanalysis Glorys/Analysis: [ *see make_OGCM_mercator.m* ]
+ - Forecast/Mediterranean high resolution Forecasts : [ *see make_OGCM_mercator_frcst.m* ]
-- Fix MOTU extraction of CMEMS data to adapt to change of data format; issue #14
+- Forecast_tools, see issue [#23](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/23)
+ - Add pause instance to download GFS datasets to avoid over rate limit violation
+ - Add dependency on time step to write on template croco_forecast.in (filled within run_croco_forecast.bash)
+ - Remove hindcast runs (and iterations for nudging OGCM data), keep only one forecast run on hindcast/forecast days.
-- Aforc_ERA5/make_ERA5.m : Fix bug when no wave variables
+- Aforc_ERA5, see issue [#23](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/23)
+ - Add python request for extraction in parallel mode
+ - Add boundary creation with WKB model
-### Changed
+## Fixed
-### Deprecated
+- Nesting_tools : fix in nested_grid, see issue [#15](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/15)
-### Removed
+- Rivers : wrong runoff positioning after first guess, fixed see issue [#18](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/18)
-### Other
+## Changed
+
+- Preprocessing_tools : Update creation of forcing files for dust and nitrogen deposition in line with the PISCES code. See issue [#19](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/19)
+
+- Oforc_OGCM : see issue [#23](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/23)
+ - Add new Copernicus Marine Toolbox to deal with mercator datasets (Please see Copernicus_Marine_Toolbox_installation.md)
+ - Launch SODA preprocessing with make_OGCM_SODA.m
+ - Lauch MERCATOR/CMEMS preprocessing with make_OGCM_mercator.m
-## [v.1.3] - 2022-11-28
+## Removed
+- No more use of ECCO datasets for oceanic reanalysis, see issue [#23](https://gitlab.inria.fr/croco-ocean/croco_tools/-/issues/23)
+
+### Deprecated
+
+### Other
diff --git a/Coupling_tools/CROCO/prepro_soda.m b/Coupling_tools/CROCO/prepro_soda.m
index 3ba9797bd55287e75ffa411903ae60496b3cf6e5..2bd90cae5a0179c9165783b3897079ed8cffaa67 100644
--- a/Coupling_tools/CROCO/prepro_soda.m
+++ b/Coupling_tools/CROCO/prepro_soda.m
@@ -1,4 +1,4 @@
clear all
close all
start ;
-make_OGCM ;
+make_OGCM_SODA ;
diff --git a/Coupling_tools/WRF_WPS/configure.namelist.wps b/Coupling_tools/WRF_WPS/configure.namelist.wps
index a2557d7196572a5ab5c7e8b15b5e0d106d5114cb..f22cb17ec6d7561cabfe0783edb7a0b432e16528 100755
--- a/Coupling_tools/WRF_WPS/configure.namelist.wps
+++ b/Coupling_tools/WRF_WPS/configure.namelist.wps
@@ -27,79 +27,8 @@
# swen.jullien@ifremer.fr
# --------------------------------------------------
-domain_name="BENGUELA"
-# Nb domains (ie nests)
-max_domains=1
-#-------------------------------------------------------------------------
-# Data Sources
-#
-# LBC_type : data source for initial and boundary conditions
-# LSM_type : data source for surface forcing
-# obc_freq_h : boundary condition frequency [hour]
-# sst_interval_m : interval between SST updates [minutes]
-#-------------------------------------------------------------------------
-LBC_type="CFSR_press_pgbh06"
-LSM_type="CFSR_sfc_flxf06"
-obc_freq_h=6
-sst_interval_m=360
-#-------------------------------------------------------------------------
-# Grid parameters
-#
-# dx : horizontal resolution in [km]
-# xdim : number of points in x
-# ydim : number of points in y
-# central_lat : latitude at the center of the domain
-# central_lon : longitude at the center of the domain
-# topo_res_d01 : horizontal resolution of orography data
-#
-# Nesting
-#
-# dimensions must check:
-# xdim_child=N*refine_coef+1
-# ydim_child=M*refine_coef+1
-#
-# Variables for real.exe
-#
-# nbvertlevel : number of vertical levels
-# nbmetlevel : number of boundary data levels
-#-------------------------------------------------------------------------
-#
-dt=150
-nbvertlevel=60
-nbmetlevel=38
-nbmetsoil=4
-ptop=5000
-#
-# Parent domain (d01)
-dx=30
-xdim_d01=56
-ydim_d01=50
-central_lat=-32.0
-central_lon=15.0
-topo_res_d01='30s'
-#topo_res_d01='3s+30s+10m'
-
-# Nest 1 (d02)
-refine_d02=5
-i_str_d02=32
-j_str_d02=153
-xdim_d02=456
-ydim_d02=476
-topo_res_d02='3s'
-#topo_res_d02='2s+3s+30s'
-#
-# Nest 2 (d03)
-refine_d03=3
-i_str_d03=35
-j_str_d03=24
-xdim_d03=277
-ydim_d03=349
-topo_res_d03='3s+30s'
-
-#-------------------------------------------------------------------------
-# Dates of parent simulation
-#-------------------------------------------------------------------------
-# real-time mode
+# Dates to process
+#-----------------
start_y=2005
start_m=01
start_d=01
@@ -110,12 +39,45 @@ end_m=01
end_d=31
end_h=18
-start_date_d01=$start_y'-'$start_m'-'$start_d'_'$start_h:00:00
-end_date_d01=$end_y'-'$end_m'-'$end_d'_'$end_h:00:00
-
-start_date_d02=$start_date_d01
-end_date_d02=$end_date_d01
+# Domains
+#---------
+max_domains=1 # Nb domains
+#
+# Parent domain (d01)
+dx=30 # horizonal resolution dx=dy in [kml]
+xdim_d01=56 # number of points in x
+ydim_d01=50 # number of points in y
+#
+# Nest 1 (d02): information read only if max_domains>1
+refine_d02=5 # refinement coefficient from parent
+i_str_d02=32 # starting index in x-dir from the parent domain
+j_str_d02=153 # starting index in y-dir from the parent domain
+xdim_d02=456 # nb of points, must check: xdim_child=N*refine_coef+1
+ydim_d02=476 # nb of points, must check: ydim_child=M*refine_coef+1
+#
+# Nest 2 (d03): information read only if max_domains>2
+refine_d03=3 # refinement coefficient from previous nest
+i_str_d03=35 # starting index in x-dir from the previous nest
+j_str_d03=24 # starting index in y-dir from the previous nest
+xdim_d03=277 # nb of points, must check: xdim_child=N*refine_coef+1
+ydim_d03=349 # nb of points, must check: ydim_child=M*refine_coef+1
-start_date_d03=$start_date_d01
-end_date_d03=$end_date_d01
+# Other information for geogrid
+#-------------------------------
+central_lat=-32.0 # central longitude of the parent domain
+central_lon=15.0 # central latitude of the parent domain
+projection='mercator' # projection used
+#
+# resolution of the topographic data to use for each domain
+topo_res_d01='30s+10m'
+topo_res_d02='3s+30s'
+topo_res_d03='3s+30s'
+# Other information for ungrib
+#------------------------------
+obc_freq_h=6 # boundary condition frequency [hour]
+#
+# suffix for Vtable to use
+LBC_type="CFSR_press_pgbh06" # for initial and boundary forcing
+LSM_type="CFSR_sfc_flxf06" # for surface data (if different from boundary data)
+
diff --git a/Coupling_tools/WRF_WPS/job.wps.pbs b/Coupling_tools/WRF_WPS/job.wps.pbs.DATARMOR
similarity index 100%
rename from Coupling_tools/WRF_WPS/job.wps.pbs
rename to Coupling_tools/WRF_WPS/job.wps.pbs.DATARMOR
diff --git a/Coupling_tools/WRF_WPS/job.wps.pbs.WCHPC b/Coupling_tools/WRF_WPS/job.wps.pbs.WCHPC
new file mode 100644
index 0000000000000000000000000000000000000000..60b19c20d52b5aa2e1360a45630361a88988895e
--- /dev/null
+++ b/Coupling_tools/WRF_WPS/job.wps.pbs.WCHPC
@@ -0,0 +1,8 @@
+#!/bin/bash
+#PBS -l select=1:ncpus=24:mpiprocs=8
+#PBS -P WCHPC
+#PBS -q smp
+#PBS -l walltime=01:00:00
+cd $PBS_O_WORKDIR
+
+./run_wps.bash configure.namelist.wps 8
diff --git a/Coupling_tools/WRF_WPS/job.wps.sh b/Coupling_tools/WRF_WPS/job.wps.sh.IRENE
similarity index 100%
rename from Coupling_tools/WRF_WPS/job.wps.sh
rename to Coupling_tools/WRF_WPS/job.wps.sh.IRENE
diff --git a/Coupling_tools/WRF_WPS/job.wps.slurm b/Coupling_tools/WRF_WPS/job.wps.slurm.JEANZAY
similarity index 100%
rename from Coupling_tools/WRF_WPS/job.wps.slurm
rename to Coupling_tools/WRF_WPS/job.wps.slurm.JEANZAY
diff --git a/Coupling_tools/WRF_WPS/job.wps.slurm.LEFTRARU b/Coupling_tools/WRF_WPS/job.wps.slurm.LEFTRARU
new file mode 100644
index 0000000000000000000000000000000000000000..aed3310ced94b6be3aa96eba08ea76d192270787
--- /dev/null
+++ b/Coupling_tools/WRF_WPS/job.wps.slurm.LEFTRARU
@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH --job-name=Run_wps
+#SBATCH --partition=slims
+#SBATCH --ntasks=1
+#SBATCH --time=12:00:00 # temps d execution maximum demande (HH:MM:SS)
+#SBATCH --output=run_wps.out
+#SBATCH --error=run_wps.err
+
+cd ${SLURM_SUBMIT_DIR}
+
+#===============================================================================
+
+umask 022
+set -u
+
+./run_wps.bash configure.namelist.wps 1
+
diff --git a/Coupling_tools/WRF_WPS/run_wps.bash b/Coupling_tools/WRF_WPS/run_wps.bash
index 9ee5e78c00ac8addd4f8206349ba766e421ad43f..2158ea45e73b72ff9f67b8ab1fbfd4c7a32052ff 100755
--- a/Coupling_tools/WRF_WPS/run_wps.bash
+++ b/Coupling_tools/WRF_WPS/run_wps.bash
@@ -107,7 +107,7 @@ source ../../myenv_mypath.sh
# WPS paths
# WPS source dir
-export WPS_EXE_DIR="${ATM}/../WPS4.2"
+export WPS_EXE_DIR="${ATM}/../WPS"
# Data dir
DATA_DIR=${CWORK}/DATA
#
@@ -120,10 +120,10 @@ export Vtable_ROOT="$PWD"
#
# Inputs directory and prefix (initial and boundary data)
export I_DATAROOT="$DATA_DIR/CFSR_grib"
-export I_DATAprefix="200901*pgbh06.gdas"
+export I_DATAprefix="200501*pgbh06.gdas"
# Surface Inputs directory and prefix (if different surface file)
export SFC_DATAROOT="$DATA_DIR/CFSR_grib"
-export SFC_DATAprefix="200901*flxf06.gdas"
+export SFC_DATAprefix="200501*flxf06.gdas"
#
# Outputs data directory
export O_DATAROOT="${ATM_FILES_DIR}/WPS_DATA"
@@ -137,9 +137,9 @@ else
fi
#
# MPI launch commands
-if [ ${MACHINE} == "JEANZAY" ]; then
+if [ ${MACHINE} == "JEANZAY" ] || [ ${MACHINE} == "LEFTRARU" ]; then
export myMPI="srun -n $NBPROCS "
-elif [ ${MACHINE} == "DATARMOR" ]; then
+elif [ ${MACHINE} == "DATARMOR" ] || [ ${MACHINE} == "WCHPC" ]; then
export myMPI="$MPI_LAUNCH -np $NBPROCS "
elif [ ${MACHINE} == "IRENE" ]; then
export myMPI="ccc_mprun -n $NBPROCS "
@@ -183,7 +183,7 @@ echo "************************************************************"
cd $MYWORKDIR
#----------------------------------------------
-# Rescale parameters from configure.namelist
+# Rescale parameters from configure.namelist.wps
#----------------------------------------------
export interval_s=`expr $obc_freq_h \* 3600`
export interval_s_SFC=$interval_s
@@ -251,6 +251,18 @@ else
exit 1
fi
+#--------------------------------------
+# Prepare dates
+#--------------------------------------
+start_date_d01=$start_y'-'$start_m'-'$start_d'_'$start_h:00:00
+end_date_d01=$end_y'-'$end_m'-'$end_d'_'$end_h:00:00
+
+start_date_d02=$start_date_d01
+end_date_d02=$end_date_d01
+
+start_date_d03=$start_date_d01
+end_date_d03=$end_date_d01
+
# O O O O O O O O O START geogrid O O O O O O O O O
if [ $switch_geogrid -eq 1 ]; then
@@ -265,7 +277,7 @@ if [ $switch_geogrid -eq 1 ]; then
echo " "
#------------------------------------------------
- # Create namelist.wps from configure.namelist
+ # Create namelist.wps from configure.namelist.wps
#------------------------------------------------
if [ -e namelist.wps ] ; then
rm -f namelist.wps
@@ -293,7 +305,7 @@ cat << End_Of_Namelist | sed -e 's/#.*//; s/ *$//' > ./namelist.wps
geog_data_res = $topo_res_d01, $topo_res_d02, $topo_res_d03,
dx = $dx_d01,
dy = $dx_d01,
- map_proj = 'mercator',
+ map_proj = $projection,
ref_lat = $central_lat
ref_lon = $central_lon
truelat1 = $central_lat,
@@ -304,10 +316,10 @@ cat << End_Of_Namelist | sed -e 's/#.*//; s/ *$//' > ./namelist.wps
/
End_Of_Namelist
-cp namelist.wps namelist.wps.geogrid.${domain_name}
+cp namelist.wps namelist.wps.geogrid
-#${myMPI}geogrid.exe >& geogrid.log
-./geogrid.exe >& geogrid.log
+${myMPI}geogrid.exe >& geogrid.log
+#./geogrid.exe >& geogrid.log
echo "% list geogrid output directory $O_DATAROOT :"
ls $O_DATAROOT
fi
@@ -405,7 +417,7 @@ cat << End_Of_Namelist | sed -e 's/#.*//; s/ *$//' > ./namelist.wps
/
End_Of_Namelist
-cp namelist.wps namelist.wps.ungrib.${LBC_type}.${domain_name}
+cp namelist.wps namelist.wps.ungrib.${LBC_type}
#-----------------------------------
# check VTABLE for LBC and make link
@@ -478,7 +490,7 @@ cat << End_Of_Namelist | sed -e 's/#.*//; s/ *$//' > ./namelist.wps
/
End_Of_Namelist
-cp namelist.wps namelist.wps.ungrib.${LSM_type}.${domain_name}
+cp namelist.wps namelist.wps.ungrib.${LSM_type}
#--------------------------
# Check VTABLE for LSM
@@ -577,10 +589,10 @@ if [ $switch_metgrid -eq 1 ]; then
/
End_Of_Namelist
-cp namelist.wps namelist.wps.metgrid.${domain_name}
+cp namelist.wps namelist.wps.metgrid
-#${myMPI}metgrid.exe >& metgrid.log
-./metgrid.exe >& metgrid.log
+${myMPI}metgrid.exe >& metgrid.log
+#./metgrid.exe >& metgrid.log
echo " ls -rtl $O_DATAROOT"
ls -rtl $O_DATAROOT*
diff --git a/Forecast_tools/CopernicusMarineToolbox/copernicusmarine_env.yml b/Forecast_tools/CopernicusMarineToolbox/copernicusmarine_env.yml
new file mode 100644
index 0000000000000000000000000000000000000000..eebe6b1d06f86018b44c46b624f6b9f378e2a64b
--- /dev/null
+++ b/Forecast_tools/CopernicusMarineToolbox/copernicusmarine_env.yml
@@ -0,0 +1,8 @@
+name: cmt_1.0
+channels:
+ - conda-forge
+dependencies:
+ - pip
+ - pip:
+ - copernicusmarine>=1.0<=2.0
+ - python>=3.9,<3.12
\ No newline at end of file
diff --git a/Forecast_tools/ForecastCharts.pdf b/Forecast_tools/ForecastCharts.pdf
deleted file mode 100644
index cfa209c29ebbae5fd52260dfdaca4d0b13fb33cc..0000000000000000000000000000000000000000
Binary files a/Forecast_tools/ForecastCharts.pdf and /dev/null differ
diff --git a/Forecast_tools/download_ECCO_frcst.m b/Forecast_tools/download_ECCO_frcst.m
deleted file mode 100644
index 64653c233bad651bf8f3ff98ec828f823cab2db6..0000000000000000000000000000000000000000
--- a/Forecast_tools/download_ECCO_frcst.m
+++ /dev/null
@@ -1,173 +0,0 @@
-function ecco_name=download_ECCO_frcst(lonmin,lonmax,latmin,latmax,...
- FRCST_dir,FRCST_prefix,url,Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subgrid from ECCO to get a CROCO forcing
-% Store that into monthly files.
-% Take care of the Greenwitch Meridian.
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 8-Sep-2006 by Pierrick Penven
-% Updated 20-Aug-2008 by Matthieu Caillaud & P. Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%
-% Get the date
-%
-rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
-[y,m,d,h,mi,s]=datevec(rundate_str);
-%
-% start
-%
-disp([' '])
-disp(['Get data for ',rundate_str])
-disp(['Minimum Longitude: ',num2str(lonmin)])
-disp(['Maximum Longitude: ',num2str(lonmax)])
-disp(['Minimum Latitude: ',num2str(latmin)])
-disp(['Maximum Latitude: ',num2str(latmax)])
-disp([' '])
-%
-% Create the directory
-%
-disp(['Making output data directory ',FRCST_dir])
-eval(['!mkdir ',FRCST_dir])
-%
-% Start
-%
-disp(['Process the dataset: ',url])
-%
-% Get the latest ECCO time
-%
-%
-% first ecco time: 06-Jan-2006 (315696)
-% first ecco time: 07-Jan-2006 (324456) !!! should be reset every year !!!
-ecco_time_start_year=359520;
-
-%
-ecco_time_start=ecco_time_start_year/24+datenum(1970,1,1)-datenum(Yorig,1,1);
-ecco_times=[ecco_time_start:10:ecco_time_start+10000];
-%htime_ecco=24*(ecco_times+datenum(Yorig,1,1)-datenum(1970,1,1));
-%
-% Get the closest ecco time
-%
-ecco_indx=max(find(ecco_times<=rundate));
-foundfile=0;
-%
-while foundfile==0
- ecco_time=ecco_times(ecco_indx);
- disp([' Testing date: ' datestr(ecco_time+datenum(Yorig,1,1))])
- [ecco_y,ecco_m,ecco_d,ecco_h,ecco_mi,ecco_s]=...
- datevec(ecco_time+datenum(Yorig,1,1));
- daysinyear=ecco_time+datenum(Yorig,1,1)-datenum(ecco_y,1,1);
- necco=round(daysinyear/10);
- nhours=necco*240;
- if nhours < 1000
- endname=['_00',num2str(nhours),'_240.cdf'];
- elseif nhours < 10000
- endname=['_0',num2str(nhours),'_240.cdf'];
- else nhours < 10000
- endname=['_',num2str(nhours),'_240.cdf'];
- end
-%
- if necco <= 9
- prefix=[url,num2str(ecco_y),'/n10day_01_0',num2str(necco),'/'];
- suffix=['_08_08.00001',endname];
- elseif necco <= 18
- prefix=[url,num2str(ecco_y),'/n10day_10_',num2str(necco),'/'];
- suffix=['_08_08.02160',endname];
- elseif necco <= 27
- prefix=[url,num2str(ecco_y),'/n10day_19_',num2str(necco),'/'];
- suffix=['_08_08.04320',endname];
- elseif necco <= 37
- prefix=[url,num2str(ecco_y),'/n10day_28_',num2str(necco),'/'];
- suffix=['_08_08.06480',endname];
- end
-%
-% test if the file exist
-%
- vname='Have';
- fname=[prefix,vname,suffix];
- warning off
- try
- x=loaddap('-A -e +v ',fname);
- foundfile=1;
- catch
- foundfile=0;
- end
- if foundfile==1 & ~isempty(x)
- disp(' File found')
- else
- foundfile=0;
- disp(' File does not exist')
- ecco_indx=ecco_indx-1;
- if ecco_indx==0
- error('DOWNLOAD_ECCO_FRCST: No file found...')
- end
- end
- warning on
-end
-%
-tindex=x.time.DODS_ML_Size;
-missval=x.Have.missing_value;
-%
-% Get the time
-%
-vname='Have';
-fname=[prefix,'Have',suffix];
-trange=['[',num2str(tindex-1),':',num2str(tindex-1),']'];
-time=readdap(fname,'time',trange);
-time=floor(time/24+datenum(1970,1,1));
-disp([' Date: ',datestr(time)])
-time=time-datenum(Yorig,1,1);
-ecco_name=[FRCST_dir,FRCST_prefix,num2str(time),'.cdf'];
-%
-%if isempty(dir(ecco_name))
-if ~exist(ecco_name)
-%
-%
-% Get a subset of the ECCO grid
-%
- vname='Have';
- fname=[prefix,vname,suffix];
- [i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- jrange,jrange_v,krange,lon,lon_u,lat,lat_v,depth]=...
- get_ECCO_subgrid(fname,lonmin,lonmax,latmin,latmax);
-%
-% Extract ECCO
-%
- extract_ECCO_frcst(FRCST_dir,FRCST_prefix,prefix,suffix,tindex,missval,...
- lon,lon_u,lat,lat_v,depth,...
- krange,jrange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- time,Yorig)
-else
- disp(' ECCO file allready exist')
-end
-return
diff --git a/Forecast_tools/download_GFS.m b/Forecast_tools/download_GFS.m
index 6060cd28ac5acc6a170772898030546b54407f75..af30f6d79cc119b4419f2496f803b907e85744c2 100644
--- a/Forecast_tools/download_GFS.m
+++ b/Forecast_tools/download_GFS.m
@@ -193,7 +193,7 @@ for ihind=1:4*hdays % loop on files until time=yesterday 12Z
radlw(n,:,:),radlw_in(n,:,:),radsw(n,:,:)]=...
get_GFS(fname,mask,tndxdap,jrange,i1min,i1max,i2min,i2max, ...
i3min,i3max,missvalue);
- end
+ end
end % ihind (nb of hindcast record)
%
%==================================================================
@@ -289,7 +289,3 @@ write_GFS(gfs_name,Yorig,lon,lat,mask,gfstime,...
disp('Download GFS: done')
%
return
-
-
-
-
diff --git a/Forecast_tools/download_mercator_frcst.m b/Forecast_tools/download_mercator_frcst.m
deleted file mode 100644
index 77a1fbf240ee257cfd3c2969d4a3c9dc31e6ae15..0000000000000000000000000000000000000000
--- a/Forecast_tools/download_mercator_frcst.m
+++ /dev/null
@@ -1,187 +0,0 @@
-function mercator_name=download_mercator_frcst(lonmin,lonmax,latmin,latmax,...
- FRCST_dir,FRCST_prefix,url,Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subgrid from ECCO to get a CROCO forcing
-% Store that into monthly files.
-% Take care of the Greenwitch Meridian.
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 8-Sep-2006 by Pierrick Penven
-% Updated 20-Aug-2008 by Matthieu Caillaud & P. Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%
-% Get the date
-%
-l=1;
-rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
-lh=5; % length of hindcast for mercator
-lf=6; % length of forecast
-%%% test if mercator forecast exist %%%
-% mercator time is in julian hours since 1950
- time=readdap(url,'time',[])/24;
-time(1)
- time=time+datenum(1950,1,1);
-time(1)
- time=time-datenum(Yorig,1,1);
- time(1)
- rundate
- size(time)
- stop
- while l==1
- try
- x=find(time==rundate+lf);
- foundtime=1;
- catch
- foundtime=0;
- end
- if foundtime==1 & ~isempty(x)
- disp('time is ok')
- else
- foundtime=0;
- disp('missing forecast')
- end
-
-if foundtime==0;
- lf=lf-1;
- l=1;
-else
- l=0;
-end
- end
-
-for i=1:lh
- time1(i)=datenum(rundate_str)-(lh+1-i);
-end
-time2=datenum(rundate_str);
-for j=1:lf
- time3(j)=datenum(rundate_str)+j;
-
-end
-if foundtime==0
- time3=[time3 time3(end)];
- end
-
-time=cat(2,time1,time2,time3);
-
-
-% Get time from Opendap
-time2=readdap(url,'time',[])/24;
-time2=time2+datenum(1950,1,1);
-%time2=time2-datenum(Yorig,1,1);
-
-% Get time index
-for i=1:length(time)
- tndx(i)=find(time2==time(i));
-end
-
-%
-% start
-%
-disp([' '])
-disp(['Get data for ',rundate_str])
-disp(['Minimum Longitude: ',num2str(lonmin)])
-disp(['Maximum Longitude: ',num2str(lonmax)])
-disp(['Minimum Latitude: ',num2str(latmin)])
-disp(['Maximum Latitude: ',num2str(latmax)])
-disp([' '])
-%
-% Create the directory
-%
-disp(['Making output data directory ',FRCST_dir])
-eval(['!mkdir ',FRCST_dir])
-%
-% Start
-%
-disp(['Process the dataset: ',url])
-%
-%
-% test if the file exist
-%
-%
-foundfile=0;
- fname=url;
- warning off
- try
- x=loaddap('-A -e +v ', fname);
- foundfile=1;
- catch
- foundfile=0;
- end
- if foundfile==1 & ~isempty(x)
- disp(' File found')
- else
- foundfile=0;
- disp(' File does not exist')
- end
- warning on
-%
-%
-%tindex=x.time.DODS_ML_Size;
-%missval=x.ssh.missing_value; %PSY3V1
-missval=x.ssh.ml__FillValue; %PSY3V2
-% Get the time
-%
-trange=['[',num2str(min(tndx)-1),':',num2str(max(tndx)-1),']'];
-fname=url;
-%
-%trange=['[',num2str(tindex-1),':',num2str(tindex-1),']'];
-%time=readdap(fname,'time',trange);
-%time=floor(time+datenum(1950,1,1));
-%disp([' Date: ',datestr(time)])
-%time=time-datenum(Yorig,1,1);
-time=time2(tndx)-datenum(Yorig,1,1);
-mercator_name=[FRCST_dir,FRCST_prefix,num2str(rundate),'.cdf'];
-%
-%if isempty(dir(mercator_name))
-if ~exist(mercator_name)
-%
-%
-% Get a subset of the ECCO grid
-%
-
-
- [i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- jrange,jrange_v,krange,lon,lon_u,lat,lat_v,depth]=...
- get_mercator_subgrid(url,lonmin,lonmax,latmin,latmax);
-%
-% Extract mercator
-%
- extract_mercator_frcst(FRCST_dir,FRCST_prefix,url,tndx,missval,...
- lon,lon_u,lat,lat_v,depth,...
- krange,jrange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- time,Yorig)
-else
- disp(' mercator file allready exist')
-end
-
-return
diff --git a/Forecast_tools/download_mercator_frcst_python.m b/Forecast_tools/download_mercator_frcst_python.m
index 0402779f8c60e4cb3eb7e10052f18a4f5c00d61d..a1c22b72b9d4ba3974c61d7688f1a025f6da0696 100644
--- a/Forecast_tools/download_mercator_frcst_python.m
+++ b/Forecast_tools/download_mercator_frcst_python.m
@@ -1,10 +1,9 @@
-function mercator_name=download_mercator_frcst_python(pathMotu,user,password,mercator_type, ...
- motu_url, service_id,product_id, ...
- lh,lf, ...
- lonmin,lonmax,latmin,latmax,zmax, ...
- FRCST_dir,FRCST_prefix,raw_mercator_name,Yorig)
+function download_mercator_frcst_python(pathCMC,user,password,mercator_type, ...
+ raw_mercator_name,product_id, ...
+ lh,lf, ...
+ lonmin,lonmax,latmin,latmax,zmax, ...
+ FRCST_dir,FRCST_prefix,date_frcst,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
% Extract a subgrid from mercator to get a CROCO forcing
% Store that into monthly files.
% Take care of the Greenwitch Meridian.
@@ -42,120 +41,116 @@ function mercator_name=download_mercator_frcst_python(pathMotu,user,password,mer
download_raw_data=1;
convert_raw2crocotools=1; % convert -> crocotools format data
%
+disp(['Making output data directory ',FRCST_dir]) % create directory
+eval(['!mkdir ',FRCST_dir, ' 2> /dev/null'])
+%
% Set variable names according to mercator type data
%
-if mercator_type==1,
- vars = {'zos' ...
- 'uo' ...
- 'vo' ...
- 'thetao' ...
- 'so'};
+if mercator_type==5
+ vars = {'zos_detided', ...
+ 'uo', ...
+ 'vo', ...
+ 'thetao', ...
+ 'so'};
else
- vars = {'zos_detided' ...
- 'uo' ...
- 'vo' ...
- 'thetao' ...
- 'so'};
+ vars = {'zos' ...
+ 'uo' ...
+ 'vo' ...
+ 'thetao' ...
+ 'so'};
end
%
% Get dates
%
rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
-
+date_run=datenum(rundate_str);
+rundate=date_run-datenum(Yorig,1,1);
for i=1:lh+1
time1(i)=datenum(rundate_str)-(lh+2-i);
end
time2=datenum(rundate_str);
-for j=1:lf+1
- time3(j)=datenum(rundate_str)+j;
+for j=1:lf+2
+ time3(j)=datenum(rundate_str)+j-1;
end
time=cat(2,time1,time2,time3);
tiempo_inicial = time1(1);
tiempo_final = time3(end);
+tiempo_p0 = time1(lh+1);
+tiempo_p1 = date_run;
+%
if (lonmin > 180)
lonmin = lonmin - 360;
end
if (lonmax > 180)
lonmax = lonmax - 360;
end
+%
disp([' '])
-disp(['Get data for ',rundate_str])
disp(['Minimum Longitude: ',num2str(lonmin)])
disp(['Maximum Longitude: ',num2str(lonmax)])
disp(['Minimum Latitude: ',num2str(latmin)])
disp(['Maximum Latitude: ',num2str(latmax)])
disp([' '])
-
+%
if download_raw_data
%
- % Get data (now in 4 different files)
+ disp(['--> Extraction Forecasts (assuming local time is after time dissemination : 12hUTC) : ', datestr(tiempo_p1,'yyyy-mm-dd')])
+ if lh ~= 0
+ for i=1:lh
+ disp(['Get Hindcasts NRT ana.: ',datestr(time1(i),'yyyy-mm-dd')])
+ end
+ disp(['Get Hindcasts P0 : ',datestr(tiempo_p0,'yyyy-mm-dd')])
+ end
+ disp(['Get ',num2str(lf+2),' Forecasts : from ',datestr(tiempo_p1,'yyyy-mm-dd'),' to ',datestr(tiempo_final, 'yyyy-mm-dd')])
+ %
+ %
+ % Get data (now splitted in 4 different files)
+ get_file_python_mercator(pathCMC, ... % SSH
+ product_id{1}, ...
+ vars(1), ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_z.nc']);
%
- % temporarily removing Matlab lib path to avoid conflict with Python,
- % (mandatory with python 2.7.X)
+ get_file_python_mercator(pathCMC, ... % U/V
+ product_id{2}, ...
+ vars(2:3), ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_u.nc']);
%
- pathdyld=getenv('DYLD_LIBRARY_PATH');
- setenv('DYLD_LIBRARY_PATH','');
- pathld=getenv('LD_LIBRARY_PATH');
- setenv('LD_LIBRARY_PATH','');
-
- get_file_python_mercator(pathMotu,mercator_type, ... % SSH
- motu_url,service_id,product_id{1}, ...
- vars(1), ...
- [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
- {datestr(tiempo_inicial,'yyyy-mm-dd') ...
- datestr(tiempo_final, 'yyyy-mm-dd')}, ...
- {user password}, ...
- [raw_mercator_name(1:end-3),'_z.nc']);
-
- get_file_python_mercator(pathMotu,mercator_type, ... % U,V
- motu_url,service_id,product_id{2}, ...
- vars(2:3), ...
- [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
- {datestr(tiempo_inicial,'yyyy-mm-dd') ...
- datestr(tiempo_final, 'yyyy-mm-dd')}, ...
- {user password}, ...
- [raw_mercator_name(1:end-3),'_u.nc']);
-
- get_file_python_mercator(pathMotu,mercator_type, ... % T
- motu_url,service_id,product_id{3}, ...
- vars(4), ...
- [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
- {datestr(tiempo_inicial,'yyyy-mm-dd') ...
- datestr(tiempo_final, 'yyyy-mm-dd')}, ...
- {user password}, ...
- [raw_mercator_name(1:end-3),'_t.nc']);
-
- get_file_python_mercator(pathMotu,mercator_type, ... % S
- motu_url,service_id,product_id{4}, ...
- vars(5), ...
- [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
- {datestr(tiempo_inicial,'yyyy-mm-dd') ...
- datestr(tiempo_final, 'yyyy-mm-dd')}, ...
- {user password}, ...
- [raw_mercator_name(1:end-3),'_s.nc']);
-
- setenv('DYLD_LIBRARY_PATH',pathdyld); % set back Matlab libs path
- setenv('LD_LIBRARY_PATH',pathld); % set back Matlab libs path
-
+ get_file_python_mercator(pathCMC, ... % T
+ product_id{3}, ...
+ vars(4), ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_t.nc']);
+ %
+ get_file_python_mercator(pathCMC, ... % S
+ product_id{4}, ...
+ vars(5), ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_s.nc']);
+%
end % download_raw_data
-
+%
if convert_raw2crocotools
%
% Convert data format and write in a more CROCOTOOLS
% compatible input file
%
- disp(['Making output data directory ',FRCST_dir]) % create directory
- eval(['!mkdir ',FRCST_dir])
- %
- mercator_name=[FRCST_dir,FRCST_prefix,num2str(rundate),'.cdf'];
- if exist(mercator_name)
- disp('Mercator file already exist => overwrite it')
- end
- write_mercator_frcst(FRCST_dir,FRCST_prefix,raw_mercator_name, ...
- mercator_type,vars,time,Yorig); % write data
+ write_mercator_multi(FRCST_dir,FRCST_prefix,raw_mercator_name, ...
+ mercator_type,vars,time,num2str(rundate),Yorig); % write data
eval(['! rm -f ',[raw_mercator_name(1:end-3),'*nc '] ]);
end
-
+%
end
-
diff --git a/Forecast_tools/extract_ECCO_frcst.m b/Forecast_tools/extract_ECCO_frcst.m
deleted file mode 100644
index 10ad8ffb066333b6b9950548940b830b07dc8afc..0000000000000000000000000000000000000000
--- a/Forecast_tools/extract_ECCO_frcst.m
+++ /dev/null
@@ -1,115 +0,0 @@
-function extract_ECCO_frcst(FRCST_dir,FRCST_prefix,prefix,suffix,tindex,missval,...
- lon,lon_u,lat,lat_v,depth,...
- krange,jrange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- time,Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subset from ECCO using DODS
-% Write it in a local file (keeping the classic
-% SODA netcdf format)
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 9-Sep-2006 by Pierrick Penven
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-disp([' Download ECCO'])
-trange=['[',num2str(tindex-1),':',num2str(tindex-1),']'];
-%
-% Get the time
-%
-%vname='Have';
-%fname=[prefix,vname,suffix];
-%time=readdap(fname,'time',trange)
-%time=floor(time/24+datenum(1970,1,1));
-%disp([' Date: ',datestr(time)])
-%time=time-datenum(Yorig,1,1)
-%
-% Get SSH
-%
-disp(' ...SSH')
-vname='Have';
-fname=[vname,suffix];
-ssh=getdap(prefix,fname,vname,...
- trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-ssh=shiftdim(ssh,2);
-ssh(ssh<=missval)=NaN;
-%
-% Get U
-%
-disp(' ...U')
-vname='Uave';
-fname=[vname,suffix];
-u=getdap(prefix,fname,vname,...
- trange,krange,jrange,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u);
-u=permute(u,[4 3 1 2]);
-u(u<=missval)=NaN;
-%
-% Get V
-%
-disp(' ...V')
-vname='Vave';
-fname=[vname,suffix];
-v=getdap(prefix,fname,vname,...
- trange,krange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-v=permute(v,[4 3 1 2]);
-v(v<=missval)=NaN;
-%
-% Get TEMP
-%
-disp(' ...TEMP')
-vname='Tave';
-fname=[vname,suffix];
-temp=getdap(prefix,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-temp=permute(temp,[4 3 1 2]);
-temp(temp<=missval)=NaN;
-%
-% Get SALT
-%
-disp(' ...SALT')
-vname='Save';
-fname=[vname,suffix];
-salt=getdap(prefix,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-salt=permute(salt,[4 3 1 2]);
-salt(salt<=missval)=NaN;
-%
-% Create the ECCO file
-%
-create_OGCM([FRCST_dir,FRCST_prefix,num2str(time),'.cdf'],...
- lon,lat,lon_u,lat,lon,lat_v,depth,time,...
- squeeze(temp),squeeze(salt),squeeze(u),...
- squeeze(v),squeeze(ssh),Yorig)
-%
-return
diff --git a/Forecast_tools/extract_mercator_frcst.m b/Forecast_tools/extract_mercator_frcst.m
deleted file mode 100644
index 72d03800af544285304716ed0cd5c56a2c8f0738..0000000000000000000000000000000000000000
--- a/Forecast_tools/extract_mercator_frcst.m
+++ /dev/null
@@ -1,116 +0,0 @@
-function extract_mercator_frcst(FRCST_dir,FRCST_prefix,url,tndx,missval,...
- lon,lon_u,lat,lat_v,depth,...
- krange,jrange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- time,Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subset from Mercator using DODS
-% Write it in a local file (keeping the classic
-% SODA netcdf format)
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 9-Sep-2006 by Pierrick Penven
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-disp([' Download MERCATOR'])
-trange=['[',num2str(min(tndx)-1),':',num2str(max(tndx)-1),']'];
-%trange=['[',num2str(tindex-1),':',num2str(tindex-1),']'];
-%
-% Get the time
-%
-%vname='Have';
-%fname=[prefix,vname,suffix];
-%time=readdap(fname,'time',trange)
-%time=floor(time/24+datenum(1970,1,1));
-%disp([' Date: ',datestr(time)])
-%time=time-datenum(Yorig,1,1)
-%
-% Get SSH
-%
-disp(' ...SSH')
-vname='ssh';
-fname='';
-ssh=getdap(url,fname,vname,...
- trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-ssh=shiftdim(ssh,2);
-ssh(ssh>=missval)=NaN;
-%
-%
-% Get U
-%
-disp(' ...U')
-vname='u';
-u=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u);
-u=permute(u,[4 3 1 2]);
-u(u>=missval)=NaN;
-%
-% Get V
-%
-disp(' ...V')
-vname='v';
-v=getdap(url,fname,vname,...
- trange,krange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-v=permute(v,[4 3 1 2]);
-v(v>=missval)=NaN;
-%
-% Get TEMP
-%
-disp(' ...TEMP')
-vname='temperature';
-temp=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-temp=permute(temp,[4 3 1 2]);
-temp(temp>=missval)=NaN;
-%
-% Get SALT
-%
-disp(' ...SALT')
-vname='salinity';
-salt=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-salt=permute(salt,[4 3 1 2]);
-salt(salt>=missval)=NaN;
-%
-%
-% Create the ECCO file
-rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
-
-create_OGCM([FRCST_dir,FRCST_prefix,num2str(rundate),'.cdf'],...
- lon,lat,lon_u,lat,lon,lat_v,depth,time,...
- squeeze(temp),squeeze(salt),squeeze(u),...
- squeeze(v),squeeze(ssh),Yorig)
-%
-return
diff --git a/Forecast_tools/get_GFS.m b/Forecast_tools/get_GFS.m
index 667463e388d902d05f92cffe7288e8e268568684..47f94e0535faa913ceec12273f466c39eb4cc3f9 100644
--- a/Forecast_tools/get_GFS.m
+++ b/Forecast_tools/get_GFS.m
@@ -47,69 +47,74 @@ t=readdap(fname,'time',trange);
disp(['TRANGE=',num2str(trange)])
disp(['GFS raw time=',sprintf('%5.3f',t)])
t=t+365; % put it in "matlab" time
-disp(['GFS: ',datestr(t)])
+disp(['GFS: ',datestr(datenum(t),'yyyy-mm-dd HH:MM:SS')])
disp('====================================================')
%disp('u...')
u=mask.*getdap('',fname,'ugrd10m',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
u(abs(u)>=missvalue)=NaN;
+pause(2)
%disp('v...')
v=mask.*getdap('',fname,'vgrd10m',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
v(abs(v)>=missvalue)=NaN;
-
-%disp('ty...')
-ty=mask.*getdap('',fname,'vflxsfc',trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-ty(abs(ty)>=missvalue)=NaN;
+pause(2)
%disp('tx...')
tx=mask.*getdap('',fname,'uflxsfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
tx(abs(tx)>=missvalue)=NaN;
+pause(2)
-
-%disp('skt...')
-%skt=mask.*getdap('',fname,'tmpsfc',trange,'',jrange,...
-% i1min,i1max,i2min,i2max,i3min,i3max);
-%skt(abs(skt)>=missvalue)=NaN;
+%disp('ty...')
+ty=mask.*getdap('',fname,'vflxsfc',trange,'',jrange,...
+ i1min,i1max,i2min,i2max,i3min,i3max);
+ty(abs(ty)>=missvalue)=NaN;
+pause(2)
%disp('tair...')
tair=mask.*getdap('',fname,'tmp2m',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
tair(abs(tair)>=missvalue)=NaN;
+pause(2)
%disp('rhum...')
rhum=mask.*getdap('',fname,'rh2m',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
rhum(abs(rhum)>=missvalue)=NaN;
+pause(2)
%disp('prate...')
prate=mask.*getdap('',fname,'pratesfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
prate(abs(prate)>=missvalue)=NaN;
+pause(2)
%disp('down radlw...')
dradlw=mask.*getdap('',fname,'dlwrfsfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
dradlw(abs(dradlw)>=missvalue)=NaN;
+pause(2)
%disp('up radlw...')
uradlw=mask.*getdap('',fname,'ulwrfsfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
uradlw(abs(uradlw)>=missvalue)=NaN;
+pause(2)
%disp('down radsw...')
dradsw=mask.*getdap('',fname,'dswrfsfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
dradsw(abs(dradsw)>=missvalue)=NaN;
+pause(2)
%disp('up radsw...')
uradsw=mask.*getdap('',fname,'uswrfsfc',trange,'',jrange,...
i1min,i1max,i2min,i2max,i3min,i3max);
uradsw(abs(uradsw)>=missvalue)=NaN;
+pause(2)
%
% Transform the variables
%
diff --git a/Forecast_tools/iteration.m b/Forecast_tools/iteration.m
deleted file mode 100644
index 9c472128427f07675c5a797b8ec8a6b6be2ef6bc..0000000000000000000000000000000000000000
--- a/Forecast_tools/iteration.m
+++ /dev/null
@@ -1,26 +0,0 @@
-
-%%%% hindcast iterations %%%
-start
-crocotools_param
-
-time=(floor(now)-datenum(Yorig,1,1)-(hdays-1)-timezone/24)*86400;
-
-% shift back restart time after first iteration
-eval(['!cp ','croco_rst.nc',' ','croco_ini.nc'])
-nc=netcdf('croco_ini.nc','write');
-nc{'scrum_time'}(1)=time;
-close(nc)
-
-for i=1:3
- disp(['I=',num2str(i+1)])
- eval(['!export OMP_NUM_THREADS=4 ; ./croco ','croco_hindcast.in ',' > ','croco_hindcast_',num2str(date),'.out']);
-
- % shift back restart time for next iteration
- eval(['!cp ','croco_rst.nc',' ','croco_ini.nc'])
- nc=netcdf('croco_ini.nc','write');
- nc{'scrum_time'}(1)=time;
- close(nc)
-
-end
-
-return
diff --git a/Forecast_tools/make_GFS.m b/Forecast_tools/make_GFS.m
index 967a7048d566a03c968f475e2b44939ce90ab740..ff01b7e2673493b57bd8a0c212b0c2c1e479fd3b 100644
--- a/Forecast_tools/make_GFS.m
+++ b/Forecast_tools/make_GFS.m
@@ -3,6 +3,8 @@
% Create and fill frc and bulk files with GFS data.
% for a forecast run
%
+% Description : 3 hourly forecasts / 0.25 deg (00z/06z/12z/18z)
+%
% The on-line reference to GFS is at
% http://nomad3.ncep.noaa.gov/
%
@@ -95,6 +97,10 @@ if Download_data==1
% Download data with DODS (the download matlab routine depends on the OGCM)
%
disp('Download data...')
+ disp('--> NB: if you receive this message during download : ')
+ disp(' " syntax error, unexpected WORD_WORD, expecting SCAN_ATTR or SCAN_DATASET or SCAN_ERROR ..."')
+ disp(' " you maybe reach the rate limit authorized, there is a ban on your IP due to an “Over Rate Limit†violation, try to wait more than 10 minutes before to do it again')
+ disp([' '])
download_GFS(today,lonmin,lonmax,latmin,latmax,FRCST_dir,Yorig,it)
%
end
@@ -121,16 +127,6 @@ create_forcing(frcname,grdname,CROCO_title,...
0,0,0,...
0,0,0,0,0,0)
nc_frc=netcdf(frcname,'write');
-% for l=1:tlen
-% nc_blk{'tair'}(l,:,:)=0;
-% nc_blk{'rhum'}(l,:,:)=0;
-% nc_blk{'prate'}(l,:,:)=0;
-% nc_blk{'radsw'}(l,:,:)=0;
-% nc_blk{'radlw'}(l,:,:)=0;
-% nc_blk{'wspd'}(l,:,:)=0;
-% nc_frc{'sustr'}(l,:,:)=0;
-% nc_frc{'svstr'}(l,:,:)=0;
-% end
%
% Loop on time
%
@@ -295,13 +291,5 @@ if makeplot==1
test_forcing(blkname,grdname,'radsw',slides,3,coastfileplot)
end
-
toc
-
-
-
-
-
-
-
diff --git a/Forecast_tools/make_OGCM_frcst.m b/Forecast_tools/make_OGCM_mercator_frcst.m
similarity index 57%
rename from Forecast_tools/make_OGCM_frcst.m
rename to Forecast_tools/make_OGCM_mercator_frcst.m
index 3c11f8e40125b08cb6a518dc362f948d6164d432..ba600e75ab7dfdc530f33914f9a6518eb41370c9 100644
--- a/Forecast_tools/make_OGCM_frcst.m
+++ b/Forecast_tools/make_OGCM_mercator_frcst.m
@@ -1,8 +1,24 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Create and fill CROCO clim and bry files with OGCM data.
-% for a forecast run
+% Create and fill CROCO clim and bry files with OGCM data
+% from mercator for a forecast run
%
+% On crocotools_param.m, available datasets:
+%
+% mercator -> 3 options for mercator_type parameter:
+%
+% 3 --> 1/12 deg Mercator global forecast (See Section 8.)
+% (daily forecast from 00h UTC up to 10 days,
+% updated daily at 12h UTC)
+% 4 --> 1/24 deg Mercator Mediterranean analysis/forecast (See Section 8.)
+% (daily forecast from 00h UTC up to 9 days,
+% updated daily at 16h UTC)
+% 5 --> the same than 4 but with detiding postprocessing on current and ssh
+%
+% Note for 3/4/5: (now -> 10days : P1-P10)
+% (now -1day : P0)
+% (7days from now -> now-1day : Near Real Time analysis)
+% (more than 15days from now : Best analysis)
%
% Further Information:
% http://www.croco-ocean.org
@@ -31,16 +47,16 @@
% Updated 20-Aug-2008 by Matthieu Caillaud & P. Marchesiello
% Updated 12-Feb-2016 by P. Marchesiello
% Updated 14-Oct-2020 by P. Marchesiello
-%
+% Updated 18-Mar-2024 by G. Cambon
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%clear all
-%close all
+clear all
+close all
tic
%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
%
% Common parameters
%
-crocotools_param
+crocotools_param;
%
% Specific to forecast
%
@@ -49,29 +65,30 @@ makeplot = 0;
% Get date
%
rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
+date_run=datenum(rundate_str);
+rundate=date_run-datenum(Yorig,1,1);
+date_frcst=rundate;
+%OGCM=mercator
+for i=1:hdays+1
+ time1(i)=date_run-(hdays+1-i);
+end
+if hdays ~= 0
+ % date_deb = rundate - hindcast days : example 2024-02-28T00:00:00Z-PT2D
+ % for a validity date 2 days before run 20240228 00hUTC ...
+ date_deb=strcat(datestr(time1(1+hdays),'yyyy-mm-ddT00:00:00') ,['-PT',num2str(hdays),'D']);
+else
+ date_deb=datestr(time1(1+hdays),'yyyy-mm-ddT00:00:00Z');
+end
%
% Set generic OGCM file name
%
-FRCST_prefix=[OGCM,'_'];
+FRCST_prefix=['mercator_'];
OGCM_name=[FRCST_dir,FRCST_prefix,num2str(rundate),'.cdf'];
%
-if strcmp(OGCM,'ECCO')
- %
- % ECCO DODS URL
- %
- % Kalman filter
- %
- url = 'http://ecco.jpl.nasa.gov/thredds/dodsC/las/kf080/kf080_';
- %
-elseif strcmp(OGCM,'mercator')
- %
- % MERCATOR : see get_file_python_mercator.m
- %
- raw_mercator_name=[FRCST_dir,'raw_motu_mercator_',num2str(rundate),'.nc'];
-else
- error(['Unknown OGCM: ',OGCM])
-end
+%
+% MERCATOR : see get_file_python_mercator.m
+%
+raw_mercator_name=[FRCST_dir,'raw_mercator_',date_deb,'.nc'];
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% end of user input parameters
@@ -95,41 +112,31 @@ pm=nc{'pm'}(:);
pn=nc{'pn'}(:);
rmask=nc{'mask_rho'}(:);
close(nc)
-
%---------------------------------------------------------------
% Extract data from the Internet
%---------------------------------------------------------------
if Download_data
- %
- % Get model limits
- %
- lonmin=min(min(lon));
- lonmax=max(max(lon));
- latmin=min(min(lat));
- latmax=max(max(lat));
- %
- % Download data (matlab routine for download depends on OGCM)
- %
- if strcmp(OGCM,'ECCO')
- disp('Download data...')
- eval(['OGCM_name=download_', ...
- OGCM,'_frcst(lonmin,lonmax,latmin,latmax,',...
- 'FRCST_dir,FRCST_prefix,url,Yorig);'])
-
- elseif strcmp(OGCM,'mercator')
%
- % Use Motu python
+ % Get model limits
+ %
+ lonmin=min(min(lon));
+ lonmax=max(max(lon));
+ latmin=min(min(lat));
+ latmax=max(max(lat));
+ %
+ % Download data (matlab routine for download depends on OGCM)
+ %
+ %
+ % Use of Copernicusmarine client (python)
+ % -> script download_mercator_frcst_python.m
%
disp('Download data...')
- eval(['OGCM_name=download_', ...
- OGCM,'_frcst_python(pathMotu,user,password,mercator_type,', ...
- 'motu_url_fcst,service_id_fcst,product_id_fcst,', ...
- 'hdays,fdays,', ...
- 'lonmin,lonmax,latmin,latmax,hmax,', ...
- 'FRCST_dir,FRCST_prefix,raw_mercator_name,Yorig);'])
- end
+ download_mercator_frcst_python(pathCMC,user,password,mercator_type, ...
+ raw_mercator_name,product_id, ...
+ hdays,fdays, ...
+ lonmin,lonmax,latmin,latmax,hmax, ...
+ FRCST_dir,FRCST_prefix,date_frcst,Yorig);
end
-
%---------------------------------------------------------------
% Get OGCM grid
%---------------------------------------------------------------
@@ -144,35 +151,28 @@ Z=-nc{'depth'}(:);
NZ=length(Z);
NZ=NZ-rmdepth;
Z=Z(1:NZ);
-
%---------------------------------------------------------------
% Get time array
%---------------------------------------------------------------
-if strcmp(OGCM,'ECCO')
- time=[90 270];
- time_cycle=360;
- trange=[1 1];
-elseif strcmp(OGCM,'mercator')
- OGCM_time=nc{'time'}(:);
- time_cycle=0;
- delta=1; % >1 if subsampling
- trange=[1:delta:length(OGCM_time)];
- time=zeros(length(trange),1);
- for i=1:length(trange)
- time(i)=OGCM_time(trange(i));
- end
+OGCM_time=nc{'time'}(:);
+time_cycle=0;
+delta=1; % >1 if subsampling
+trange=[1:delta:length(OGCM_time)];
+time=zeros(length(trange),1);
+for i=1:length(trange)
+ time(i)=OGCM_time(trange(i));
end
close(nc)
-
%---------------------------------------------------------------
% Initial file
%---------------------------------------------------------------
if makeini==1
- ininame=[ini_prefix,num2str(rundate),nc_suffix];
- disp(['Create an initial file for ',num2str(rundate);])
+ %
+ ininame=[ini_prefix,num2str(date_frcst),nc_suffix];
+ disp(['-> Create an initial file for date ',num2str(date_deb);])
create_inifile(ininame,grdname,CROCO_title,...
theta_s,theta_b,hc,N,...
- rundate-hdays,'clobber',vtransform); % starts at 00:00
+ date_frcst-hdays,'clobber',vtransform); % starts at 00:00
nc_ini=netcdf(ininame,'write');
interp_OGCM_frcst(OGCM_name,Roa,interp_method,...
@@ -180,19 +180,22 @@ if makeini==1
nc_ini,[],lon,lat,angle,h,pm,pn,rmask,...
1,vtransform,obc)
close(nc_ini)
- if (isoctave == 0)
- eval(['!cp ',ininame,' ',ini_prefix,'hct',nc_suffix])
- else
- eval(['cp ',ininame,' ',ini_prefix,'hct',nc_suffix])
+ if hdays ~= 0
+ if (isoctave == 0)
+ eval(['!cp ',ininame,' ',ini_prefix,'hct_',num2str(date_frcst),nc_suffix])
+ else
+ eval(['cp ',ininame,' ',ini_prefix,'hct_',num2str(date_frcst),nc_suffix])
+ end
end
end
-
%---------------------------------------------------------------
% Clim and Bry files
%---------------------------------------------------------------
if makeclim==1 | makebry==1
if makebry==1
- bryname=[bry_prefix,num2str(rundate),nc_suffix];
+ bryname=[bry_prefix,num2str(date_frcst),nc_suffix];
+ disp([' '])
+ disp(['-> Create bry files from ',num2str(date_deb);])
create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
theta_s,theta_b,hc,N,...
time,time_cycle,'clobber',vtransform);
@@ -201,7 +204,8 @@ if makeclim==1 | makebry==1
nc_bry=[];
end
if makeclim==1
- clmname=[clm_prefix,num2str(rundate),nc_suffix];
+ clmname=[clm_prefix,num2str(date_frcst),nc_suffix];
+ disp(['-> Create clim files from ',num2str(date_deb);])
create_climfile(clmname,grdname,CROCO_title,...
theta_s,theta_b,hc,N,...
time,time_cycle,'clobber',vtransform);
@@ -209,18 +213,16 @@ if makeclim==1 | makebry==1
else
nc_clm=[];
end
-
%---------------------------------------------------------------
% Perform interpolations for all selected records
%---------------------------------------------------------------
-for tndx=1:length(time)
- disp([' Time step : ',num2str(tndx),' of ',num2str(length(time)),' :'])
- interp_OGCM_frcst(OGCM_name,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,trange(tndx),...
- nc_clm,nc_bry,lon,lat,angle,h,pm,pn,rmask, ...
- tndx,vtransform,obc)
-end
-
+ for tndx=1:length(time)
+ disp([' Time step : ',num2str(tndx),' of ',num2str(length(time)),' :'])
+ interp_OGCM_frcst(OGCM_name,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,trange(tndx),...
+ nc_clm,nc_bry,lon,lat,angle,h,pm,pn,rmask, ...
+ tndx,vtransform,obc)
+ end
%
% Close CROCO files
%
@@ -239,21 +241,21 @@ if makeplot==1
disp(' ')
disp(' Make a few plots...')
if makeini==1
- ininame=[ini_prefix,num2str(rundate),nc_suffix];
+ ininame=[ini_prefix,num2str(date_frcst),nc_suffix];
figure
test_clim(ininame,grdname,'temp',1,coastfileplot)
figure
test_clim(ininame,grdname,'salt',1,coastfileplot)
end
if makeclim==1
- clmname=[clm_prefix,num2str(rundate),nc_suffix];
+ clmname=[clm_prefix,num2str(date_frcst),nc_suffix];
figure
test_clim(clmname,grdname,'temp',1,coastfileplot)
figure
test_clim(clmname,grdname,'salt',1,coastfileplot)
end
if makebry==1
- bryname=[bry_prefix,num2str(rundate),nc_suffix];
+ bryname=[bry_prefix,num2str(frcst),nc_suffix];
figure
test_bry(bryname,grdname,'temp',1,obc)
figure
diff --git a/Forecast_tools/make_forecast.m b/Forecast_tools/make_forecast.m
index 4f1c4ff026ed8c73b9d0b3e3a0f1685969ec2558..4f449259b6fc4a5b2802e89b4d52e3ff5f3bb297 100644
--- a/Forecast_tools/make_forecast.m
+++ b/Forecast_tools/make_forecast.m
@@ -1,86 +1,90 @@
-%
-% make_forecast.m
-%
-% Preparation of the files for the forecast system:
-% - launch make_OGCM_frcst and make_GFS
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 8-Sep-2006 by Pierrick Penven
-% Updated 12-Feb-2016 by P. Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-start
-tic
-crocotools_param
-
-%
-% Get the lateral boundary conditions
-%
-make_OGCM_frcst
-%
-% Get the surface forcing
-%
-make_GFS
-%
-% Copy the resulting files
-%
-rundate=datenum(date)-datenum(Yorig,1,1); nc_suffix='.nc';
-eval(['!cp ',bry_prefix,num2str(rundate),nc_suffix,' ',bry_prefix,'0',nc_suffix])
-eval(['!cp ',blk_prefix,num2str(rundate),nc_suffix,' ',blk_prefix,'0',nc_suffix])
-eval(['!cp ',frc_prefix,num2str(rundate),nc_suffix,' ',frc_prefix,'0',nc_suffix])
-eval(['!cp ',clm_prefix,num2str(rundate),nc_suffix,' ',clm_prefix,'0',nc_suffix])
-eval(['!cp ',ini_prefix,num2str(rundate),nc_suffix,' ',ini_prefix,'0',nc_suffix])
-%
-% Add tidal data in forcing file
-%
-if add_tides_fcst==1
- disp(['Add tidal data ... '])
- frcname=[CROCO_files_dir,'croco_frc_GFS_0.nc'];
- [Y,M,d,h,mi,s] = datevec(date);
- add_tidal_data(tidename,grdname,frcname,Ntides,tidalrank, ...
- Yorig,Y,M,coastfileplot,sal_tides,salname)
-end
-%
-% Set the clock right:
-% - copy croco_ini.nc in FORECAST/croco_ini.nc if not available
-% - update scrum_time in FORECAST/croco_ini.nc using timezone information
-% In this case, initial scrum_time is the UTC time corresponding to
-% local midnight of day=now-hdays (scrum_time needs to be a UTC time
-% since all forcing fields are referenced to UTC time).
-%
-disp('Set the clock right in initial file using Time Zone information')
-time=(floor(now)-datenum(Yorig,1,1)-hdays-timezone/24)*86400;
-ininame='FORECAST/croco_ini.nc';
-nc=netcdf(ininame,'write');
-if isempty(nc)
- rundate=datenum(date)-datenum(Yorig,1,1); nc_suffix='.nc';
- disp('No restart file available in CROCO_FILES, copy OGCM inifile')
- eval(['!cp ',ini_prefix,num2str(rundate),nc_suffix,' ',ininame])
- nc=netcdf(ininame,'write');
-end
-nc{'scrum_time'}(:)=time;
-close(nc)
-toc
-return
+%
+% make_forecast.m
+%
+% Preparation of the files for the forecast system:
+% - launch make_OGCM_frcst and make_GFS
+%
+% Further Information:
+% http://www.croco-ocean.org
+%
+% This file is part of CROCOTOOLS
+%
+% CROCOTOOLS is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published
+% by the Free Software Foundation; either version 2 of the License,
+% or (at your option) any later version.
+%
+% CROCOTOOLS is distributed in the hope that it will be useful, but
+% WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program; if not, write to the Free Software
+% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
+% MA 02111-1307 USA
+%
+% Copyright (c) 2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
+%
+% Updated 8-Sep-2006 by Pierrick Penven
+% Updated 12-Feb-2016 by P. Marchesiello
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+start
+tic
+crocotools_param
+
+%
+% Get the lateral boundary conditions
+%
+make_OGCM_mercator_frcst
+%
+% Get the surface forcing
+%
+make_GFS
+%
+% Copy the resulting files
+%
+rundate=datenum(date)-datenum(Yorig,1,1);
+nc_suffix='.nc';
+eval(['!cp ',bry_prefix,num2str(rundate),nc_suffix,' ',bry_prefix,'0',nc_suffix])
+eval(['!cp ',blk_prefix,num2str(rundate),nc_suffix,' ',blk_prefix,'0',nc_suffix])
+eval(['!cp ',frc_prefix,num2str(rundate),nc_suffix,' ',frc_prefix,'0',nc_suffix])
+eval(['!cp ',clm_prefix,num2str(rundate),nc_suffix,' ',clm_prefix,'0',nc_suffix])
+eval(['!cp ',ini_prefix,num2str(rundate),nc_suffix,' ',ini_prefix,'0',nc_suffix])
+%
+% Add tidal data in forcing file
+%
+if add_tides_fcst==1
+ disp(['Add tidal data ... '])
+ frcname=[CROCO_files_dir,'croco_frc_GFS_0.nc'];
+ [Y,M,d,h,mi,s] = datevec(date);
+ add_tidal_data(tidename,grdname,frcname,Ntides,tidalrank, ...
+ Yorig,Y,M,coastfileplot,sal_tides,salname)
+end
+%
+% Set the clock right:
+% - copy croco_ini.nc in FORECAST/croco_ini.nc if not available
+% - update scrum_time in FORECAST/croco_ini.nc using timezone information
+% In this case, initial scrum_time is the UTC time corresponding to
+% local midnight of day=now-hdays (scrum_time needs to be a UTC time
+% since all forcing fields are referenced to UTC time).
+%
+disp('Set the clock right in initial file using Time Zone information')
+time=(floor(now)-datenum(Yorig,1,1)-hdays-timezone/24)*86400;
+if ~exist('FORECAST', 'dir')
+ mkdir('FORECAST');
+end
+ininame='FORECAST/croco_ini.nc';
+nc=netcdf(ininame,'write');
+if isempty(nc)
+ rundate=datenum(date)-datenum(Yorig,1,1); nc_suffix='.nc';
+ disp('No restart file available in CROCO_FILES, copy OGCM inifile')
+ eval(['!cp ',ini_prefix,num2str(rundate),nc_suffix,' ',ininame])
+ nc=netcdf(ininame,'write');
+end
+nc{'scrum_time'}(:)=time;
+close(nc)
+toc
+return
diff --git a/Forecast_tools/motuclient-python/LICENSE b/Forecast_tools/motuclient-python/LICENSE
deleted file mode 100755
index f0156c535521aefeac49856f5e1299fb00070c60..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/LICENSE
+++ /dev/null
@@ -1,165 +0,0 @@
- GNU LESSER GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-
- This version of the GNU Lesser General Public License incorporates
-the terms and conditions of version 3 of the GNU General Public
-License, supplemented by the additional permissions listed below.
-
- 0. Additional Definitions.
-
- As used herein, "this License" refers to version 3 of the GNU Lesser
-General Public License, and the "GNU GPL" refers to version 3 of the GNU
-General Public License.
-
- "The Library" refers to a covered work governed by this License,
-other than an Application or a Combined Work as defined below.
-
- An "Application" is any work that makes use of an interface provided
-by the Library, but which is not otherwise based on the Library.
-Defining a subclass of a class defined by the Library is deemed a mode
-of using an interface provided by the Library.
-
- A "Combined Work" is a work produced by combining or linking an
-Application with the Library. The particular version of the Library
-with which the Combined Work was made is also called the "Linked
-Version".
-
- The "Minimal Corresponding Source" for a Combined Work means the
-Corresponding Source for the Combined Work, excluding any source code
-for portions of the Combined Work that, considered in isolation, are
-based on the Application, and not on the Linked Version.
-
- The "Corresponding Application Code" for a Combined Work means the
-object code and/or source code for the Application, including any data
-and utility programs needed for reproducing the Combined Work from the
-Application, but excluding the System Libraries of the Combined Work.
-
- 1. Exception to Section 3 of the GNU GPL.
-
- You may convey a covered work under sections 3 and 4 of this License
-without being bound by section 3 of the GNU GPL.
-
- 2. Conveying Modified Versions.
-
- If you modify a copy of the Library, and, in your modifications, a
-facility refers to a function or data to be supplied by an Application
-that uses the facility (other than as an argument passed when the
-facility is invoked), then you may convey a copy of the modified
-version:
-
- a) under this License, provided that you make a good faith effort to
- ensure that, in the event an Application does not supply the
- function or data, the facility still operates, and performs
- whatever part of its purpose remains meaningful, or
-
- b) under the GNU GPL, with none of the additional permissions of
- this License applicable to that copy.
-
- 3. Object Code Incorporating Material from Library Header Files.
-
- The object code form of an Application may incorporate material from
-a header file that is part of the Library. You may convey such object
-code under terms of your choice, provided that, if the incorporated
-material is not limited to numerical parameters, data structure
-layouts and accessors, or small macros, inline functions and templates
-(ten or fewer lines in length), you do both of the following:
-
- a) Give prominent notice with each copy of the object code that the
- Library is used in it and that the Library and its use are
- covered by this License.
-
- b) Accompany the object code with a copy of the GNU GPL and this license
- document.
-
- 4. Combined Works.
-
- You may convey a Combined Work under terms of your choice that,
-taken together, effectively do not restrict modification of the
-portions of the Library contained in the Combined Work and reverse
-engineering for debugging such modifications, if you also do each of
-the following:
-
- a) Give prominent notice with each copy of the Combined Work that
- the Library is used in it and that the Library and its use are
- covered by this License.
-
- b) Accompany the Combined Work with a copy of the GNU GPL and this license
- document.
-
- c) For a Combined Work that displays copyright notices during
- execution, include the copyright notice for the Library among
- these notices, as well as a reference directing the user to the
- copies of the GNU GPL and this license document.
-
- d) Do one of the following:
-
- 0) Convey the Minimal Corresponding Source under the terms of this
- License, and the Corresponding Application Code in a form
- suitable for, and under terms that permit, the user to
- recombine or relink the Application with a modified version of
- the Linked Version to produce a modified Combined Work, in the
- manner specified by section 6 of the GNU GPL for conveying
- Corresponding Source.
-
- 1) Use a suitable shared library mechanism for linking with the
- Library. A suitable mechanism is one that (a) uses at run time
- a copy of the Library already present on the user's computer
- system, and (b) will operate properly with a modified version
- of the Library that is interface-compatible with the Linked
- Version.
-
- e) Provide Installation Information, but only if you would otherwise
- be required to provide such information under section 6 of the
- GNU GPL, and only to the extent that such information is
- necessary to install and execute a modified version of the
- Combined Work produced by recombining or relinking the
- Application with a modified version of the Linked Version. (If
- you use option 4d0, the Installation Information must accompany
- the Minimal Corresponding Source and Corresponding Application
- Code. If you use option 4d1, you must provide the Installation
- Information in the manner specified by section 6 of the GNU GPL
- for conveying Corresponding Source.)
-
- 5. Combined Libraries.
-
- You may place library facilities that are a work based on the
-Library side by side in a single library together with other library
-facilities that are not Applications and are not covered by this
-License, and convey such a combined library under terms of your
-choice, if you do both of the following:
-
- a) Accompany the combined library with a copy of the same work based
- on the Library, uncombined with any other library facilities,
- conveyed under the terms of this License.
-
- b) Give prominent notice with the combined library that part of it
- is a work based on the Library, and explaining where to find the
- accompanying uncombined form of the same work.
-
- 6. Revised Versions of the GNU Lesser General Public License.
-
- The Free Software Foundation may publish revised and/or new versions
-of the GNU Lesser General Public License from time to time. Such new
-versions will be similar in spirit to the present version, but may
-differ in detail to address new problems or concerns.
-
- Each version is given a distinguishing version number. If the
-Library as you received it specifies that a certain numbered version
-of the GNU Lesser General Public License "or any later version"
-applies to it, you have the option of following the terms and
-conditions either of that published version or of any later version
-published by the Free Software Foundation. If the Library as you
-received it does not specify a version number of the GNU Lesser
-General Public License, you may choose any version of the GNU Lesser
-General Public License ever published by the Free Software Foundation.
-
- If the Library as you received it specifies that a proxy can decide
-whether future versions of the GNU Lesser General Public License shall
-apply, that proxy's public statement of acceptance of any version is
-permanent authorization for you to choose that version for the
-Library.
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/MANIFEST.in b/Forecast_tools/motuclient-python/MANIFEST.in
deleted file mode 100755
index 4f24fe0853d877a1ab9433602fafc6b10068c24a..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/MANIFEST.in
+++ /dev/null
@@ -1,8 +0,0 @@
-# Author: CLS, smarty@cls.fr
-include LICENSE
-include pom.xml
-include README.md
-include setup.cfg
-include setup.py
-include src/python/motu_utils/cfg/log.ini
-include src/python/motu_utils/cfg/messages.properties
diff --git a/Forecast_tools/motuclient-python/README.md b/Forecast_tools/motuclient-python/README.md
deleted file mode 100755
index d1cabd5f31d0dd965842f224f1c146f5c628e9c1..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/README.md
+++ /dev/null
@@ -1,334 +0,0 @@
-# Motu Client Python Project
-@author Product owner <tjolibois@cls.fr>
-@author Scrum master, software architect <smarty@cls.fr>
-@author Quality assurance, continuous integration manager <smarty@cls.fr>
-
->How to read this file?
-Use a markdown reader:
-plugins [chrome](https://chrome.google.com/webstore/detail/markdown-preview/jmchmkecamhbiokiopfpnfgbidieafmd?utm_source=chrome-app-launcher-info-dialog) exists (Once installed in Chrome, open URL chrome://extensions/, and check "Markdown Preview"/Authorise access to file URL.),
-or for [firefox](https://addons.mozilla.org/fr/firefox/addon/markdown-viewer/) (anchor tags do not work)
-and also plugin for [notepadd++](https://github.com/Edditoria/markdown_npp_zenburn).
-
->Be careful: Markdown format has issue while rendering underscore "\_" character which can lead to bad variable name or path.
-
-
-# Summary
-* [Overview](#Overview)
-* [Build](#Build)
-* [Installation](#Installation)
- * [Prerequisites](#InstallationPre)
- * [Using PIP](#InstallationPIP)
- * [From tar.gz file](#InstallationTGZ)
-* [Configuration](#Configuration)
-* [Usage and options](#Usage)
- * [Usage from PIP installation](#UsagePIP)
- * [Usage from tar.gz installation](#UsageTGZ)
-* [Usage examples](#UsageExamples)
- * [Download](#UsageExamplesDownload)
- * [GetSize](#UsageExamplesGetSize)
- * [DescribeProduct](#UsageExamplesDescribeProduct)
-* [Licence](#Licence)
-* [Troubleshooting](#Troubleshooting)
- * [Unable to download the latest version watched on GitHub from PIP](#Troubleshooting)
- * [From Windows, Parameter error](#TroubleshootingWinArgErr)
-
-# <a name="Overview">Overview</a>
-Motu client "motuclient-python" is a python script used to connect to Motu HTTP server in order to:
-
-* __extract__ the data of a dataset, with geospatial, temporal and variable criterias (default option)
-* __get the size__ of an extraction with geospatial, temporal and variable criterias
-* __get information__ about a dataset
-
-This program can be integrated into a processing chain in order to automate the downloading of products via the Motu.
-
-
-# <a name="Build">Build</a>
-From the root folder runs the command:
-
-```
-./patchPOMtoBuild.sh
-mvn clean install -Dmaven.test.skip=true
-[...]
-[INFO] BUILD SUCCESS
-[...]
-```
-
-This creates two archives in the target folder:
-
-* motuclient-python-$version-$buildTimestamp-src.tar.gz: Archive containing all the source code
-* motuclient-python-$version-$buildTimestamp-bin.tar.gz: Archive ready to be installed
-
-
-
-# <a name="Installation">Installation</a>
-
-## <a name="InstallationPre">Prerequisites</a>
-You must use python version 2.7.X or later.
-This program is fully compatible with Python 3.X versions.
-There is two methods to install the client, by using PIP or from a tar.gz file.
- [setuptools](#InstallationSetuptools) python package has be installed in order to display the motuclient version successfully.
-
-## <a name="InstallationPIP">Using PIP</a>
-Python Package Index is used to ease installation.
-If your host needs a PROXY set it, for example:
-```
-export HTTPS_PROXY=http://myCompanyProxy:8080
-```
-
-Then run:
-
-```
-pip install motuclient
-```
-
-Now "motuclient" is installed, you can [configured it](#Configuration) and [use it](#UsagePIP).
-
-
-## <a name="InstallationTGZ">From tar.gz file</a>
-Deploy the archive (file motuclient-python-$version-bin.tar.gz available from [GitHub release](https://github.com/clstoulouse/motu-client-python/releases)) in the directory of your choice.
-```
-tar xvzf motuclient-python-$version-$buildTimestamp-bin.tar.gz
-```
-
-Create a [configuration file](#Configuration) and set the user and password to use to connect to the CAS server.
-
-## <a name="InstallationSetuptools">Install setuptools python package</a>
-"[Setuptools](https://pypi.python.org/pypi/setuptools)" python package has to be installed in order to display the version with option --version, here is how to install it:
-
-If your host needs a PROXY set it, for example:
-```
-export HTTPS_PROXY=http://myCompanyProxy:8080
-```
-
-Then run:
-
-```
-sudo apt install python-pip
-pip install --upgrade setuptools
-```
-
-# <a name="Configuration">Configuration</a>
-All parameters can be defined as command line options or can be written in a configuration file.
-The configuration file is a .ini file. This file is located in the following directory:
-
-* on __Unix__ platforms: $HOME/motuclient/motuclient-python.ini
-* on __Windows__ platforms: %USERPROFILE%\motuclient\motuclient-python.ini
-
-The expected structure of file is:
-```
-[Main]
-# Motu credentials
-user=john
-pwd=secret
-
-motu=http://motu-ip-server:port/motu-web/Motu
-service_id=GLOBAL_ANALYSIS_FORECAST_PHY_001_024-TDS
-product_id=global-analysis-forecast-phy-001-024-hourly-t-u-v-ssh
-date_min=2019-03-27
-date_max=2019-03-27
-latitude_min=-30
-latitude_max=40.0
-longitude_min=-10
-longitude_max=179.9166717529297
-depth_min=0.493
-depth_max=0.4942
-# Empty or non set means all variables
-# 1 or more variables separated by a coma and identified by their standard name
-variable=sea_water_potential_temperature,sea_surface_height_above_geoid
-# Accept relative or absolute path. The dot character "." is the current folder
-out_dir=./out_dir
-out_name=test.nc
-
-# Logging
-# https://docs.python.org/3/library/logging.html#logging-levels
-# log_level=X {CRITICAL:50, ERROR:40, WARNING:30, INFO:20, DEBUG:10, TRACE:0}
-log_level=0
-
-# block_size block used to download file (integer expressing bytes) default=65535
-# block_size=65535
-socket_timeout=120000
-
-# Http proxy to connect to Motu server
-# proxy_server=proxy.domain.net:8080
-# proxy_user=john
-# proxy_pwd=secret
-```
-
-A configuration file in another location can be specified by the `--config-file` option. It is even possible to split the configuration into two or more files. This is useful, for example, to keep server configuration in one file and dataset configuration in another:
-```
-./motuclient.py --config-file ~/server.ini --config-file ~/mercator.ini
-```
-If by chance there is a parameter listed in both configuration files, the value in the last file (e.g. `mercator.ini`) is the one actually used.
-
-# <a name="Usage">Usage</a>
-Starts the motu python client.
-
-## <a name="UsagePIP">Usage from PIP installation</a>
-Since version 1.8.0:
-```
-motuclient -h
-motuclient [options]
-```
-Before version 1.8.0:
-```
-python -m motu-client -h
-python -m motu-client [options]
-```
-
-[Options](#UsageOptions) are listed below.
-Method to used when it has been installed with [PIP method](#InstallationPIP).
-
-
-## <a name="UsageTGZ">Usage from tar.gz installation</a>
-```
-./motuclient.py -h
-motuclient.py [options]
-```
-Method to used when it has been installed with [tar.gz method](#InstallationTGZ).
-Usefull if host is offline and has no Internet access.
-
-### <a name="UsageOptions">__Options:__</a>
-
-
-* __-h, --help__ show this help message and exit
-* __-q, --quiet__ print logs with level WARN in stdout, used to prevent any output in stdout
-* __--noisy__ print logs with level TRACE in stdout
-* __--verbose__ print logs with level DEBUG in stdout
-* __--version__ show program's version number and exit, [setuptools](#InstallationSetuptools) python package has be installed to run it successfully
-
-* __--proxy-server=PROXY_SERVER__ Proxy server (url) used to contact Motu
-* __--proxy-user=PROXY_USER__ Proxy user name (string)
-* __--proxy-pwd=PROXY_PWD__ Proxy password (string)
-
-* __--auth-mode=AUTH_MODE__ the authentication mode: [default: cas]
- * __none__ for no authentication
- * __basic__ for basic authentication
- * __cas__ for Central Authentication Service
-* __-u USER, --user=USER__ User name (string) for the specified authentication mode
-* __-p PWD, --pwd=PWD__ the user password (string) for the specified authentication mode. Special characters can be used.
- * __Example 1__ From a Windows batch, if your password contains a percent character, double the percent character: If password is CMS2017@%! then enter -u username-p CMS2017@%%!
- * __Example 2__ From a Windows batch, if your password contains a space character, set password between double quotes: If password is CMS2017 @%! then enter -u username-p "CMS2017 @%%!"
- * __Example 3__ From a Linux shell, if your password contains a space character, set password between simple quotes: If password is CMS2017 @%! then enter -u username-p 'CMS2017 @%!'
-
-* __-m MOTU, --motu=MOTU__ Motu server url, e.g. "-m http://localhost:8080/motu-web/Motu"
-* __-s SERVICE_ID, --service-id=SERVICE_ID__ The service identifier (string), e.g. -s Mercator_Ocean_Model_Global-TDS
-* __-d PRODUCT_ID, --product-id=PRODUCT_ID__ The product (data set) to download (string), e.g. -d dataset-mercator-psy4v3-gl12-bestestimate-uv
-* __-t DATE_MIN, --date-min=DATE_MIN__ The min date with optional hour resolution (string following format YYYY-MM-DD [HH:MM:SS]), e.g. -t "2016-06-10" or -t "2016-06-10 12:00:00". Be careful to not forget double quotes around the date.
-* __-T DATE_MAX, --date-max=DATE_MAX__ The max date with optional hour resolution (string following format YYYY-MM-DD [HH:MM:SS ]), e.g. -T "2016-06-11" or -T "2016-06-10 12:00:00". Be careful to not forget double quotes around the date.
-* __-y LATITUDE_MIN, --latitude-min=LATITUDE_MIN__ The min latitude (float in the interval [-90 ; 90 ]), e.g. -y -80.5
-* __-Y LATITUDE_MAX, --latitude-max=LATITUDE_MAX__ The max latitude (float in the interval [-90 ; 90 ]), e.g. -Y 80.5
-* __-x LONGITUDE_MIN, --longitude-min=LONGITUDE_MIN__ The min longitude (float in the interval [-180 ; 180 ]), e.g. -x -180
-* __-X LONGITUDE_MAX, --longitude-max=LONGITUDE_MAX__ The max longitude (float in the interval [-180 ; 180 ]), e.g. -X 35.5
-* __-z DEPTH_MIN, --depth-min=DEPTH_MIN__ The min depth (float in the interval [0 ; 2e31 ] or string 'Surface'), e.g. -z 0.49
-* __-Z DEPTH_MAX, --depth-max=DEPTH_MAX__ The max depth (float in the interval [0 ; 2e31 ] or string 'Surface'), e.g. -Z 0.50
-* __-v VARIABLE, --variable=VARIABLE__ The variable (list of strings), e.g. -v salinity -v sst
-* __-S, --sync-mode__ Sets the download mode to synchronous (not recommended). If this parameter is set, Motu server is called with parameter [console](https://github.com/clstoulouse/motu#download-product). Otherwise
-, Motu server is called with parameter [status](https://github.com/clstoulouse/motu#download-product).
-
-
-* __-o OUT_DIR, --out-dir=OUT_DIR__ The output dir where result (download file) is written (string). If it starts with "console", behaviour is the same as with --console-mode.
-* __-f OUT_NAME, --out-name=OUT_NAME__ The output file name (string)
-* __--console-mode__ Write result on stdout. In case of an extraction, write the nc file http URL where extraction result can be downloaded. In case of a getSize or a describeProduct request, display the XML result.
-
-* __-D, --describe-product__ Get all updated information on a dataset. Output is in XML format, [API details](https://github.com/clstoulouse/motu#describe-product)
-* __--size__ Get the size of an extraction. Output is in XML format, [API details](https://github.com/clstoulouse/motu#get-size)
-
-* __--block-size=BLOCK_SIZE__ The block used to download file (integer expressing bytes), default=65535 bytes
-* __--socket-timeout=SOCKET_TIMEOUT__ Set a timeout on blocking socket operations (float expressing seconds)
-* __--user-agent=USER_AGENT__ Set the identification string (user-agent) for HTTP requests. By default this value is 'Python-urllib/x.x' (where x.x is the version of the python interpreter)
-
-
-# <a name="UsageExamples">Usage examples</a>
-In the following examples, variable ${MOTU\_USER} and ${MOTU\_PASSWORD} are user name and user password used to connect to the CAS server for single sign on.
-${MOTU\_SERVER\_URL} is the URL on the MOTU HTTP(s) server. For example http://localhost:8080/motu-web/Motu.
-Commands "./motuclient.py" has to be replaced by "python -m motuclient" if it has been installed with [PIP method](#UsagePIP).
-
-
-## <a name="UsageExamplesDownload">Download</a>
-### Download and save extracted file on the local machine
-This command writes the extraction result data in file: /data/test.nc
-
-```
-./motuclient.py --verbose --auth-mode=none -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -z 0.49 -Z 0.50 -x -70 -X 25 -y -75 -Y 10 -t "2016-06-10" -T "2016-06-11" -v salinity -o /data -f test.nc
-```
-
-### Display on stdout the HTTP(s) URL of the NC file available on the Motu server
-The HTTP(s) URL is displayed on stdout. This URL is a direct link to the file which is available to be downloaded.
-
-```
-./motuclient.py --quiet --auth-mode=cas -u ${MOTU_USER} -p ${MOTU_PASSWORD} -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -z 0.49 -Z 0.50 -x -70 -X 25 -y -75 -Y 10 -t "2016-06-10" -T "2016-06-11" -v salinity -o console
-```
-
-## <a name="UsageExamplesGetSize">GetSize</a>
-See [https://github.com/clstoulouse/motu#ClientAPI_GetSize](https://github.com/clstoulouse/motu#ClientAPI_GetSize) for more details about XML result.
-
-### Get the XML file which contains the extraction size on the local machine
-```
-./motuclient.py --size --auth-mode=cas -u ${MOTU_USER} -p ${MOTU_PASSWORD} -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -z 0.49 -Z 0.50 -x -70 -X 25 -y -75 -Y 10 -t "2016-06-10" -T "2016-06-11" -v salinity -o /data -f getSizeResult.xml
-```
-
-### Display the extraction size as XML on stdout
-```
-./motuclient.py --quiet --size --auth-mode=cas -u ${MOTU_USER} -p ${MOTU_PASSWORD} -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -z 0.49 -Z 0.50 -x -70 -X 25 -y -75 -Y 10 -t "2016-06-10" -T "2016-06-11" -v salinity -o console
-```
-
-
-## <a name="UsageExamplesDescribeProduct">DescribeProduct</a>
-See [https://github.com/clstoulouse/motu#describe-product](https://github.com/clstoulouse/motu#describe-product) for more details about XML result.
-
-### Get the XML file which contains the dataset description on the local machine
-```
-./motuclient.py -D --auth-mode=cas -u ${MOTU_USER} -p ${MOTU_PASSWORD} -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -o /data -f describeProductResult.xml
-```
-
-### Display the dataset description XML result on stdout
-```
-./motuclient.py --quiet -D --auth-mode=cas -u ${MOTU_USER} -p ${MOTU_PASSWORD} -m ${MOTU_SERVER_URL} -s HR_MOD_NCSS-TDS -d HR_MOD -o console
-```
-
-
-
-
-# <a name="Licence">Licence</a>
-This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
-
-This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
-
-You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-# <a name="Troubleshooting">Troubleshooting</a>
-# <a name="TroubleshootingPIPCache">Unable to download the latest version watched on GitHub from PIP</a>
-Example:
-```
-pip install motuclient
-Collecting motuclient
- Using cached https://test-files.pythonhosted.org/packages/4a/7d/41c3bdd973baf119371493c193248349c9b7107477ebf343f3889cabbf48/motuclient-X.Y.Z.zip
-Installing collected packages: motuclient
- Running setup.py install for motuclient ... done
-Successfully installed motuclient-X.Y.Z
-```
-
-Clear your PIP cache: On Windows, delete the folder %HOMEPATH%/pip. On archlinux pip cache is located at ~/.cache/pip.
-After re run the command:
-```
-pip install motuclient
-Collecting motuclient
- Using https://test-files.pythonhosted.org/packages/4a/7d/41c3bdd973baf119371493c193248349c9b7107477ebf343f3889cabbf48/motuclient-X.Y.Z.zip
-Installing collected packages: motuclient
- Running setup.py install for motuclient ... done
-Successfully installed motuclient-X.Y.Z
-```
-
-# <a name="TroubleshootingWinArgErr">From Windows, Parameter error</a>
-From Windows, the command "motuclient.py --version" returns an error.
-10:44:24 [ERROR] Execution failed: [Excp 13] User (option 'user') is mandatory when 'cas' authentication is set. Please provide it.
-
-__Analyse:__
-This issue comes from the fact that Windows command line does not pass parameters to python command.
-
-__Solution:__
-```
-Edit the Windows Registry Key "HKEY_CLASSES_ROOT\py_auto_file\shell\open\command" and append at the end of the value %*
-Exemple: "C:\dvltSoftware\python\Python27\python.exe" "%1" %*
-```
-
diff --git a/Forecast_tools/motuclient-python/motu-client.py b/Forecast_tools/motuclient-python/motu-client.py
deleted file mode 100755
index 623f3587b1a19ab8d9d5a1a95582957d75e9e03b..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu-client.py
+++ /dev/null
@@ -1,28 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Deprecated
-# Only for retrocompatibility of Motu <= v1.7
-import logging
-import motuclient
-
-deprecatedWarnMsg='"motu-client" module is deprecated since version1.8. A new Python module named "motuclient" without a dash separator between motu and client shall be used instead of "motu-client".'
-motuclient.initLogger()
-motuclient.log.warn( deprecatedWarnMsg )
-
-
-def get_client_version():
- #motuclient.log.warn( deprecatedWarnMsg + 'e.g. motuclient.get_client_version()')
- return motuclient.get_client_version()
-
-def get_client_artefact():
- #motuclient.log.warn( deprecatedWarnMsg + ', e.g. motuclient.get_client_artefact()')
- return motuclient.get_client_artefact()
-
-def main():
- #motuclient.log.warn( deprecatedWarnMsg + ', e.g. motuclient.main()')
- motuclient.main()
-
-if __name__ == '__main__':
- #motuclient.log.warn( deprecatedWarnMsg + ', e.g. motuclient.main()')
- motuclient.main()
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/__init__.py b/Forecast_tools/motuclient-python/motu_utils/__init__.py
deleted file mode 100755
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Forecast_tools/motuclient-python/motu_utils/cfg/log.ini b/Forecast_tools/motuclient-python/motu_utils/cfg/log.ini
deleted file mode 100755
index ff8a4ee6a1fa985dd55e8c9f2f9f40e8a36dce36..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/cfg/log.ini
+++ /dev/null
@@ -1,24 +0,0 @@
-[loggers]
-keys=root
-
-[handlers]
-keys=console
-
-[formatters]
-keys=default
-
-[logger_root]
-level=NOTSET
-handlers=console
-qualname=motuclient
-
-[handler_console]
-class=StreamHandler
-level=NOTSET
-formatter=default
-args=(sys.stdout,)
-stream=sys.stdout
-
-[formatter_default]
-format=%(asctime)s.%(msecs)03d [%(levelname)5s] %(message)s
-datefmt = %Y-%m-%d %H:%M:%S
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/cfg/messages.properties b/Forecast_tools/motuclient-python/motu_utils/cfg/messages.properties
deleted file mode 100755
index 1b73d07e535d345467a61491c26a11af6ebe0cdc..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/cfg/messages.properties
+++ /dev/null
@@ -1,17 +0,0 @@
-motuclient.exception.option.mandatory=[Excp 1] Option '%s' is mandatory. Please provide it.
-motuclient.exception.option.mandatory.user=[Excp 13] User (option '%s') is mandatory when '%s' authentication is set. Please provide it.
-motuclient.exception.option.mandatory.mode=[Excp 17] Authentication mode other than '%s' (option '%s') is mandatory when a user ('%s') is set. Please provide it.
-motuclient.exception.option.mandatory.password=[Excp 14] Password (option '%s') is mandatory for user '%s'. Please provide it.
-motuclient.exception.option.outdir-notexist=[Excp 2] The given output directory '%s' does not exist.
-motuclient.exception.option.outdir-notwritable=[Excp 3] The given output directory (%s) is not writable.
-motuclient.exception.option.not-url=[Excp 4] Option '%s' has a bad url scheme "%s".
-motuclient.exception.option.linked=[Excp 5] Option '%s' and '%s' must be provided both, or none.
-motuclient.exception.option.out-of-range=[Excp 6] Option '%s' is out of range for value '%s'.
-motuclient.exception.option.invalid=[Excp 12] Value '%s' is not valid for option '%s'. Expected one of %s.
-motuclient.exception.option.geographic-box=[Excp 7] Geographic coverage is not fully defined. Missing '%s' parameters.
-motuclient.exception.authentication.unfound-url=[Excp 8] CAS Url Server can't be found in '%s'. Check the contacted service use CAS for authentication.
-motuclient.exception.authentication.not-redirected=[Excp 15] Service '%s' seems to not have been redirected to the CAS service. Check the contacted service use CAS for authentication.
-motuclient.exception.authentication.redirected=[Excp 16] Service '%s' seems to have been redirected to the CAS service ('%s'). Check the contacted service doesn't need a CAS authentication first.
-motuclient.exception.authentication.tgt=[Excp 9] Unable to retrieve the Ticket Granting Ticket (TGT) when authenticating with CAS mode.
-motuclient.exception.motu.error=[Excp 10] Motu server failed to process the request. Response returned is the following: '%s'.
-motuclient.exception.download.too-short=[Excp 11] "Dataset retrival incomplete. Got only %i out of %i bytes.
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/motu_api.py b/Forecast_tools/motuclient-python/motu_utils/motu_api.py
deleted file mode 100755
index 21600cd8d539a5cd7da9032acd328bd31cdba16e..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/motu_api.py
+++ /dev/null
@@ -1,652 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-import sys
-
-
-if sys.version_info > (3, 0):
- import urllib.request, urllib.error
- from urllib.request import BaseHandler
- from urllib.parse import unquote, quote_plus, urlparse
-else:
- from urllib import quote_plus, quote
- from urlparse import urlparse
-
-
-import os
-import re
-import datetime
-import time
-import socket
-from xml.dom import minidom
-from pkg_resources import get_distribution
-
-# Import project libraries
-from motu_utils import utils_http, utils_stream, utils_cas, utils_log, utils_messages, utils_unit, \
- stop_watch, pom_version
-from motu_utils import utils_collection
-import logging
-
-# constant for authentication modes
-AUTHENTICATION_MODE_NONE = 'none'
-AUTHENTICATION_MODE_BASIC = 'basic'
-AUTHENTICATION_MODE_CAS = 'cas'
-
-# constant for date time string format
-DATETIME_FORMAT = "%Y-%m-%d% %H:%M:%S"
-
-
-# shared logger
-log = None
-
-def get_client_version():
- """Return the version (as a string) of this client.
-
- The value is automatically set by the maven processing build, so don't
- touch it unless you know what you are doing."""
- version = 'unknown'
- try:
- version = get_distribution('motuclient').version
- except:
- version = pom_version.getPOMVersion()
- return version
-
-def get_client_artefact():
- """Return the artifact identifier (as a string) of this client.
-
- The value is automatically set by the maven processing build, so don't
- touch it unless you know what you are doing."""
- return 'motuclient-python'
-
-def build_params(_options):
- """Function that builds the query string for Motu according to the given options"""
- temporal = ''
- geographic = ''
- vertical = ''
- other_opt = ''
-
- """
- Build the main url to connect to
- """
- query_options = utils_collection.ListMultimap()
-
- # describeProduct in XML format (sync) / productDownload (sync/async)
- if _options.describe:
- query_options.insert( action = 'describeProduct',
- service = _options.service_id,
- product = _options.product_id
- )
- elif _options.size:
- query_options.insert( action = 'getSize',
- service = _options.service_id,
- product = _options.product_id
- )
- else:
- # synchronous/asynchronous mode
- if _options.sync:
- log.info('Synchronous mode set')
- query_options.insert( action = 'productdownload',
- scriptVersion = quote_plus(get_client_version()),
- mode = 'console',
- service = _options.service_id,
- product = _options.product_id
- )
- else:
- log.info('Asynchronous mode set')
- query_options.insert( action = 'productdownload',
- scriptVersion = quote_plus(get_client_version()),
- mode = 'status',
- service = _options.service_id,
- product = _options.product_id
- )
-
- # geographical parameters
- if _options.extraction_geographic:
- query_options.insert( x_lo = _options.longitude_min,
- x_hi = _options.longitude_max,
- y_lo = _options.latitude_min,
- y_hi = _options.latitude_max
- )
-
- if _options.extraction_vertical:
- query_options.insert( z_lo = _options.depth_min,
- z_hi = _options.depth_max
- )
-
- if _options.extraction_output:
- query_options.insert(output=_options.outputWritten)
- else:
- query_options.insert(output="netcdf")
-
- if _options.extraction_temporal:
- # date are strings, and they are send to Motu "as is". If not, we convert them into string
- if _options.date_min is not None or _options.date_min != None:
- date_min = _options.date_min
- if not isinstance(date_min, str):
- date_min = date_min.strftime(DATETIME_FORMAT)
- query_options.insert( t_lo = date_min )
-
- if _options.date_max is not None or _options.date_max != None:
- date_max = _options.date_max
- if not isinstance(date_max, str):
- date_max = date_max.strftime(DATETIME_FORMAT)
- query_options.insert( t_hi = date_max )
-
- variable = _options.variable
- if variable is not None:
- for i, opt in enumerate(variable):
- query_options.insert( variable = opt )
-
-
- if _options.console_mode or _options.out_dir.startswith("console") :
- query_options.insert(mode="console")
-
- return utils_http.encode(query_options)
-
-def check_options(_options):
- """function that checks the given options for coherency."""
-
- # Check Mandatory Options
- if (_options.auth_mode != AUTHENTICATION_MODE_NONE and
- _options.auth_mode != AUTHENTICATION_MODE_BASIC and
- _options.auth_mode != AUTHENTICATION_MODE_CAS):
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.invalid'] % (_options.auth_mode, 'auth-mode', [AUTHENTICATION_MODE_NONE, AUTHENTICATION_MODE_BASIC, AUTHENTICATION_MODE_CAS]))
-
- # if authentication mode is set we check both user & password presence
- if (_options.user == None and
- _options.auth_mode != AUTHENTICATION_MODE_NONE):
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory.user'] % ('user', _options.auth_mode))
-
- # check that if a user is set, a password should be set also
- if (_options.pwd == None and
- _options.user != None):
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory.password'] % ('pwd', _options.user))
-
- #check that if a user is set, an authentication mode should also be set
- if (_options.user != None and
- _options.auth_mode == AUTHENTICATION_MODE_NONE):
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory.mode'] % (AUTHENTICATION_MODE_NONE, 'auth-mode', _options.user))
-
- # those following parameters are required
- if _options.motu == None :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory'] % 'motu')
-
- if _options.service_id == None :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory'] % 'service-id')
-
- if _options.product_id == None :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory'] % 'product-id')
-
- if _options.out_dir == None :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.mandatory'] % 'out-dir')
-
- out_dir = _options.out_dir
- if not out_dir.startswith("console"):
- # check directory existence
- if not os.path.exists(out_dir):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.outdir-notexist'] % out_dir)
- # check whether directory is writable or not
- if not os.access(out_dir, os.W_OK):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.outdir-notwritable'] % out_dir)
-
- if _options.out_name == None :
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.mandatory'] % 'out-name')
-
- # Check PROXY Options
- _options.proxy = False
- if (_options.proxy_server != None) and (len(_options.proxy_server) != 0):
- _options.proxy = True
- # check that proxy server is a valid url
- url = _options.proxy_server
- p = re.compile('^(ftp|http|https):\/\/(\w+:{0,1}\w*@)?(\S+)(:[0-9]+)?(\/|\/([\w#!:.?+=&%@!\-\/]))?')
- m = p.match(url)
-
- if not m :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.not-url'] % ('proxy-server', url))
- # check that if proxy-user is defined then proxy-pwd shall be also, and reciprocally.
- if (_options.proxy_user != None) != ( _options.proxy_pwd != None ) :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.linked'] % ('proxy-user', 'proxy-name'))
-
-
- # Check VERTICAL Options
- _options.extraction_vertical = False
- if _options.depth_min != None or _options.depth_max != None :
- _options.extraction_vertical = True
-
- # Check TEMPORAL Options
- _options.extraction_temporal = False
- if _options.date_min != None or _options.date_max != None :
- _options.extraction_temporal = True
-
- #Check OUTPUT Options
- _options.extraction_output = False
- if _options.outputWritten != None :
- _options.extraction_output = True
-
- # Check GEOGRAPHIC Options
- _options.extraction_geographic = False
- if _options.latitude_min != None or _options.latitude_max != None or _options.longitude_min != None or _options.longitude_max != None :
- _options.extraction_geographic = True
- if( _options.latitude_min == None ):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.geographic-box'] % 'latitude_min')
-
- if( _options.latitude_max == None ):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.geographic-box'] % 'latitude_max')
-
- if( _options.longitude_min == None ):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.geographic-box'] % 'longitude_min')
-
- if( _options.longitude_max == None ):
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.option.geographic-box'] % 'longitude_max')
-
- tempvalue = float(_options.latitude_min)
- if tempvalue < -90 or tempvalue > 90 :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.out-of-range'] % ('latitude_min', str(tempvalue)))
- tempvalue = float(_options.latitude_max)
- if tempvalue < -90 or tempvalue > 90 :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.out-of-range'] % ('latitude_max', str(tempvalue)))
- tempvalue = float(_options.longitude_min)
- tempvalue = normalize_longitude(tempvalue)
- if tempvalue < -180 or tempvalue > 180 :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.out-of-range'] % ('logitude_min', str(tempvalue)))
- tempvalue = float(_options.longitude_max)
- tempvalue = normalize_longitude(tempvalue)
- if tempvalue < -180 or tempvalue > 180 :
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.option.out-of-range'] % ('longitude_max', str(tempvalue)))
-
-def normalize_longitude(lon):
- if lon > 180:
- while lon > 180:
- lon -= 360
- elif lon < -180:
- while lon < -180:
- lon += 360
- return lon
-
-def total_seconds(td):
- return total_milliseconds(td) / 10**3
-
-def total_milliseconds(td):
- return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 10**6) / 10**3
-
-def get_url_config(_options, data = None):
- # prepare arguments
- kargs = {}
- # proxy
- if _options.proxy:
- #proxyUrl = _options.proxy_server.partition(':')
- proxyUrl = urlparse(_options.proxy_server)
- kargs['proxy'] = { "scheme": proxyUrl.scheme,
- "netloc": proxyUrl.netloc }
- if _options.proxy_user != None:
- kargs['proxy']['user'] = _options.proxy_user
- kargs['proxy']['password'] = _options.proxy_pwd
- # authentication
- if _options.auth_mode == AUTHENTICATION_MODE_BASIC:
- kargs['authentication'] = { 'mode' : 'basic',
- 'user' : _options.user,
- 'password': _options.pwd }
- # headers
- kargs['headers'] = {"X-Client-Id" : get_client_artefact(),
- "X-Client-Version": quote_plus(get_client_version())}
- # data
- if data != None:
- kargs['data'] = data
-
- return kargs
-
-def get_requestUrl(dl_url, server, _options, **options):
- """ Get the request url."""
- stopWatch = stop_watch.localThreadStopWatch()
- start_time = datetime.datetime.now()
- stopWatch.start('get_request')
- log.info( "Requesting file to download (this can take a while)..." )
-
- # Get request id
- m = utils_http.open_url(dl_url, **options)
- responseStr = m.read()
- dom = minidom.parseString(responseStr)
- node = dom.getElementsByTagName('statusModeResponse')[0]
- status = node.getAttribute('status')
- if status == "2":
- msg = node.getAttribute('msg')
- log.error(msg)
- get_req_url = None
- else:
- requestId = node.getAttribute('requestId')
- # Get request url
- get_req_url = server + '?action=getreqstatus&requestid=' + requestId + "&service=" + _options.service_id + "&product=" + _options.product_id
-
- stopWatch.stop('get_request')
-
- return get_req_url
-
-def wait_till_finished(reqUrlCAS, **options):
- stopWatch = stop_watch.localThreadStopWatch()
- start_time = datetime.datetime.now()
-
-
-lastProgressPercentValue=0.0
-
-def dl_2_file(dl_url, fh, block_size = 65535, isADownloadRequest = None, **options):
- """ Download the file with the main url (of Motu) file.
-
- Motu can return an error message in the response stream without setting an
- appropriate http error code. So, in that case, the content-type response is
- checked, and if it is text/plain, we consider this as an error.
-
- dl_url: the complete download url of Motu
- fh: file handler to use to write the downstream"""
-
- stopWatch = stop_watch.localThreadStopWatch()
- start_time = datetime.datetime.now()
- lastProgressPercentValue=0.0
- log.info("Downloading file (this can take a while)..." )
-
- # download file
- temp = None
- if not fh.startswith("console"):
- temp = open(fh, 'w+b')
-
- try:
- stopWatch.start('processing')
-
- m = utils_http.open_url(dl_url, **options)
- try:
- # check the real url (after potential redirection) is not a CAS Url scheme
- match = re.search(utils_cas.CAS_URL_PATTERN, m.url)
- if match is not None:
- service, _, _ = dl_url.partition('?')
- redirection, _, _ = m.url.partition('?')
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.authentication.redirected'] % (service, redirection))
-
- # check that content type is not text/plain
- headers = m.info()
- if "Content-Type" in headers and len(headers['Content-Type']) > 0 and isADownloadRequest and (headers['Content-Type'].startswith('text') or headers['Content-Type'].find('html') != -1):
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.motu.error'] % m.read())
-
- log.info( 'File type: %s' % headers['Content-Type'] )
- # check if a content length (size of the file) has been send
- size = -1
- if "Content-Length" in headers:
- try:
- # it should be an integer
- size = int(headers["Content-Length"])
- log.info( 'File size: %s (%i B)' % (utils_unit.convert_bytes(size), size))
- except Exception as e:
- size = -1
- log.warn( 'File size is not an integer: %s' % headers["Content-Length"] )
- elif temp is not None:
- log.warn( 'File size: %s' % 'unknown' )
-
- processing_time = datetime.datetime.now();
- stopWatch.stop('processing')
- stopWatch.start('downloading')
-
- # performs the download
- log.info( 'Downloading file %s' % os.path.abspath(fh) )
-
- def progress_function(sizeRead):
- global lastProgressPercentValue
- percent = sizeRead*100./size
- if percent - lastProgressPercentValue> 1 or (lastProgressPercentValue != 100 and percent >= 100) :
- log.info( "- %s (%.1f%%)", utils_unit.convert_bytes(size).rjust(8), percent)
- lastProgressPercentValue = percent
-
- def none_function(sizeRead):
- global lastProgressPercentValue
- percent = 100
- log.info( "- %s (%.1f%%)", utils_unit.convert_bytes(size).rjust(8), percent)
- lastProgressPercentValue = percent
-
- if temp is not None:
- read = utils_stream.copy(m, temp, progress_function if size != -1 else none_function, block_size)
- else:
- if isADownloadRequest:
- #Console mode, only display the NC file URL on stdout
- read = len(m.url)
- print((m.url))
- else:
- import io
- output = io.StringIO()
- utils_stream.copy(m, output, progress_function if size != -1 else none_function, block_size)
- read = len(output.getvalue())
- print((output.getvalue()))
-
- end_time = datetime.datetime.now()
- stopWatch.stop('downloading')
-
- log.info( "Processing time : %s", str(processing_time - init_time) )
- log.info( "Downloading time : %s", str(end_time - processing_time) )
- log.info( "Total time : %s", str(end_time - init_time) )
- log.info( "Download rate : %s/s", utils_unit.convert_bytes((read / total_milliseconds(end_time - start_time)) * 10 ** 3))
- finally:
- m.close()
- finally:
- if temp is not None:
- temp.flush()
- temp.close()
-
- # raise exception if actual size does not match content-length header
- if temp is not None and size >= 0 and read < size:
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.download.too-short'] % (read, size))
-
-def execute_request(_options):
- """
- the main function that submit a request to motu. Available options are:
-
- * Proxy configuration (with eventually user credentials)
- - proxy_server: 'http://my-proxy.site.com:8080'
- - proxy_user : 'john'
- - proxy_pwd :'doe'
-
- * Autorisation mode: 'cas', 'basic', 'none'
- - auth_mode: 'cas'
-
- * User credentials for authentication 'cas' or 'basic'
- - user: 'john'
- - pwd: 'doe'
-
- * Motu service URL
- - motu: 'http://atoll-dev.cls.fr:30080/mis-gateway-servlet/Motu'
-
- * Dataset identifier to download
- - product_id: 'dataset-duacs-global-nrt-madt-merged-h'
-
- * Service identifier to use for retrieving dataset
- - service_id: 'http://purl.org/myocean/ontology/service/database#yourduname'
-
- * Geographic extraction parameters
- - latitude_max : 10.0
- - latitude_min : -10.0
- - longitude_max: -0.333333333369
- - longitude_min: 0.0
-
- * Vertical extraction parameters
- - depth_max: 1000
- - depth_min: 0
-
- * Temporal extraction parameters, as a datetime instance or a string (format: '%Y-%m-%d %H:%M:%S')
- - date_max: 2010-04-25 12:05:36
- - date_min: 2010-04-25
-
- * Variable extraction
- - variable: ['variable1','variable2']
-
- * The file name and the directory of the downloaded dataset
- - out_dir : '.'
- - out_name: 'dataset'
-
- * The block size used to perform download
- - block_size: 12001
-
- * The socket timeout configuration
- - socket_timeout: 515
-
- * The user agent to use when performing http requests
- - user_agent: 'motu-api-client'
-
- """
- global log
- global init_time
-
- init_time = datetime.datetime.now()
- stopWatch = stop_watch.localThreadStopWatch()
- stopWatch.start()
- try:
- log = logging.getLogger("motu_api")
-
- # at first, we check given options are ok
- check_options(_options)
-
- # print some trace info about the options set
- log.log(utils_log.TRACE_LEVEL, '-' * 60)
-
- for option in dir(_options):
- if not option.startswith('_'):
- log.log(utils_log.TRACE_LEVEL, "%s=%s" % (option, getattr(_options, option)))
-
- log.log(utils_log.TRACE_LEVEL, '-' * 60)
-
- # start of url to invoke
- url_service = _options.motu
-
- # parameters of the invoked service
- url_params = build_params(_options)
-
- url_config = get_url_config(_options)
-
- # check if question mark is in the url
- questionMark = '?'
- if url_service.endswith(questionMark) :
- questionMark = ''
- url = url_service+questionMark+url_params
-
- if _options.describe == True or _options.size == True:
- _options.out_name = _options.out_name.replace('.nc','.xml')
-
- # set-up the socket timeout if any
- if _options.socket_timeout != None:
- log.debug("Setting timeout %s" % _options.socket_timeout)
- socket.setdefaulttimeout(_options.socket_timeout)
-
- if _options.auth_mode == AUTHENTICATION_MODE_CAS:
- stopWatch.start('authentication')
- # perform authentication before acceding service
- download_url = utils_cas.authenticate_CAS_for_URL(url,
- _options.user,
- _options.pwd, **url_config)
- url_service = download_url.split("?")[0]
- stopWatch.stop('authentication')
- else:
- # if none, we do nothing more, in basic, we let the url requester doing the job
- download_url = url
-
- # create a file for storing downloaded stream
- fh = os.path.join(_options.out_dir,_options.out_name)
- if _options.console_mode:
- fh = "console"
-
- try:
- # Synchronous mode
- if _options.sync == True or _options.describe == True or _options.size == True:
- is_a_download_request=False
- if _options.describe == False and _options.size == False:
- is_a_download_request=True
- dl_2_file(download_url, fh, _options.block_size, is_a_download_request, **url_config)
- log.info( "Done" )
- # Asynchronous mode
- else:
- stopWatch.start('wait_request')
- requestUrl = get_requestUrl(download_url, url_service, _options, **url_config)
-
- if requestUrl != None:
- # asynchronous mode
- status = 0
- dwurl = ""
- msg = ""
-
- while True:
- if _options.auth_mode == AUTHENTICATION_MODE_CAS:
- stopWatch.start('authentication')
- # perform authentication before acceding service
- requestUrlCas = utils_cas.authenticate_CAS_for_URL(requestUrl,
- _options.user,
- _options.pwd, **url_config)
- stopWatch.stop('authentication')
- else:
- # if none, we do nothing more, in basic, we let the url requester doing the job
- requestUrlCas = requestUrl
-
-
- m = utils_http.open_url(requestUrlCas, **url_config)
- motu_reply=m.read()
- dom = minidom.parseString(motu_reply)
-
- for node in dom.getElementsByTagName('statusModeResponse'):
- status = node.getAttribute('status')
- dwurl = node.getAttribute('remoteUri')
- msg = node.getAttribute('msg')
-
- # Check status
- if status == "0" or status == "3": # in progress/pending
- log.info('Product is not yet available (request in progress)')
- time.sleep(10)
- else: # finished (error|success)
- break
-
- if status == "2":
- log.error(msg)
- if status == "1":
- log.info('The product is ready for download')
- if dwurl != "":
- dl_2_file(dwurl, fh, _options.block_size, not (_options.describe or _options.size), **url_config)
- log.info( "Done" )
- else:
- log.error("Couldn't retrieve file")
-
- stopWatch.stop('wait_request')
-
- except:
- try:
- if (os.path.isfile(fh)):
- os.remove(fh)
- except:
- pass
- raise
- finally:
- stopWatch.stop()
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/pom_version.py b/Forecast_tools/motuclient-python/motu_utils/pom_version.py
deleted file mode 100755
index 958faea73e10b84c6204d1b796bc404c6d9c5fd7..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/pom_version.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from xml.etree import ElementTree
-import os
-
-def getPOMVersion():
- version="Unknown"
- try:
- # For production tree, while run from cur folder
- abspath = os.path.abspath(__file__)
- dname = os.path.dirname(abspath)
- version = __getPOMVersion(os.path.join(dname, "..", "pom.xml") )
- except:
- # For development tree
- try:
- version = __getPOMVersion(os.path.join(dname, "..", "..", "pom.xml") )
- except :
- version = __getPOMVersion(os.path.join(dname, "..", "..", "..", "pom.xml") )
- finally:
- return version
-
-def __getPOMVersion(POM_FILE):
- namespaces = {'xmlns' : 'http://maven.apache.org/POM/4.0.0'}
- tree = ElementTree.parse(POM_FILE)
- root = tree.getroot()
- version = root.find("xmlns:version", namespaces=namespaces)
- return str(version.text)
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/stop_watch.py b/Forecast_tools/motuclient-python/motu_utils/stop_watch.py
deleted file mode 100755
index fe294f035972153e01c8d14cb6ebd40feb009e28..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/stop_watch.py
+++ /dev/null
@@ -1,107 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-from threading import Thread, local
-
-import time
-import threading
-
-# global stats
-tsl = local()
-
-class StopWatch(object):
- TIME = "time"
- GLOBAL = "global"
-
- def __init__(self):
- # contains the computed times
- self.times = {}
- # contains the current timers
- self.timers = {}
-
- def clear(self):
- self.timers = {}
- self.times = {}
-
- def start(self,label = GLOBAL):
- """Starts a new counter
- Returns the time the counter has been recorded.
- """
- self.timers[label] = self.__time()
- return self.timers[label]
-
- def stop(self,label=GLOBAL):
- """Stops the clock for the given counter.
- Returns the time at which the instance was stopped.
- """
- self.times[label] = self.elapsed(label)
- del self.timers[label]
-
- return self.times[label]
-
- def isRunning(self, label=GLOBAL):
- return label in self.timers
-
- def elapsed(self,label=GLOBAL):
- """The number of seconds since the current time that the StopWatch
- object was created. If stop() was called, it is the number
- of seconds from the instance creation until stop() was called.
- """
- t0 = self.times[label] if label in self.times else 0.
- t1 = self.timers[label] if label in self.timers else 0.
- t2 = self.__time() if label in self.timers else 0.
-
- return t0 + (t2 - t1)
-
- def getTimes(self):
- return self.times
-
- def __time(self):
- """Wrapper for time.time() to allow unit testing.
- """
- return time.time()
-
- def __str__(self):
- """Nicely format the elapsed time
- """
- keys = list(self.times.keys()) + [x for x in list(self.timers.keys()) if x not in list(self.times.keys())]
- txt = ""
- for key in keys:
- txt = txt + key + " : " + str(self.elapsed(key)) + " s " + ("(running)" if self.isRunning(key) else "(stopped)")+"\n"
- return txt
-
-def localThreadStopWatch():
- if not hasattr(tsl,'timer'):
- lock = threading.Lock()
- lock.acquire()
- try:
- if not hasattr(tsl,'timer'):
- tsl.timer = StopWatch()
- finally:
- lock.release()
- return tsl.timer
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_cas.py b/Forecast_tools/motuclient-python/motu_utils/utils_cas.py
deleted file mode 100755
index e59de858326b0fca28e290f869b48cbadd924b8c..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_cas.py
+++ /dev/null
@@ -1,152 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-import logging
-import re
-import sys
-
-
-if sys.version_info > (3, 0):
- import urllib.request, urllib.error
- from urllib.parse import parse_qs, urlparse, quote, quote_plus
-else:
- from urllib import quote_plus, quote
- from urlparse import urlparse, parse_qs
-
-from motu_utils import utils_http, utils_log, utils_html, utils_messages
-from motu_utils import utils_collection
-
-
-# pattern used to search for a CAS url within a response
-CAS_URL_PATTERN = '(.*)/login.*'
-
-def authenticate_CAS_for_URL(url, user, pwd, **url_config):
- """Performs a CAS authentication for the given URL service and returns
- the service url with the obtained credential.
-
- The following algorithm is done:
- 1) A connection is opened on the given URL
- 2) We check that the response is an HTTP redirection
- 3) Redirected URL contains the CAS address
- 4) We ask for a ticket for the given user and password
- 5) We ask for a service ticket for the given service
- 6) Then we return a new url with the ticket attached
-
- url: the url of the service to invoke
- user: the username
- pwd: the password"""
-
- log = logging.getLogger("utils_cas:authenticate_CAS_for_URL")
-
- server, sep, options = url.partition( '?' )
-
- log.info( 'Authenticating user %s for service %s' % (user,server) )
-
- connexion = utils_http.open_url(url, **url_config)
-
- # connexion response code must be a redirection, else, there's an error (user can't be already connected since no cookie or ticket was sent)
- if connexion.url == url:
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.authentication.not-redirected'] % server)
-
- # find the cas url from the redirected url
- redirected_url = connexion.url
- p = parse_qs(urlparse(connexion.url).query, keep_blank_values=False)
- redirectServiceUrl = p['service'][0]
-
-
- m = re.search(CAS_URL_PATTERN, redirected_url)
-
- if m is None:
- raise Exception(
- utils_messages.get_external_messages()['motuclient.exception.authentication.unfound-url'] % redirected_url)
-
- url_cas = m.group(1) + '/v1/tickets'
-
- opts = utils_http.encode(utils_collection.ListMultimap(username = quote(user), password = quote(pwd)))
-
- utils_log.log_url(log, "login user into CAS:\t", url_cas + '?' + opts)
- url_config['data']=opts.encode()
- try:
- connexion = utils_http.open_url(url_cas, **url_config)
- except Exception as e:
- if e.code == 400:
- log.error( """Error: Bad user login or password:
-
- On *nix OS, you must use the single quote, otherwise it may expand specific characters.
- [...] -u 'string' or --user 'string' [...]
-
- On Windows OS, you must use the double quote, because single quotes are treated literally.
- [...] -p "string" or --pwd "string" [...]
- """)
-
- raise e
-
- fp = utils_html.FounderParser()
- for line in connexion:
- log.log(utils_log.TRACE_LEVEL, 'utils_html.FounderParser() line: %s', line)
- # py3 compatibility
- if (isinstance(line, bytes)):
- fp.feed(line.decode())
- else:
- fp.feed(line)
-
- tgt = fp.action_[fp.action_.rfind('/') + 1:]
- log.log(utils_log.TRACE_LEVEL, 'TGT: %s', tgt)
-
- # WARNING : don't use 'fp.action_' as url : it seems protocol is always http never https
- # use 'url_cas', extract TGT from 'fp.action_' , then construct url_ticket.
- # url_ticket = fp.action_
- url_ticket = url_cas + '/' + tgt
-
- if url_ticket is None:
- raise Exception(utils_messages.get_external_messages()['motuclient.exception.authentication.tgt'])
-
- utils_log.log_url(log, "found url ticket:\t", url_ticket)
-
- opts = utils_http.encode(utils_collection.ListMultimap(service = quote_plus(redirectServiceUrl)))
-
- utils_log.log_url(log, 'Granting user for service\t', url_ticket + '?' + opts)
- url_config['data']=opts.encode()
-
- ticket = utils_http.open_url(url_ticket, **url_config).readline()
-
- # py3 compatibility
- if (isinstance(ticket, bytes)):
- ticket = ticket.decode()
-
- utils_log.log_url(log, "found service ticket:\t", ticket)
-
- # we append the download url with the ticket and return the result
- service_url = redirectServiceUrl + '&ticket=' + ticket
-
- utils_log.log_url(log, "service url is:\t", service_url)
-
- return service_url
-
-
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_collection.py b/Forecast_tools/motuclient-python/motu_utils/utils_collection.py
deleted file mode 100755
index ab2792551b691afc7b956f1f3ee54ed5782b8a29..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_collection.py
+++ /dev/null
@@ -1,110 +0,0 @@
-"""
-The multimap data structure associates multiple values to a key.
-
-In this module the multimap is implemented by a dictionary in which each key is
-associated to a container, which can be a list, a dictionary, or a set.
-
-These containers are created, accessed, and extended using the usual array
-notation, e.g. m["a"] = 1, m["a"] = 2 creates a container for key "a"
-containing 1 and 2. An item within a container can be removed using the
-"remove" method.
-
-Requires Python 2.7.
-"""
-
-import collections
-
-class Map(object):
- """ Map wraps a dictionary. It is essentially an abstract class from which
- specific multimaps are subclassed. """
- def __init__(self):
- self._dict = {}
-
- def __repr__(self):
- return "%s(%s)" % (self.__class__.__name__, repr(self._dict))
-
- __str__ = __repr__
-
- def __getitem__(self, key):
- return self._dict[key]
-
- def __setitem__(self, key, value):
- self._dict[key] = value
-
- def __delitem__(self, key):
- del self._dict[key]
-
- def insert(self, **values):
- for k, v in values.items():
- self.__setitem__(k, v)
-
- def remove(self, key, value):
- del self._dict[key]
-
- def dict(self):
- """ Allows access to internal dictionary, if necessary. Caution: multimaps
- will break if keys are not associated with proper container."""
- return self._dict
-
-class ListMultimap(Map):
- """ ListMultimap is based on lists and allows multiple instances of same value. """
- def __init__(self, **values):
- self._dict = collections.defaultdict(list)
- self.insert(**values)
-
- def __setitem__(self, key, value):
- self._dict[key].append(value)
-
- def remove(self, key, value):
- self._dict[key].remove(value)
-
-class SetMultimap(Map):
- """ SetMultimap is based on sets and prevents multiple instances of same value. """
- def __init__(self):
- self._dict = collections.defaultdict(set)
-
- def __setitem__(self, key, value):
- self._dict[key].add(value)
-
- def remove(self, key, value):
- self._dict[key].remove(value)
-
-class DictMultimap(Map):
- """ DictMultimap is based on dicts and allows fast tests for membership. """
- def __init__(self):
- self._dict = collections.defaultdict(dict)
-
- def __setitem__(self, key, value):
- self._dict[key][value] = True
-
- def remove(self, key, value):
- del self._dict[key][value]
-
-def test():
- def test_multimap(m):
- print("__________________________________")
- print(m["a"])
- m["a"] = 1
- m["a"] = 2
- m["a"] = 2
- m["a"] = 3
- m["a"] = 4
- m.insert( b = 'v1', c = 'v2' )
- print(m)
- m.remove("a", 4)
- print(m)
- print(("a" in m.dict()))
- print(m["a"])
- m["a"] = 5
- m["b"] = 6
- print(m)
- del m["b"]
- print(m)
- print((3 in m["a"]))
-
- test_multimap(ListMultimap())
- test_multimap(SetMultimap())
- test_multimap(DictMultimap())
-
-if __name__ == "__main__":
- test()
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_configpath.py b/Forecast_tools/motuclient-python/motu_utils/utils_configpath.py
deleted file mode 100755
index 607a86885852bb2ea7c1d6ca700f15d0916bedfd..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_configpath.py
+++ /dev/null
@@ -1,20 +0,0 @@
-import sys
-import os
-
-MOTU_CLIENT_CONFIG_PATH = os.path.join("motu_utils", "cfg")
-LINUX_CONFIG_PATH = os.path.join("/usr", "local", MOTU_CLIENT_CONFIG_PATH)
-WINDOWS_CONFIG_PATH = os.path.join(sys.prefix, MOTU_CLIENT_CONFIG_PATH)
-VIT_ENV_CONFIG_PATH = MOTU_CLIENT_CONFIG_PATH
-LOCAL_CONFIG_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "motu_utils", "cfg")
-
-def getConfigPath():
- if os.path.isdir(LINUX_CONFIG_PATH):
- return LINUX_CONFIG_PATH
- elif os.path.isdir(WINDOWS_CONFIG_PATH):
- return WINDOWS_CONFIG_PATH
- elif os.path.isdir(LOCAL_CONFIG_PATH):
- return LOCAL_CONFIG_PATH
- elif os.path.isdir(VIT_ENV_CONFIG_PATH):
- return VIT_ENV_CONFIG_PATH
- else:
- return ""
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_html.py b/Forecast_tools/motuclient-python/motu_utils/utils_html.py
deleted file mode 100755
index 6d6976d1b188aceef2be62c3055b50d2d53c41ad..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_html.py
+++ /dev/null
@@ -1,48 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-import sys
-if sys.version_info > (3, 0):
- from html.parser import HTMLParser
-else:
- from HTMLParser import HTMLParser
-
-
-
-class FounderParser(HTMLParser):
- """
- Parser witch found the form/action section an return it
- """
- def __init__(self, *args, **kargs):
- HTMLParser.__init__(self, *args, **kargs)
- self.action_ = None
-
- def handle_starttag(self, tag, attrs):
- d = dict(attrs)
- if tag == 'form' and 'action' in d:
- self.action_ = d['action']
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_http.py b/Forecast_tools/motuclient-python/motu_utils/utils_http.py
deleted file mode 100755
index d3ab68c99be7f98df986447368934c16fe7d0023..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_http.py
+++ /dev/null
@@ -1,181 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-import sys
-
-
-if sys.version_info > (3, 0):
- import urllib.request, urllib.error
- from urllib.request import HTTPCookieProcessor, Request
- from urllib.request import HTTPSHandler, HTTPHandler, install_opener, build_opener, \
- HTTPRedirectHandler, ProxyHandler, HTTPBasicAuthHandler, HTTPPasswordMgrWithDefaultRealm
- from urllib.request import HTTPErrorProcessor as HTTPErrorProcessor_
- from http.client import HTTPConnection, HTTPSConnection
- from http.cookiejar import CookieJar
-else:
- from httplib import HTTPConnection, HTTPSConnection
- from urllib2 import HTTPSHandler, install_opener, build_opener, \
- HTTPRedirectHandler, HTTPRedirectHandler, ProxyHandler, HTTPBasicAuthHandler, \
- HTTPPasswordMgrWithDefaultRealm, HTTPCookieProcessor, HTTPSHandler, HTTPHandler, Request
- from urllib2 import HTTPErrorProcessor as HTTPErrorProcessor_
- from cookielib import CookieJar
-
-from motu_utils import utils_log
-import logging
-import ssl
-import socket
-
-
-class TLS1v2Connection(HTTPSConnection):
- """Like HTTPSConnection but more specific"""
- def __init__(self, host, **kwargs):
- HTTPSConnection.__init__(self, host, **kwargs)
-
- def connect(self):
- """Overrides HTTPSConnection.connect to specify TLS version"""
- # Standard implementation from HTTPSConnection, which is not
- # designed for extension, unfortunately
- sock = socket.create_connection((self.host, self.port),
- self.timeout, self.source_address)
- if getattr(self, '_tunnel_host', None):
- self.sock = sock
- self._tunnel()
-
- # This is the only difference; default wrap_socket uses SSLv23
- self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file,
- ssl_version=ssl.PROTOCOL_TLSv1_2)
-
-class TLS1v2Handler(HTTPSHandler):
- """Like HTTPSHandler but more specific"""
- def __init__(self):
- HTTPSHandler.__init__(self)
-
- def https_open(self, req):
- return self.do_open(TLS1v2Connection, req)
-
-# Overide default handler
-install_opener(build_opener(TLS1v2Handler()))
-
-
-class HTTPErrorProcessor(HTTPErrorProcessor_):
- def https_response(self, request, response):
- # Consider error codes that are not 2xx (201 is an acceptable response)
- code, msg, hdrs = response.code, response.msg, response.info()
- if code >= 300:
- response = self.parent.error('http', request, response, code, msg, hdrs)
- return response
-
-
-class SmartRedirectHandler(HTTPRedirectHandler):
-
- def http_error_302(self, req, fp, code, msg, headers):
- result = HTTPRedirectHandler.http_error_302(
- self, req, fp, code, msg, headers)
- result.status = code
- return result
-
-
-def open_url(url, **kargsParam):
- """open an url and return an handler on it.
- arguments can be :
- headers : http headers to send
- headers = {"Accept": "text/plain",
- "User-Agent": "a user agent"
- }
-
- proxy : the proxy to use when connecting to the url
- proxy = { "url": "http://aproxy.server",
- "port": 8080,
- "user": "username",
- "password": "userpassword"
- }
-
- authentication: the authentication information
- authentication = { "mode": "basic",
- "user": "username",
- "password": "password" }
- """
- data = None
- log = logging.getLogger("utils_http:open_url")
- kargs = kargsParam.copy()
- # common handlers
- handlers = [SmartRedirectHandler(),
- HTTPCookieProcessor(CookieJar()),
- HTTPHandler(),
- TLS1v2Handler(),
- utils_log.HTTPDebugProcessor(log),
- HTTPErrorProcessor()
- ]
-
- # add handlers for managing proxy credentials if necessary
- if 'proxy' in kargs:
- urlProxy = ''
- if 'user' in kargs['proxy']:
- urlProxy = kargs['proxy']['user'] + ':' + kargs['proxy']['password'] + '@'
-
- urlProxy += kargs['proxy']['netloc']
-
- handlers.append( ProxyHandler({'http':urlProxy, 'https':urlProxy}) )
- handlers.append( HTTPBasicAuthHandler() )
-
- del kargs['proxy']
-
- if 'authentication' in kargs:
- # create the password manager
- #password_mgr = HTTPPasswordMgrWithDefaultRealm(ssl_version=ssl.PROTOCOL_TLSv1)
- password_mgr = HTTPPasswordMgrWithDefaultRealm()
- urlPart = url.partition('?')
- password_mgr.add_password(None, urlPart, kargs['authentication']['user'], kargs['authentication']['password'])
- # add the basic authentication handler
- handlers.append(HTTPSHandler(password_mgr))
- del kargs['authentication']
-
- if 'data' in kargs:
- data = kargs['data']
- del kargs['data']
-
- _opener = build_opener(*handlers)
- log.log(utils_log.TRACE_LEVEL, 'list of handlers:')
- for h in _opener.handlers:
- log.log(utils_log.TRACE_LEVEL, ' . %s', str(h))
-
- # create the request
- if( data != None ):
- r = Request(url, data, **kargs)
- else:
- r = Request(url, **kargs)
-
- # open the url, but let the exception propagates to the caller
- return _opener.open(r)
-
-def encode(options):
- opts = []
- for k, vset in options.dict().items():
- for v in vset:
- opts.append('%s=%s' % (str(k), str(v).replace('#','%23').replace(' ','%20')))
- return '&'.join(opts)
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_log.py b/Forecast_tools/motuclient-python/motu_utils/utils_log.py
deleted file mode 100755
index 0457164d9626ac1602d653d0af203f03eb662149..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_log.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-
-import sys
-if sys.version_info > (3, 0):
- import urllib.request, urllib.error
- from urllib.request import BaseHandler
- from urllib.parse import unquote
-else:
-
- from urllib2 import BaseHandler
- from urllib2 import unquote
-
-
-
-import logging
-
-# trace level
-TRACE_LEVEL = 1
-
-def log_url(log, message, url, level = logging.DEBUG ):
- """Nicely logs the given url.
-
- Print out the url with the first part (protocol, host, port, authority,
- user info, path, ref) and in sequence all the query parameters.
-
- log: the log into which write the message
- message: a message to print before the url
- url: the url to log
- level: (optional) the log level to use"""
-
- urls = url.split('?')
- log.log( level, message + unquote(urls[0]) )
- if len(urls) > 1:
- for a in sorted(urls[1].split('&')):
- param = a.split('=')
- if( len(param) < 2 ):
- param.append('')
- log.log( level, ' . %s = %s', unquote(param[0]), unquote(param[1]) )
-
-
-class HTTPDebugProcessor(BaseHandler):
- """ Track HTTP requests and responses with this custom handler.
- """
- def __init__(self, log, log_level=TRACE_LEVEL):
- self.log_level = log_level
- self.log = log
-
- def http_request(self, request):
- host, full_url = request.host, request.get_full_url()
- url_path = full_url[full_url.find(host) + len(host):]
- log_url ( self.log, "Requesting: ", request.get_full_url(), TRACE_LEVEL )
- self.log.log(self.log_level, "%s %s" % (request.get_method(), url_path))
-
- for header in request.header_items():
- self.log.log(self.log_level, " . %s: %s" % header[:])
-
- return request
-
- def http_response(self, request, response):
- code, msg, headers = response.code, response.msg, response.info().items()
- self.log.log(self.log_level, "Response:")
- self.log.log(self.log_level," HTTP/1.x %s %s" % (code, msg))
-
- for key, value in headers:
- self.log.log(self.log_level, " . %s: %s" % (key, value))
-
- return response
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_messages.py b/Forecast_tools/motuclient-python/motu_utils/utils_messages.py
deleted file mode 100755
index 1878288ff25384cb06004a996eabd6c2457e7c6b..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_messages.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-from motu_utils import utils_configpath
-import os, sys
-_messages = None
-
-MESSAGES_FILE = utils_configpath.getConfigPath() + '/messages.properties'
-
-
-def _process_content(content):
- propDict = dict()
- for propLine in content:
- propDef = propLine.strip()
- if len(propDef) == 0:
- continue
- if propDef[0] in ('!', '#'):
- continue
- punctuation = [propDef.find(c) for c in ':= '] + [len(propDef)]
- found = min([pos for pos in punctuation if pos != -1])
- name = propDef[:found].rstrip()
- value = propDef[found:].lstrip(":= ").rstrip()
- propDict[name] = value
-
- _messages = propDict
- return _messages
-
-
-def _process_file_py3(path):
- with open(path) as propFile:
- return _process_content(propFile.readlines())
-
-
-def _process_file_py2(path):
- propFile = file(path, "rU")
- processed_content = _process_content(propFile)
- propFile.close()
- return processed_content
-
-
-def get_external_messages():
- """Return a table of externalized messages.
-
- The table is lazzy instancied (loaded once when called the first time)."""
- global _messages
- if _messages is None:
- if sys.version_info > (3, 0):
- return _process_file_py3(MESSAGES_FILE)
- return _process_file_py2(MESSAGES_FILE)
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_stream.py b/Forecast_tools/motuclient-python/motu_utils/utils_stream.py
deleted file mode 100755
index 27680c66a75ce09d5abbfa95ff1693e7c44b4619..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_stream.py
+++ /dev/null
@@ -1,66 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-import io, sys
-
-def copy(sourceHandler, destHandler, callback = None, blockSize = 65535 ):
- """Copy the available content through the given handler to another one. Process
- can be monitored with the (optional) callback function.
-
- sourceHandler: the handler through witch downloading content
- destHandler: the handler into which writing data
- callback: the callback function called for each block read. Signature: f: sizeRead -> void
- blockSize: the size of the block used to read data
-
- returns the total size read
- """
- read = 0
- while 1:
- block = sourceHandler.read(blockSize)
- exit_condition = ''
- if(isinstance(block, bytes)):
- exit_condition = b''
- if block == exit_condition:
- break
- read += len(block)
- try:
- if type(destHandler) == io.StringIO:
- strBlock=str(block)
- if sys.version_info > (3, 0):
- destHandler.write( str(block, 'utf-8') )
- else:
- destHandler.write( unicode(block, 'utf-8') )
- else:
- destHandler.write(block)
- except Exception as inst:
- print(type(inst)) # the exception instance
- print(inst.args) # arguments stored in .args
- print(inst)
-
- callback(read)
-
- return read
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motu_utils/utils_unit.py b/Forecast_tools/motuclient-python/motu_utils/utils_unit.py
deleted file mode 100755
index 60a9142440e218eeb20d6057263240f3005b1838..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motu_utils/utils_unit.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-# SI unit prefixes
-SI_K, SI_M, SI_G, SI_T = 10 ** 3, 10 ** 6, 10 ** 9, 10 ** 12
-
-def convert_bytes(n):
- """Converts the given bytes into a string with the most appropriate
- unit power.
-
- Note that prefixes like M, G, T are power of 10 (ISO/IEC 80000-13:2008) and
- not power of 2."""
- if n >= SI_T:
- return '%.1f TB' % (float(n) / SI_T)
- elif n >= SI_G:
- return '%.1f GB' % (float(n) / SI_G)
- elif n >= SI_M:
- return '%.1f MB' % (float(n) / SI_M)
- elif n >= SI_K:
- return '%.1f kB' % (float(n) / SI_K)
- else:
- return '%d B' % n
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/motuclient.py b/Forecast_tools/motuclient-python/motuclient.py
deleted file mode 100755
index 35e6b52f027c8555d9b9cf6317727e04198043c1..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/motuclient.py
+++ /dev/null
@@ -1,329 +0,0 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Python motu client
-#
-# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
-# Data Dissemination.
-#
-# http://cls-motu.sourceforge.net/
-#
-# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
-# http://www.cls.fr - and Contributors
-#
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation; either version 2.1 of the License, or
-# (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-# License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
-
-
-import sys
-from cgi import log
-if sys.version_info > (3, 0):
- import urllib
- import configparser as ConfigParser
-else:
- import urllib2 as urllib
- import ConfigParser
-
-import traceback
-import platform
-import sys
-import os
-import datetime
-import logging
-import logging.config
-
-import optparse
-from motu_utils import utils_configpath
-
-# error code to use when exiting after exception catch
-ERROR_CODE_EXIT=1
-
-# the config file to load from
-CFG_FILE = '~/motuclient/motuclient-python.ini'
-LOG_CFG_FILE = './motu_utils/cfg/log.ini'
-
-SECTION = 'Main'
-
-# shared logger
-log = None
-
-# shared variables to download
-_variables = []
-
-# project libraries path
-LIBRARIES_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'motu_utils')
-# Manage imports of project libraries
-if not os.path.exists(LIBRARIES_PATH):
- sys.stderr.write('\nERROR: can not find project libraries path: %s\n\n' % os.path.abspath(LIBRARIES_PATH))
- sys.exit(1)
-sys.path.append(LIBRARIES_PATH)
-
-# Import project libraries
-import utils_log
-import utils_messages
-import motu_api
-
-def get_client_version():
- """Return the version (as a string) of this client.
-
- The value is automatically set by the maven processing build, so don't
- touch it unless you know what you are doing."""
- return motu_api.get_client_version()
-
-def get_client_artefact():
- """Return the artifact identifier (as a string) of this client.
-
- The value is automatically set by the maven processing build, so don't
- touch it unless you know what you are doing."""
- return motu_api.get_client_artefact()
-
-def load_options():
- """load options to handle"""
-
- _options = None
-
- # create option parser
- parser = optparse.OptionParser(version=get_client_artefact() + ' v' + get_client_version())
-
- # add available options
- parser.add_option( '--quiet', '-q',
- help = "prevent any output in stdout",
- action = 'store_const',
- const = logging.WARN,
- dest='log_level')
-
- parser.add_option( '--verbose',
- help = "print information in stdout",
- action='store_const',
- const = logging.DEBUG,
- dest='log_level')
-
- parser.add_option( '--noisy',
- help = "print more information (traces) in stdout",
- action='store_const',
- const = utils_log.TRACE_LEVEL,
- dest='log_level')
-
- parser.add_option( '--user', '-u',
- help = "the user name (string)")
-
- parser.add_option( '--pwd', '-p',
- help = "the user password (string)")
-
- parser.add_option( '--auth-mode',
- default = motu_api.AUTHENTICATION_MODE_CAS,
- help = "the authentication mode: '" + motu_api.AUTHENTICATION_MODE_NONE +
- "' (for no authentication), '"+ motu_api.AUTHENTICATION_MODE_BASIC +
- "' (for basic authentication), or '"+motu_api.AUTHENTICATION_MODE_CAS +
- "' (for Central Authentication Service) [default: %default]")
-
- parser.add_option( '--proxy-server',
- help = "the proxy server (url)")
-
- parser.add_option( '--proxy-user',
- help = "the proxy user (string)")
-
- parser.add_option( '--proxy-pwd',
- help = "the proxy password (string)")
-
- parser.add_option( '--motu', '-m',
- help = "the motu server to use (url)")
-
- parser.add_option( '--service-id', '-s',
- help = "The service identifier (string)")
-
- parser.add_option( '--product-id', '-d',
- help = "The product (data set) to download (string)")
-
- parser.add_option( '--date-min', '-t',
- help = "The min date with optional hour resolution (string following format YYYY-MM-DD [HH:MM:SS])")
-
- parser.add_option( '--date-max', '-T',
- help = "The max date with optional hour resolution (string following format YYYY-MM-DD [HH:MM:SS])",
- default = datetime.date.today().isoformat())
-
- parser.add_option( '--latitude-min', '-y',
- type = 'float',
- help = "The min latitude (float in the interval [-90 ; 90])")
-
- parser.add_option( '--latitude-max', '-Y',
- type = 'float',
- help = "The max latitude (float in the interval [-90 ; 90])")
-
- parser.add_option( '--longitude-min', '-x',
- type = 'float',
- help = "The min longitude (float in the interval [-180 ; 180])")
-
- parser.add_option( '--longitude-max', '-X',
- type = 'float',
- help = "The max longitude (float in the interval [-180 ; 180])")
-
- parser.add_option( '--depth-min', '-z',
- type = 'string',
- help = "The min depth (float in the interval [0 ; 2e31] or string 'Surface')")
-
- parser.add_option( '--depth-max', '-Z',
- type = 'string',
- help = "The max depth (float in the interval [0 ; 2e31] or string 'Surface')")
-
- parser.add_option( '--variable', '-v',
- help = "The variable (list of strings)",
- callback=option_callback_variable,
- dest="variable",
- type="string",
- action="callback")
-
- parser.add_option( '--sync-mode', '-S',
- help = "Sets the download mode to synchronous (not recommended)",
- action='store_true',
- dest='sync')
-
- parser.add_option( '--describe-product', '-D',
- help = "Get all updated information on a dataset. Output is in XML format",
- action='store_true',
- dest='describe')
-
- parser.add_option( '--size',
- help = "Get the size of an extraction. Output is in XML format",
- action='store_true',
- dest='size')
-
- parser.add_option( '--out-dir', '-o',
- help = "The output dir where result (download file) is written (string). If it starts with 'console', behaviour is the same as with --console-mode. ",
- default=".")
-
- parser.add_option( '--out-name', '-f',
- help = "The output file name (string)",
- default="data.nc")
-
- parser.add_option( '--block-size',
- type = 'int',
- help = "The block used to download file (integer expressing bytes)",
- default="65536")
-
- parser.add_option( '--socket-timeout',
- type = 'float',
- help = "Set a timeout on blocking socket operations (float expressing seconds)")
- parser.add_option( '--user-agent',
- help = "Set the identification string (user-agent) for HTTP requests. By default this value is 'Python-urllib/x.x' (where x.x is the version of the python interpreter)")
-
- parser.add_option( '--outputWritten',
- help = "Optional parameter used to set the format of the file returned by the download request: netcdf or netcdf4. If not set, netcdf is used.")
-
- parser.add_option( '--console-mode',
- help = "Optional parameter used to display result on stdout, either URL path to download extraction file, or the XML content of getSize or describeProduct requests.",
- action='store_true',
- dest='console_mode')
-
- parser.add_option( '--config-file',
- help = "Path of the optional configuration file [default: %s]" % CFG_FILE,
- action='append',
- dest="config_file",
- type="string")
-
- # create config parser
- conf_parser = ConfigParser.ConfigParser()
-
- # read configuration file name from cli arguments or use default
- # cant set default in parser.add_option due to optparse/argparse bug:
- # https://bugs.python.org/issue16399
- config_file = parser.parse_args()[0].config_file
- if config_file is None:
- config_file = [CFG_FILE]
- config_file=[os.path.expanduser(x) for x in config_file]
- conf_parser.read(config_file)
-
- # set default values by picking from the configuration file
- default_values = {}
- default_variables = []
- for option in parser.option_list:
- if (option.dest != None) and conf_parser.has_option(SECTION, option.dest):
- if option.dest == "variable":
- variablesInCfgFile = conf_parser.get(SECTION, option.dest)
- if (not variablesInCfgFile is None) and variablesInCfgFile.strip():
- allVariablesArray = variablesInCfgFile.split(",")
- default_variables = default_variables + allVariablesArray
- default_values[option.dest] = default_variables
- else:
- default_values[option.dest] = conf_parser.get(SECTION, option.dest)
-
- parser.set_defaults( **default_values )
-
- return parser.parse_args()
-
-def option_callback_variable(option, opt, value, parser):
- global _variables
- _variables.append(value)
- setattr(parser.values, option.dest, _variables)
-
-
-def initLogger():
- logging.addLevelName(utils_log.TRACE_LEVEL, 'TRACE')
- logging.config.fileConfig( os.path.join(os.path.dirname(__file__),LOG_CFG_FILE) )
- global log
- log = logging.getLogger(__name__)
-
- logging.getLogger().setLevel(logging.INFO)
-#===============================================================================
-# The Main function
-#===============================================================================
-def main():
- start_time = datetime.datetime.now()
-
- initLogger()
-
- try:
- # we prepare options we want
- (_options, args) = load_options()
-
- if _options.log_level != None:
- logging.getLogger().setLevel(int(_options.log_level))
-
- motu_api.execute_request(_options)
- except Exception as e:
- log.error( "Execution failed: %s", e )
- if hasattr(e, 'reason'):
- log.info( ' . reason: %s', e.reason )
- if hasattr(e, 'code'):
- log.info( ' . code %s: ', e.code )
- if hasattr(e, 'read'):
- log.log( utils_log.TRACE_LEVEL, ' . detail:\n%s', e.read() )
-
- log.debug( '-'*60 )
- log.debug( "Stack trace exception is detailed herafter:" )
- exc_type, exc_value, exc_tb = sys.exc_info()
- x = traceback.format_exception(exc_type, exc_value, exc_tb)
- for stack in x:
- log.debug( ' . %s', stack.replace('\n', '') )
- log.debug( '-'*60 )
- log.log( utils_log.TRACE_LEVEL, 'System info is provided hereafter:' )
- system, node, release, version, machine, processor = platform.uname()
- log.log( utils_log.TRACE_LEVEL, ' . system : %s', system )
- log.log( utils_log.TRACE_LEVEL, ' . node : %s', node )
- log.log( utils_log.TRACE_LEVEL, ' . release : %s', release )
- log.log( utils_log.TRACE_LEVEL, ' . version : %s', version )
- log.log( utils_log.TRACE_LEVEL, ' . machine : %s', machine )
- log.log( utils_log.TRACE_LEVEL, ' . processor: %s', processor )
- log.log( utils_log.TRACE_LEVEL, ' . python : %s', sys.version )
- log.log( utils_log.TRACE_LEVEL, ' . client : %s', get_client_version() )
- log.log( utils_log.TRACE_LEVEL, '-'*60 )
-
- sys.exit(ERROR_CODE_EXIT)
-
- finally:
- log.debug( "Elapsed time : %s", str(datetime.datetime.now() - start_time) )
-
-if __name__ == '__main__':
- main()
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/pom.xml b/Forecast_tools/motuclient-python/pom.xml
deleted file mode 100755
index fb4c1380e70371ebd04b0de5f3c8c9017a72a473..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/pom.xml
+++ /dev/null
@@ -1,83 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>cls.atoll.motu.client</groupId>
- <artifactId>motuclient-python</artifactId>
- <version>1.8.4</version>
- <packaging>pom</packaging>
-
- <name>Motu Client Python</name>
- <description>This package holds the python scripts used to address Motu servers for ordering, extracting and
- downloading oceanographic data.
- </description>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- </properties>
-
- <build>
- <scriptSourceDirectory>${basedir}/src</scriptSourceDirectory>
- <testSourceDirectory>${basedir}/bin</testSourceDirectory>
- <outputDirectory>${basedir}/bin</outputDirectory>
- <testOutputDirectory>${basedir}/bin</testOutputDirectory>
- <plugins>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <version>2.4</version>
- <configuration>
- <finalName>${project.artifactId}-${project.version}-${build-timestamp}</finalName>
- <descriptors>
- <descriptor>${basedir}/assembly/bin.xml</descriptor>
- <descriptor>${basedir}/assembly/src.xml</descriptor>
- </descriptors>
- </configuration>
- <executions>
- <execution>
- <id>make-assembly</id>
- <phase>package</phase>
- <goals>
- <goal>single</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- <!-- Used to build a "build-timestamp" property, this property could be overridden by ANT calls from /motu-distribution/build.xml -->
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>buildnumber-maven-plugin</artifactId>
- <version>1.4</version>
- <configuration>
- <revisionOnScmFailure>no.scm.config.in.pom</revisionOnScmFailure>
- </configuration>
- <executions>
- <execution>
- <id>create-timestamp-id</id>
- <phase>validate</phase>
- <goals>
- <goal>create-timestamp</goal>
- </goals>
- <configuration>
- <timestampFormat>yyyyMMddHHmmssSSS</timestampFormat>
- <timestampPropertyName>build-timestamp</timestampPropertyName>
- <!-- formats the timestamp all together like 2016-04-04 14:17:05.123
- and puts it in the ${myBuildNumberVariable} buildProperty -->
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
-
- <organization>
- <name>CLS (Collecte Localisation Satelite)</name>
- <url>http://www.cls.fr</url>
- </organization>
-
- <licenses>
- <license>
- <name>GNU Lesser General Public License (LGPL)</name>
- <url>http://www.gnu.org/licenses/lgpl.html</url>
- <distribution>repo</distribution>
- <comments>A business-friendly Open Source license</comments>
- </license>
- </licenses>
-</project>
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/setup.cfg b/Forecast_tools/motuclient-python/setup.cfg
deleted file mode 100755
index a2f3748e2ae31f02aaef0168927480f8fae39a27..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[metadata]
-description-file = README.md
\ No newline at end of file
diff --git a/Forecast_tools/motuclient-python/setup.py b/Forecast_tools/motuclient-python/setup.py
deleted file mode 100755
index b0fab61c4aa10b415d7570a8d0c3a7b319bdad81..0000000000000000000000000000000000000000
--- a/Forecast_tools/motuclient-python/setup.py
+++ /dev/null
@@ -1,61 +0,0 @@
-import os
-import sys
-
-from setuptools import setup, find_packages
-
-# project libraries path
-LIBRARIES_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'src', 'python')
-
-# Manage imports of project libraries
-if not os.path.exists(LIBRARIES_PATH):
- sys.stderr.write('\nERROR: can not find project libraries path: %s\n\n' % os.path.abspath(LIBRARIES_PATH))
- sys.exit(1)
-sys.path.append(LIBRARIES_PATH)
-
-from motu_utils import pom_version
-
-setup(
- name='motuclient',
- version=pom_version.getPOMVersion(),
- python_requires='>=2.7',
- description='Extract and download gridded data through a python command line from Motu web server. Used in CMEMS context http://marine.copernicus.eu/',
- long_description='Motu is a high efficient and robust Web Server which fills the gap between heterogeneous data providers to end users. Motu handles, extracts and transforms oceanographic huge volumes of data without performance collapse. This client enables to extract and download data through a python command line.',
- keywords=[
- 'Copernicus',
- 'CMEMS',
- 'CLS',
- 'Motu',
- 'motuclient-python',
- 'Dissemination Unit'
- ],
-
- author='Sylvain MARTY, CLS',
- author_email='smarty@cls.fr',
- platforms=['any'],
-
- url='https://github.com/clstoulouse/motu-client-python',
- license='LGPL',
-
- package_dir = {'': 'src/python', 'motu_utils': 'src/python/motu_utils'},
- packages=['motu_utils'],
- py_modules = ['motuclient', 'motu-client'],
- include_package_data=True,
-
- download_url='https://github.com/clstoulouse/motu-client-python/releases/',
-
- classifiers=[
- 'Development Status :: 5 - Production/Stable',
- 'Programming Language :: Python :: 2.7',
- 'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',
- 'Topic :: Scientific/Engineering :: GIS',
- 'Environment :: Console',
- 'Natural Language :: English',
- 'Operating System :: OS Independent'
- ],
-
- entry_points={
- 'console_scripts': [
- 'motuclient = motuclient:main'
- ]
- }
-)
diff --git a/Forecast_tools/plot_forecast_croco.m b/Forecast_tools/plot_forecast_croco.m
index 82375860ceed13c236559114fe34acbdbb54aeb9..48bd8fde2cd88ba32a8990cb6954d93deedbc820 100644
--- a/Forecast_tools/plot_forecast_croco.m
+++ b/Forecast_tools/plot_forecast_croco.m
@@ -1,5 +1,5 @@
%*********************************************************
-% plot CROCO forecast analysis at noon for each day
+% plot CROCO forecast analysis at noon of each day
%*********************************************************
clear all
close all
@@ -16,35 +16,33 @@ dirout = './Figs/';
eval(['!mkdir ',dirout])
grdname = [dirin,'SCRATCH/croco_grd.nc'];
frcname = [dirin,'SCRATCH/croco_frc_GFS_0.nc'];
+hisname = [dirin,'SCRATCH/croco_his.nc'];
avgname = [dirin,'SCRATCH/croco_avg.nc'];
coastfile = [dirin,'coastline_l.mat'];
-%lonmin=8; lonmax=22; latmin=-38; latmax=-26;
-
skip_wnd = 2;
skip_cur = 2;
zoom = 0;
fsize = 14; % Font size
-nx = 3; % number of days
-titlemark = ['IRD: ',datestr(now)];
+nx = 3; % number of forecast days
+%
+titlemark = ['CROCO: ',datestr(now)];
mean_currents = 0; % 1: plot 0-500 mean currents
% 0: surface currents
plot_fig_1 = 0; % wind
-plot_fig_2 = 0; % surface currents
+plot_fig_2 = 1; % surface currents
plot_fig_3 = 1; % SST + surface currents
plot_fig_4 = 1; % SSH
-plot_fig_5 = 0; % HBL
+plot_fig_5 = 1; % HBL
-% offset to convert UTC model time
-% into local matlab time (days]
+% offset to convert UTC model time
+% into local matlab time [days]
days_off = timezone/24+datenum(Yorig,1,1);
%
%************ End of users's defined parameter ************
%
-% time (in matlab time)
-%
today=floor(now);
%
% date in 'Yorig' time
@@ -75,7 +73,6 @@ dzv=zv(2:end,:,:)-zv(1:end-1,:,:);
% coastline
%bounds=[lonmin lonmax latmin latmax]; res='l';
%coastfile=make_coast2(bounds,res)
-
%
barwidth=0.5;
barheight=0.04;
@@ -89,14 +86,14 @@ if plot_fig_1,
%
% 1: wind
%
- disp('PLot winds ...')
+ disp('Plot winds ...')
itime=0;
cmin=0; cint=5; cmax=30; cff_wnd=.4; % winds
[LON,LAT]=meshgrid([lonmin:1/3:lonmax],[latmin:1/3:latmax]);
nc=netcdf(frcname);
smstime=nc{'sms_time'}(:);
smstime0=floor(now)-datenum(Yorig,1,1)-1/24-1; %midday
- for tndx=1:nx;
+ for tndx=hdays+1:nx+hdays
smstime0=smstime0+1;
itime=itime+1;
disp(['Day ',num2str(itime)])
@@ -137,7 +134,12 @@ if plot_fig_1,
h=m_streamslice(LON,LAT,U,V,1); hold on;
%m_streamslice(lonr,latr,ur,vr,1); hold on;
set(h,'color','b');
- m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ if ~isempty(coastfile)
+ m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ %m_usercoast(coastfile,'line', 'color', 'black', 'linewidth', 2);
+ else
+ m_gshhs_f('patch',[.7 .7 .7],'edgecolor','k')
+ end
hold off
m_grid('box','fancy','tickdir','in','FontSize',fsize);
set(findobj('tag','m_grid_color'),'facecolor','white')
@@ -159,8 +161,9 @@ if plot_fig_1,
xlabel('Wind [knots]','FontSize',fsize)
set(gcf, 'PaperPositionMode', 'auto');
- export_fig -transparent file.pdf
- eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ export_fig -transparent file.jpg
+ eval(['! mv -f file.jpg ',dirout,outname,'.jpg']);
+ %eval(['print -bestfit -dpdf',dirout,outname,'.pdf']);
end
close(nc)
end % plot_fig_1
@@ -169,7 +172,7 @@ if plot_fig_2,
%
% 2: Surface currents
%
-disp('PLot surface currents ...')
+disp('Plot surface currents ...')
itime=0;
cmin=0; cint=0.1; cmax=2.0; cff_cur=2;
for tndx=hdays+1:nx+hdays
@@ -211,7 +214,7 @@ for tndx=hdays+1:nx+hdays
close(nc)
spd=1.94384*mask.*sqrt((u2rho_2d(u)).^2+(v2rho_2d(v)).^2);
- spd=get_missing_val(lon,lat,spd);
+ %spd=get_missing_val(lon,lat,spd); % in batch mode, do not render properly with m_contour + m_usercoast
[ur,vr,lonr,latr,maskr]=uv_vec2rho(u,v,lon,lat,angle,mask,skip_cur,[0 0 0 0]);
m_proj('mercator',...
@@ -222,7 +225,12 @@ for tndx=hdays+1:nx+hdays
caxis([cmin cmax])
hold on
m_quiver(lonr,latr,cff_cur*ur,cff_cur*vr,0,'k');
- m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ if ~isempty(coastfile)
+ m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ %m_usercoast(coastfile,'line', 'color', 'black', 'linewidth', 2);
+ else
+ m_gshhs_f('patch',[.7 .7 .7],'edgecolor','k')
+ end
hold off
m_grid('box','fancy','tickdir','in','FontSize',fsize);
set(findobj('tag','m_grid_color'),'facecolor','white')
@@ -247,8 +255,9 @@ for tndx=hdays+1:nx+hdays
end
set(gcf, 'PaperPositionMode', 'auto');
- export_fig -transparent file.pdf
- eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ export_fig -transparent file.jpg
+ eval(['! mv -f file.jpg ',dirout,outname,'.jpg']);
+ %eval(['print -bestfit -dpdf ',dirout,outname,'.pdf
end
end
end % plot_fig_2
@@ -257,7 +266,7 @@ if plot_fig_3,
%
% 3: SST and Surface Currents
%
-disp('PLot SST and surface currents ...')
+disp('Plot SST and surface currents ...')
itime=0;
nc=netcdf(avgname);
sst=mask.*squeeze(nc{'temp'}(1,N,:,:));
@@ -285,9 +294,9 @@ for tndx=hdays+1:nx+hdays
close(nc)
[ur,vr,lonr,latr,maskr]=uv_vec2rho(u,v,lon,lat,angle,mask,skip_cur,[0 0 0 0]);
spdr=sqrt(ur.^2+vr.^2);
- sst=get_missing_val(lon,lat,sst);
- ur=get_missing_val(lonr,latr,ur);
- vr=get_missing_val(lonr,latr,vr);
+ %sst=get_missing_val(lon,lat,sst); % in batch mode, do not render properly with m_contour + m_usercoast
+ %ur=get_missing_val(lonr,latr,ur);
+ %vr=get_missing_val(lonr,latr,vr);
%plot_res=1/3;
%[LON,LAT]=meshgrid([lonmin:plot_res:lonmax],[latmin:plot_res:latmax]);
@@ -298,12 +307,18 @@ for tndx=hdays+1:nx+hdays
'lon',[lonmin lonmax],...
'lat',[latmin latmax]);
[C0,h0]=m_contourf(lon,lat,sst,[cmin:cint:cmax],'k');
+ %m_pcolor(lon,lat,sst);
shading flat
caxis([cmin cmax])
hold on
m_quiver(lonr,latr,cff_cur*ur,cff_cur*vr,0,'k');
%m_streamslice(LON,LAT,U,V,2);
- m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ if ~isempty(coastfile)
+ m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ %m_usercoast(coastfile,'line', 'color', 'black', 'linewidth', 2);
+ else
+ m_gshhs_f('patch',[.7 .7 .7],'edgecolor','k')
+ end
hold off
m_grid('box','fancy','tickdir','in','FontSize',fsize-2);
set(findobj('tag','m_grid_color'),'facecolor','white')
@@ -324,8 +339,11 @@ for tndx=hdays+1:nx+hdays
xlabel('SST [^{o}C]','FontSize',fsize)
set(gcf, 'PaperPositionMode', 'auto');
- export_fig -transparent file.pdf
- eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ export_fig -transparent file.jpg
+ eval(['! mv -f file.jpg ',dirout,outname,'.jpg']);
+ %export_fig -transparent file.pdf
+ %eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ %eval(['print -bestfit -dpdf ',dirout,outname,'.pdf']);
end
end
end % plot_fig_3
@@ -334,7 +352,7 @@ if plot_fig_4,
%
% 4: Sea Surface Height
%
-disp('PLot SSH ...')
+disp('Plot SSH ...')
itime=0;
cmin=-50; cint=5; cmax=50;
for tndx=hdays+1:nx+hdays
@@ -353,13 +371,18 @@ for tndx=hdays+1:nx+hdays
ssh=100*squeeze(nc{'zeta'}(tndx,:,:));
ssh=(ssh-mean(mean(ssh))).*mask;
close(nc)
- ssh=get_missing_val(lon,lat,ssh);
+ %ssh=get_missing_val(lon,lat,ssh); % in batch mode, do not render properly with m_contour + m_usercoast
m_proj('mercator','lon',[lonmin lonmax],'lat',[latmin latmax]);
[C0,h0]=m_contourf(lon,lat,ssh,[cmin:cint:cmax]);
-% shading flat
+ shading flat
caxis([cmin cmax])
- m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ if ~isempty(coastfile)
+ m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ %m_usercoast(coastfile,'line', 'color', 'black', 'linewidth', 2);
+ else
+ m_gshhs_f('patch',[.7 .7 .7],'edgecolor','k')
+ end
m_grid('box','fancy','tickdir','in','FontSize',fsize-2);
set(findobj('tag','m_grid_color'),'facecolor','white')
title([datestr(scrumtime,1)],'FontSize',fsize+1)
@@ -379,8 +402,9 @@ for tndx=hdays+1:nx+hdays
xlabel('SSH [cm]','FontSize',fsize)
set(gcf, 'PaperPositionMode', 'auto');
- export_fig -transparent file.pdf
- eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ export_fig -transparent file.jpg
+ eval(['! mv -f file.jpg ',dirout,outname,'.jpg']);
+ %eval(['print -bestfit -dpdf ',dirout,outname,'.pdf']);
end
end
end % plot_fig_4
@@ -389,7 +413,7 @@ if plot_fig_5,
%
% 5: Surface Boundary Layer Depth
%
-disp('PLot HBL ...')
+disp('Plot HBL ...')
itime=0;
cmin=0; cint=10; cmax=100;
for tndx=hdays+1:nx+hdays
@@ -406,13 +430,19 @@ for tndx=hdays+1:nx+hdays
if ~isempty(scrumtime)
hbl=mask.*squeeze(nc{'hbl'}(tndx,:,:));
close(nc)
-% hbl=get_missing_val(lon,lat,hbl);
+ %hbl=get_missing_val(lon,lat,hbl); % in batch mode, do not render properly with m_contour + m_usercoast
m_proj('mercator','lon',[lonmin lonmax],'lat',[latmin latmax]);
- m_pcolor(lon,lat,hbl);
- shading flat
+ %[C0,h0]=m_contourf(lon,lat,ssh,[cmin:cint:cmax]);
+ %shading flat
+ m_pcolor(lon,lat,hbl);shading flat;
caxis([cmin cmax])
- m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ if ~isempty(coastfile)
+ m_usercoast(coastfile,'patch',[.0 .0 .0]);
+ %m_usercoast(coastfile,'line', 'color', 'black', 'linewidth', 2);
+ else
+ m_gshhs_f('patch',[.7 .7 .7],'edgecolor','k');
+ end
m_grid('box','fancy','tickdir','in','FontSize',fsize-2);
set(findobj('tag','m_grid_color'),'facecolor','white')
title([datestr(scrumtime,1)],'FontSize',fsize+1)
@@ -432,8 +462,11 @@ for tndx=hdays+1:nx+hdays
xlabel('HBL [m]','FontSize',fsize)
set(gcf, 'PaperPositionMode', 'auto');
- export_fig -transparent file.pdf
- eval(['! mv -f file.pdf ',dirout,outname,'.pdf']);
+ export_fig -transparent file.jpg
+ eval(['! mv -f file.jpg ',dirout,outname,'.jpg']);
+ %eval(['print -bestfit -dpdf ',dirout,outname,'.pdf']);
end
end
end % plot_fig_5
+
+
diff --git a/Forecast_tools/plot_quick_forecast.m b/Forecast_tools/plot_quick_forecast.m
deleted file mode 100644
index 9fc96d737266b9f7eefeff4ece8af2e88000cb67..0000000000000000000000000000000000000000
--- a/Forecast_tools/plot_quick_forecast.m
+++ /dev/null
@@ -1,334 +0,0 @@
-%
-% forecast_analysis.m
-%
-% Create an image from the forecast results and send it to the
-% forecast web page.
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 8-Sep-2006 by Pierrick Penven
-% Updated 5-Oct-2006 by Pierrick Penven (changes in file names)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-start
-disp('Forecast analysis')
-%
-% Common parameters
-%
-crocotools_param
-%
-% plot the wind speed at noon for each day
-%
-skip=5;
-zoom=0;
-X=30;
-Y=22;
-% time (in matlab time)
-%
-today=floor(now);
-%
-% date in 'Yorig' time
-%
-rundate=datenum(today)-datenum(Yorig,1,1);
-%
-nc=netcdf(grdname);
-lon=nc{'lon_rho'}(:);
-lat=nc{'lat_rho'}(:);
-mask=nc{'mask_rho'}(:);
-angle=nc{'angle'}(:);
-close(nc)
-mask(mask==0)=NaN;
-%
-lonmin=min(min(lon))-zoom;
-lonmax=max(max(lon))+zoom;
-latmin=min(min(lat))-zoom;
-latmax=max(max(lat))+zoom;
-%
-close all
-figure('Units','centimeters',...
- 'Position',[1 1 X Y],...
- 'PaperPosition',[1 1 X Y],...
- 'PaperUnits','centimeters')
-%
-fsize=8;
-nx=6;
-cff1=4;
-cff2=2;
-%
-barwidth=0.2;
-barheight=0.01;
-titleheight=0.01;
-hmargin=0.025;
-vmargin=0.06;
-%
-width=(1-(1+nx)*hmargin)/(nx);
-height=(1-6.6*vmargin-3*barheight-titleheight)/3;
-%
-left1=hmargin;
-%
-bot1=vmargin;
-bot2=bot1+barheight+0.5*vmargin;
-bot3=bot2+height+1.5*vmargin;
-bot4=bot3+barheight+0.5*vmargin;
-bot5=bot4+height+1.5*vmargin;
-bot6=bot5+barheight+0.5*vmargin;
-bot7=bot6+height+1.5*vmargin;
-%
-% title
-%
-subplot('Position',[0.5-0.5*barwidth bot7 barwidth titleheight])
-set(gca,'XTickLabel',[' '])
-xlabel(['CROCO experiment: ',datestr(today)],'FontSize',10)
-%
-% 1: wind stress
-%
-left=left1;
-bot=bot6;
-for tndx=4*5:4:4*5+4*(nx)
- subplot('Position',[left bot width height])
- nc=netcdf('SCRATCH/croco_frc_GFS_0.nc');
- smstime=[];
- smstime=nc{'sms_time'}(tndx);
- if ~isempty(smstime)
- u=squeeze(nc{'sustr'}(tndx,:,:));
- v=squeeze(nc{'svstr'}(tndx,:,:));
- close(nc)
- stress=mask.*sqrt((u2rho_2d(u)).^2+(v2rho_2d(v)).^2);
- [ur,vr,lonr,latr,spd]=uv_vec2rho(u,v,lon,lat,angle,mask,skip,[0 0 0 0]);
- m_proj('mercator',...
- 'lon',[lonmin lonmax],...
- 'lat',[latmin latmax]);
- [C0,h0]=m_contourf(lon,lat,stress,[0:0.04:0.3],'k');
- shading flat
- caxis([0 0.3])
- hold on
- m_quiver(lonr,latr,cff1*ur,cff1*vr,0,'k');
- m_usercoast(coastfileplot,'patch',[.9 .9 .9]);
- hold off
- m_grid('box','fancy','xtick',5,'ytick',5,'tickdir','out',...
- 'FontSize',fsize-2);
- set(findobj('tag','m_grid_color'),'facecolor','white')
- title([datestr(smstime+datenum(Yorig,1,1))],'FontSize',fsize)
- left=left+width+hmargin;
- end
-end
-subplot('Position',[0.5-0.5*barwidth bot5 barwidth barheight])
-x=[0:1];
-y=[0:0.04:0.3];
-[X,Y]=meshgrid(x,y);
-contourf(Y,X,Y,y)
-caxis([0 0.3])
-set(gca,'XTick',[0:0.04:0.3],'YTickLabel',[' '])
-set(gca,'FontSize',fsize)
-xlabel('Wind stress [N.m^{-2}]','FontSize',fsize)
-%
-% 2: Surface currents
-%
-left=left1;
-bot=bot4;
-for tndx=1:nx
- subplot('Position',[left bot width height])
- nc=netcdf('SCRATCH/croco_avg.nc');
- scrumtime=[];
- scrumtime=(nc{'scrum_time'}(tndx))/(24*3600);
- if ~isempty(scrumtime)
- N=length(nc('s_rho'));
- u=squeeze(nc{'u'}(tndx,N,:,:));
- v=squeeze(nc{'v'}(tndx,N,:,:));
- close(nc)
- spd=mask.*sqrt((u2rho_2d(u)).^2+(v2rho_2d(v)).^2);
- [ur,vr,lonr,latr,spdr]=uv_vec2rho(u,v,lon,lat,angle,mask,skip,[0 0 0 0]);
- m_proj('mercator',...
- 'lon',[lonmin lonmax],...
- 'lat',[latmin latmax]);
- [C0,h0]=m_contourf(lon,lat,100*spd,[0:10:80],'k');
- shading flat
- caxis([0 80])
- hold on
- m_quiver(lonr,latr,cff2*ur,cff2*vr,0,'k');
- m_usercoast(coastfileplot,'patch',[.9 .9 .9]);
- hold off
- m_grid('box','fancy','xtick',5,'ytick',5,'tickdir','out',...
- 'FontSize',fsize-2);
- set(findobj('tag','m_grid_color'),'facecolor','white')
- title([datestr(scrumtime+datenum(Yorig,1,1))],'FontSize',fsize)
- left=left+width+hmargin;
- end
-end
-subplot('Position',[0.5-0.5*barwidth bot3 barwidth barheight])
-x=[0:1];
-y=[0:10:80];
-[X,Y]=meshgrid(x,y);
-caxis([0 80])
-contourf(Y,X,Y,y)
-set(gca,'XTick',[0:10:80],'YTickLabel',[' '])
-set(gca,'FontSize',fsize)
-xlabel('Surface currents [cm.s^{-1}]','FontSize',fsize)
-%
-% 3: SST
-%
-left=left1;
-bot=bot2;
-for tndx=1:nx
- subplot('Position',[left bot width height])
- nc=netcdf('SCRATCH/croco_avg.nc');
- scrumtime=[];
- scrumtime=(nc{'scrum_time'}(tndx))/(24*3600);
- if ~isempty(scrumtime)
- N=length(nc('s_rho'));
- sst=squeeze(nc{'temp'}(tndx,N,:,:));
- close(nc)
- m_proj('mercator',...
- 'lon',[lonmin lonmax],...
- 'lat',[latmin latmax]);
- [C0,h0]=m_contourf(lon,lat,sst,[10:1:25],'k');
- shading flat
- caxis([10 25])
- hold on
- m_usercoast(coastfileplot,'patch',[.9 .9 .9]);
- hold off
- m_grid('box','fancy','xtick',5,'ytick',5,'tickdir','out',...
- 'FontSize',fsize-2);
- set(findobj('tag','m_grid_color'),'facecolor','white')
- title([datestr(scrumtime+datenum(Yorig,1,1))],'FontSize',fsize)
- left=left+width+hmargin;
- end
-end
-subplot('Position',[0.5-0.5*barwidth bot1 barwidth barheight])
-x=[0:1];
-y=[10:1:25];
-[X,Y]=meshgrid(x,y);
-caxis([10 25])
-contourf(Y,X,Y,y)
-set(gca,'XTick',[10:2:25],'YTickLabel',[' '])
-set(gca,'FontSize',fsize)
-xlabel('SST [^{o}C]','FontSize',fsize)
-%
-% Print the image
-%
-eval(['print -depsc2 croco_',num2str(rundate),'.eps'])
-eval(['!convert -density 85 croco_',num2str(rundate),...
- '.eps croco_',num2str(rundate),'.jpg'])
-eval(['!mv -f croco_',num2str(rundate),'.jpg croco_realtime.jpg'])
-%
-% send the file to the web site
-%
-% %!./envoi.csh croco_realtime.jpg
-% %
-% close all
-% %
-% nc=netcdf('SCRATCH/croco_sta_hindcast.nc');
-% t1=nc{'scrum_time'}(:)/(24*3600);
-% sst1=squeeze(nc{'temp'}(:,1,32));
-% bott1=squeeze(nc{'temp'}(:,1,1));
-% temp1=squeeze(nc{'temp'}(:,1,:));
-% z1=squeeze(nc{'depth'}(:,1,:));
-% u1=1e3*squeeze(nc{'u'}(:,1,:));
-% v1=1e3*squeeze(nc{'v'}(:,1,:));
-% close(nc)
-% tmin=min(t1);
-% sst1(1)=NaN;
-% bott1(1)=NaN;
-% u1(1,:)=NaN;
-% v1(1,:)=NaN;
-% temp1(1,:)=NaN;
-%
-% nc=netcdf('SCRATCH/croco_sta_forecast.nc');
-% t2=nc{'scrum_time'}(:)/(24*3600);
-% sst2=squeeze(nc{'temp'}(:,1,32));
-% bott2=squeeze(nc{'temp'}(:,1,1));
-% temp2=squeeze(nc{'temp'}(:,1,:));
-% z2=squeeze(nc{'depth'}(:,1,:));
-% u2=1e3*squeeze(nc{'u'}(:,1,:));
-% v2=1e3*squeeze(nc{'v'}(:,1,:));
-% close(nc)
-% temp2=temp2(2:end,:);
-% u2=u2(2:end,:);
-% v2=v2(2:end,:);
-% z2=z2(2:end,:);
-% t2=t2(2:end);
-% sst2=sst2(2:end);
-% bott2=bott2(2:end);
-% z=squeeze(z2(1,:));
-% t1=t1-tmin;
-% t2=t2-tmin;
-%
-% figure('Units','centimeters',...
-% 'Position',[1 1 20 20],...
-% 'PaperPosition',[1 1 20 20],...
-% 'PaperUnits','centimeters')
-%
-% subplot(3,1,1)
-% pcolor(t1,z,u1')
-% hold on
-% pcolor(t2,z,u2')
-% axis([0 9 -30 0])
-% shading flat
-% caxis([-250 250])
-% colorbar
-% title(['Velocity East [mm/s]'])
-% ylabel('Depth')
-% set(gca,'Xticklabel',[])
-%
-% subplot(3,1,2)
-% pcolor(t1,z,v1')
-% hold on
-% pcolor(t2,z,v2')
-% axis([0 9 -30 0])
-% shading flat
-% caxis([-250 250])
-% colorbar
-% title(['Velocity North [mm/s]'])
-% ylabel('Depth')
-% set(gca,'Xticklabel',[])
-%
-% subplot(3,1,3)
-% pcolor(t1,z,temp1')
-% hold on
-% pcolor(t2,z,temp2')
-% axis([0 9 -30 0])
-% shading flat
-% caxis([10 15])
-% colorbar
-% title(['Temperature [^oC]'])
-% ylabel('Depth')
-% set(gca,'Xtick',[0.5:1:9],...
-% 'Xticklabel',datestr(tmin+[0.5:1:9]+datenum(Yorig,1,1),19))
-% %
-% % Print the image
-% %
-% eval(['print -depsc2 -painters bob_',num2str(rundate),'.eps'])
-% eval(['!convert -density 85 bob_',num2str(rundate),...
-% '.eps bob_',num2str(rundate),'.jpg'])
-% eval(['!cp -f bob_',num2str(rundate),'.jpg bob_realtime.jpg'])
-% %
-% % send the file to the web site
-% %
-% %!./envoi.csh bob_realtime.jpg
-
-
-
-
-
diff --git a/Nesting_tools/create_nestedclim.m b/Nesting_tools/create_nestedclim.m
index 49768926c11b9070e7e8bf3539e662f1899a5f3e..ace52e95a325f0f73eea18c9cec81dc9a246a850 100644
--- a/Nesting_tools/create_nestedclim.m
+++ b/Nesting_tools/create_nestedclim.m
@@ -126,8 +126,8 @@ ncclim{'theta_s'} = ncdouble('one') ;
ncclim{'theta_b'} = ncdouble('one') ;
ncclim{'Tcline'} = ncdouble('one') ;
ncclim{'hc'} = ncdouble('one') ;
-ncclim{'sc_r'} = ncdouble('s_rho') ;
-ncclim{'Cs_r'} = ncdouble('s_rho') ;
+ncclim{'s_rho'} = ncdouble('s_rho') ;
+ncclim{'Cs_rho'} = ncdouble('s_rho') ;
ncclim{'tclm_time'} = ncdouble('tclm_time') ;
ncclim{'sclm_time'} = ncdouble('sclm_time') ;
ncclim{'uclm_time'} = ncdouble('uclm_time') ;
@@ -180,23 +180,23 @@ ncclim{'hc'}.long_name = 'S-coordinate parameter, critical depth';
ncclim{'hc'}.units = ncchar('meter');
ncclim{'hc'}.units = 'meter';
%
-ncclim{'sc_r'}.long_name = ncchar('S-coordinate at RHO-points');
-ncclim{'sc_r'}.long_name = 'S-coordinate at RHO-points';
-ncclim{'sc_r'}.units = ncchar('nondimensional');
-ncclim{'sc_r'}.units = 'nondimensional';
-ncclim{'sc_r'}.valid_min = -1;
-ncclim{'sc_r'}.valid_max = 0;
-ncclim{'sc_r'}.field = ncchar('sc_r, scalar');
-ncclim{'sc_r'}.field = 'sc_r, scalar';
-%
-ncclim{'Cs_r'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
-ncclim{'Cs_r'}.long_name = 'S-coordinate stretching curves at RHO-points';
-ncclim{'Cs_r'}.units = ncchar('nondimensional');
-ncclim{'Cs_r'}.units = 'nondimensional';
-ncclim{'Cs_r'}.valid_min = -1;
-ncclim{'Cs_r'}.valid_max = 0;
-ncclim{'Cs_r'}.field = ncchar('Cs_r, scalar');
-ncclim{'Cs_r'}.field = 'Cs_r, scalar';
+ncclim{'s_rho'}.long_name = ncchar('S-coordinate at RHO-points');
+ncclim{'s_rho'}.long_name = 'S-coordinate at RHO-points';
+ncclim{'s_rho'}.units = ncchar('nondimensional');
+ncclim{'s_rho'}.units = 'nondimensional';
+ncclim{'s_rho'}.valid_min = -1;
+ncclim{'s_rho'}.valid_max = 0;
+ncclim{'s_rho'}.field = ncchar('s_rho, scalar');
+ncclim{'s_rho'}.field = 's_rho, scalar';
+%
+ncclim{'Cs_rho'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
+ncclim{'Cs_rho'}.long_name = 'S-coordinate stretching curves at RHO-points';
+ncclim{'Cs_rho'}.units = ncchar('nondimensional');
+ncclim{'Cs_rho'}.units = 'nondimensional';
+ncclim{'Cs_rho'}.valid_min = -1;
+ncclim{'Cs_rho'}.valid_max = 0;
+ncclim{'Cs_rho'}.field = ncchar('Cs_rho, scalar');
+ncclim{'Cs_rho'}.field = 'Cs_rho, scalar';
%
ncclim{'tclm_time'}.long_name = ncchar('time for temperature climatology');
ncclim{'tclm_time'}.long_name = 'time for temperature climatology';
@@ -308,7 +308,7 @@ ncclim.history = history;
%
result = endef(ncclim);
%
-[sc_r,Cs_r,sc_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
+[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
%
% Write variables
%
@@ -320,8 +320,8 @@ ncclim{'theta_s'}(:) = theta_s;
ncclim{'theta_b'}(:) = theta_b;
ncclim{'Tcline'}(:) = Tcline;
ncclim{'hc'}(:) = hc;
-ncclim{'sc_r'}(:) = sc_r;
-ncclim{'Cs_r'}(:) = Cs_r;
+ncclim{'s_rho'}(:) = s_rho;
+ncclim{'Cs_rho'}(:) = Cs_rho;
ncclim{'tclm_time'}(:) = ttime;
ncclim{'sclm_time'}(:) = stime;
ncclim{'uclm_time'}(:) = utime ;
diff --git a/Nesting_tools/create_nestedinitial.m b/Nesting_tools/create_nestedinitial.m
index c4bb989d582921cb8b7fd5fe04976b164cb25a7f..7bb1e37ec0b8e055d06d9e02787e24d651d95d08 100644
--- a/Nesting_tools/create_nestedinitial.m
+++ b/Nesting_tools/create_nestedinitial.m
@@ -110,8 +110,8 @@ ncini{'theta_s'} = ncdouble('one') ;
ncini{'theta_b'} = ncdouble('one') ;
ncini{'Tcline'} = ncdouble('one') ;
ncini{'hc'} = ncdouble('one') ;
-ncini{'sc_r'} = ncdouble('s_rho') ;
-ncini{'Cs_r'} = ncdouble('s_rho') ;
+ncini{'s_rho'} = ncdouble('s_rho') ;
+ncini{'Cs_rho'} = ncdouble('s_rho') ;
ncini{'scrum_time'} = ncdouble('time') ;
ncini{'u'} = ncdouble('time','s_rho','eta_u','xi_u') ;
ncini{'v'} = ncdouble('time','s_rho','eta_v','xi_v') ;
@@ -169,23 +169,23 @@ ncini{'hc'}.long_name = 'S-coordinate parameter, critical depth';
ncini{'hc'}.units = ncchar('meter');
ncini{'hc'}.units = 'meter';
%
-ncini{'sc_r'}.long_name = ncchar('S-coordinate at RHO-points');
-ncini{'sc_r'}.long_name = 'S-coordinate at RHO-points';
-ncini{'sc_r'}.units = ncchar('nondimensional');
-ncini{'sc_r'}.units = 'nondimensional';
-ncini{'sc_r'}.valid_min = -1;
-ncini{'sc_r'}.valid_max = 0;
-ncini{'sc_r'}.field = ncchar('sc_r, scalar');
-ncini{'sc_r'}.field = 'sc_r, scalar';
-%
-ncini{'Cs_r'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
-ncini{'Cs_r'}.long_name = 'S-coordinate stretching curves at RHO-points';
-ncini{'Cs_r'}.units = ncchar('nondimensional');
-ncini{'Cs_r'}.units = 'nondimensional';
-ncini{'Cs_r'}.valid_min = -1;
-ncini{'Cs_r'}.valid_max = 0;
-ncini{'Cs_r'}.field = ncchar('Cs_r, scalar');
-ncini{'Cs_r'}.field = 'Cs_r, scalar';
+ncini{'s_rho'}.long_name = ncchar('S-coordinate at RHO-points');
+ncini{'s_rho'}.long_name = 'S-coordinate at RHO-points';
+ncini{'s_rho'}.units = ncchar('nondimensional');
+ncini{'s_rho'}.units = 'nondimensional';
+ncini{'s_rho'}.valid_min = -1;
+ncini{'s_rho'}.valid_max = 0;
+ncini{'s_rho'}.field = ncchar('s_rho, scalar');
+ncini{'s_rho'}.field = 's_rho, scalar';
+%
+ncini{'Cs_rho'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
+ncini{'Cs_rho'}.long_name = 'S-coordinate stretching curves at RHO-points';
+ncini{'Cs_rho'}.units = ncchar('nondimensional');
+ncini{'Cs_rho'}.units = 'nondimensional';
+ncini{'Cs_rho'}.valid_min = -1;
+ncini{'Cs_rho'}.valid_max = 0;
+ncini{'Cs_rho'}.field = ncchar('Cs_rho, scalar');
+ncini{'Cs_rho'}.field = 'Cs_rho, scalar';
%
ncini{'scrum_time'}.long_name = ncchar('time since initialization');
ncini{'scrum_time'}.long_name = 'time since initialization';
@@ -290,7 +290,7 @@ ncini.creation_method = 'Nestgui @ CROCOTOOLS';
% Leave define mode
%
%%result = endef(ncini);
-[sc_r,Cs_r,sc_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
+[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
%
% Write variables
%
@@ -302,8 +302,8 @@ ncini{'theta_s'}(:)=theta_s;
ncini{'theta_b'}(:)=theta_b;
ncini{'Tcline'}(:)=Tcline;
ncini{'hc'}(:)=hc;
-ncini{'sc_r'}(:)=sc_r;
-ncini{'Cs_r'}(:)=Cs_r;
+ncini{'s_rho'}(:)=s_rho;
+ncini{'Cs_rho'}(:)=Cs_rho;
ncini{'scrum_time'}(1)=time;
ncini{'u'}(:)=0;
ncini{'v'}(:)=0;
diff --git a/Nesting_tools/create_nestedrestart.m b/Nesting_tools/create_nestedrestart.m
index b328c8f8eef03e8415127e273c30e42bcafe30a2..cdc87b2736d6f0bc84f04d9a5eeb94e4bad560bb 100644
--- a/Nesting_tools/create_nestedrestart.m
+++ b/Nesting_tools/create_nestedrestart.m
@@ -292,10 +292,10 @@ disp('Get the vertical grid')
ncrst.theta_s=ncprt.theta_s(:);
ncrst.theta_b=ncprt.theta_b(:);
ncrst.hc=ncprt.hc(:);
-ncrst.sc_w=ncprt.sc_w(:);
+ncrst.s_w=ncprt.s_w(:);
ncrst.Cs_w=ncprt.Cs_w(:);
-ncrst.sc_r=ncprt.sc_r(:);
-ncrst.Cs_r=ncprt.Cs_r(:);
+ncrst.s_rho=ncprt.s_rho(:);
+ncrst.Cs_rho=ncprt.Cs_rho(:);
ncrst.ntimes=ncprt.ntimes(:);
ncrst.ndtfast=ncprt.ndtfast(:);
ncrst.dt=ncprt.dt(:);
diff --git a/Nesting_tools/nested_grid.m b/Nesting_tools/nested_grid.m
index 9280ae2dcb823a443967f637f3ca650848112d32..60caeba52ae6342d64460427b4e0af3b17ba3e2b 100644
--- a/Nesting_tools/nested_grid.m
+++ b/Nesting_tools/nested_grid.m
@@ -152,8 +152,6 @@ while (bbound_east | bbound_west | bbound_south | bbound_north)
disp(' ')
disp(' Do the interpolations...')
lonpchild=interp2(igrd_p,jgrd_p,lonp_parent,ichildgrd_p,jchildgrd_p,'cubic');
- lonpchild(1,1);
- lonp_parent(imin,1);
latpchild=interp2(igrd_p,jgrd_p,latp_parent,ichildgrd_p,jchildgrd_p,'cubic');
xpchild=interp2(igrd_p,jgrd_p,xp_parent,ichildgrd_p,jchildgrd_p,'cubic');
ypchild=interp2(igrd_p,jgrd_p,yp_parent,ichildgrd_p,jchildgrd_p,'cubic');
diff --git a/Oforc_OGCM/Copernicus_Marine_Toolbox_installation.md b/Oforc_OGCM/Copernicus_Marine_Toolbox_installation.md
new file mode 100644
index 0000000000000000000000000000000000000000..3e99a2e225edb81e196dca467dcd4c49904e8316
--- /dev/null
+++ b/Oforc_OGCM/Copernicus_Marine_Toolbox_installation.md
@@ -0,0 +1,74 @@
+# Copernicus Marine Toolbox installation
+
+The Copernicus Marine Toolbox is used to download and extract data from the Copernicus Marine Data Store (Global Ocean Physics Reanalysis, Global Ocean Physics Analysis and Forecast, ...) to create oceanic open boundary and initial conditions. [ https://data.marine.copernicus.eu/products ]
+
+
+All the instructions can be found here :
+ * 1) https://help.marine.copernicus.eu/en/collections/4060068-copernicus-marine-toolbox
+ * 2) https://help.marine.copernicus.eu/en/articles/7970514-copernicus-marine-toolbox-installation
+
+
+Prerequisites:
+ * python version >= 3.9 & <3.12
+
+
+---
+## 2 ways to download it:
+
+ 1) typing :
+ ```console
+ python -m pip install copernicusmarine
+ ```
+
+
+ 2) Use of conda/mamba package (replace conda by mamba command below)
+
+ * Install a dedicated environment, by default named cmt_1.0 . First, you need to copy the file copernicusmarine_env.yml from the directory Forecast_tools/CopernicusMarineToolbox/
+
+ ```console
+ conda env create -f copernicusmarine_env.yml
+ ```
+
+ Note that you can use micromamba instead of mamba to install the python environment
+
+
+ Firstly, you need to activate the environment cmt_1.0 :
+
+ ```console
+ conda activate cmt_1.0
+ ```
+
+ The location of the executable (here after pathCMC) will be found typing :
+
+ ```console
+ ls $CONDA_PREFIX/bin/copernicusmarine
+ ```
+ Note that the value returned by your terminal here, will be your pathCMC to fill in your
+ crocotools_param.m and download_glorys_data.sh script
+
+
+---
+## When it's installed :
+
+You will have access to the copernicusmarine executable with various sub-command, very useful to get, extract and download data from the Copernicus Marine Data Store :
+
+```console
+copernicusmarine -h
+```
+
+Or alternatively:
+
+```console
+$CONDA_PREFIX/bin/copernicusmarine -h
+```
+
+
+To be used in the Matlab croco_tools, in the crocotools_param.m, you need to :
+
+- define the path to the copernicusmarine executable (`pathCMC`) in crocotools_param.m at *section 7, Option for make_OGCM_frcst or make_OGCM_mercator*
+- define your copernicus marine `login` and `password` in crocotools_param.m at *section 7, Options for for make_OGCM_frcst or make_OGCM_mercator*
+
+
+
+
+
diff --git a/Oforc_OGCM/README b/Oforc_OGCM/README
deleted file mode 100644
index e6c1fb9025401f548d2fd508d1c2042509bafab5..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/README
+++ /dev/null
@@ -1,24 +0,0 @@
-==
-make_OGCM.m is a way to get initial and boundary conditions
-for CROCO simulations from different global oceanic models.
-for the moment it works with SODA and ECCO.
-it uses DODS to extract the subgrids.
-
-Pierrick 2006/1/19.
-
-==
-Update:
-Now it use the ECCO2 data, every 3 days
-Gildas 2014/2/14
-
-==
-24-11-2020 : Update by Gildas Cambon
-Now you can process oceanic frocing from the global daily glorys12 reanalysis
-at 1/12 degree resolution.
-It is distributed by copernicus/mecator => https://resources.marine.copernicus.eu/
-
-It use the python-motu client to download a space and time
-extraction of the reanalysis.
-Have a look at the routines :
-- download_mercator_frcst_python.m
-- get_file_python_mercator.m
diff --git a/Oforc_OGCM/README.md b/Oforc_OGCM/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..31f4a7caa65eb28e987352656969cbe0d0a60ef5
--- /dev/null
+++ b/Oforc_OGCM/README.md
@@ -0,0 +1,20 @@
+## 23-02-2024 : Update to use the Copernicus Marine Toolbox
+
+ - see Copernicus_Marine_Toolbox_installation.md
+
+## 24-11-2020 : Update by Gildas Cambon
+Now you can process oceanic forcing from the global daily glorys12 reanalysis
+at 1/12 degree resolution.
+It is distributed by copernicus/mecator => https://resources.marine.copernicus.eu/
+
+It use the python-motu client to download a space and time
+extraction of the reanalysis.
+Have a look at the routines :
+- download_mercator_frcst_python.m
+- get_file_python_mercator.m
+
+## 14-02-2014 : Gildas Cambon
+Now it use the ECCO2 data, every 3 days
+
+## 01-19-2006 : Pierrick Penven
+make_OGCM.m is a way to get initial and boundary conditions. For CROCO simulations from different global oceanic models. For the moment it works with SODA and ECCO. it uses DODS to extract the subgrids
diff --git a/Oforc_OGCM/create_OGCM.m b/Oforc_OGCM/create_OGCM.m
index 24e4ae1e8f4ec52bcc54ac3e318122b3fbacfa05..88f0469002ac1d2a37c6e9b7521ee2bb1d33b7b0 100644
--- a/Oforc_OGCM/create_OGCM.m
+++ b/Oforc_OGCM/create_OGCM.m
@@ -80,6 +80,18 @@ nc{'vbar'}.long_name='MERIDIONAL BAROTROPIC VELOCITY';
nc{'vbar'}.units=ncchar('m/sec');
nc{'vbar'}.units='m/sec';
nc{'vbar'}.missing_value=missval;
+%nc{'taux'}=ncfloat('time','latU','lonU') ;
+%nc{'taux'}.long_name=ncchar('TAU_X');
+%nc{'taux'}.long_name='TAU_X';
+%nc{'taux'}.units=ncchar('N.m-2');
+%nc{'taux'}.units='N.m-2';
+%nc{'taux'}.missing_value=missval;
+%nc{'tauy'}=ncfloat('time','latV','lonV') ;
+%nc{'tauy'}.long_name=ncchar('TAU_Y');
+%nc{'tauy'}.long_name='TAU_Y';
+%nc{'tauy'}.units=ncchar('N.m-2');
+%nc{'tauy'}.units='N.m-2';
+%nc{'tauy'}.missing_value=missval;
nc{'ssh'}=ncfloat('time','latT','lonT') ;
nc{'ssh'}.long_name=ncchar('SEA LEVEL HEIGHT');
nc{'ssh'}.long_name='SEA LEVEL HEIGHT';
@@ -129,6 +141,8 @@ nc{'time'}(tndx)=time(tndx);
%
if length(time)==1
nc{'ssh'}(tndx,:,:)=ssh;
+% nc{'taux'}(tndx,:,:)=taux;
+% nc{'tauy'}(tndx,:,:)=tauy;
u1=u;
v1=v;
nc{'u'}(tndx,:,:,:)=u1;
@@ -137,6 +151,8 @@ nc{'time'}(tndx)=time(tndx);
nc{'salt'}(tndx,:,:,:)=salt;
else
nc{'ssh'}(tndx,:,:)=squeeze(ssh(tndx,:,:));
+% nc{'taux'}(tndx,:,:)=squeeze(taux(tndx,:,:));
+% nc{'tauy'}(tndx,:,:)=squeeze(tauy(tndx,:,:));
u1=squeeze(u(tndx,:,:,:));
v1=squeeze(v(tndx,:,:,:));
nc{'u'}(tndx,:,:,:)=u1;
diff --git a/Oforc_OGCM/create_SODA.m b/Oforc_OGCM/create_SODA.m
deleted file mode 100644
index 2d22d123b97a58a92e485ded16cd7094e04e2bae..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/create_SODA.m
+++ /dev/null
@@ -1,199 +0,0 @@
-function create_SODA(fname,lonT,latT,lonU,latU,lonV,latV,depth,time,...
- temp,salt,u,v,ssh,taux,tauy,Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Create the OGCM file
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2005-2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 6-Sep-2006 by Pierrick Penven
-% Updated 7-Oct-2013 by Gildas Cambon
-% Updated 14-Fev-2013 by Gildas Cambon
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-missval=NaN;
-disp(' Create the OGCM file')
-nc=netcdf(fname,'clobber');
-redef(nc);
-nc('lonT')=length(lonT);
-nc('latT')=length(latT);
-nc('lonU')=length(lonU);
-nc('latU')=length(latU);
-nc('lonV')=length(lonV);
-nc('latV')=length(latV);
-nc('depth')=length(depth);
-nc('time')=length(time);
-nc{'temp'}=ncfloat('time','depth','latT','lonT') ;
-nc{'temp'}.long_name=ncchar('TEMPERATURE');
-nc{'temp'}.long_name='TEMPERATURE';
-nc{'temp'}.units=ncchar('deg. C');
-nc{'temp'}.units='deg. C';
-nc{'temp'}.missing_value=missval;
-nc{'salt'}=ncfloat('time','depth','latT','lonT') ;
-nc{'salt'}.long_name=ncchar('SALINITY');
-nc{'salt'}.long_name='SALINITY';
-nc{'salt'}.units=ncchar('ppt');
-nc{'salt'}.units='ppt';
-nc{'salt'}.missing_value=missval;
-nc{'u'}=ncfloat('time','depth','latU','lonU') ;
-nc{'u'}.long_name=ncchar('ZONAL VELOCITY');
-nc{'u'}.long_name='ZONAL VELOCITY';
-nc{'u'}.units=ncchar('m/sec');
-nc{'u'}.units='m/sec';
-nc{'u'}.missing_value=missval;
-nc{'v'}=ncfloat('time','depth','latV','lonV') ;
-nc{'v'}.long_name=ncchar('MERIDIONAL VELOCITY');
-nc{'v'}.long_name='MERIDIONAL VELOCITY';
-nc{'v'}.units=ncchar('m/sec');
-nc{'v'}.units='m/sec';
-nc{'v'}.missing_value=missval;
-nc{'ubar'}=ncfloat('time','latU','lonU') ;
-nc{'ubar'}.long_name=ncchar('ZONAL BAROTROPIC VELOCITY');
-nc{'ubar'}.long_name='ZONAL BAROTROPIC VELOCITY';
-nc{'ubar'}.units=ncchar('m/sec');
-nc{'ubar'}.units='m/sec';
-nc{'ubar'}.missing_value=missval;
-nc{'vbar'}=ncfloat('time','latV','lonV') ;
-nc{'vbar'}.long_name=ncchar('MERIDIONAL BAROTROPIC VELOCITY');
-nc{'vbar'}.long_name='MERIDIONAL BAROTROPIC VELOCITY';
-nc{'vbar'}.units=ncchar('m/sec');
-nc{'vbar'}.units='m/sec';
-nc{'vbar'}.missing_value=missval;
-nc{'taux'}=ncfloat('time','latU','lonU') ;
-nc{'taux'}.long_name=ncchar('TAU_X');
-nc{'taux'}.long_name='TAU_X';
-nc{'taux'}.units=ncchar('N.m-2');
-nc{'taux'}.units='N.m-2';
-nc{'taux'}.missing_value=missval;
-nc{'tauy'}=ncfloat('time','latV','lonV') ;
-nc{'tauy'}.long_name=ncchar('TAU_Y');
-nc{'tauy'}.long_name='TAU_Y';
-nc{'tauy'}.units=ncchar('N.m-2');
-nc{'tauy'}.units='N.m-2';
-nc{'tauy'}.missing_value=missval;
-nc{'ssh'}=ncfloat('time','latT','lonT') ;
-nc{'ssh'}.long_name=ncchar('SEA LEVEL HEIGHT');
-nc{'ssh'}.long_name='SEA LEVEL HEIGHT';
-nc{'ssh'}.units=ncchar('m');
-nc{'ssh'}.units='m';
-nc{'ssh'}.missing_value=missval;
-nc{'lonT'}=ncdouble('lonT') ;
-nc{'lonT'}.units=ncchar('degrees_east');
-nc{'lonT'}.units='degrees_east';
-nc{'latT'}=ncdouble('latT') ;
-nc{'latT'}.units=ncchar('degrees_north');
-nc{'latT'}.units='degrees_north';
-nc{'lonU'}=ncdouble('lonU') ;
-nc{'lonU'}.units=ncchar('degrees_east');
-nc{'lonU'}.units='degrees_east';
-nc{'latU'}=ncdouble('latU') ;
-nc{'latU'}.units=ncchar('degrees_north');
-nc{'latU'}.units='degrees_north';
-nc{'lonV'}=ncdouble('lonV') ;
-nc{'lonV'}.units=ncchar('degrees_east');
-nc{'lonV'}.units='degrees_east';
-nc{'latV'}=ncdouble('latV') ;
-nc{'latV'}.units=ncchar('degrees_north');
-nc{'latV'}.units='degrees_north';
-nc{'depth'}=ncdouble('depth') ;
-nc{'depth'}.units=ncchar('meters');
-nc{'depth'}.units='meters';
-nc{'time'}=ncdouble('time') ;
-eval(['nc{''time''}.units = ncchar(''days since 1-Jan-',num2str(Yorig),' 00:00:0.0'');'])
-eval(['nc{''time''}.units = ''days since 1-Jan-',num2str(Yorig),' 00:00:0.0'';'])
-endef(nc);
-%
-% File the file
-%
-disp(' Fill the OGCM file')
-nc{'depth'}(:)=depth;
-nc{'latT'}(:)=latT;
-nc{'lonT'}(:)=lonT;
-nc{'latU'}(:)=latU;
-nc{'lonU'}(:)=lonU;
-nc{'latV'}(:)=latV;
-nc{'lonV'}(:)=lonV;
-%
-for tndx=1:length(time)
-%
-nc{'time'}(tndx)=time(tndx);
-%
-if length(time)==1
- nc{'ssh'}(tndx,:,:)=ssh;
- nc{'taux'}(tndx,:,:)=taux;
- nc{'tauy'}(tndx,:,:)=tauy;
- u1=u;
- v1=v;
- nc{'u'}(tndx,:,:,:)=u1;
- nc{'v'}(tndx,:,:,:)=v1;
- nc{'temp'}(tndx,:,:,:)=temp;
- nc{'salt'}(tndx,:,:,:)=salt;
-else
- nc{'ssh'}(tndx,:,:)=squeeze(ssh(tndx,:,:));
- nc{'taux'}(tndx,:,:)=squeeze(taux(tndx,:,:));
- nc{'tauy'}(tndx,:,:)=squeeze(tauy(tndx,:,:));
- u1=squeeze(u(tndx,:,:,:));
- v1=squeeze(v(tndx,:,:,:));
- nc{'u'}(tndx,:,:,:)=u1;
- nc{'v'}(tndx,:,:,:)=v1;
- nc{'temp'}(tndx,:,:,:)=squeeze(temp(tndx,:,:,:));
- nc{'salt'}(tndx,:,:,:)=squeeze(salt(tndx,:,:,:));
-end
-%
-% Compute the barotropic velocities
-%
-masku=isfinite(u1);
-maskv=isfinite(v1);
-u1(isnan(u1))=0;
-v1(isnan(v1))=0;
-dz=gradient(depth);
-NZ=length(depth);
-du=0*squeeze(u1(1,:,:));
-zu=du;
-dv=0*squeeze(v1(1,:,:));
-zv=dv;
-for k=1:NZ
- du=du+dz(k)*squeeze(u1(k,:,:));
- zu=zu+dz(k)*squeeze(masku(k,:,:));
- dv=dv+dz(k)*squeeze(v1(k,:,:));
- zv=zv+dz(k)*squeeze(maskv(k,:,:));
-end
-du(zu==0)=NaN;
-dv(zv==0)=NaN;
-zu(zu==0)=NaN;
-zv(zv==0)=NaN;
-ubar=du./zu;
-vbar=dv./zv;
-%
-nc{'ubar'}(tndx,:,:)=ubar;
-nc{'vbar'}(tndx,:,:)=vbar;
-%
-end
-%
-close(nc)
-%
-return
-
-end
-
diff --git a/Oforc_OGCM/download_ECCO.m b/Oforc_OGCM/download_ECCO.m
deleted file mode 100644
index 144424cc46b97763cbeb9de9e023bc8cfa36cee1..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/download_ECCO.m
+++ /dev/null
@@ -1,102 +0,0 @@
-function download_ECCO (Ymin,Ymax,Mmin,Mmax,lonmin,lonmax,latmin,latmax,...
- OGCM_dir,OGCM_prefix,url,Yorig)
-%
-% Extract a subgrid from ECCO to get a CROCO forcing
-% Store that into monthly files.
-% Take care of the Greenwitch Meridian.
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 6-Sep-2006 by Pierrick Penven
-% Updated 14-Feb-2014 by Gildas cambon : ECCO2 server
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-disp([' '])
-disp(['Get data from Y',num2str(Ymin),'M',num2str(Mmin),...
- ' to Y',num2str(Ymax),'M',num2str(Mmax)])
-disp(['Minimum Longitude: ',num2str(lonmin)])
-disp(['Maximum Longitude: ',num2str(lonmax)])
-disp(['Minimum Latitude: ',num2str(latmin)])
-disp(['Maximum Latitude: ',num2str(latmax)])
-disp([' '])
-%
-% Catalogue vvname for ECCO2
-%
-catalog_vname={'THETA','SALT','UVEL','VVEL','SSH'};
-catalog_vname2={'temp','salt','u','v','ssh'};
-%
-% Create the directory
-%
-disp(['Making output data directory ',OGCM_dir])
-eval(['!mkdir ',OGCM_dir])
-%
-% Start
-%
-disp(['Process the dataset: ',url])
-%
-% Find a subset of the ECCO grid
-%
-fname=[url,'THETA.nc/THETA.1440x720x50.19920102.nc'];
-[i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- jrange,jrange_v,krange,lon,lon_u,lat,lat_v,depth]=...
- get_ECCO_subgrid(fname,lonmin,lonmax,latmin,latmax);
-
-time0=readdap(fname,'TIME',[]);
-%
-% Loop on the years
-%
-for Y=Ymin:Ymax
- disp(['Processing year: ',num2str(Y)])
- %
- % Loop on the months
- %
- if Y==Ymin
- mo_min=Mmin;
- else
- mo_min=1;
- end
- if Y==Ymax
- mo_max=Mmax;
- else
- mo_max=12;
- end
- for M=mo_min:mo_max
- disp([' Processing month: ',num2str(M)])
- ECCO_file=[OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf'];
- %
- % Extract ECCO data
- %
- extract_ECCO(OGCM_dir,OGCM_prefix,url,Y,M,...
- catalog_vname,catalog_vname2,...
- lon,lat,depth,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max,Yorig)
-
- end
-end
-return
-
-end
-
diff --git a/Oforc_OGCM/download_glorys_data.sh b/Oforc_OGCM/download_glorys_data.sh
index 7c85633f1dd2870f727391ff666f1cd3d0b51123..8b20c40a142649eef765cf9a5ea86858ecf95afb 100755
--- a/Oforc_OGCM/download_glorys_data.sh
+++ b/Oforc_OGCM/download_glorys_data.sh
@@ -1,6 +1,6 @@
#!/bin/bash
set -e
-source ../../myenv_mypath.sh
+#source ../../myenv_mypath.sh
##########################
# python
# ======
@@ -10,27 +10,14 @@ source ../../myenv_mypath.sh
#
# motuclient
# ==========
-# 1- Use croco's motuclient (pathMotu => Forecast_tools) or ...
-# 2- Install your own motuclient:
-# To update/upgrade and get the latest version of motuclient
-# from a previous version (<= v1.8.3), type in the following:
-# $ python -m pip install --upgrade motuclient
-# Otherwise (if there is no previous installation of motuclient),
-# type in the following:
-# $ python -m pip install motuclient
-# It should install and display motuclient package v1.8.4 (Oct. 2019).
-# To make sure, display the version:
-# $ python -m motuclient --version
-# If it does not return: "motuclient-python v1.8.X" ("X" >= "4"),
-# then type in the following:
-# $ python -m pip install motuclient==1.8.4
+# 1- Use copernicusmarine client ...
#### USER INFORMATIONS ####
user='XXXXXXXXX'
-password='XXXXXXXXXX'
+password='XXXXXXXXX'
###
-### motu client ###
-path_to_motu="${OCE}/../../croco_tools" # Use croco's motuclient croco_tools/Forecast_tools
-# if you want to use your own motu, leave empty
+### Copernicus marine client ###
+# this is the pathCMC (described on the readme file Copernicus_Marine_Toolbox_installation.md)
+path_to_cmt="/home/to/your/bin/copernicusmarine"
###
YEAR_START=2017
MONTH_START=1
@@ -49,7 +36,8 @@ DT_TIME= # Value in days. Default value when empty is 1 month.
kdata="MONTHLY" # DAILY or MONTHLY
####################
READ_GRD=1 # read croco_grid to find lon/lat min-max
-INPUT_GRD="${OCE_FILES_DIR}/croco_grd.nc"
+#INPUT_GRD="${OCE_FILES_DIR}/croco_grd.nc"
+INPUT_GRD="CROCO_FILES/croco_grd.nc"
# In case you don't want to read croco_grd
# Please use -180/180 -90/90 format
lon_min="-90"
@@ -72,16 +60,14 @@ for field in ${vars}; do
done
###
-### motu command ###
-if [[ -z ${path_to_motu} ]]; then
- command_line="python -m motuclient"
+if [[ -z ${path_to_cmt} ]]; then
+ echo "You need to define your path_to_cmt variable ..."
+ exit 12
else
- command_line="${path_to_motu}/Forecast_tools/motuclient-python/motuclient.py"
+ command_line=${path_to_cmt}" "
fi
-## motu info
-motu_url_reana='http://my.cmems-du.eu/motu-web/Motu'
-service_id_reana='GLOBAL_MULTIYEAR_PHY_001_030-TDS'
+## cmt info
if [[ ${kdata} == "DAILY" ]]; then
product_id_reana='cmems_mod_glo_phy_my_0.083_P1D-m'
elif [[ ${kdata} == "MONTHLY" ]]; then
@@ -126,18 +112,20 @@ for YEAR in `seq ${YEAR_START} ${YEAR_END}`; do
daystrt=1
start_date=$( printf "%04d-%02d-%02d" $YEAR $MONTH $daystrt)
end_date=$(printf `date +"%Y-%m-%d" -d "${start_date} +1 month - 1 day"`)
- OUTNAME="${OUTDIR}/raw_motu_${PREFIX}_Y${YEAR}M${MONTH}.nc"
- ${command_line} --motu ${motu_url_reana} --service-id ${service_id_reana} --product-id ${product_id_reana} --longitude-min ${lon_min} --longitude-max ${lon_max} --latitude-min ${lat_min} --latitude-max ${lat_max} --date-min "${start_date} 12:00:00" --date-max "${end_date} 12:00:00" --depth-min 0.493 --depth-max 5727.918 ${variables} --out-dir ./ --out-name ${OUTNAME} --user ${user} --pwd ${password}
+ OUTNAME="${OUTDIR}/raw_${PREFIX}_Y${YEAR}M${MONTH}.nc"
+ echo "${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${OUTNAME} --username ${user} --password ${password} --force-download"
+ ${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${OUTNAME} --username ${user} --password ${password} --force-download
elif [[ ${kdata} == "DAILY" ]]; then
if [ -z ${DT_TIME} ]; then
start_date=$( printf "%04d-%02d-%02d" $YEAR $MONTH $daystrt)
end_date=$(printf `date +"%Y-%m-%d" -d "${start_date} +1 month - 1 day"`)
- OUTNAME="${OUTDIR}/raw_motu_${PREFIX}_Y${YEAR}M${MONTH}.nc"
- ${command_line} --motu ${motu_url_reana} --service-id ${service_id_reana} --product-id ${product_id_reana} --longitude-min ${lon_min} --longitude-max ${lon_max} --latitude-min ${lat_min} --latitude-max ${lat_max} --date-min "${start_date} 12:00:00" --date-max "${end_date} 12:00:00" --depth-min 0.493 --depth-max 5727.918 ${variables} --out-dir ./ --out-name ${OUTNAME} --user ${user} --pwd ${password}
+ OUTNAME="${OUTDIR}/raw_${PREFIX}_Y${YEAR}M${MONTH}.nc"
+ echo "${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${OUTNAME} --username ${user} --password ${password} --force-download"
+ ${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${OUTNAME} --username ${user} --password ${password} --force-download
else
for DAY in `seq ${dstart} ${DT_TIME} ${dend}`; do
- tmpoutname="${OUTDIR}/raw_motu_${PREFIX}_Y${YEAR}M${MONTH}D${DAY}.nc"
+ tmpoutname="${OUTDIR}/raw_${PREFIX}_Y${YEAR}M${MONTH}D${DAY}.nc"
start_date=$( printf "%04d-%02d-%02d" $YEAR $MONTH $DAY )
end_date=$( date +"%Y-%m-%d" -d "${start_date} +${DT_TIME} day - 1 day" )
tmpsdate=$( echo `date -d ${start_date} +"%Y%m"` )
@@ -150,12 +138,13 @@ for YEAR in `seq ${YEAR_START} ${YEAR_END}`; do
nbdays=$(( (${second_date} - ${first_date})/86400 ))
end_date=$( date +"%Y-%m-%d" -d "${end_date} - ${nbdays} day" )
fi
- ${command_line} --motu ${motu_url_reana} --service-id ${service_id_reana} --product-id ${product_id_reana} --longitude-min ${lon_min} --longitude-max ${lon_max} --latitude-min ${lat_min} --latitude-max ${lat_max} --date-min "${start_date} 12:00:00" --date-max "${end_date} 12:00:00" --depth-min 0.493 --depth-max 5727.918 ${variables} --out-dir ./ --out-name ${tmpoutname} --user ${user} --pwd ${password}
+ echo "${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${tmpoutname} --username ${user} --password ${password} --force-download"
+ ${command_line} subset -i ${product_id_reana} -x ${lon_min} -X ${lon_max} -y ${lat_min} -Y ${lat_max} -t "${start_date}" -T "${end_date}" -z 0.493 -Z 5727.918 ${variables} -o ./ -f ${tmpoutname} --username ${user} --password ${password} --force-download
ncks -O -F --mk_rec_dmn time ${tmpoutname} ${tmpoutname}
done
cd ${OUTDIR}
- ncrcat -O raw_motu_${PREFIX}_Y${YEAR}M${MONTH}D*.nc raw_motu_${PREFIX}_Y${YEAR}M${MONTH}.nc
- rm -r raw_motu_${PREFIX}_Y${YEAR}M${MONTH}D*.nc
+ ncrcat -O raw_${PREFIX}_Y${YEAR}M${MONTH}D*.nc raw_${PREFIX}_Y${YEAR}M${MONTH}.nc
+ rm -r raw_${PREFIX}_Y${YEAR}M${MONTH}D*.nc
cd -
fi
fi
diff --git a/Oforc_OGCM/download_mercator_python.m b/Oforc_OGCM/download_mercator_python.m
index eb98f398503619748aaeda2822c4cda7e63cea6c..31d4ea5445894f277440c5144312b33bc4129644 100644
--- a/Oforc_OGCM/download_mercator_python.m
+++ b/Oforc_OGCM/download_mercator_python.m
@@ -1,5 +1,5 @@
-function download_mercator_python(pathMotu,user,password,mercator_type, ...
- motu_url,service_id,product_id, ...
+function download_mercator_python(pathCMC,user,password,mercator_type, ...
+ product_id, ...
Y,M, ...
lonmin,lonmax,latmin,latmax,zmax, ...
OGCM_dir,OGCM_prefix,thedatemonth,Yorig)
@@ -37,7 +37,6 @@ function download_mercator_python(pathMotu,user,password,mercator_type, ...
% Updated 20-Aug-2008 by Matthieu Caillaud & P. Marchesiello
% Update 23-Oct-2020 by Gildas Cambon
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% pathMotu is a deprecated parameter !
download_raw_data=1;
convert_raw2crocotools=1; % convert -> crocotools format data
%
@@ -48,7 +47,7 @@ vars = {'zos' ...
'vo' ...
'thetao' ...
'so'};
-
+%
disp([' '])
disp(['Get data for Y',num2str(Y),'M',num2str(M)])
disp(['Minimum Longitude: ',num2str(lonmin)])
@@ -60,8 +59,7 @@ disp([' '])
% Create the directory
%
disp(['Making output data directory ',OGCM_dir])
-eval(['!mkdir ',OGCM_dir])
-
+eval(['!mkdir ',OGCM_dir, ' 2> /dev/null'])
%
% Get files and dates
%
@@ -69,7 +67,6 @@ eval(['!mkdir ',OGCM_dir])
time1=datenum(Y,M,01);
time2=datenum(Y,M+1,01) - 1;
%time2=datenum(Y,M,02); %for debug
-%e debug
time=cat(2,time1,time2);
tiempo_inicial = time(1);
tiempo_final = time(end);
@@ -80,47 +77,84 @@ end
if (lonmax > 180)
lonmax = lonmax - 360;
end
-raw_mercator_name=[OGCM_dir,'raw_motu_',OGCM_prefix,thedatemonth,'.nc'];
+raw_mercator_name=[OGCM_dir,'raw_',OGCM_prefix,thedatemonth,'.nc'];
if download_raw_data
%
- % Get data
- % (temporarily removing Matlab lib path to avoid conflict with Python, mandatory with python 2.7.X)
- % for example problem like :
- % Execution failed: /usr/lib/python2.7/lib-dynload/pyexpat.x86_64-linux-gnu.so:
- % undefined symbol: XML_SetHashSalt" )
-
- pathdyld=getenv('DYLD_LIBRARY_PATH');
- setenv('DYLD_LIBRARY_PATH','');
- pathld=getenv('LD_LIBRARY_PATH');
- setenv('LD_LIBRARY_PATH','');
-
- get_file_python_mercator(pathMotu,mercator_type, ...
- motu_url,service_id,product_id, ...
+ % Get data
+ if mercator_type==1
+ get_file_python_mercator(pathCMC, ...
+ product_id, ...
vars, ...
[lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
{datestr(tiempo_inicial,'yyyy-mm-dd') ...
datestr(tiempo_final, 'yyyy-mm-dd')}, ...
{user password}, ...
- raw_mercator_name);
-
- setenv('DYLD_LIBRARY_PATH',pathdyld); % set back Matlab libs path
- setenv('LD_LIBRARY_PATH',pathld); % set back Matlab libs path
-end %end download_raw_data
+ raw_mercator_name);
+
+ elseif mercator_type==2
+ %zos
+ get_file_python_mercator(pathCMC,...
+ product_id{1}, ...
+ vars{1}, ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_z.nc']);
+ %uo/vo
+ get_file_python_mercator(pathCMC, ...
+ product_id{2}, ...
+ {vars{2:3}}, ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_u.nc']);
+ %thetao
+ get_file_python_mercator(pathCMC, ...
+ product_id{3}, ...
+ vars{4}, ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_t.nc']);
+ %so
+ get_file_python_mercator(pathCMC, ...
+ product_id{4}, ...
+ vars{5}, ...
+ [lonmin-1 lonmax+1 latmin-1 latmax+1 0 zmax], ...
+ {datestr(tiempo_inicial,'yyyy-mm-dd') ...
+ datestr(tiempo_final, 'yyyy-mm-dd')}, ...
+ {user password}, ...
+ [raw_mercator_name(1:end-3),'_s.nc']);
+ end
+%
+end %end download_raw_data
+%
if convert_raw2crocotools
%
% Convert data format and write in a more CROCOTOOLS
% compatible input file
%
- mercator_name=[OGCM_dir,'raw_motu_',OGCM_prefix,thedatemonth,'.nc'];
+ mercator_name=[OGCM_dir,'raw_',OGCM_prefix,thedatemonth,'.nc'];
if exist(mercator_name)
disp('Mercator file already exist => overwrite it')
end
- write_mercator(OGCM_dir,OGCM_prefix,raw_mercator_name, ...
- mercator_type,vars,time,thedatemonth,Yorig); % write data
- eval(['! rm -f ',raw_mercator_name]);
+ if mercator_type==1
+ write_mercator(OGCM_dir,OGCM_prefix,raw_mercator_name, ...
+ mercator_type,vars,time,thedatemonth,Yorig); % write data
+% eval(['! rm -f ',raw_mercator_name]);
+ elseif mercator_type==2
+ write_mercator_multi(OGCM_dir,OGCM_prefix,raw_mercator_name, ...
+ mercator_type,vars,time,thedatemonth,Yorig); % write data
+% eval(['! rm -f ',raw_mercator_name(1:end-3),'*.nc']);
+ end
+
+
end
end
diff --git a/Oforc_OGCM/extract_ECCO.m b/Oforc_OGCM/extract_ECCO.m
deleted file mode 100644
index 936831af9fedd44fb4032d59486c374d7afa67c2..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/extract_ECCO.m
+++ /dev/null
@@ -1,172 +0,0 @@
-function extract_ECCO(OGCM_dir,OGCM_prefix,url,Y,M,catalog_vname,...
- catalog_vname2,...
- lon,lat,depth,...
- krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max,......
- Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subset from ECCO using DODS
-% Write it in a local file (keeping the classic
-% SODA netcdf format)
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 6-Sep-2006 by Pierrick Penven
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-disp([' Download ECCO2 for ',num2str(Y),...
- ' - ',num2str(M)])
-%
-% Get Matlab version
-%
-matversion=version('-release');
-matlab_new=~verLessThan('matlab','7.14');
-disp([' Matlab version : ',matversion])
-disp([' !!! WARNING !!! '])
-if matlab_new
- disp([' Matlab version >= 2012a '])
- disp([' --> use Matlab built-in support for OPeNDAP'])
- disp([' with Matlab scripts in Opendap_tools_no_loaddap'])
- disp([' (set path in start.m)'])
-else
- disp([' Matlab version < 2012a '])
- disp([' --> use Matlab scripts in Opendap_tools'])
- disp([' (set path in start.m)'])
-end
-disp([' !!! WARNING !!! '])
-%
-% Get the number of days in the month
-%
-nmax=daysinmonth(Y,M);
-%%nmax=5;
-Lm=length(lon);
-Mm=length(lat);
-N=length(depth);
-%int_3D=3; % Interval in days between ECCO2 data for 3D variables
-%int_2D=1; % Interval in days between ECCO2 data for 2D variables
-for vv=1:length(catalog_vname)
- vname=char(catalog_vname(vv));
- vname2=char(catalog_vname2(vv));
- prefix=[char(vname),'.nc/'];
- % Get starting day of month
- if strcmp(vname,'THETA')
- Dst=1;
- disp(['-->'])
- disp([' Check ',vname,' for ',datestr(datenum(Y,M,Dst,0,0,0))])
- fname0=get_filename_ECCO(vname,Y,M,Dst);
- fname=[url,prefix,fname0];
- % Determine if dap file exists at day D0
- % --> if not, increment
- dok=[];
- try; dok=loaddap('-A -e +v ',fname); end;
- while isempty(dok)==1
- Dst=Dst+1;
- fname0=get_filename_ECCO(vname,Y,M,Dst);
- fname=[url,prefix,fname0];
- try; dok=loaddap('-A -e +v ',fname); end;
- end
- end
- % Compute 3D variable every 3 days
- if ~strcmp(vname,'SSH')% v-> name='UVEL, VVEL'
- var0=nan*zeros(N,Mm,Lm);
- tndx=0;
- for D=Dst:3:nmax
- tndx=tndx+1;
- disp(['===>'])
- disp([' Downloading ',vname,' for ',datestr(datenum(Y,M,D,0,0,0))])
- fname0=get_filename_ECCO(vname,Y,M,D);
- fname=[url,prefix,fname0];
- time=readdap(fname,'TIME',[]);
- time3d(tndx)=time+datenum(1992,1,1)-datenum(Yorig,1,1);
- x=readattribute(fname);
- eval(['missing_value=x.',vname,'.missing_value;'])
- var0=getdap('',fname,vname,'[0:0]', ...
- krange,jrange,i1min,i1max,i2min,i2max,i3min,i3max);
- var0(var0<=-2000)=NaN;
- if matlab_new
- var(tndx,:,:,:)=var0;
- else
- var(tndx,:,:,:)=permute(var0,[3 1 2]); % old readdap version
- end
- %size(var)
- end
- if strcmp(vname,'UVEL')
- u=var;
- elseif strcmp(vname,'VVEL')
- v=var;
- elseif strcmp(vname,'THETA')
- temp=var;
- elseif strcmp(vname,'SALT')
- salt=var;
- end
- % disp(['Write variable ',vname2])
- % create_ECCO_3D([OGCM_dir,vname2,'_Y',num2str(Y),'M',num2str(M),'.cdf'], ...
- % vname2,lon,lat,depth,time3d,var,Yorig)
- clear var
-
- else
-
- % Compute 2D variable every 3 days also!
- var0=nan*zeros(Mm,Lm);
- tndx=0;
- for D=Dst:3:nmax
- tndx=tndx+1;
- disp(['===>'])
- disp([' Downloading ',vname,' for ',datestr(datenum(Y,M,D,0,0,0))])
- fname0=get_filename_ECCO(vname,Y,M,D);
- fname=[url,prefix,fname0];
- time=readdap(fname,'TIME',[]);
- time3d(tndx)=time+datenum(1992,1,1)-datenum(Yorig,1,1);
- x=readattribute(fname);
- eval(['missing_value=x.',vname,'.missing_value;'])
- var0=getdap('',fname,vname,'[0:0]','', ...
- jrange,i1min,i1max,i2min,i2max,i3min,i3max);
- var0(var0<=-2000)=NaN;
- var(tndx,:,:)=var0;
- end
- if strcmp(vname,'SSH')
- ssh=var;
- end
- % disp(['Write variable ',vname2])
- % create_ECCO_2D([OGCM_dir,vname2,'_Y',num2str(Y),'M',num2str(M),'.cdf'], ...
- % vname2,lon,lat,time3d,var,Yorig)
- clear var
-
- end %-> if
-
-end %-> catalogue_vname list
-
-%
-% Create ECCO file and write variables
-%
-create_OGCM([OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf'],...
- lon,lat,lon,lat,lon,lat,depth,time3d,temp,salt,u,v,ssh,Yorig)
-
-return
-
-end
-
diff --git a/Oforc_OGCM/extract_SODA.m b/Oforc_OGCM/extract_SODA.m
index acc6507727bfbbcc04c9caa57148ee24e6977832..77c7936bd008ddb45a7ebeaf505ccca1f408fe34 100644
--- a/Oforc_OGCM/extract_SODA.m
+++ b/Oforc_OGCM/extract_SODA.m
@@ -32,8 +32,10 @@ function extract_SODA(SODA_dir,SODA_prefix,url,year,month,...
% e-mail:Pierrick.Penven@ird.fr
%
% Updated 6-Sep-2006 by Pierrick Penven
-% Updated : 23-Oct-2009 by Gildas Cambon Adaptation for the special tratment
+% Updated : 23-Oct-2009 by Gildas Cambon Adaptation for the special treatement
% for the bry file
+% Updated 18-March-2024 by Gildas Cambon
+% - remove download of taux and tauy
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
disp([' Download SODA for ',num2str(year),...
@@ -62,33 +64,33 @@ if missval<0
else
ssh(ssh>=(0.9*missval))=NaN;
end
-%
-% Get TAUX
-%
-disp(' ...TAUX')
-taux=getdap(url,'',...
- 'taux',trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-eval(['missval=double(x.taux.',missname,');'])
-if missval<0
- taux(taux<=(0.9*missval))=NaN;
-else
- taux(taux>=(0.9*missval))=NaN;
-end
-%
-% Get TAUY
-%
-disp(' ...TAUY')
-tauy=getdap(url,'',...
- 'tauy',trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-eval(['missval=double(x.tauy.',missname,');'])
-if missval<0
- tauy(tauy<=(0.9*missval))=NaN;
-else
- tauy(tauy>=(0.9*missval))=NaN;
-end
-%
+% %
+% % Get TAUX
+% %
+% disp(' ...TAUX')
+% taux=getdap(url,'',...
+% 'taux',trange,'',jrange,...
+% i1min,i1max,i2min,i2max,i3min,i3max);
+% eval(['missval=double(x.taux.',missname,');'])
+% if missval<0
+% taux(taux<=(0.9*missval))=NaN;
+% else
+% taux(taux>=(0.9*missval))=NaN;
+% end
+% %
+% % Get TAUY
+% %
+% disp(' ...TAUY')
+% tauy=getdap(url,'',...
+% 'tauy',trange,'',jrange,...
+% i1min,i1max,i2min,i2max,i3min,i3max);
+% eval(['missval=double(x.tauy.',missname,');'])
+% if missval<0
+% tauy(tauy<=(0.9*missval))=NaN;
+% else
+% tauy(tauy>=(0.9*missval))=NaN;
+% end
+% %
% Get U
%
disp(' ...U')
@@ -147,8 +149,11 @@ end
%
% Create the SODA file
%
-create_SODA([SODA_dir,SODA_prefix,'Y',num2str(year),'M',num2str(month),'.cdf'],...
+% create_SODA([SODA_dir,SODA_prefix,'Y',num2str(year),'M',num2str(month),'.cdf'],...
+% lon,lat,lon,lat,lon,lat,depth,time,...
+% temp,salt,u,v,ssh,taux,tauy,Yorig)
+create_OGCM([SODA_dir,SODA_prefix,'Y',num2str(year),'M',num2str(month),'.cdf'],...
lon,lat,lon,lat,lon,lat,depth,time,...
- temp,salt,u,v,ssh,taux,tauy,Yorig)
+ temp,salt,u,v,ssh,Yorig)
%
return
diff --git a/Oforc_OGCM/extract_mercator.m b/Oforc_OGCM/extract_mercator.m
deleted file mode 100644
index 6842dea339cfcba39a969e4aac1a355996a8996d..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/extract_mercator.m
+++ /dev/null
@@ -1,212 +0,0 @@
-function extract_mercator(OGCM_dir,OGCM_prefix,url,Y,M,...
- lon,lon_u,lat,lat_v,depth,...
- krange,jrange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- Yorig)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extract a subset from ECCO using DODS
-% Write it in a local file (keeping the classic
-% SODA netcdf format)
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 6-Sep-2006 by Pierrick Penven
-% Updated 20-Aug-2008 by Matthieu Caillaud & P. Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-disp([' Download mercator for ',num2str(Y),...
- ' - ',num2str(M)])
-
-%
-% Get the dataset attributes
-%
-
-% test if the file exist
-%
-%
-foundfile=0;
- fname=url;
- warning off
- try
- x=loaddap('-A -e +v ', fname);
- foundfile=1;
- catch
- foundfile=0;
- end
- if foundfile==1 & ~isempty(x)
- disp(' File found')
- else
- foundfile=0;
- disp(' File does not exist')
- end
- warning on
-%
-%
-missval=x.ssh.missing_value; %PSY3V1
-
-%missval=x.ssh.ml__FillValue; %PSY3V2
-
-
-
-%
-% Get the time range
-%
-time=readdap(fname,'time',[]);
-%
-% Process the time
-%
-time=time+datenum(1950,1,1);
-
-disp(datestr(time));
-c=datevec(time);
-y0=c(:,1);
-m0=c(:,2);
-d0=c(:,3);
-oktime=1;
-d=[12;13;14;15;16;17;18];
-if Y~=mean(y0)
- disp(['Warning: dates are not all for year: ',num2str(Y)])
- oktime=0;
-end
-tndx=find(m0==M & y0==Y);
-if isempty(tndx)
- error('Time problem: did not find the corresponding month')
-end
-%
-if oktime==0 & M==12 % to get the value of 1 jan of next year %
- tndx=[tndx;tndx(end)+1];
-end
-
-trange=['[',num2str(min(tndx)-1),':',num2str(max(tndx)-1),']'];
-
-
-% tndx=find(m0==M & y0==Y);
- % trange=['[',num2str(tndx(1)-1),']'];
-
-%
-% Put the time into "Yorig time"
-%
-time=time(tndx)-datenum(Yorig,1,1);
-%
-% Get SSH
-%
-disp(' ...SSH')
-vname='ssh';
-fname='';
-ssh=getdap(url,fname,vname,...
- trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-
-
-
-ssh=shiftdim(ssh,2);
-%missval=x.ssh.missing_value;
-ssh(ssh>=missval)=NaN;
-%
-% Get TAUX
-%
-disp(' ...TAUX')
-taux=getdap(url,fname,...
- 'taux',trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-
-
-%missval=x.taux.missing_value;
-taux(taux>=missval)=NaN;
-%
-% Get TAUY
-%
-disp(' ...TAUY')
-tauy=getdap(url,fname,...
- 'tauy',trange,'',jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-%missval=x.tauy.missing_value;
-tauy(tauy>=missval)=NaN;
-%
-
-% Get U
-%
-disp(' ...U')
-vname='u';
-u=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u);
-u=permute(u,[4 3 1 2]);
-%u=shiftdim(u,2);
-%missval=x.u.missing_value;
-u(u>=missval)=NaN;
-%
-% Get V
-%
-disp(' ...V')
-vname='v';
-v=getdap(url,fname,vname,...
- trange,krange,jrange_v,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-v=permute(v,[4 3 1 2]);
-%missval=x.v.missing_value;
-v(v>=missval)=NaN;
-%
-% Get TEMP
-%
-disp(' ...TEMP')
-vname='temperature';
-temp=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-temp=permute(temp,[4 3 1 2]);
-
-%temp=shiftdim(temp,2);
-%missval=x.temperature.missing_value;
-temp(temp>=missval)=NaN;
-%
-% Get SALT
-%
-disp(' ...SALT')
-vname='salinity';
-salt=getdap(url,fname,vname,...
- trange,krange,jrange,...
- i1min,i1max,i2min,i2max,i3min,i3max);
-salt=permute(salt,[4 3 1 2]);
-%salt=shiftdim(salt,2);
-%missval=x.salinity.missing_value;
-salt(salt>=missval)=NaN;
-%
-% Create the ECCO file
-%
-fname=url
-%
-%
-create_OGCM([OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf'],...
- lon,lat,lon_u,lat,lon,lat_v,depth,time,...
- temp,salt,u,v,ssh,Yorig)
-%
-return
-
-end
-
diff --git a/Oforc_OGCM/get_ECCO_subgrid.m b/Oforc_OGCM/get_ECCO_subgrid.m
deleted file mode 100644
index f7488716e3991ba3ce6835a2243c0252e2642ff4..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/get_ECCO_subgrid.m
+++ /dev/null
@@ -1,138 +0,0 @@
-function [i1min,i1max,i2min,i2max,i3min,i3max,...
- i1min_u,i1max_u,i2min_u,i2max_u,i3min_u,i3max_u,...
- jrange,jrange_v,krange,lon,lon_u,lat,lat_v,depth]=...
- get_ECCO_subgrid(path,lonmin,lonmax,latmin,latmax)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Get the indices for a ECCO subgrid
-%
-%
-% Further Information:
-% http://www.croco-ocean.org
-%
-% This file is part of CROCOTOOLS
-%
-% CROCOTOOLS is free software; you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published
-% by the Free Software Foundation; either version 2 of the License,
-% or (at your option) any later version.
-%
-% CROCOTOOLS is distributed in the hope that it will be useful, but
-% WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program; if not, write to the Free Software
-% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
-% MA 02111-1307 USA
-%
-% Copyright (c) 2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-% Updated 6-Sep-2006 by Pierrick Penven
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-dl=1;
-lonmin=lonmin-dl;
-lonmax=lonmax+dl;
-latmin=latmin-dl;
-latmax=latmax+dl;
-%
-% Get the global grid
-%
-lon=readdap(path,'LONGITUDE_T',[]);
-lat=readdap(path,'LATITUDE_T',[]);
-depth=readdap(path,'DEPTH_T',[]);
-%
-% Quick fix because lon_u and lat_v are
-%
-disp('GET_ECCO_SUBGRID: Warning lon_u and lat_v are no more downloaded from the server')
-lon_u=lon-0.5;
-lat_v=lat-0.5;
-%
-% Get a subgrid
-%
-%
-% 1 Longitude: take care of greenwitch
-%
-i1=find(lon-360>=lonmin & lon-360<=lonmax);
-i2=find(lon>=lonmin & lon<=lonmax);
-i3=find(lon+360>=lonmin & lon+360<=lonmax);
-%
-lon=cat(1,lon(i1)-360,lon(i2),lon(i3)+360);
-%
-if ~isempty(i1)
- i1min=min(i1)-1;
- i1max=max(i1)-1;
-else
- i1min=[];
- i1max=[];
-end
-if ~isempty(i2)
- i2min=min(i2)-1;
- i2max=max(i2)-1;
-else
- i2min=[];
- i2max=[];
-end
-if ~isempty(i3)
- i3min=min(i3)-1;
- i3max=max(i3)-1;
-else
- i3min=[];
- i3max=[];
-end
-%
-i1_u=find(lon_u-360>=lonmin & lon_u-360<=lonmax);
-i2_u=find(lon_u>=lonmin & lon_u<=lonmax);
-i3_u=find(lon_u+360>=lonmin & lon_u+360<=lonmax);
-%
-lon_u=cat(1,lon_u(i1_u)-360,lon_u(i2_u),lon(i3_u)+360);
-%
-if ~isempty(i1_u)
- i1min_u=min(i1_u)-1;
- i1max_u=max(i1_u)-1;
-else
- i1min_u=[];
- i1max_u=[];
-end
-if ~isempty(i2_u)
- i2min_u=min(i2_u)-1;
- i2max_u=max(i2_u)-1;
-else
- i2min_u=[];
- i2max_u=[];
-end
-if ~isempty(i3_u)
- i3min_u=min(i3_u)-1;
- i3max_u=max(i3_u)-1;
-else
- i3min_u=[];
- i3max_u=[];
-end
-%
-% 2 Latitude
-%
-j=find(lat>=latmin & lat<=latmax);
-lat=lat(j);
-jmin=min(j)-1;
-jmax=max(j)-1;
-jrange=['[',num2str(jmin),':',num2str(jmax),']'];
-%
-j_v=find(lat_v>=latmin & lat_v<=latmax);
-lat_v=lat_v(j_v);
-jmin_v=min(j_v)-1;
-jmax_v=max(j_v)-1;
-jrange_v=['[',num2str(jmin_v),':',num2str(jmax_v),']'];
-%
-% 3 Depth
-%
-k=length(depth);
-krange=['[',num2str(0),':',num2str(k-1),']'];
-%
-return
-
-end
-
diff --git a/Oforc_OGCM/get_file_python_mercator.m b/Oforc_OGCM/get_file_python_mercator.m
index 4320a577d1b9c49c84d543eda371e3afd694eb2d..1fe41bcf8da615bfdae7ddf7e8687642429499da 100644
--- a/Oforc_OGCM/get_file_python_mercator.m
+++ b/Oforc_OGCM/get_file_python_mercator.m
@@ -1,7 +1,8 @@
-function outname = get_file_python_mercator(pathmotu,mercator_type,...
- motu_url,service_id,product_id, ...
- vars, ...
- geom,date,info,outname)
+function outname = get_file_python_mercator(pathCMC,...
+ product_id,...
+ vars,...
+ geom,date,...
+ info,outname)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Extract a subgrid from MERCATOR to get a CROCO forcing
@@ -33,115 +34,36 @@ function outname = get_file_python_mercator(pathmotu,mercator_type,...
%
% Updated 12-Feb-2016 by P. Marchesiello
% Updated 26-Nov-2020 by G. Cambon
+% Updated 22-Feb-2024 by G. Cambon
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Usage:
-%=======
-% get_file_python_mercator(pathMotu,mercator_type,...
-% motu_url,service_id,product_id, ...
-% {'varname1' 'varname2'}, ...
-% [lonmin lonmax latmin latmax, depthmin depthmax], ...
-% {'startdate' 'enddate'},{user password},
-% 'outname.nc');
-%
-% For GLORYS 12 reanalysis
-% ========================
-% motu_url='http://my.cmems-du.eu/motu-web/Motu';
-% service_id='GLOBAL_REANALYSIS_PHY_001_030-TDS';
-% product_id='global-reanalysis-phy-001-030-daily';
-%
-% For Mercator 1/12 forecast
-% ==========================
-% motu_url='http://nrt.cmems-du.eu/motu-web/Motu';
-% service_id='GLOBAL_ANALYSIS_FORECAST_PHY_001_024-TDS';
-% product_id='global-analysis-forecast-phy-001-024';
-%
-% For Met-Office 1/4 forecast
-% ===========================
-% motu_url='http://nrtcmems.mercator-ocean.fr/motu-web/Motu';
-% service_id='GLOBAL_ANALYSIS_FORECAST_PHYS_001_015-TDS';
-% product_id='global-analysis-forecast-phys-001-015';
-%
-% Check http://marine.copernicus.eu/web/34-products-and-services-faq.php
-% for changes in the command line: addresses, file names, variable names ...
-%
-% Currently needs Python2.7.X (with X >= 10) or Python 3.X (with >=4)
-% and motuclient.py v.1.8.X (where "X" is equal or higher to "4")
-% from https://marine.copernicus.eu/services-portfolio/technical-faq/#motu-client
-%
-% python
-% ======
-% Type:
-% python --version
-% It should return: "Python 2.7.10+" or "Python 3.4+".
-%
-% motuclient
-% ==========
-% 1- Use croco's motuclient (pathMotu => Forecast_tools) or ...
-% 2- Install your own motuclient:
-% To update/upgrade and get the latest version of motuclient
-% from a previous version (<= v1.8.3), type in the following:
-% $ python -m pip install --upgrade motuclient
-% Otherwise (if there is no previous installation of motuclient),
-% type in the following:
-% $ python -m pip install motuclient
-% It should install and display motuclient package v1.8.4 (Oct. 2019).
-% To make sure, display the version:
-% $ python -m motuclient --version
-% If it does not return: "motuclient-python v1.8.X" ("X" >= "4"),
-% then type in the following:
-% $ python -m pip install motuclient==1.8.4
-%=======
-%
-eval(['! rm ',outname])
+% Informations :
+% => https://help.marine.copernicus.eu/en/collections/4060068-copernicus-marine-toolbox
+% => https://help.marine.copernicus.eu/en/articles/8206131-how-to-download-a-copernicus-marine-toolbox-request-in-matlab
+%
+eval(['! rm -f ',outname])
+disp([' '])
+disp(['Extraction of product: ', product_id])
+disp([' '])
+command = { sprintf('export PYTHONWARNINGS="ignore"; ')
+ sprintf('%s',pathCMC)
+ sprintf(' subset')
+ sprintf(' --username %s --password %s',info{1},info{2})
+ sprintf(' -i %s',product_id)
+ sprintf(' -t %s -T %s',['"',date{1},'"'],['"',date{2},'"'])
+ sprintf(' -x %f -X %f',geom(1),geom(2))
+ sprintf(' -y %f -Y %f',geom(3),geom(4))
+ sprintf(' -z %f -Z %f',geom(5),geom(6))
+ sprintf(' -o ./')
+ sprintf(' -f %s',outname)
+ sprintf(' --force-download')};
-if isempty(pathmotu), % use your own motuclient
-
- command = {'!python -m motuclient'
- sprintf(' -u %s -p %s',info{1},info{2})
- sprintf(' -m %s',motu_url)
- sprintf(' -s %s',service_id)
- sprintf(' -d %s',product_id)
- sprintf(' -t %s -T %s',date{1},date{2})
- sprintf(' -x %f -X %f',geom(1),geom(2))
- sprintf(' -y %f -Y %f',geom(3),geom(4))
- sprintf(' -z %f -Z %f',geom(5),geom(6))
- sprintf(' -o ./')
- sprintf(' --out-name %s',outname)};
-
-else % use croco's motuclient
-
- command = {'!'
- sprintf('%s',pathmotu)
- 'motuclient-python/motuclient.py'
- sprintf(' -u %s -p %s',info{1},info{2})
- sprintf(' -m %s',motu_url)
- sprintf(' -s %s',service_id)
- sprintf(' -d %s',product_id)
- sprintf(' -t %s -T %s',date{1},date{2})
- sprintf(' -x %f -X %f',geom(1),geom(2))
- sprintf(' -y %f -Y %f',geom(3),geom(4))
- sprintf(' -z %f -Z %f',geom(5),geom(6))
- sprintf(' -o ./')
- sprintf(' --out-name %s',outname)};
-end
-
-for k =1:length(vars)
- command{end+1}=sprintf(' -v %s ',vars{k});
+if isa(vars,'cell')
+ for k =1:size(vars,2)
+ command{end+1}=sprintf(' -v %s',vars{k});
+ end
end
-%===
-% If using a proxy server, uncomment the following line and replace by your
-% proxy url and port server. Beware that a SPACE is needed between
-% "--proxy-server=" and "the proxy-server-name" !
-%
-%command{end+2}=sprintf('--proxy-server= http://your_proxy_server:your_proxy_port');
-%===
disp([command{:}])
-eval([command{:}])
+system([command{:}]);
-%
-% example of a python motuclient commands
-%
-%python -m motuclient --motu http://my.cmems-du.eu/motu-web/Motu --service-id GLOBAL_REANALYSIS_PHY_001_030-TDS --product-id global-reanalysis-phy-001-030-daily --longitude-min 15 --longitude-max 20 --latitude-min -40 --latitude-max -25 --date-min "2004-12-31 12:00:00" --date-max "2005-02-01 12:00:00" --depth-min 0.493 --depth-max 5727.918 --variable so --variable thetao --variable uo --variable vo --variable zos --out-dir <OUTPUT_DIRECTORY> --out-name <OUTPUT_FILENAME> --user <USERNAME> --pwd <PASSWORD>
-end
diff --git a/Oforc_OGCM/get_filename_ECCO.m b/Oforc_OGCM/get_filename_ECCO.m
deleted file mode 100644
index 02893a34c70139d3dabda2d175dfd65d4d9b9cee..0000000000000000000000000000000000000000
--- a/Oforc_OGCM/get_filename_ECCO.m
+++ /dev/null
@@ -1,24 +0,0 @@
-function fname=get_filename_ECCO(vname,Y,M,D)
-
-stryear=num2str(Y);
-if M<10
- strmonth=['0',num2str(M)];
-else
- strmonth=[num2str(M)];
-end
-
-if D<10
- strday=['0',num2str(D)];
-else
- strday=[num2str(D)];
-end
-
-if strcmp(vname,'SSH')
- fname=[vname,'.1440x720.',stryear,strmonth,strday,'.nc'] ;
-else
- fname=[vname,'.1440x720x50.',stryear,strmonth,strday,'.nc'] ;
-end
-return
-
-end
-
diff --git a/Oforc_OGCM/make_OGCM.m b/Oforc_OGCM/make_OGCM_SODA.m
similarity index 93%
rename from Oforc_OGCM/make_OGCM.m
rename to Oforc_OGCM/make_OGCM_SODA.m
index 13b070e9821bd97de7051930c4bda69620b791f4..f59e5e54c0f8ec650b2a2044832c2bf95b552635 100644
--- a/Oforc_OGCM/make_OGCM.m
+++ b/Oforc_OGCM/make_OGCM_SODA.m
@@ -1,6 +1,6 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Create and fill CROCO clim and bry files with OGCM data.
+% Create and fill CROCO clim and bry files with OGCM SODA data.
%
% The on-line reference to SODA is at
% http://iridl.ldeo.columbia.edu./SOURCES/.CARTON-GIESE/.SODA/
@@ -45,35 +45,13 @@ close all
% Common parameters
%
crocotools_param
-%
-if strcmp(OGCM,'SODA')
+
%
% SODA DODS URL
%
- % SODA 2.0.2-4
- %url= 'http://apdrc.soest.hawaii.edu:80/dods/public_data/SODA/soda_pop2.0.4'
-
- % SODA_2.1.6 [ ERA40/QSCAT 1958-2008 / POP2.1 / WOD09 ]
- %%url='http://iridl.ldeo.columbia.edu/SOURCES/.CARTON-GIESE/.SODA/.v2p1p6' ;
- %url='http://apdrc.soest.hawaii.edu:80/dods/public_data/SODA/soda_pop2.1.6' ;
-
% SODA_2.2.4/ [ C20R-2 1871-2008 / POP2.1 ]
%%url='http://iridl.ldeo.columbia.edu/SOURCES/.CARTON-GIESE/.SODA/.v2p2p4' ;
url='http://apdrc.soest.hawaii.edu:80/dods/public_data/SODA/soda_pop2.2.4' ;
-
-elseif strcmp(OGCM,'ECCO')
- %
- % ECCO DODS URL
- %
- % Kalman filter
- %
- % url = 'http://ecco.jpl.nasa.gov/thredds/dodsC/las/kf080/kf080_';
- url = 'http://ecco2.jpl.nasa.gov:80/opendap/data1/cube/cube92/lat_lon/quart_90S_90N/'
- %
-else
- error(['Unknown OGCM: ',OGCM])
- % for mercator/glorys12 reanalysis use make_OGCM_mercator.m
-end
%
itolap_tot=itolap_a + itolap_p;
disp(['Overlap before =',num2str(itolap_a)])
@@ -118,8 +96,8 @@ if Download_data==1
% Download data with DODS (the download matlab routine depends on the OGCM)
%
disp('Download data...')
- eval(['download_',OGCM,'(Ymin,Ymax,Mmin,Mmax,lonmin,lonmax,latmin,latmax,',...
- 'OGCM_dir,OGCM_prefix,url,Yorig)'])
+ download_SODA(Ymin,Ymax,Mmin,Mmax,lonmin,lonmax,latmin,latmax,...
+ OGCM_dir,OGCM_prefix,url,Yorig)
end
%
%------------------------------------------------------------------------------------
@@ -322,10 +300,10 @@ if makeclim==1 | makebry==1
Yp=Y;
for aa=1:itolap_p
tndx_OGCM(aa)=ntimes;
- end
+ end
else
for aa=1:itolap_p
- tndx_OGCM(aa)=aa;
+ tndx_OGCM(aa)=aa;
end;
end
%
diff --git a/Oforc_OGCM/make_OGCM_mercator.m b/Oforc_OGCM/make_OGCM_mercator.m
index 1619d15f8212497dd5b874344065d7cfd2e9b291..510f206909ca6e8244e58c6ac518481c1d041e25 100644
--- a/Oforc_OGCM/make_OGCM_mercator.m
+++ b/Oforc_OGCM/make_OGCM_mercator.m
@@ -3,6 +3,19 @@
% Create and fill CROCO clim and bry files with OGCM
% MERCATOR data.
%
+% On crocotools_param.m, available datasets:
+% SODA -> Description : 1/4 deg SODA v2.2.4 monthly means
+% (187101 -> 201012)
+% mercator -> 2 options for mercator_type parameter:
+%
+% 1 --> 1/12 deg Mercator global reanalysis (1993 -> 202101)
+% (Monthly or Daily product)
+% 2 --> 1/12 deg Mercator global analysis (202011 -> )
+%
+% Note for 2:
+% (7days from now -> now-1day : Near Real Time analysis)
+% (more than 15days from now : Best analysis)
+%
% Online reference to MERCATOR is at http://marine.copernicus.eu
%
% Further Information:
@@ -109,10 +122,9 @@ if Download_data==1
mo_max=12;
end
for M=mo_min:mo_max
- %motu_url_reana
thedatemonth=['Y',num2str(Y),'M',num2str(M)];
- download_mercator_python(pathMotu,user,password,1,...
- motu_url_reana,service_id_reana,product_id_reana, ...
+ download_mercator_python(pathCMC,user,password,mercator_type,...
+ product_id, ...
Y,M, ...
lonmin,lonmax,latmin,latmax,hmax, ...
OGCM_dir,OGCM_prefix,thedatemonth,Yorig)
@@ -154,7 +166,8 @@ if makeini==1
% Process the time in Yorig time (i.e days since Yorig-01-01)
%
tini=datenum(Ymin,Mmin,1)-datenum(Yorig,1,1);
- disp(['Create an initial file for ',datestr(tini+datenum(Yorig,1,1));])
+ disp([' '])
+ disp(['=> Create an initial file for ',datestr(tini+datenum(Yorig,1,1));])
create_inifile(ininame,grdname,CROCO_title,...
theta_s,theta_b,hc,N,...
tini,'clobber', vtransform);
@@ -211,10 +224,10 @@ if makeclim==1 | makebry==1
OGCM_time=nc{'time'}(:);
ntimes=length(OGCM_time);
if ntimes==1
- dt=30; % monthly files (SODA..)
+ dt=30; % monthly files
itolap_a=1; itolap_p=1;
itolap_tot=itolap_a + itolap_p;
- disp(['Reduced overlap for monthly SODA files'])
+ disp(['Reduced overlap for monthly files'])
disp(['...'])
else
dt=max(gradient(OGCM_time));
@@ -254,6 +267,8 @@ if makeclim==1 | makebry==1
if makebry==1
bryname=[bry_prefix,'Y',num2str(Y),...
'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ disp([' '])
+ disp(['=> Create bry file : ', bryname ])
create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
theta_s,theta_b,hc,N,...
croco_time,0,'clobber',vtransform);
diff --git a/Oforc_OGCM/prepro_soda.m b/Oforc_OGCM/prepro_soda.m
index 3ba9797bd55287e75ffa411903ae60496b3cf6e5..2bd90cae5a0179c9165783b3897079ed8cffaa67 100644
--- a/Oforc_OGCM/prepro_soda.m
+++ b/Oforc_OGCM/prepro_soda.m
@@ -1,4 +1,4 @@
clear all
close all
start ;
-make_OGCM ;
+make_OGCM_SODA ;
diff --git a/Oforc_OGCM/write_mercator.m b/Oforc_OGCM/write_mercator.m
index 1a765e567cbda7e7a7c0307f46d4c0108d95c683..353f1e9f6c8a27ced212223662bf60889f0c3034 100644
--- a/Oforc_OGCM/write_mercator.m
+++ b/Oforc_OGCM/write_mercator.m
@@ -2,8 +2,8 @@ function write_mercator(OGCM_dir,OGCM_prefix,raw_mercator_name,...
mercator_type,vars,time,thedatemonth,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Extract a subset from Mercator in the case of hindcast
-% using python motu client (cls)
+% Extract a subset from Mercator in the case of hindcast
+% using python copernicusmarine client
% Write it in a local file (keeping the classic SODA netcdf format)
%
% Further Information:
@@ -35,18 +35,16 @@ function write_mercator(OGCM_dir,OGCM_prefix,raw_mercator_name,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-disp([' writing MERCATOR file'])
+disp([' Writing MERCATOR file'])
%
% Get grid and time frame
%
nc = netcdf(raw_mercator_name);
-if mercator_type==1,
- lon = nc{'longitude'}(:);
- lat = nc{'latitude'}(:);
- depth = nc{'depth'}(:);
- time = nc{'time'}(:);
- time = time / 24 + datenum(1950,1,1) - datenum(Yorig,1,1);
-end
+lon = nc{'longitude'}(:);
+lat = nc{'latitude'}(:);
+depth = nc{'depth'}(:);
+time = nc{'time'}(:);
+time = time / 24 + datenum(1950,1,1) - datenum(Yorig,1,1);
%
% Get SSH
%
@@ -95,9 +93,8 @@ temp=ncc(:);
missval=ncc.FillValue_(:);
scale_factor=ncc.scale_factor(:);
add_offset=ncc.add_offset(:);
-ktoc=272.15;
temp(temp<=missval)=NaN;
-temp = temp.*scale_factor + add_offset; % - ktoc;
+temp = temp.*scale_factor + add_offset;
%
% Get SALT
%
diff --git a/Forecast_tools/write_mercator_frcst.m b/Oforc_OGCM/write_mercator_multi.m
similarity index 65%
rename from Forecast_tools/write_mercator_frcst.m
rename to Oforc_OGCM/write_mercator_multi.m
index e82e36165942b54f7f7d5efb1b0ee92d16a3c655..75779986369b35dae2216d03266933eec7155ef2 100644
--- a/Forecast_tools/write_mercator_frcst.m
+++ b/Oforc_OGCM/write_mercator_multi.m
@@ -1,9 +1,10 @@
-function write_mercator_frcst(FRCST_dir,FRCST_prefix,raw_mercator_name,...
- mercator_type,vars,time,Yorig)
+function write_mercator_multi(OGCM_dir,OGCM_prefix,raw_mercator_name,...
+ mercator_type,vars,time,thedatemonth,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Extract a subset from Marcator using python motu client (cls)
-% Write it in a local file (keeping the classic SODA netcdf format)
+% Extract a subset from Mercator in the case of
+% using python
+% Write mercator multi files for analysis and forecast
%
% Further Information:
% http://www.croco-ocean.org
@@ -31,10 +32,10 @@ function write_mercator_frcst(FRCST_dir,FRCST_prefix,raw_mercator_name,...
% Updated 9-Sep-2006 by Pierrick Penven
% Updated 19-May-2011 by Andres Sepulveda & Gildas Cambon
% Updated 12-Feb-2016 by P. Marchesiello
-% Updated 06-May-2023 by Efrain Rodriguez-Rubio & P. Marchesiello
+%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-disp([' writing MERCATOR file'])
+disp([' Writing MERCATOR multifiles '])
fname_z=[raw_mercator_name(1:end-3),'_z.nc'];
fname_u=[raw_mercator_name(1:end-3),'_u.nc'];
@@ -44,51 +45,51 @@ fname_s=[raw_mercator_name(1:end-3),'_s.nc'];
%
% Get grid and time frame
%
-nc = netcdf(fname_u,'r');
-if mercator_type==1,
- lon = nc{'longitude'}(:);
- lat = nc{'latitude'}(:);
- depth = nc{'depth'}(:);
- time = nc{'time'}(:);
- time = time / 24 + datenum(1950,1,1) - datenum(Yorig,1,1);
+nc = netcdf(fname_u);
+lon = nc{'longitude'}(:);
+lat = nc{'latitude'}(:);
+depth = nc{'depth'}(:);
+time = nc{'time'}(:);
+%
+if (mercator_type == 4) | (mercator_type == 5)
+ time = time / (24*60) + datenum(1900,1,1) - datenum(Yorig,1,1);
else
- lon = nc{'lon'}(:);
- lat = nc{'lat'}(:);
- depth = nc{'depth'}(:);
- time = nc{'time'}(:);
- time = time / 86400 + datenum(2014,1,9) - datenum(Yorig,1,1);
+ time = time / 24 + datenum(1950,1,1) - datenum(Yorig,1,1);
end
close(nc)
%
% Get SSH
%
-%missval = -32767;
disp(' ...SSH')
nc = netcdf(fname_z,'r');
vname=sprintf('%s',vars{1});
ncc=nc{vname};
ssh=ncc(:);
missval=ncc.FillValue_(:);
-scale_factor=1; %ncc.scale_factor(:);
-add_offset=0.; %ncc.add_offset(:);
+scale_factor=1;
+add_offset=0;
ssh(ssh>=missval)=NaN;
+%scale_factor=ncc.scale_factor(:);
+%add_offset=ncc.add_offset(:);
+%ssh(ssh<=missval)=NaN;
ssh = ssh.*scale_factor + add_offset;
-close(nc)
+close(nc) % close raw_mercator_name
%
%
-% Get U
-%
disp(' ...U')
nc = netcdf(fname_u,'r');
vname=sprintf('%s',vars{2});
ncc=nc{vname};
u=ncc(:);
missval=ncc.FillValue_(:);
-scale_factor=1; %ncc.scale_factor(:);
-add_offset=0.; %ncc.add_offset(:);
+scale_factor=1;
+add_offset=0;
u(u>=missval)=NaN;
+%scale_factor=ncc.scale_factor(:);
+%add_offset=ncc.add_offset(:);
+%u(u<=missval)=NaN;
u = u.*scale_factor + add_offset;
-close(nc)
+close(nc) % close raw_mercator_name
%
% Get V
%
@@ -98,11 +99,14 @@ vname=sprintf('%s',vars{3});
ncc=nc{vname};
v=ncc(:);
missval=ncc.FillValue_(:);
-scale_factor=1; %ncc.scale_factor(:);
-add_offset=0.; %ncc.add_offset(:);
+scale_factor=1;
+add_offset=0;
v(v>=missval)=NaN;
+%scale_factor=ncc.scale_factor(:);
+%add_offset=ncc.add_offset(:);
+%v(v<=missval)=NaN;
v = v.*scale_factor + add_offset;
-close(nc)
+close(nc) % close raw_mercator_name
%
% Get TEMP
%
@@ -112,12 +116,14 @@ vname=sprintf('%s',vars{4});
ncc=nc{vname};
temp=ncc(:);
missval=ncc.FillValue_(:);
-scale_factor=1; %ncc.scale_factor(:);
-add_offset=0.; %ncc.add_offset(:);
-ktoc=272.15;
+scale_factor=1;
+add_offset=0;
temp(temp>=missval)=NaN;
-temp = temp.*scale_factor + add_offset; % - ktoc;
-close(nc)
+%scale_factor=ncc.scale_factor(:);
+%add_offset=ncc.add_offset(:);
+%temp(temp<=missval)=NaN;
+temp = temp.*scale_factor + add_offset;
+close(nc) % close raw_mercator_name
%
% Get SALT
%
@@ -127,18 +133,18 @@ vname=sprintf('%s',vars{5});
ncc=nc{vname};
salt=ncc(:);
missval=ncc.FillValue_(:);
-scale_factor=1; %ncc.scale_factor(:);
-add_offset=0.; %ncc.add_offset(:);
+scale_factor=1;
+add_offset=0;
salt(salt>=missval)=NaN;
+%scale_factor=ncc.scale_factor(:);
+%add_offset=ncc.add_offset(:);
+%salt(salt<=missval)=NaN;
salt = salt.*scale_factor + add_offset;
-close(nc)
+close(nc) % close raw_mercator_name
%
% Create the Mercator file
%
-rundate_str=date;
-rundate=datenum(rundate_str)-datenum(Yorig,1,1);
-
-create_OGCM([FRCST_dir,FRCST_prefix,num2str(rundate),'.cdf'],...
+create_OGCM([OGCM_dir,OGCM_prefix,thedatemonth,'.cdf'],...
lon,lat,lon,lat,lon,lat,depth,time,...
squeeze(temp),squeeze(salt),squeeze(u),...
squeeze(v),squeeze(ssh),Yorig)
diff --git a/Preprocessing_tools/Bio/add_bry_pisces.m b/Preprocessing_tools/Bio/add_bry_pisces.m
index 19410b0e2f7ef4f83ac5981bd4d338f2df78e3d8..966f75274ee33c4eb9ad9981b26ab728a74dc387 100644
--- a/Preprocessing_tools/Bio/add_bry_pisces.m
+++ b/Preprocessing_tools/Bio/add_bry_pisces.m
@@ -1,4 +1,4 @@
-function add_bry_pisces(bryname,obc,time,cycle,clobber);
+function add_bry_pisces(bryname,obc,time,cycle,makequota,clobber);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function add_bry_pisces(bryname,grdname,title,obc...
@@ -64,8 +64,10 @@ nc('talk_time') = length(time);
nc('si_time') = length(time);
nc('fer_time') = length(time);
nc('o2_time') = length(time);
-nc('dop_time') = length(time);
-nc('don_time') = length(time);
+if makequota
+ nc('dop_time') = length(time);
+ nc('don_time') = length(time);
+end
nc('one') = 1;
%
% Create variables and attributes
@@ -119,20 +121,6 @@ nc{'doc_time'}.units = ncchar('day');
nc{'doc_time'}.units = 'day';
nc{'doc_time'}.cycle_length = cycle;%
%
-nc{'dop_time'} = ncdouble('dop_time') ;
-nc{'dop_time'}.long_name = ncchar('time for DOP climatology');
-nc{'dop_time'}.long_name = 'time for DOP climatology';
-nc{'dop_time'}.units = ncchar('day');
-nc{'dop_time'}.units = 'day';
-nc{'dop_time'}.cycle_length = cycle;%
-%
-nc{'don_time'} = ncdouble('don_time') ;
-nc{'don_time'}.long_name = ncchar('time for DON climatology');
-nc{'don_time'}.long_name = 'time for DON climatology';
-nc{'don_time'}.units = ncchar('day');
-nc{'don_time'}.units = 'day';
-nc{'don_time'}.cycle_length = cycle;%
-%
nc{'fer_time'} = ncdouble('fer_time') ;
nc{'fer_time'}.long_name = ncchar('time for FER climatology');
nc{'fer_time'}.long_name = 'time for FER climatology';
@@ -140,6 +128,23 @@ nc{'fer_time'}.units = ncchar('day');
nc{'fer_time'}.units = 'day';
nc{'fer_time'}.cycle_length = cycle;%
%
+if makequota
+ nc{'dop_time'} = ncdouble('dop_time') ;
+ nc{'dop_time'}.long_name = ncchar('time for DOP climatology');
+ nc{'dop_time'}.long_name = 'time for DOP climatology';
+ nc{'dop_time'}.units = ncchar('day');
+ nc{'dop_time'}.units = 'day';
+ nc{'dop_time'}.cycle_length = cycle;%
+%
+ nc{'don_time'} = ncdouble('don_time') ;
+ nc{'don_time'}.long_name = ncchar('time for DON climatology');
+ nc{'don_time'}.long_name = 'time for DON climatology';
+ nc{'don_time'}.units = ncchar('day');
+ nc{'don_time'}.units = 'day';
+ nc{'don_time'}.cycle_length = cycle;%
+end
+%
+%
if obc(1)==1
%
% Southern boundary
@@ -185,24 +190,26 @@ if obc(1)==1
nc{'DOC_south'}.long_name = 'southern boundary DOC';
nc{'DOC_south'}.units = ncchar('mMol N m-3');
nc{'DOC_south'}.units = 'mMol N m-3';
-%
- nc{'DOP_south'} = ncdouble('dop_time','s_rho','xi_rho') ;
- nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
- nc{'DOP_south'}.long_name = 'southern boundary DOP';
- nc{'DOP_south'}.units = ncchar('mMol N m-3');
- nc{'DOP_south'}.units = 'mMol N m-3';
-%
- nc{'DON_south'} = ncdouble('don_time','s_rho','xi_rho') ;
- nc{'DON_south'}.long_name = ncchar('southern boundary DON');
- nc{'DON_south'}.long_name = 'southern boundary DON';
- nc{'DON_south'}.units = ncchar('mMol N m-3');
- nc{'DON_south'}.units = 'mMol N m-3';
%
nc{'FER_south'} = ncdouble('fer_time','s_rho','xi_rho') ;
nc{'FER_south'}.long_name = ncchar('southern boundary Iron');
nc{'FER_south'}.long_name = 'southern boundary Iron';
nc{'FER_south'}.units = ncchar('mMol N m-3');
nc{'FER_south'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_south'} = ncdouble('dop_time','s_rho','xi_rho') ;
+ nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
+ nc{'DOP_south'}.long_name = 'southern boundary DOP';
+ nc{'DOP_south'}.units = ncchar('mMol N m-3');
+ nc{'DOP_south'}.units = 'mMol N m-3';
+%
+ nc{'DON_south'} = ncdouble('don_time','s_rho','xi_rho') ;
+ nc{'DON_south'}.long_name = ncchar('southern boundary DON');
+ nc{'DON_south'}.long_name = 'southern boundary DON';
+ nc{'DON_south'}.units = ncchar('mMol N m-3');
+ nc{'DON_south'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -251,24 +258,26 @@ if obc(2)==1
nc{'DOC_east'}.long_name = 'eastern boundary DOC';
nc{'DOC_east'}.units = ncchar('mMol N m-3');
nc{'DOC_east'}.units = 'mMol N m-3';
-%
- nc{'DOP_east'} = ncdouble('dop_time','s_rho','eta_rho') ;
- nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
- nc{'DOP_east'}.long_name = 'eastern boundary DOP';
- nc{'DOP_east'}.units = ncchar('mMol N m-3');
- nc{'DOP_east'}.units = 'mMol N m-3';
-%
- nc{'DON_east'} = ncdouble('don_time','s_rho','eta_rho') ;
- nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
- nc{'DON_east'}.long_name = 'eastern boundary DON';
- nc{'DON_east'}.units = ncchar('mMol N m-3');
- nc{'DON_east'}.units = 'mMol N m-3';
%
nc{'FER_east'} = ncdouble('fer_time','s_rho','eta_rho') ;
nc{'FER_east'}.long_name = ncchar('eastern boundary Iron');
nc{'FER_east'}.long_name = 'eastern boundary Iron';
nc{'FER_east'}.units = ncchar('mMol N m-3');
nc{'FER_east'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_east'} = ncdouble('dop_time','s_rho','eta_rho') ;
+ nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
+ nc{'DOP_east'}.long_name = 'eastern boundary DOP';
+ nc{'DOP_east'}.units = ncchar('mMol N m-3');
+ nc{'DOP_east'}.units = 'mMol N m-3';
+%
+ nc{'DON_east'} = ncdouble('don_time','s_rho','eta_rho') ;
+ nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
+ nc{'DON_east'}.long_name = 'eastern boundary DON';
+ nc{'DON_east'}.units = ncchar('mMol N m-3');
+ nc{'DON_east'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -317,24 +326,26 @@ if obc(3)==1
nc{'DOC_north'}.long_name = 'northern boundary DOC';
nc{'DOC_north'}.units = ncchar('mMol N m-3');
nc{'DOC_north'}.units = 'mMol N m-3';
-%
- nc{'DOP_north'} = ncdouble('dop_time','s_rho','xi_rho') ;
- nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
- nc{'DOP_north'}.long_name = 'northern boundary DOP';
- nc{'DOP_north'}.units = ncchar('mMol N m-3');
- nc{'DOP_north'}.units = 'mMol N m-3';
-%
- nc{'DON_north'} = ncdouble('don_time','s_rho','xi_rho') ;
- nc{'DON_north'}.long_name = ncchar('northern boundary DON');
- nc{'DON_north'}.long_name = 'northern boundary DON';
- nc{'DON_north'}.units = ncchar('mMol N m-3');
- nc{'DON_north'}.units = 'mMol N m-3';
%
nc{'FER_north'} = ncdouble('fer_time','s_rho','xi_rho') ;
nc{'FER_north'}.long_name = ncchar('northern boundary Iron');
nc{'FER_north'}.long_name = 'northern boundary Iron';
nc{'FER_north'}.units = ncchar('mMol N m-3');
nc{'FER_north'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_north'} = ncdouble('dop_time','s_rho','xi_rho') ;
+ nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
+ nc{'DOP_north'}.long_name = 'northern boundary DOP';
+ nc{'DOP_north'}.units = ncchar('mMol N m-3');
+ nc{'DOP_north'}.units = 'mMol N m-3';
+%
+ nc{'DON_north'} = ncdouble('don_time','s_rho','xi_rho') ;
+ nc{'DON_north'}.long_name = ncchar('northern boundary DON');
+ nc{'DON_north'}.long_name = 'northern boundary DON';
+ nc{'DON_north'}.units = ncchar('mMol N m-3');
+ nc{'DON_north'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -383,24 +394,26 @@ if obc(4)==1
nc{'DOC_west'}.long_name = 'western boundary DOC';
nc{'DOC_west'}.units = ncchar('mMol N m-3');
nc{'DOC_west'}.units = 'mMol N m-3';
-%
- nc{'DOP_west'} = ncdouble('dop_time','s_rho','eta_rho') ;
- nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
- nc{'DOP_west'}.long_name = 'western boundary DOP';
- nc{'DOP_west'}.units = ncchar('mMol N m-3');
- nc{'DOP_west'}.units = 'mMol N m-3';
-%
- nc{'DON_west'} = ncdouble('don_time','s_rho','eta_rho') ;
- nc{'DON_west'}.long_name = ncchar('western boundary DON');
- nc{'DON_west'}.long_name = 'western boundary DON';
- nc{'DON_west'}.units = ncchar('mMol N m-3');
- nc{'DON_west'}.units = 'mMol N m-3';
%
nc{'FER_west'} = ncdouble('fer_time','s_rho','eta_rho') ;
nc{'FER_west'}.long_name = ncchar('western boundary Iron');
nc{'FER_west'}.long_name = 'western boundary Iron';
nc{'FER_west'}.units = ncchar('mMol N m-3');
nc{'FER_west'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_west'} = ncdouble('dop_time','s_rho','eta_rho') ;
+ nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
+ nc{'DOP_west'}.long_name = 'western boundary DOP';
+ nc{'DOP_west'}.units = ncchar('mMol N m-3');
+ nc{'DOP_west'}.units = 'mMol N m-3';
+%
+ nc{'DON_west'} = ncdouble('don_time','s_rho','eta_rho') ;
+ nc{'DON_west'}.long_name = ncchar('western boundary DON');
+ nc{'DON_west'}.long_name = 'western boundary DON';
+ nc{'DON_west'}.units = ncchar('mMol N m-3');
+ nc{'DON_west'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -418,8 +431,10 @@ nc{'talk_time'}(:) = time;
nc{'si_time'}(:) = time;
nc{'fer_time'}(:) = time;
nc{'o2_time'}(:) = time;
-nc{'dop_time'}(:) = time;
-nc{'don_time'}(:) = time;
+if makequota
+ nc{'dop_time'}(:) = time;
+ nc{'don_time'}(:) = time;
+end
if obc(1)==1
nc{'NO3_south'}(:) = 0;
nc{'PO4_south'}(:) = 0;
@@ -429,8 +444,10 @@ if obc(1)==1
nc{'TALK_south'}(:) = 0;
nc{'DOC_south'}(:) = 0;
nc{'FER_south'}(:) = 0;
- nc{'DOP_south'}(:) = 0;
- nc{'DON_south'}(:) = 0;
+ if makequota
+ nc{'DOP_south'}(:) = 0;
+ nc{'DON_south'}(:) = 0;
+ end
end
if obc(2)==1
nc{'NO3_east'}(:) = 0;
@@ -441,8 +458,10 @@ if obc(2)==1
nc{'TALK_east'}(:) = 0;
nc{'DOC_east'}(:) = 0;
nc{'FER_east'}(:) = 0;
- nc{'DOP_east'}(:) = 0;
- nc{'DON_east'}(:) = 0;
+ if makequota
+ nc{'DOP_east'}(:) = 0;
+ nc{'DON_east'}(:) = 0;
+ end
end
if obc(3)==1
nc{'NO3_north'}(:) = 0;
@@ -453,8 +472,10 @@ if obc(3)==1
nc{'TALK_north'}(:) = 0;
nc{'DOC_north'}(:) = 0;
nc{'FER_north'}(:) = 0;
- nc{'DOP_north'}(:) = 0;
- nc{'DON_north'}(:) = 0;
+ if makequota
+ nc{'DOP_north'}(:) = 0;
+ nc{'DON_north'}(:) = 0;
+ end
end
if obc(4)==1
nc{'NO3_west'}(:) = 0;
@@ -465,8 +486,10 @@ if obc(4)==1
nc{'TALK_west'}(:) = 0;
nc{'DOC_west'}(:) = 0;
nc{'FER_west'}(:) = 0;
- nc{'DOP_west'}(:) = 0;
- nc{'DON_west'}(:) = 0
+ if makequota
+ nc{'DOP_west'}(:) = 0;
+ nc{'DON_west'}(:) = 0
+ end
end
close(nc)
return
diff --git a/Preprocessing_tools/Bio/add_bry_pisces_Z.m b/Preprocessing_tools/Bio/add_bry_pisces_Z.m
index 995a4b8f36b71cfcdccbb27e80945360568f79fb..69bde9cd1fab7f65d4f4d5e1991c91ccc0b22394 100644
--- a/Preprocessing_tools/Bio/add_bry_pisces_Z.m
+++ b/Preprocessing_tools/Bio/add_bry_pisces_Z.m
@@ -1,4 +1,4 @@
-function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,clobber);
+function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,makequota,clobber);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% function add_bry_pisces_Z(zbryname,obc,... %
@@ -42,8 +42,10 @@ nc('talk_time') = length(time);
nc('si_time') = length(time);
nc('fer_time') = length(time);
nc('o2_time') = length(time);
-nc('dop_time') = length(time);
-nc('don_time') = length(time);
+if makequota
+ nc('dop_time') = length(time);
+ nc('don_time') = length(time);
+end
nc('one') = 1;
%
if obc(1)==1
@@ -91,24 +93,27 @@ if obc(1)==1
nc{'DOC_south'}.long_name = 'southern boundary DOC';
nc{'DOC_south'}.units = ncchar('mMol N m-3');
nc{'DOC_south'}.units = 'mMol N m-3';
-%
- nc{'DOP_south'} = ncdouble('dop_time','Z','xi_rho') ;
- nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
- nc{'DOP_south'}.long_name = 'southern boundary DOP';
- nc{'DOP_south'}.units = ncchar('mMol N m-3');
- nc{'DOP_south'}.units = 'mMol N m-3';
-%
- nc{'DON_south'} = ncdouble('don_time','Z','xi_rho') ;
- nc{'DON_south'}.long_name = ncchar('southern boundary DON');
- nc{'DON_south'}.long_name = 'southern boundary DON';
- nc{'DON_south'}.units = ncchar('mMol N m-3');
- nc{'DON_south'}.units = 'mMol N m-3';
-%
+ %
nc{'FER_south'} = ncdouble('fer_time','Z','xi_rho') ;
nc{'FER_south'}.long_name = ncchar('southern boundary Iron');
nc{'FER_south'}.long_name = 'southern boundary Iron';
nc{'FER_south'}.units = ncchar('mMol N m-3');
nc{'FER_south'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_south'} = ncdouble('dop_time','Z','xi_rho') ;
+ nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
+ nc{'DOP_south'}.long_name = 'southern boundary DOP';
+ nc{'DOP_south'}.units = ncchar('mMol N m-3');
+ nc{'DOP_south'}.units = 'mMol N m-3';
+%
+ nc{'DON_south'} = ncdouble('don_time','Z','xi_rho') ;
+ nc{'DON_south'}.long_name = ncchar('southern boundary DON');
+ nc{'DON_south'}.long_name = 'southern boundary DON';
+ nc{'DON_south'}.units = ncchar('mMol N m-3');
+ nc{'DON_south'}.units = 'mMol N m-3';
+ end
+%
end
%
if obc(2)==1
@@ -156,24 +161,26 @@ if obc(2)==1
nc{'DOC_east'}.long_name = 'eastern boundary DOC';
nc{'DOC_east'}.units = ncchar('mMol N m-3');
nc{'DOC_east'}.units = 'mMol N m-3';
-%
- nc{'DOP_east'} = ncdouble('dop_time','Z','eta_rho') ;
- nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
- nc{'DOP_east'}.long_name = 'eastern boundary DOP';
- nc{'DOP_east'}.units = ncchar('mMol N m-3');
- nc{'DOP_east'}.units = 'mMol N m-3';
-%
- nc{'DON_east'} = ncdouble('don_time','Z','eta_rho') ;
- nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
- nc{'DON_east'}.long_name = 'eastern boundary DON';
- nc{'DON_east'}.units = ncchar('mMol N m-3');
- nc{'DON_east'}.units = 'mMol N m-3';
%
nc{'FER_east'} = ncdouble('fer_time','Z','eta_rho') ;
nc{'FER_east'}.long_name = ncchar('eastern boundary Iron');
nc{'FER_east'}.long_name = 'eastern boundary Iron';
nc{'FER_east'}.units = ncchar('mMol N m-3');
nc{'FER_east'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_east'} = ncdouble('dop_time','Z','eta_rho') ;
+ nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
+ nc{'DOP_east'}.long_name = 'eastern boundary DOP';
+ nc{'DOP_east'}.units = ncchar('mMol N m-3');
+ nc{'DOP_east'}.units = 'mMol N m-3';
+%
+ nc{'DON_east'} = ncdouble('don_time','Z','eta_rho') ;
+ nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
+ nc{'DON_east'}.long_name = 'eastern boundary DON';
+ nc{'DON_east'}.units = ncchar('mMol N m-3');
+ nc{'DON_east'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -222,24 +229,26 @@ if obc(3)==1
nc{'DOC_north'}.long_name = 'northern boundary DOC';
nc{'DOC_north'}.units = ncchar('mMol N m-3');
nc{'DOC_north'}.units = 'mMol N m-3';
-%
- nc{'DOP_north'} = ncdouble('dop_time','Z','xi_rho') ;
- nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
- nc{'DOP_north'}.long_name = 'northern boundary DOP';
- nc{'DOP_north'}.units = ncchar('mMol N m-3');
- nc{'DOP_north'}.units = 'mMol N m-3';
-%
- nc{'DON_north'} = ncdouble('don_time','Z','xi_rho') ;
- nc{'DON_north'}.long_name = ncchar('northern boundary DON');
- nc{'DON_north'}.long_name = 'northern boundary DON';
- nc{'DON_north'}.units = ncchar('mMol N m-3');
- nc{'DON_north'}.units = 'mMol N m-3';
%
nc{'FER_north'} = ncdouble('fer_time','Z','xi_rho') ;
nc{'FER_north'}.long_name = ncchar('northern boundary Iron');
nc{'FER_north'}.long_name = 'northern boundary Iron';
nc{'FER_north'}.units = ncchar('mMol N m-3');
nc{'FER_north'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_north'} = ncdouble('dop_time','Z','xi_rho') ;
+ nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
+ nc{'DOP_north'}.long_name = 'northern boundary DOP';
+ nc{'DOP_north'}.units = ncchar('mMol N m-3');
+ nc{'DOP_north'}.units = 'mMol N m-3';
+%
+ nc{'DON_north'} = ncdouble('don_time','Z','xi_rho') ;
+ nc{'DON_north'}.long_name = ncchar('northern boundary DON');
+ nc{'DON_north'}.long_name = 'northern boundary DON';
+ nc{'DON_north'}.units = ncchar('mMol N m-3');
+ nc{'DON_north'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -288,24 +297,26 @@ if obc(4)==1
nc{'DOC_west'}.long_name = 'western boundary DOC';
nc{'DOC_west'}.units = ncchar('mMol N m-3');
nc{'DOC_west'}.units = 'mMol N m-3';
-%
- nc{'DOP_west'} = ncdouble('dop_time','Z','eta_rho') ;
- nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
- nc{'DOP_west'}.long_name = 'western boundary DOP';
- nc{'DOP_west'}.units = ncchar('mMol N m-3');
- nc{'DOP_west'}.units = 'mMol N m-3';
-%
- nc{'DON_west'} = ncdouble('don_time','Z','eta_rho') ;
- nc{'DON_west'}.long_name = ncchar('western boundary DON');
- nc{'DON_west'}.long_name = 'western boundary DON';
- nc{'DON_west'}.units = ncchar('mMol N m-3');
- nc{'DON_west'}.units = 'mMol N m-3';
%
nc{'FER_west'} = ncdouble('fer_time','Z','eta_rho') ;
nc{'FER_west'}.long_name = ncchar('western boundary Iron');
nc{'FER_west'}.long_name = 'western boundary Iron';
nc{'FER_west'}.units = ncchar('mMol N m-3');
nc{'FER_west'}.units = 'mMol N m-3';
+%
+ if makequota
+ nc{'DOP_west'} = ncdouble('dop_time','Z','eta_rho') ;
+ nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
+ nc{'DOP_west'}.long_name = 'western boundary DOP';
+ nc{'DOP_west'}.units = ncchar('mMol N m-3');
+ nc{'DOP_west'}.units = 'mMol N m-3';
+%
+ nc{'DON_west'} = ncdouble('don_time','Z','eta_rho') ;
+ nc{'DON_west'}.long_name = ncchar('western boundary DON');
+ nc{'DON_west'}.long_name = 'western boundary DON';
+ nc{'DON_west'}.units = ncchar('mMol N m-3');
+ nc{'DON_west'}.units = 'mMol N m-3';
+ end
%
end
%
@@ -323,8 +334,10 @@ nc('talk_time') = time;
nc('si_time') = time;
nc('fer_time') = time;
nc('o2_time') = time;
-nc('dop_time') = time;
-nc('don_time') = time;
+ if makequota
+ nc('dop_time') = time;
+ nc('don_time') = time;
+ end
if obc(1)==1
nc{'NO3_south'}(:) = 0;
nc{'PO4_south'}(:) = 0;
@@ -334,8 +347,10 @@ if obc(1)==1
nc{'TALK_south'}(:) = 0;
nc{'DOC_south'}(:) = 0;
nc{'FER_south'}(:) = 0;
- nc{'DOP_south'}(:) = 0;
- nc{'DON_south'}(:) = 0;
+ if makequota
+ nc{'DOP_south'}(:) = 0;
+ nc{'DON_south'}(:) = 0;
+ end
end
if obc(2)==1
nc{'NO3_east'}(:) = 0;
@@ -346,8 +361,10 @@ if obc(2)==1
nc{'TALK_east'}(:) = 0;
nc{'DOC_east'}(:) = 0;
nc{'FER_east'}(:) = 0;
- nc{'DOP_east'}(:) = 0;
- nc{'DON_east'}(:) = 0;
+ if makequota
+ nc{'DOP_east'}(:) = 0;
+ nc{'DON_east'}(:) = 0;
+ end
end
if obc(3)==1
nc{'NO3_north'}(:) = 0;
@@ -358,8 +375,10 @@ if obc(3)==1
nc{'TALK_north'}(:) = 0;
nc{'DOC_north'}(:) = 0;
nc{'FER_north'}(:) = 0;
- nc{'DOP_north'}(:) = 0;
- nc{'DON_north'}(:) = 0;
+ if makequota
+ nc{'DOP_north'}(:) = 0;
+ nc{'DON_north'}(:) = 0;
+ end
end
if obc(4)==1
nc{'NO3_west'}(:) = 0;
@@ -370,8 +389,10 @@ if obc(4)==1
nc{'TALK_west'}(:) = 0;
nc{'DOC_west'}(:) = 0;
nc{'FER_west'}(:) = 0;
- nc{'DOP_west'}(:) = 0;
- nc{'DON_west'}(:) = 0;
+ if makequota
+ nc{'DOP_west'}(:) = 0;
+ nc{'DON_west'}(:) = 0;
+ end
end
close(nc)
return
diff --git a/Preprocessing_tools/Bio/add_don.m b/Preprocessing_tools/Bio/add_don.m
index 19c9079e79e24b07b77329aed1e6941e615e4bf0..7618b93feb932f0101249b56252b5b5604c2540e 100644
--- a/Preprocessing_tools/Bio/add_don.m
+++ b/Preprocessing_tools/Bio/add_don.m
@@ -1,5 +1,5 @@
function add_don(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
+ ann_datafile,cycle,makeoa,makeclim,makequota);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
diff --git a/Preprocessing_tools/Bio/add_dop.m b/Preprocessing_tools/Bio/add_dop.m
index 6f487614af5041b12db1670daa6390cf491afa5c..bfb63a43ab7b30c697ea2fb3feb2c8b44fa99078 100644
--- a/Preprocessing_tools/Bio/add_dop.m
+++ b/Preprocessing_tools/Bio/add_dop.m
@@ -1,5 +1,5 @@
function add_dop(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
+ ann_datafile,cycle,makeoa,makeclim,makequota);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,dop]=add_dop(climfile,gridfile,...
diff --git a/Preprocessing_tools/Bio/add_ini_pisces.m b/Preprocessing_tools/Bio/add_ini_pisces.m
index 95649b850a81ea08c0f95d5e654a9d130d8ac8b3..179eff727c961bb859212e482763d8bac97d47f5 100644
--- a/Preprocessing_tools/Bio/add_ini_pisces.m
+++ b/Preprocessing_tools/Bio/add_ini_pisces.m
@@ -1,4 +1,4 @@
-function add_ini_pisces(inifile,clobber)
+function add_ini_pisces(inifile,clobber,makequota)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright (c) 2000 IRD %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -42,9 +42,11 @@ nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'DIC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'TALK'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'DON'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'FER'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+if makequota
+ nc{'DON'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+ nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+end
%
% Create attributes
@@ -91,23 +93,25 @@ nc{'DOC'}.units = ncchar('mMol C m-3');
nc{'DOC'}.units = 'mMol C m-3';
%
%
-nc{'DON'}.long_name = ncchar('DON');
-nc{'DON'}.long_name = 'DON';
-nc{'DON'}.units = ncchar('mMol C m-3');
-nc{'DON'}.units = 'mMol C m-3';
-%
-%
-nc{'DOP'}.long_name = ncchar('DOP');
-nc{'DOP'}.long_name = 'DOP';
-nc{'DOP'}.units = ncchar('mMol C m-3');
-nc{'DOP'}.units = 'mMol C m-3';
-%
-%
nc{'FER'}.long_name = ncchar('FER');
nc{'FER'}.long_name = 'FER';
nc{'FER'}.units = ncchar('mMol Fe m-3');
nc{'FER'}.units = 'mMol Fe m-3';
%
+%
+if makequota
+ nc{'DON'}.long_name = ncchar('DON');
+ nc{'DON'}.long_name = 'DON';
+ nc{'DON'}.units = ncchar('mMol C m-3');
+ nc{'DON'}.units = 'mMol C m-3';
+%
+%
+ nc{'DOP'}.long_name = ncchar('DOP');
+ nc{'DOP'}.long_name = 'DOP';
+ nc{'DOP'}.units = ncchar('mMol C m-3');
+ nc{'DOP'}.units = 'mMol C m-3';
+end
+%
% Leave define mode
%
%%result = endef(nc);
@@ -121,9 +125,11 @@ nc{'O2'}(:) = 0;
nc{'DIC'}(:) = 0;
nc{'TALK'}(:) = 0;
nc{'DOC'}(:) = 0;
-nc{'DON'}(:) = 0;
-nc{'DOP'}(:) = 0;
nc{'FER'}(:) = 0;
+if makequota
+ nc{'DON'}(:) = 0;
+ nc{'DOP'}(:) = 0;
+end
%
% Synchronize on disk
%
diff --git a/Preprocessing_tools/Bio/make_biol.m b/Preprocessing_tools/Bio/make_biol.m
index 750cca383a6d7f9b3242458ba0333ea736b4c455..0e22f38d6b86efe0810c7de8446c49d7ac184190 100644
--- a/Preprocessing_tools/Bio/make_biol.m
+++ b/Preprocessing_tools/Bio/make_biol.m
@@ -113,6 +113,9 @@ if (makeini)
disp('------------------------')
disp('Iron deposition file')
make_dust
+ disp('------------------------')
+ disp('Nitrogen deposition')
+ make_ndepo
end
if (makebioebus)
disp('========================')
diff --git a/Preprocessing_tools/Bio/make_bry_pisces.m b/Preprocessing_tools/Bio/make_bry_pisces.m
index 700070e4cdfeb97452b3a095091104b6262450a1..bb9d5406f8dc38148086fb67a29577bb7448fe8d 100644
--- a/Preprocessing_tools/Bio/make_bry_pisces.m
+++ b/Preprocessing_tools/Bio/make_bry_pisces.m
@@ -126,7 +126,7 @@ if (makebry)
disp('======================================================== ')
disp('=> You need the croco_bry_Z.nc file created by make_bry.m ')
disp('======================================================== ')
- add_bry_pisces(bryname,obc,time,cycle,'write');
+ add_bry_pisces(bryname,obc,time,cycle,makequota,'write');
end
%
% Redefine the boundary file in Z-coordinates
@@ -142,7 +142,7 @@ if (makeZbry)
kmax=max(find(Z<hmax))-1;
Z=Z(1:kmax);
close(nc)
- add_bry_pisces_Z(Zbryname,obc,Z,time,cycle,'write');
+ add_bry_pisces_Z(Zbryname,obc,Z,time,cycle,makequota,'write');
disp(' ')
disp(' Horizontal extrapolations')
%
@@ -184,7 +184,7 @@ if (makeZbry)
disp(' Dissolved Organic Carbon...')
bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
'doc',['DOC',suffix],obcndx,Roa);
- if makequota
+ if makequota
disp(' Dissolved Organic Nitrogen...')
bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
'doc',['DON',suffix],obcndx,Roa);
@@ -276,12 +276,15 @@ figure
test_bry(bryname,grdname,'TALK',6,obc)
figure
test_bry(bryname,grdname,'DOC',6,obc)
-if makequota
-figure
-test_bry(bryname,grdname,'DON',6,obc)
-end
figure
test_bry(bryname,grdname,'FER',6,obc)
+figure
+ if makequota
+ test_bry(bryname,grdname,'DON',6,obc)
+ figure
+ test_bry(bryname,grdname,'DOP',6,obc)
+ figure
+ end
end
%
% End
diff --git a/Preprocessing_tools/Bio/make_clim_pisces.m b/Preprocessing_tools/Bio/make_clim_pisces.m
index 8b1499a25cd31d8de40451b942f04f727e2297ef..4cd0afe9d136b60f7459e85a08a3812a06aed880 100644
--- a/Preprocessing_tools/Bio/make_clim_pisces.m
+++ b/Preprocessing_tools/Bio/make_clim_pisces.m
@@ -235,12 +235,13 @@ figure
test_clim(clmname,grdname,'TALK',1,coastfileplot)
figure
test_clim(clmname,grdname,'DOC',1,coastfileplot)
-if makequota
figure
+if makequota
test_clim(clmname,grdname,'DON',1,coastfileplot)
-end
figure
+end
test_clim(clmname,grdname,'FER',1,coastfileplot)
+figure
end
%
% End
diff --git a/Preprocessing_tools/Bio/make_dust.m b/Preprocessing_tools/Bio/make_dust.m
index a65183ad7bd76bf8a448aac96fd5cc848c9cb54d..a58d90167e8d544bc09dacf8ed741e7275ff8352 100644
--- a/Preprocessing_tools/Bio/make_dust.m
+++ b/Preprocessing_tools/Bio/make_dust.m
@@ -41,7 +41,8 @@ crocotools_param
%
%dust_file=[woapisces_dir,'dust.iron.cdf'];
%dust_name='irondep';
-dust_file=[woapisces_dir,'dust_seas.cdf'];
+%dust_file=[woapisces_dir,'dust_seas.cdf'];
+dust_file=[woapisces_dir,'DUST_INCA_new_r360x180.nc'];
dust_name='dust';
%time=woa_time;
time=[0.5:1:11.5];
@@ -67,6 +68,7 @@ close(nc);
%
disp(' Creating file')
nc = netcdf(bioname, 'clobber');
+%nc = netcdf(bioname, 'write');
%%result = redef(nc);
%
nc('xi_u') = L;
@@ -78,7 +80,11 @@ nc('eta_rho') = Mp;
%
nc('dust_time') = length(time);
nc{'dust_time'} = ncdouble('dust_time') ;
-nc{'dust'} = ncdouble('dust_time','eta_rho','xi_rho') ;
+nc{'dust'} = ncdouble('dust_time','eta_rho','xi_rho') ;
+nc{'dustfer'} = ncdouble('dust_time','eta_rho','xi_rho') ;
+nc{'dustpo4'} = ncdouble('dust_time','eta_rho','xi_rho') ;
+nc{'dustsi'} = ncdouble('dust_time','eta_rho','xi_rho') ;
+nc{'solubility2'} = ncdouble('dust_time','eta_rho','xi_rho') ;
%
nc{'dust_time'}.long_name = ncchar('time for dust');
nc{'dust_time'}.long_name = 'time for dust';
@@ -88,13 +94,41 @@ if cycle~=0
nc{'dust_time'}.cycle_length = cycle;
end
%
-nc{'dust'}.long_name = ncchar('Fe Dust Deposition');
-nc{'dust'}.long_name = 'Fe Dust Deposition';
-nc{'dust'}.units = ncchar('nMol Fe m-3');
-nc{'dust'}.units = 'nmol Fe m-3';
+nc{'dust'}.long_name = ncchar('Dust Deposition');
+nc{'dust'}.long_name = 'Dust Deposition';
+nc{'dust'}.units = ncchar('Kg m-2 s-1');
+nc{'dust'}.units = 'Kg m-2 s-1';
nc{'dust'}.fields = ncchar('dust, scalar, series');
nc{'dust'}.fields = 'dust, scalar, series';
%
+nc{'dustfer'}.long_name = ncchar('Fe Dust Deposition');
+nc{'dustfer'}.long_name = 'Fe Dust Deposition';
+nc{'dustfer'}.units = ncchar('Kg m-2 s-1');
+nc{'dustfer'}.units = 'Kg m-2 s-1';
+nc{'dustfer'}.fields = ncchar('dustfer, scalar, series');
+nc{'dustfer'}.fields = 'dustfer, scalar, series';
+%
+nc{'dustpo4'}.long_name = ncchar('PO4 Dust Deposition');
+nc{'dustpo4'}.long_name = 'PO4 Dust Deposition';
+nc{'dustpo4'}.units = ncchar('Kg m-2 s-1');
+nc{'dustpo4'}.units = 'Kg m-2 s-1';
+nc{'dustpo4'}.fields = ncchar('dustpo4, scalar, series');
+nc{'dustpo4'}.fields = 'dustpo4, scalar, series';
+%
+nc{'dustsi'}.long_name = ncchar('Si Dust Deposition');
+nc{'dustsi'}.long_name = 'Si Dust Deposition';
+nc{'dustsi'}.units = ncchar('Kg m-2 s-1');
+nc{'dustsi'}.units = 'Kg m-2 s-1';
+nc{'dustsi'}.fields = ncchar('dustsi, scalar, series');
+nc{'dustsi'}.fields = 'dustsi, scalar, series';
+%
+nc{'solubility2'}.long_name = ncchar('Fe solubility from Mahowald');
+nc{'solubility2'}.long_name = 'Fe solubility from Mahowald';
+nc{'solubility2'}.units = ncchar('%');
+nc{'solubility2'}.units = '%';
+nc{'solubility2'}.fields = ncchar('solubility2, scalar, series');
+nc{'solubility2'}.fields = 'solubility2, scalar, series';
+%
%%endef(nc);
% Create global attributes
@@ -118,7 +152,15 @@ nc=netcdf(bioname,'write');
%
for tindex=1:length(time)
time=nc{'dust_time'}(tindex);
- nc{'dust'}(tindex,:,:)=ext_data(dust_file,dust_name,tindex,...
+ nc{'dust'}(tindex,:,:)=ext_data(dust_file,'dust',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'dustfer'}(tindex,:,:)=ext_data(dust_file,'dustfer',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'dustpo4'}(tindex,:,:)=ext_data(dust_file,'dustpo4',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'dustsi'}(tindex,:,:)=ext_data(dust_file,'dustsi',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'solubility2'}(tindex,:,:)=ext_data(dust_file,'solubility2',tindex,...
lon,lat,time,Roa,1);
end
close(nc)
@@ -128,6 +170,9 @@ if (makeplot)
%
disp(' Make a few plots...')
test_bioforcing(bioname,grdname,'dust',[1 4 7 10],3,coastfileplot)
+test_bioforcing(bioname,grdname,'dustfer',[1 4 7 10],3,coastfileplot)
+test_bioforcing(bioname,grdname,'dustpo4',[1 4 7 10],3,coastfileplot)
+test_bioforcing(bioname,grdname,'dustsi',[1 4 7 10],3,coastfileplot)
end % if makeplot
%
% End
diff --git a/Preprocessing_tools/Bio/make_ini_pisces.m b/Preprocessing_tools/Bio/make_ini_pisces.m
index c2e6cd4e458759558e2f0b8cc433ab9041fe25f6..80a3afa418a8d90b02292a208b71b01926da6f7d 100644
--- a/Preprocessing_tools/Bio/make_ini_pisces.m
+++ b/Preprocessing_tools/Bio/make_ini_pisces.m
@@ -65,7 +65,7 @@ disp([' Adding PISCES data into initial file: ',ininame])
%
% Initial file
%
-add_ini_pisces(ininame,'write');
+add_ini_pisces(ininame,'write',makequota);
%
% Horizontal and vertical interp/extrapolations
%
@@ -101,14 +101,14 @@ ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
'doc','DOC','r',tini);
if makequota
-disp(' ')
-disp('Dissolved Organic Nitrogen...')
-ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
- 'doc','DON','r',tini);
-disp(' ')
-disp('Dissolved Organic Phosphorus...')
-ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
- 'doc','DOP','r',tini);
+ disp(' ')
+ disp('Dissolved Organic Nitrogen...')
+ ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
+ 'doc','DON','r',tini);
+ disp(' ')
+ disp('Dissolved Organic Phosphorus...')
+ ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
+ 'doc','DOP','r',tini);
end
disp(' ')
@@ -134,9 +134,14 @@ if (makeplot == 1)disp(' ')
figure
test_clim(ininame,grdname,'DOC',1,coastfileplot)
figure
- test_clim(ininame,grdname,'DON',1,coastfileplot)
- figure
test_clim(ininame,grdname,'FER',1,coastfileplot)
+ figure
+ if makequota
+ test_clim(ininame,grdname,'DON',1,coastfileplot)
+ figure
+ test_clim(ininame,grdname,'DOP',1,coastfileplot)
+ figure
+ end
end
end %if makeini
diff --git a/Preprocessing_tools/Bio/make_ndepo.m b/Preprocessing_tools/Bio/make_ndepo.m
new file mode 100644
index 0000000000000000000000000000000000000000..3ad96fe77707ae2284ed0a202b325504c58fab12
--- /dev/null
+++ b/Preprocessing_tools/Bio/make_ndepo.m
@@ -0,0 +1,157 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Build a PISCES forcing file
+%
+% Extrapole and interpole surface data to get surface boundary
+% conditions for PISCES (forcing netcdf file)
+%
+% Data input format (netcdf):
+% ndep(T, Y, X)
+% T : time [Months]
+% Y : Latitude [degree north]
+% X : Longitude [degree east]
+%
+% Data source : IRI/LDEO Climate Data Library
+% (Atlas of Surface Marine Data 1994)
+%
+% http://ingrid.ldgo.columbia.edu/
+% http://iridl.ldeo.columbia.edu/SOURCES/.DASILVA/
+%
+% Pierrick Penven, IRD, 2005. %
+% Olivier Aumont the master, IRD, 2006. %
+% Patricio Marchesiello, chief, IRD, 2007. %
+% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+clear all
+close all
+%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
+disp(' ')
+disp('Creating biology forcing file')
+%
+% Title - Grid file name - Forcing file name
+%
+crocotools_param
+%
+% bioname
+%
+%bioname='croco_frcbio.nc'
+%
+% Nitrogen deposition file
+%
+ndep_file=[woapisces_dir,'Ndep_CMIP_NCAR-CCMI-2-0_gn_199001-201012-clim.nc'];
+ndep_name='ndep';
+%time=woa_time;
+time=[0.5:1:11.5];
+cycle=woa_cycle;
+disp(' ')
+%
+%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
+%
+% Read in the grid
+%
+disp(' ')
+disp(' Read in the grid...')
+nc=netcdf(grdname,'r');
+Lp=length(nc('xi_rho'));
+Mp=length(nc('eta_rho'));
+L=Lp-1;
+M=Mp-1;
+lon=nc{'lon_rho'}(:);
+lat=nc{'lat_rho'}(:);
+angle=nc{'angle'}(:);
+close(nc);
+%
+% create dust forcing file
+%
+disp(' Creating file')
+%nc = netcdf(bioname, 'clobber');
+nc = netcdf(bioname, 'write');
+%%result = redef(nc);
+%
+nc('xi_u') = L;
+nc('xi_v') = Lp;
+nc('xi_rho') = Lp;
+nc('eta_u') = Mp;
+nc('eta_v') = M;
+nc('eta_rho') = Mp;
+%
+nc('ndep_time') = length(time);
+nc{'ndep_time'} = ncdouble('ndep_time') ;
+nc{'ndep'} = ncdouble('ndep_time','eta_rho','xi_rho') ;
+nc{'noyndepo'} = ncdouble('ndep_time','eta_rho','xi_rho') ;
+nc{'nhxndepo'} = ncdouble('ndep_time','eta_rho','xi_rho') ;
+%
+nc{'ndep_time'}.long_name = ncchar('time for nitrogen deposition');
+nc{'ndep_time'}.long_name = 'time for nitrogen deposition';
+nc{'ndep_time'}.units = ncchar('day');
+nc{'ndep_time'}.units = 'day';
+if cycle~=0
+ nc{'ndep_time'}.cycle_length = cycle;
+end
+%
+nc{'ndep'}.long_name = ncchar('Nitrogen Deposition');
+nc{'ndep'}.long_name = 'Nitrogen Deposition';
+nc{'ndep'}.units = ncchar('KgN m-2 s-1');
+nc{'ndep'}.units = 'KgN m-2 s-1';
+nc{'ndep'}.fields = ncchar('ndep, scalar, series');
+nc{'ndep'}.fields = 'ndep, scalar, series';
+%
+nc{'noyndepo'}.long_name = ncchar('NOy Deposition');
+nc{'noyndepo'}.long_name = 'NOy Deposition';
+nc{'noyndepo'}.units = ncchar('KgN m-2 s-1');
+nc{'noyndepo'}.units = 'KgN m-2 s-1';
+nc{'noyndepo'}.fields = ncchar('noyndepo, scalar, series');
+nc{'noyndepo'}.fields = 'noyndepo, scalar, series';
+%
+nc{'nhxndepo'}.long_name = ncchar('NHx Deposition');
+nc{'nhxndepo'}.long_name = 'NHx Deposition';
+nc{'nhxndepo'}.units = ncchar('KgN m-2 s-1');
+nc{'nhxndepo'}.units = 'KgN m-2 s-1';
+nc{'nhxndepo'}.fields = ncchar('nhxndepo, scalar, series');
+nc{'nhxndepo'}.fields = 'nhxndepo, scalar, series';
+%
+%%endef(nc);
+
+% Create global attributes
+nc.title = ncchar(CROCO_title);
+nc.title = CROCO_title;
+nc.date = ncchar(date);
+nc.date = date;
+nc.grd_file = ncchar(bioname);
+nc.grd_file = grdname;
+nc.type = ncchar('CROCO biology forcing file');
+nc.type = 'CROCO biology forcing file';
+
+% Write time variable
+nc{'ndep_time'}(:)=time.*30; % if time in month in the dataset !!!
+
+close(nc)
+
+nc=netcdf(bioname,'write');
+%
+% Loop on time
+for tindex=1:length(time)
+ time=nc{'ndep_time'}(tindex);
+ nc{'ndep'}(tindex,:,:)=ext_data(ndep_file,'ndep',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'noyndepo'}(tindex,:,:)=ext_data(ndep_file,'noyndepo',tindex,...
+ lon,lat,time,Roa,1);
+ nc{'nhxndepo'}(tindex,:,:)=ext_data(ndep_file,'nhxndepo',tindex,...
+ lon,lat,time,Roa,1);
+end
+%
+close(nc)
+if (makeplot)
+%
+% Make a few plots
+%
+disp(' Make a few plots...')
+test_bioforcing(bioname,grdname,'ndep',[1 4 7 10],3,coastfileplot)
+test_bioforcing(bioname,grdname,'noyndepo',[1 4 7 10],3,coastfileplot)
+test_bioforcing(bioname,grdname,'nhxndepo',[1 4 7 10],3,coastfileplot)
+end % if makeplot
+%
+% End
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Preprocessing_tools/create_bryfile.m b/Preprocessing_tools/create_bryfile.m
index e2c3af8a2fc287e00494777a85da8129f70a3297..e36dde8a424dba55eb23d715dc26d29afe2877d6 100644
--- a/Preprocessing_tools/create_bryfile.m
+++ b/Preprocessing_tools/create_bryfile.m
@@ -163,47 +163,47 @@ nc{'hc'}.long_name = 'S-coordinate parameter, critical depth';
nc{'hc'}.units = ncchar('meter');
nc{'hc'}.units = 'meter';
%
-nc{'sc_r'} = ncdouble('s_rho') ;
-nc{'sc_r'}.long_name = ncchar('S-coordinate at RHO-points');
-nc{'sc_r'}.long_name = 'S-coordinate at RHO-points';
-nc{'sc_r'}.valid_min = -1.;
-nc{'sc_r'}.valid_max = 0.;
-nc{'sc_r'}.positive = ncchar('up');
-nc{'sc_r'}.positive = 'up';
+nc{'s_rho'} = ncdouble('s_rho') ;
+nc{'s_rho'}.long_name = ncchar('S-coordinate at RHO-points');
+nc{'s_rho'}.long_name = 'S-coordinate at RHO-points';
+nc{'s_rho'}.valid_min = -1.;
+nc{'s_rho'}.valid_max = 0.;
+nc{'s_rho'}.positive = ncchar('up');
+nc{'s_rho'}.positive = 'up';
if (vtransform == 1)
- nc{'sc_r'}.standard_name = ncchar('ocean_s_coordinate_g1');
- nc{'sc_r'}.standard_name = 'ocean_s_coordinate_g1';
+ nc{'s_rho'}.standard_name = ncchar('ocean_s_coordinate_g1');
+ nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g1';
elseif (vtransform == 2)
- nc{'sc_r'}.standard_name = ncchar('ocean_s_coordinate_g2');
- nc{'sc_r'}.standard_name = 'ocean_s_coordinate_g2';
+ nc{'s_rho'}.standard_name = ncchar('ocean_s_coordinate_g2');
+ nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g2';
end
-nc{'sc_r'}.formula_terms = ncchar('s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc');
-nc{'sc_r'}.formula_terms = 's: s_rho C: Cs_r eta: zeta depth: h depth_c: hc';
-%
-nc{'sc_w'} = ncdouble('s_w') ;
-nc{'sc_w'}.long_name = ncchar('S-coordinate at W-points');
-nc{'sc_w'}.long_name = 'S-coordinate at W-points';
-nc{'sc_w'}.valid_min = -1. ;
-nc{'sc_w'}.valid_max = 0. ;
-nc{'sc_w'}.positive = ncchar('up');
-nc{'sc_w'}.positive = 'up';
+nc{'s_rho'}.formula_terms = ncchar('s: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc');
+nc{'s_rho'}.formula_terms = 's: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc';
+%
+nc{'s_w'} = ncdouble('s_w') ;
+nc{'s_w'}.long_name = ncchar('S-coordinate at W-points');
+nc{'s_w'}.long_name = 'S-coordinate at W-points';
+nc{'s_w'}.valid_min = -1. ;
+nc{'s_w'}.valid_max = 0. ;
+nc{'s_w'}.positive = ncchar('up');
+nc{'s_w'}.positive = 'up';
if (vtransform == 1)
- nc{'sc_w'}.standard_name = ncchar('ocean_s_coordinate_g1');
- nc{'sc_w'}.standard_name = 'ocean_s_coordinate_g1';
+ nc{'s_w'}.standard_name = ncchar('ocean_s_coordinate_g1');
+ nc{'s_w'}.standard_name = 'ocean_s_coordinate_g1';
elseif (vtransform == 2)
- nc{'sc_w'}.standard_name = ncchar('ocean_s_coordinate_g2');
- nc{'sc_w'}.standard_name = 'ocean_s_coordinate_g2';
+ nc{'s_w'}.standard_name = ncchar('ocean_s_coordinate_g2');
+ nc{'s_w'}.standard_name = 'ocean_s_coordinate_g2';
end
-nc{'sc_w'}.formula_terms = ncchar('s: s_w C: Cs_w eta: zeta depth: h depth_c: hc');
-nc{'sc_w'}.formula_terms = 's: s_w C: Cs_w eta: zeta depth: h depth_c: hc';
+nc{'s_w'}.formula_terms = ncchar('s: s_w C: Cs_w eta: zeta depth: h depth_c: hc');
+nc{'s_w'}.formula_terms = 's: s_w C: Cs_w eta: zeta depth: h depth_c: hc';
%
-nc{'Cs_r'} = ncdouble('s_rho') ;
-nc{'Cs_r'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
-nc{'Cs_r'}.long_name = 'S-coordinate stretching curves at RHO-points';
-nc{'Cs_r'}.units = ncchar('nondimensional');
-nc{'Cs_r'}.units = 'nondimensional';
-nc{'Cs_r'}.valid_min = -1;
-nc{'Cs_r'}.valid_max = 0;
+nc{'Cs_rho'} = ncdouble('s_rho') ;
+nc{'Cs_rho'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
+nc{'Cs_rho'}.long_name = 'S-coordinate stretching curves at RHO-points';
+nc{'Cs_rho'}.units = ncchar('nondimensional');
+nc{'Cs_rho'}.units = 'nondimensional';
+nc{'Cs_rho'}.valid_min = -1;
+nc{'Cs_rho'}.valid_max = 0;
%
nc{'Cs_w'} = ncdouble('s_w') ;
nc{'Cs_w'}.long_name = ncchar('S-coordinate stretching curves at W-points');
@@ -582,7 +582,7 @@ nc.history = history;
%
% Compute S coordinates
%
-[sc_r,Cs_r,sc_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
+[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
%disp(['vtransform=',num2str(vtransform)])
%
% Write variables
@@ -596,9 +596,9 @@ nc{'theta_s'}(:) = theta_s;
nc{'theta_b'}(:) = theta_b;
nc{'Tcline'}(:) = hc;
nc{'hc'}(:) = hc;
-nc{'sc_r'}(:) = sc_r;
-nc{'sc_w'}(:) = sc_w;
-nc{'Cs_r'}(:) = Cs_r ;
+nc{'s_rho'}(:) = s_rho;
+nc{'s_w'}(:) = s_w;
+nc{'Cs_rho'}(:) = Cs_rho ;
nc{'Cs_w'}(:) = Cs_w;
nc{'tclm_time'}(:) = time;
nc{'temp_time'}(:) = time;
diff --git a/Preprocessing_tools/create_climfile.m b/Preprocessing_tools/create_climfile.m
index f8bda105d7894d1ff746d974cb761f361d0ba4b6..7e2bee7a33a668d18c5356820ae84ec11a07c08b 100644
--- a/Preprocessing_tools/create_climfile.m
+++ b/Preprocessing_tools/create_climfile.m
@@ -124,9 +124,9 @@ nc{'theta_s'} = ncdouble('one') ;
nc{'theta_b'} = ncdouble('one') ;
nc{'Tcline'} = ncdouble('one') ;
nc{'hc'} = ncdouble('one') ;
-nc{'sc_r'} = ncdouble('s_rho') ;
-nc{'sc_w'} = ncdouble('s_w') ;
-nc{'Cs_r'} = ncdouble('s_rho') ;
+nc{'s_rho'} = ncdouble('s_rho') ;
+nc{'s_w'} = ncdouble('s_w') ;
+nc{'Cs_rho'} = ncdouble('s_rho') ;
nc{'Cs_w'} = ncdouble('s_w') ;
nc{'tclm_time'} = ncdouble('tclm_time') ;
nc{'temp_time'} = ncdouble('temp_time') ;
@@ -192,44 +192,44 @@ nc{'hc'}.long_name = 'S-coordinate parameter, critical depth';
nc{'hc'}.units = ncchar('meter');
nc{'hc'}.units = 'meter';
%
-nc{'sc_r'}.long_name = ncchar('S-coordinate at RHO-points');
-nc{'sc_r'}.long_name = 'S-coordinate at RHO-points';
-nc{'sc_r'}.valid_min = -1.;
-nc{'sc_r'}.valid_max = 0.;
-nc{'sc_r'}.positive = ncchar('up');
-nc{'sc_r'}.positive = 'up';
+nc{'s_rho'}.long_name = ncchar('S-coordinate at RHO-points');
+nc{'s_rho'}.long_name = 'S-coordinate at RHO-points';
+nc{'s_rho'}.valid_min = -1.;
+nc{'s_rho'}.valid_max = 0.;
+nc{'s_rho'}.positive = ncchar('up');
+nc{'s_rho'}.positive = 'up';
if (vtransform ==1)
- nc{'sc_r'}.standard_name = ncchar('ocean_s_coordinate_g1');
- nc{'sc_r'}.standard_name = 'ocean_s_coordinate_g1';
+ nc{'s_rho'}.standard_name = ncchar('ocean_s_coordinate_g1');
+ nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g1';
elseif (vtransform ==2)
- nc{'sc_r'}.standard_name = ncchar('ocean_s_coordinate_g2');
- nc{'sc_r'}.standard_name = 'ocean_s_coordinate_g2';
+ nc{'s_rho'}.standard_name = ncchar('ocean_s_coordinate_g2');
+ nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g2';
end
-nc{'sc_r'}.formula_terms = ncchar('s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc');
-nc{'sc_r'}.formula_terms = 's: s_rho C: Cs_r eta: zeta depth: h depth_c: hc';
-%
-nc{'sc_w'}.long_name = ncchar('S-coordinate at W-points');
-nc{'sc_w'}.long_name = 'S-coordinate at W-points';
-nc{'sc_w'}.valid_min = -1. ;
-nc{'sc_w'}.valid_max = 0. ;
-nc{'sc_w'}.positive = ncchar('up');
-nc{'sc_w'}.positive = 'up';
+nc{'s_rho'}.formula_terms = ncchar('s: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc');
+nc{'s_rho'}.formula_terms = 's: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc';
+%
+nc{'s_w'}.long_name = ncchar('S-coordinate at W-points');
+nc{'s_w'}.long_name = 'S-coordinate at W-points';
+nc{'s_w'}.valid_min = -1. ;
+nc{'s_w'}.valid_max = 0. ;
+nc{'s_w'}.positive = ncchar('up');
+nc{'s_w'}.positive = 'up';
if (vtransform == 1)
- nc{'sc_w'}.standard_name = ncchar('ocean_s_coordinate_g1');
- nc{'sc_w'}.standard_name = 'ocean_s_coordinate_g1';
+ nc{'s_w'}.standard_name = ncchar('ocean_s_coordinate_g1');
+ nc{'s_w'}.standard_name = 'ocean_s_coordinate_g1';
elseif (vtransform == 2)
- nc{'sc_w'}.standard_name = ncchar('ocean_s_coordinate_g2');
- nc{'sc_w'}.standard_name = 'ocean_s_coordinate_g2';
+ nc{'s_w'}.standard_name = ncchar('ocean_s_coordinate_g2');
+ nc{'s_w'}.standard_name = 'ocean_s_coordinate_g2';
end
-nc{'sc_w'}.formula_terms = ncchar('s: s_w C: Cs_w eta: zeta depth: h depth_c: hc');
-nc{'sc_w'}.formula_terms = 's: s_w C: Cs_w eta: zeta depth: h depth_c: hc';
+nc{'s_w'}.formula_terms = ncchar('s: s_w C: Cs_w eta: zeta depth: h depth_c: hc');
+nc{'s_w'}.formula_terms = 's: s_w C: Cs_w eta: zeta depth: h depth_c: hc';
%
-nc{'Cs_r'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
-nc{'Cs_r'}.long_name = 'S-coordinate stretching curves at RHO-points';
-nc{'Cs_r'}.units = ncchar('nondimensional');
-nc{'Cs_r'}.units = 'nondimensional';
-nc{'Cs_r'}.valid_min = -1;
-nc{'Cs_r'}.valid_max = 0;
+nc{'Cs_rho'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
+nc{'Cs_rho'}.long_name = 'S-coordinate stretching curves at RHO-points';
+nc{'Cs_rho'}.units = ncchar('nondimensional');
+nc{'Cs_rho'}.units = 'nondimensional';
+nc{'Cs_rho'}.valid_min = -1;
+nc{'Cs_rho'}.valid_max = 0;
%
nc{'Cs_w'}.long_name = ncchar('S-coordinate stretching curves at W-points');
nc{'Cs_w'}.long_name = 'S-coordinate stretching curves at W-points';
@@ -411,17 +411,17 @@ nc.history = history;
%
% Set S-Curves in domain [-1 < sc < 0] at vertical W- and RHO-points.
%
-[sc_r,Cs_r,sc_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
+[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
%disp(['vtransform=',num2str(vtransform)])
% cff1=1./sinh(theta_s);
% cff2=0.5/tanh(0.5*theta_s);
-% sc_r=((1:N)-N-0.5)/N;
-% Cs_r=(1.-theta_b)*cff1*sinh(theta_s*sc_r)...
-% +theta_b*(cff2*tanh(theta_s*(sc_r+0.5))-0.5);
-% sc_w=((0:N)-N)/N;
-% Cs_w=(1.-theta_b)*cff1*sinh(theta_s*sc_w)...
-% +theta_b*(cff2*tanh(theta_s*(sc_w+0.5))-0.5);
+% s_rho=((1:N)-N-0.5)/N;
+% Cs_rho=(1.-theta_b)*cff1*sinh(theta_s*s_rho)...
+% +theta_b*(cff2*tanh(theta_s*(s_rho+0.5))-0.5);
+% s_w=((0:N)-N)/N;
+% Cs_w=(1.-theta_b)*cff1*sinh(theta_s*s_w)...
+% +theta_b*(cff2*tanh(theta_s*(s_w+0.5))-0.5);
%
@@ -436,9 +436,9 @@ nc{'theta_s'}(:) = theta_s;
nc{'theta_b'}(:) = theta_b;
nc{'Tcline'}(:) = hc;
nc{'hc'}(:) = hc;
-nc{'sc_r'}(:) = sc_r;
-nc{'sc_w'}(:) = sc_w;
-nc{'Cs_r'}(:) = Cs_r;
+nc{'s_rho'}(:) = s_rho;
+nc{'s_w'}(:) = s_w;
+nc{'Cs_rho'}(:) = Cs_rho;
nc{'Cs_w'}(:) = Cs_w;
nc{'tclm_time'}(:) = time;
nc{'temp_time'}(:) = time;
diff --git a/Preprocessing_tools/create_inifile.m b/Preprocessing_tools/create_inifile.m
index 8a2e8332df778509725dc5284037714d1a20916d..acdc9abc116e2aa64d463824ebe5cf63a5fa17d2 100644
--- a/Preprocessing_tools/create_inifile.m
+++ b/Preprocessing_tools/create_inifile.m
@@ -109,8 +109,8 @@ nc{'theta_s'} = ncdouble('one') ;
nc{'theta_b'} = ncdouble('one') ;
nc{'Tcline'} = ncdouble('one') ;
nc{'hc'} = ncdouble('one') ;
-nc{'sc_r'} = ncdouble('s_rho') ;
-nc{'Cs_r'} = ncdouble('s_rho') ;
+nc{'s_rho'} = ncdouble('s_rho') ;
+nc{'Cs_rho'} = ncdouble('s_rho') ;
nc{'ocean_time'} = ncdouble('time') ;
nc{'scrum_time'} = ncdouble('time') ;
nc{'u'} = ncdouble('time','s_rho','eta_u','xi_u') ;
@@ -159,19 +159,19 @@ nc{'hc'}.long_name = 'S-coordinate parameter, critical depth';
nc{'hc'}.units = ncchar('meter');
nc{'hc'}.units = 'meter';
%
-nc{'sc_r'}.long_name = ncchar('S-coordinate at RHO-points');
-nc{'sc_r'}.long_name = 'S-coordinate at RHO-points';
-nc{'sc_r'}.units = ncchar('nondimensional');
-nc{'sc_r'}.units = 'nondimensional';
-nc{'sc_r'}.valid_min = -1;
-nc{'sc_r'}.valid_max = 0;
+nc{'s_rho'}.long_name = ncchar('S-coordinate at RHO-points');
+nc{'s_rho'}.long_name = 'S-coordinate at RHO-points';
+nc{'s_rho'}.units = ncchar('nondimensional');
+nc{'s_rho'}.units = 'nondimensional';
+nc{'s_rho'}.valid_min = -1;
+nc{'s_rho'}.valid_max = 0;
%
-nc{'Cs_r'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
-nc{'Cs_r'}.long_name = 'S-coordinate stretching curves at RHO-points';
-nc{'Cs_r'}.units = ncchar('nondimensional');
-nc{'Cs_r'}.units = 'nondimensional';
-nc{'Cs_r'}.valid_min = -1;
-nc{'Cs_r'}.valid_max = 0;
+nc{'Cs_rho'}.long_name = ncchar('S-coordinate stretching curves at RHO-points');
+nc{'Cs_rho'}.long_name = 'S-coordinate stretching curves at RHO-points';
+nc{'Cs_rho'}.units = ncchar('nondimensional');
+nc{'Cs_rho'}.units = 'nondimensional';
+nc{'Cs_rho'}.valid_min = -1;
+nc{'Cs_rho'}.valid_max = 0;
%
nc{'ocean_time'}.long_name = ncchar('time since initialization');
nc{'ocean_time'}.long_name = 'time since initialization';
@@ -239,7 +239,7 @@ nc.history = history;
%
% Compute S coordinates
%
-[sc_r,Cs_r,sc_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
+[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
%disp(['vtransform=',num2str(vtransform)])
%
% Write variables
@@ -253,8 +253,8 @@ nc{'theta_s'}(:) = theta_s;
nc{'theta_b'}(:) = theta_b;
nc{'Tcline'}(:) = hc;
nc{'hc'}(:) = hc;
-nc{'sc_r'}(:) = sc_r;
-nc{'Cs_r'}(:) = Cs_r;
+nc{'s_rho'}(:) = s_rho;
+nc{'Cs_rho'}(:) = Cs_rho;
nc{'scrum_time'}(1) = time*24*3600;
nc{'ocean_time'}(1) = time*24*3600;
nc{'u'}(:) = 0;
diff --git a/Preprocessing_tools/geost_currents.m b/Preprocessing_tools/geost_currents.m
index 73026f9bd479c9032b2eca2e13825576656a6a65..2363074ba8615dc757597c21333ba0236cdfcf33 100644
--- a/Preprocessing_tools/geost_currents.m
+++ b/Preprocessing_tools/geost_currents.m
@@ -162,8 +162,8 @@ for l=1:tlen
%
% Ekman transport
%
- if ~isempty(frcname)
-% disp('Add the Ekman transport')
+ if exist(frcname)
+ disp('Add the Ekman transport')
sustr(:,:)=nfrc{'sustr'}(l,:,:);
svstr(:,:)=nfrc{'svstr'}(l,:,:);
% rhoA=1.3; Cd=1.4e-3;
diff --git a/Preprocessing_tools/geost_currents_bry.m b/Preprocessing_tools/geost_currents_bry.m
index cc0f2e0ae463df34d5f3a7912c92cbf7c6d10104..eaad7517df7a78442456ee9a37786ce11391afe5 100644
--- a/Preprocessing_tools/geost_currents_bry.m
+++ b/Preprocessing_tools/geost_currents_bry.m
@@ -193,8 +193,8 @@ for l=1:tlen
%
% Ekman transport
%
- if ~isempty(frcname)
-% disp('Add the Ekman transport')
+ if exist(frcname)
+ disp('Add the Ekman transport')
if obcndx==1
tmp=squeeze(nfrc{'sustr'}(l,1,:));
sustr=0*h;
diff --git a/Preprocessing_tools/make_config.m b/Preprocessing_tools/make_config.m
index d6e53acfd725406bd8d52759e8a505097c1f2ef4..94b89ab97f69c3e85168aa23229b533262110466 100644
--- a/Preprocessing_tools/make_config.m
+++ b/Preprocessing_tools/make_config.m
@@ -47,5 +47,5 @@ make_clim
% Interannual forcing
%
%make_NCEP
-%make_OGCM
+%make_OGCM_mercator (SODA)
return
diff --git a/Preprocessing_tools/zlevs.m b/Preprocessing_tools/zlevs.m
index 619c1101d3c11995d39d6425efe50a8f218b4781..4d154c4da4e89ac498b7ca7481658e30bd68adeb 100644
--- a/Preprocessing_tools/zlevs.m
+++ b/Preprocessing_tools/zlevs.m
@@ -107,11 +107,9 @@ end
% transformation metrics compute evolving depths of of the three-
% dimensional model grid. Also adjust zeta for dry cells.
%
-h(h==0)=1.e-2;
Dcrit=0.01; % min water depth in dry cells
zeta(zeta<(Dcrit-h))=Dcrit-h(zeta<(Dcrit-h));
%
-hinv=1./h;
z=zeros(N,M,L);
if (vtransform == 2)
if type=='w'
@@ -123,14 +121,16 @@ if (vtransform == 2)
cff2=sc_r+1;
sc=sc_r;
end
- h2=(h+hc);
+ h2=(abs(h)+hc);
cff=hc*sc;
h2inv=1./h2;
for k=1:N
- z0=cff(k)+cff1(k)*h;
+ z0=cff(k)+cff1(k)*abs(h);
z(k,:,:)=z0.*h./(h2) + zeta.*(1.+z0.*h2inv);
end
else
+ h(h==0)=1.e-2;
+ hinv=1./h;
cff1=Cs;
cff2=sc+1;
cff=hc*(sc-Cs);
@@ -152,7 +152,6 @@ end
% end
%end
-
return
diff --git a/Preprocessing_tools/zlevs_1d.m b/Preprocessing_tools/zlevs_1d.m
index 45292a515a41425de38bfe37beb6a163d9826b14..3c856873a46d20c18265a8b4bfe623d34d448cbe 100644
--- a/Preprocessing_tools/zlevs_1d.m
+++ b/Preprocessing_tools/zlevs_1d.m
@@ -42,8 +42,6 @@ function z = zlevs_1d(h, zeta, theta_s, theta_b, hc, N, type, vtransform)
%
% Set S-Curves in domain [-1 < sc < 0] at vertical W- and RHO-points.
%
-cff1 = 1./sinh(theta_s);
-cff2 = 0.5/tanh(0.5*theta_s);
if type=='w'
sc = ((0:N) - N) / N;
N = N + 1;
@@ -51,8 +49,23 @@ else
sc=((1:N)-N-0.5) / N;
end
-Cs = (1.-theta_b) * cff1 * sinh(theta_s * sc)...
- + theta_b * (cff2 * tanh(theta_s * (sc + 0.5)) - 0.5);
+if (vtransform==1)
+ cff1=1./sinh(theta_s);
+ cff2=0.5/tanh(0.5*theta_s);
+ Cs=(1.-theta_b)*cff1*sinh(theta_s*sc)...
+ + theta_b*(cff2*tanh(theta_s*(sc+0.5))- 0.5);
+elseif (vtransform==2)
+ if theta_s>0.,
+ csrf=(1.-cosh(theta_s*sc))/(cosh(theta_s)-1.);
+ else
+ csrf=-sc.^2;
+ end
+ if theta_b>0.,
+ Cs=(exp(theta_b*csrf)-1.)/(1.-exp(-theta_b));
+ else
+ Cs=csrf;
+ end
+end
%
% Create S-coordinate system: based on model topography h(i,j),
% fast-time-averaged free-surface field and vertical coordinate
@@ -72,11 +85,11 @@ if (vtransform==1)
end
elseif (vtransform==2)
disp('--- using new s-coord')
- hinv=1./(h+hc);
+ hinv=1./(abs(h)+hc);
cff=hc*sc;
cff1=Cs;
for k=1:N
- z(k)=zeta+(zeta+h).*(cff(k)+cff1(k)*h).*hinv;
+ z(k)=zeta+(zeta+h).*(cff(k)+cff1(k)*abs(h)).*hinv;
end
else
error('wrong argument in zlevs_1d');
diff --git a/README.md b/README.md
index b7c105c438b96ea250085e768ce3609dc0e95bc5..6bf35917b473af68a636385d9c1c05ac516d962e 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,21 @@
CROCO_TOOLS
-----------
-CROCO preprocessing tools, CROCO_TOOLS, have been developed under Matlab software by IRD researchers (former Roms_tools). Note: These tools have been made to build easily regional configurations using climatological data. To use interannual data, some facilities are available (NCEP, CFSR, QuickScat data for atmospheric forcing, SODA and ECCO for lateral boundaries). However, to use other data, you will need to adapt the scripts. All utilities/toolbox requested for matlab crocotools programs are provided within the UTILITIES directory, or can be downloaded here: http://www.croco-ocean.org/download
+CROCO preprocessing tools, CROCO_TOOLS, have been developed under Matlab software by IRD researchers (former Roms_tools). Note: These tools have been made to build easily regional configurations using climatological data. To use interannual data, some facilities are available (ERA5, ERA-Interim, NCEP, CFSR, QuickScat data for atmospheric forcing, GLORYS, SODA and ECCO for lateral boundaries). However, to use other data, you will need to adapt the scripts. All utilities/toolbox requested for matlab crocotools programs are provided within the UTILITIES directory, or can be downloaded at https://www.croco-ocean.org in the Download section.
+
+More informations on the croco website at
+https://www.croco-ocean.org
+
+CROCO_TOOLS documentation is available at
+https://croco-ocean.gitlabpages.inria.fr/croco_doc
+
+and more specifically at
+https://croco-ocean.gitlabpages.inria.fr/croco_doc/tutos
+
+Remember you can also subscribe at CROCO forum at
+https://forum.croco-ocean.org
+
+
+
diff --git a/Rivers/create_runoff.m b/Rivers/create_runoff.m
index e783d78c7406a1a12e773ea4bd99d3028338c4d7..4cedbe46dcf854e30c3daaeae52857f25fe029c8 100644
--- a/Rivers/create_runoff.m
+++ b/Rivers/create_runoff.m
@@ -1,6 +1,6 @@
function create_runoff(runoffname,grdname,title,...
qbart,qbarc,rivername,rivernumber,...
- runoffname_StrLen,dir,psource_ncfile_ts,biol)
+ runoffname_StrLen,dir,psource_ncfile_ts,biol,pisces,quota)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf runoff file
@@ -91,7 +91,72 @@ if psource_ncfile_ts
nw{'NO3_src'} = ncdouble('n_qbar','qbar_time');
nw{'NO3_src'}.long_name = ncchar('runoff no3 conc.');
- nw{'NO3_src'}.units = ncchar('mmol.s-1');
+ nw{'NO3_src'}.units = ncchar('mmol.m-3');
+ if pisces
+ nw{'po4_src_time'} = ncdouble('qbar_time');
+ nw{'po4_src_time'}.long_name = ncchar('runoff time');
+ nw{'po4_src_time'}.units = ncchar('days');
+ nw{'po4_src_time'}.cycle_length = 360;
+
+ nw{'PO4_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'PO4_src'}.long_name = ncchar('runoff po4 conc.');
+ nw{'PO4_src'}.units = ncchar('mmol.m-3');
+
+ nw{'si_src_time'} = ncdouble('qbar_time');
+ nw{'si_src_time'}.long_name = ncchar('runoff time');
+ nw{'si_src_time'}.units = ncchar('days');
+ nw{'si_src_time'}.cycle_length = 360;
+
+ nw{'Si_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'Si_src'}.long_name = ncchar('runoff si conc.');
+ nw{'Si_src'}.units = ncchar('mmol.m-3');
+
+ nw{'dic_src_time'} = ncdouble('qbar_time');
+ nw{'dic_src_time'}.long_name = ncchar('runoff time');
+ nw{'dic_src_time'}.units = ncchar('days');
+ nw{'dic_src_time'}.cycle_length = 360;
+
+ nw{'DIC_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'DIC_src'}.long_name = ncchar('runoff dic conc.');
+ nw{'DIC_src'}.units = ncchar('mmol.m-3');
+
+ nw{'doc_src_time'} = ncdouble('qbar_time');
+ nw{'doc_src_time'}.long_name = ncchar('runoff time');
+ nw{'doc_src_time'}.units = ncchar('days');
+ nw{'doc_src_time'}.cycle_length = 360;
+
+ nw{'DOC_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'DOC_src'}.long_name = ncchar('runoff doc conc.');
+ nw{'DOC_src'}.units = ncchar('mmol.m-3');
+
+ nw{'talk_src_time'} = ncdouble('qbar_time');
+ nw{'talk_src_time'}.long_name = ncchar('runoff time');
+ nw{'talk_src_time'}.units = ncchar('days');
+ nw{'talk_src_time'}.cycle_length = 360;
+
+ nw{'TALK_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'TALK_src'}.long_name = ncchar('runoff talk conc.');
+ nw{'TALK_src'}.units = ncchar('mmol.m-3');
+ if quota
+ nw{'don_src_time'} = ncdouble('qbar_time');
+ nw{'don_src_time'}.long_name = ncchar('runoff time');
+ nw{'don_src_time'}.units = ncchar('days');
+ nw{'don_src_time'}.cycle_length = 360;
+
+ nw{'DON_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'DON_src'}.long_name = ncchar('runoff don conc.');
+ nw{'DON_src'}.units = ncchar('mmol.m-3');
+
+ nw{'dop_src_time'} = ncdouble('qbar_time');
+ nw{'dop_src_time'}.long_name = ncchar('runoff time');
+ nw{'dop_src_time'}.units = ncchar('days');
+ nw{'dop_src_time'}.cycle_length = 360;
+
+ nw{'DOP_src'} = ncdouble('n_qbar','qbar_time');
+ nw{'DOP_src'}.long_name = ncchar('runoff dop conc.');
+ nw{'DOP_src'}.units = ncchar('mmol.m-3');
+ end
+ end
end
end
%%%result = endef(nw);
@@ -115,11 +180,22 @@ if psource_ncfile_ts
nw{'temp_src_time'} (:) = qbart;
nw{'salt_src_time'} (:) = qbart;
if biol
- % nw{'no3_src_time'} (:) = no3t;
+ nw{'no3_src_time'} (:) = qbart;
+ if pisces
+ nw{'po4_src_time'} (:) = qbart;
+ nw{'si_src_time'} (:) = qbart;
+ nw{'dic_src_time'} (:) = qbart;
+ nw{'doc_src_time'} (:) = qbart;
+ nw{'talk_src_time'} (:) = qbart;
+ if quota
+ nw{'don_src_time'} (:) = qbart;
+ nw{'dop_src_time'} (:) = qbart;
+ end
+ end
end
end
for k=1:rivernumber
nw{'runoff_name'}(k,:) = rivername(k,:);
end
%
-close(nw)
+close (nw)
diff --git a/Rivers/locate_runoff.m b/Rivers/locate_runoff.m
index 547004132174a70c538562e724d27a8d62541cc0..6394fc25d2e51eb61390f30708946a2c9a2b5968 100644
--- a/Rivers/locate_runoff.m
+++ b/Rivers/locate_runoff.m
@@ -53,39 +53,42 @@ if dir(1)==0
if dir(2)==1 % >> : west - east => TESTED
while mask(j,i) == 1
i=i-1;
- disp(['MASK:',num2str(mask(j,i))])
- end
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKU:',num2str(masku(j,i))])
+ % disp(['MASK:',num2str(mask(j,i))])
+ end
+ %in this case add +1 in i to get back into last wet cell
+ i=i+1;
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKU:',num2str(masku(j,i))])
elseif dir(2)==-1 % << : east - west => TESTED
while mask(j,i) == 1
i=i+1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- %in this case add +1 in i to get back into last wet cell
- j=j+1;
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKU:',num2str(masku(j,i))])
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKU:',num2str(masku(j,i))])
end
else %inland
if dir(2) == 1 % >> : west-est => TESTED
while mask(j,i) ~= 1
i=i+1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKU:',num2str(masku(j,i))])
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKU:',num2str(masku(j,i))])
elseif dir(2) == -1 % << : east-west => TESTED
while mask(j,i) ~= 1
i=i-1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKU:',num2str(masku(j,i))])
+ % Modif GC 01/2024
+ %in this case add +1 in i to get back into last wet cell
+ i=i+1
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKU:',num2str(masku(j,i))])
end
end
else %dir(k,1)=1
@@ -93,43 +96,46 @@ else %dir(k,1)=1
if dir(2) == 1 % ^ : sud - nord => TESTED
while mask(j,i) == 1
j=j-1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
%in this case add +1 in j to get back into last wet cell
j=j+1;
%
- disp(['-- ^^ start insea'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKV:',num2str(maskv(j,i))])
+ %disp(['-- ^^ start insea'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKV:',num2str(maskv(j,i))])
elseif dir(2) == -1 % v : nord - sud => TESTED
while mask(j,i) == 1
j=j+1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKV:',num2str(maskv(j,i))])
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKV:',num2str(maskv(j,i))])
end
else %inland
if dir(2) == 1 % ^: sud-nord => TESTED
while mask(j,i) ~= 1
j=j+1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- disp(['--^^ start inland'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKV:',num2str(maskv(j,i))])
+ %disp(['--^^ start inland'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKV:',num2str(maskv(j,i))])
elseif dir(2) == -1 % v : nord-sud => TESTED
while mask(j,i) ~= 1
j=j-1;
- disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASK:',num2str(mask(j,i))])
end
- disp(['--'])
- disp(['MASK:',num2str(mask(j,i))])
- disp(['MASKV:',num2str(maskv(j,i))])
+ % Modif GC 01/2024
+ %in this case add +1 in j to get back into last wet cell
+ j=j+1;
+ %disp(['--'])
+ %disp(['MASK:',num2str(mask(j,i))])
+ %disp(['MASKV:',num2str(maskv(j,i))])
end
end
end
@@ -139,15 +145,17 @@ j2=j; i2=i;
j2for=j-1; i2for=i-1;
% regarding the flow direction, sense and landmask surrounding
-% -- toward west >>
+% -- toward east >>
if ( dir(1) == 0 & dir(2) == 1 ) ;
j2for_out = j2for ;
i2for_out = i2for ;
end
-% -- toward est <<
+% -- toward west <<
if ( dir(1) == 0 & dir(2) == -1 );
j2for_out = j2for ;
- i2for_out = i2for + 1 ;
+ % Modif GC 01/2024
+ % i2for_out = i2for + 1 ;
+ i2for_out = i2for ;
end
% -- toward north ^^
if ( dir(1) == 1 & dir(2) == 1 );
@@ -156,7 +164,9 @@ if ( dir(1) == 1 & dir(2) == 1 );
end
% -- toward south vv
if ( dir(1) == 1 & dir(2) == -1 );
- j2for_out = j2for + 1 ;
+ % Modif GC 01/2024
+ % j2for_out = j2for + 1 ;
+ j2for_out = j2for ;
i2for_out = i2for ;
end
diff --git a/Rivers/make_runoff.m b/Rivers/make_runoff.m
index 3040b96ccfb310456cfce68df469fc663363c2ab..edef1e76f59041576962d1cb7a9186c92ded7894 100644
--- a/Rivers/make_runoff.m
+++ b/Rivers/make_runoff.m
@@ -72,7 +72,7 @@ end
%=========================================================================================
% Choose if you process variable tracer concentration(temp, salt, NO3, ...)
-psource_ncfile_ts=0;
+psource_ncfile_ts=1;
if psource_ncfile_ts
psource_ncfile_ts_auto=1 ;
@@ -104,7 +104,7 @@ plotting_zoom=0;
%
%=========================================================================================
% Add biogeochemical variables
-if (makenpzd | makepisces | makebioebus) makebio = 1;
+if (makenpzd | makepisces | makebioebus | makequota) makebio = 1;
else
makebio = 0;
end
@@ -156,7 +156,7 @@ if rivernumber == 0 %%at least a river
disp(['Create a "fictive" runoff forcing file : river with no discharge'])
create_runoff(rivname,grdname,title_name,...
qbar_time,qbar_cycle, ...
- 'fictiveriver_@nest',1,18,1,psource_ncfile_ts,makebio)
+ 'fictiveriver_@nest',1,18,1,psource_ncfile_ts,makebio,makepisces,makequota)
my_flow=0;
nw=netcdf(rivname,'w');
disp(['Write in runoff file'])
@@ -166,6 +166,17 @@ if rivernumber == 0 %%at least a river
nw{'salt_src'}(:) = my_salt_src';
if makebio
nw{'NO3_src'}(:) = my_no3_src';
+ if makepisces
+ nw{'PO4_src'}(:) = my_po4_src';
+ nw{'Si_src'}(:) = my_sil_src';
+ nw{'DIC_src'}(:) = my_dic_src';
+ nw{'DOC_src'}(:) = my_doc_src';
+ nw{'TALK_src'}(:) = my_talk_src';
+ if makequota
+ nw{'DON_src'}(:) = my_don_src';
+ nw{'DOP_src'}(:) = my_dop_src';
+ end
+ end
end
end
close(nw)
@@ -379,7 +390,7 @@ else
disp(' Create the runoff file...')
create_runoff(rivname,grdname,title_name,...
qbar_time,qbar_cycle, ...
- rivername,number_rivertoprocess,rivname_StrLen,dir,psource_ncfile_ts,makebio)
+ rivername,number_rivertoprocess,rivname_StrLen,dir,psource_ncfile_ts,makebio,makepisces,makequota)
%%
%% Adjust the rivers positions relative to the mask
%%
@@ -425,6 +436,17 @@ else
my_salt_src0=zeros(rivernumber ,length(woa_time));
if makebio==1
my_no3_src0=zeros(rivernumber,length(woa_time));
+ if makepisces==1
+ my_po4_src0=zeros(rivernumber,length(woa_time));
+ my_sil_src0=zeros(rivernumber,length(woa_time));
+ my_dic_src0=zeros(rivernumber,length(woa_time));
+ my_doc_src0=zeros(rivernumber,length(woa_time));
+ my_talk_src0=zeros(rivernumber,length(woa_time));
+ if makequota==1
+ my_don_src0=zeros(rivernumber,length(woa_time));
+ my_dop_src0=zeros(rivernumber,length(woa_time));
+ end
+ end
end
if psource_ncfile_ts_auto
@@ -463,6 +485,24 @@ else
if makebio==1
NO3=squeeze(ncclim{'NO3'}(:,N,j_rho,i_rho));
my_no3_src0(k,:)=NO3';
+ if makepisces==1
+ PO4=squeeze(ncclim{'PO4'}(:,N,j_rho,i_rho));
+ my_po4_src0(k,:)=PO4';
+ Si=squeeze(ncclim{'Si'}(:,N,j_rho,i_rho));
+ my_sil_src0(k,:)=Si';
+ DIC=squeeze(ncclim{'DIC'}(:,N,j_rho,i_rho));
+ my_dic_src0(k,:)=DIC';
+ DOC=squeeze(ncclim{'DOC'}(:,N,j_rho,i_rho));
+ my_doc_src0(k,:)=DOC';
+ TALK=squeeze(ncclim{'TALK'}(:,N,j_rho,i_rho));
+ my_talk_src0(k,:)=TALK';
+ if makequota==1
+ DON=squeeze(ncclim{'DON'}(:,N,j_rho,i_rho));
+ my_don_src0(k,:)=DON';
+ DOP=squeeze(ncclim{'DOP'}(:,N,j_rho,i_rho));
+ my_dop_src0(k,:)=DOP';
+ end
+ end
end
end
close(ncclim)
@@ -588,6 +628,17 @@ else
my_salt_src= my_salt_src0(find(indomain_last==1),:);
if makebio
my_no3_src = my_no3_src0(find(indomain_last==1),:);
+ if makepisces
+ my_po4_src = my_po4_src0(find(indomain_last==1),:);
+ my_sil_src = my_sil_src0(find(indomain_last==1),:);
+ my_dic_src = my_dic_src0(find(indomain_last==1),:);
+ my_doc_src = my_doc_src0(find(indomain_last==1),:);
+ my_talk_src = my_talk_src0(find(indomain_last==1),:);
+ if makequota
+ my_don_src = my_don_src0(find(indomain_last==1),:);
+ my_dop_src = my_dop_src0(find(indomain_last==1),:);
+ end
+ end
end
end
%%
@@ -740,6 +791,24 @@ else
if makebio
nw{'NO3_src'}(:) = my_no3_src';
disp(['... NO3 concentration'])
+ if makepisces
+ nw{'PO4_src'}(:) = my_po4_src';
+ disp(['... PO4 concentration'])
+ nw{'Si_src'}(:) = my_sil_src';
+ disp(['... Si concentration'])
+ nw{'DIC_src'}(:) = my_dic_src';
+ disp(['... DIC concentration'])
+ nw{'DOC_src'}(:) = my_doc_src';
+ disp(['... DOC concentration'])
+ nw{'TALK_src'}(:) = my_talk_src';
+ disp(['... TALK concentration'])
+ if makequota
+ nw{'DON_src'}(:) = my_don_src';
+ disp(['... DON concentration'])
+ nw{'DOP_src'}(:) = my_dop_src';
+ disp(['... DOP concentration'])
+ end
+ end
end
end
if psource_ncfile_ts == 1
@@ -788,14 +857,58 @@ else
if psource_ncfile_ts==1
T=mean(my_temp_src0(k,:));
S=mean(my_salt_src0(k,:));
+ if makebio
+ N=mean(my_no3_src0(k,:));
+ if makepisces
+ P=mean(my_po4_src0(k,:));
+ S=mean(my_sil_src0(k,:));
+ A=mean(my_talk_src0(k,:));
+ Di=mean(my_dic_src0(k,:));
+ Dc=mean(my_doc_src0(k,:));
+ if makequota
+ Dn=mean(my_don_src0(k,:));
+ Dp=mean(my_dop_src0(k,:));
+ end
+ end
+ end
else
T=20;
S=15;
+ if makebio
+ N=10;
+ if makepisces
+ P=1;
+ S=10;
+ A=2300;
+ Di=2100;
+ Dc=28;
+ if makequota
+ Dn=10;
+ Dp=1;
+ end
+ end
+ end
end
%Print the listing
- disp([' ',num2str(I2for_out(k)),' ',num2str(J2for_out(k)),...
- ' ',num2str(dir(k,1)),' ',num2str(dir(k,2)),' T T ',...
- num2str(T),' ',num2str(S)])
+ if makebio==0
+ disp([' ',num2str(I2for_out(k)),' ',num2str(J2for_out(k)),...
+ ' ',num2str(dir(k,1)),' ',num2str(dir(k,2)),' T T ',...
+ num2str(T),' ',num2str(S)])
+ else
+ if makepisces==0
+ disp([' ',num2str(I2for_out(k)),' ',num2str(J2for_out(k)),...
+ ' ',num2str(dir(k,1)),' ',num2str(dir(k,2)),' T T T ',...
+ num2str(T),' ',num2str(S),' ',num2str(N)])
+ else
+ if makequota==0
+ disp([' ',num2str(I2for_out(k)),' ',num2str(J2for_out(k)),...
+ ' ',num2str(dir(k,1)),' ',num2str(dir(k,2)),' 4*T 2*F T F T 2*F T 12*F T 2*F'])
+ else
+ disp([' ',num2str(I2for_out(k)),' ',num2str(J2for_out(k)),...
+ ' ',num2str(dir(k,1)),' ',num2str(dir(k,2)),' 4*T 2*F T F T 2*F T 12*F T 2*F 2*T 13*F '])
+ end
+ end
+ end
end
disp(['-----------------------------------------------------------------'])
@@ -804,7 +917,7 @@ else
%%
figure(30)
if psource_ncfile_ts==1
- subplot(3,1,1)
+ subplot(3,2,1)
end
hold on
plot([1:12],my_flow)
@@ -814,17 +927,39 @@ else
xlabel(['\bf Month']);ylabel(['\bf Discharge in m3/s'])
set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
if psource_ncfile_ts==1
- subplot(3,1,2)
+ subplot(3,2,3)
plot([1:12],my_temp_src)
box on, grid on
xlabel(['\bf Month']);ylabel(['\bf Temp [C]'])
set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
%
- subplot(3,1,3)
+ subplot(3,2,5)
plot([1:12],my_salt_src)
box on, grid on
xlabel(['\bf Month']);ylabel(['\bf Salt [psu]'])
set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
+ %
+ if makebio
+ subplot(3,2,2)
+ plot([1:12],my_no3_src)
+ box on, grid on
+ xlabel(['\bf Month']);ylabel(['\bf NO3 [mmol/m3]'])
+ set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
+ %
+ if makepisces
+ subplot(3,2,4)
+ plot([1:12],my_doc_src)
+ box on, grid on
+ xlabel(['\bf Month']);ylabel(['\bf DOC [mmol/m3]'])
+ set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
+ %
+ subplot(3,2,6)
+ plot([1:12],my_sil_src)
+ box on, grid on
+ xlabel(['\bf Month']);ylabel(['\bf Si [mmol/m3]'])
+ set(gca,'Xtick',[0.5:11.5],'XtickLabel',['J';'F';'M';'A';'M';'J';'J';'A';'S';'O';'N';'D']);
+ end
+ end
end
end %% end at least one river !
diff --git a/Tides/add_tidal_data.m b/Tides/add_tidal_data.m
index 6beb3b0eb58262c669e25abb7fe75dbd0b8fb5e4..1144ab6edc26fc82e7cc43251cf85957bedc001f 100644
--- a/Tides/add_tidal_data.m
+++ b/Tides/add_tidal_data.m
@@ -214,7 +214,7 @@ if makeplot==1
%
% Plot tidal potential
%
- ncfrc=netcdf(frcname);
+ ncfrc=netcdf(frcname,'r');
domaxis=[min(min(lonr)) max(max(lonr)) min(min(latr)) max(max(latr))];
% M2 AMP
Pamp=squeeze(ncfrc{'tide_Pamp'}(1,:,:));
diff --git a/Tides/make_tides.m b/Tides/make_tides.m
index 5e79833527e534965b2c5c3ac3bb9b182a50468d..128f8079e5e53ee69ee16b0d7ccfdc5150715582 100644
--- a/Tides/make_tides.m
+++ b/Tides/make_tides.m
@@ -237,7 +237,7 @@ if makeplot==1
%
% Plot tidal potential
%
- ncfrc=netcdf(frcname);
+ ncfrc=netcdf(frcname,'r');
domaxis=[min(min(lonr)) max(max(lonr)) min(min(latr)) max(max(latr))];
% M2 AMP
Pamp=squeeze(ncfrc{'tide_Pamp'}(1,:,:));
diff --git a/UTILITIES/export_fig/.ignore/ghostscript.txt b/UTILITIES/export_fig/.ignore/ghostscript.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb5075252008b85d5406fb74f27fc9343f4e955b
--- /dev/null
+++ b/UTILITIES/export_fig/.ignore/ghostscript.txt
@@ -0,0 +1 @@
+gs
\ No newline at end of file
diff --git a/UTILITIES/export_fig/.ignore/gs_font_path.txt b/UTILITIES/export_fig/.ignore/gs_font_path.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf71a1b34d8793c467671f5bd2bc2f229d24b6ac
--- /dev/null
+++ b/UTILITIES/export_fig/.ignore/gs_font_path.txt
@@ -0,0 +1 @@
+UTILITIES/export_fig/.ignore/ghostscript.txt /usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype
\ No newline at end of file
diff --git a/Visualization_tools/time_series.m b/Visualization_tools/time_series.m
index 78cc9715c85b482342b6514580e10019abf5d9e7..043f460145ceb850fe58e26cae6894a25df1ea85 100644
--- a/Visualization_tools/time_series.m
+++ b/Visualization_tools/time_series.m
@@ -1,7 +1,7 @@
function time_series(hisfile,gridfile,lon0,lat0,vname,vlevel,coef)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Get a vertical Profile
+% Get a time series
%
% Further Information:
% http://www.croco-ocean.org
diff --git a/croco_pyvisu/CrocoXarray.py b/croco_pyvisu/CrocoXarray.py
deleted file mode 100644
index ef26ddd7175ee471ebd5e072364bbc33f9e912f8..0000000000000000000000000000000000000000
--- a/croco_pyvisu/CrocoXarray.py
+++ /dev/null
@@ -1,358 +0,0 @@
-# -*- coding: UTF-8 -*-
-#
-# generated by wxGlade 0.8.0b3 on Tue Jan 30 13:49:27 2018
-#
-
-import os
-import re
-import numpy as np
-import xarray as xr
-from croco_wrapper import CrocoWrapper
-
-second2day = 1. / 86400.
-
-
-class Croco(object):
- '''
- Croco class grouping all the methods relative to the variables
- '''
- def __init__(self):
- '''
- Initialise the Croco object
- '''
-
- self.wrapper = CrocoWrapper()
-
- # Mean earth radius in metres (from scalars.h)
- self.r_earth = 6371315.
-
- # An index along either x or y dimension
- self.ij = None
-
- self.ListOfVariables = self.list_of_variables()
- self.ListOfDerived = self.list_of_derived()
-
- self.rho0 = 1027.
- self.g = 9.81
-
- def list_of_variables(self):
- '''
- return names of variables depending on time and having at least 3 dimensions
- '''
- # open file
- # ds = return_xarray_dataset(self.crocofile)
- # retrieve real name for time dimension
- # timedim = self.wrapper.keymap_dimensions['tdim']
- ds = self.wrapper.dsvar
- keys = []
- self.variables = {}
- # retrieve variable name
- for key in ds.data_vars.keys():
- if ('t' in ds[key].dims and len(ds[key].dims) > 2):
- self.variables[key] = ds[key]
- keys.append(key)
- return keys
-
- def list_of_derived(self):
- ''' List of calculated variables implemented '''
- keys = []
- keys.append('pv_ijk')
- keys.append('zeta_k')
- keys.append('dtdz')
- keys.append('log(Ri)')
- return keys
-
- def get_variable(self, variableName, tindex=None, xindex=None, yindex=None, zindex=None):
-
- dims = self.variables[variableName].dims
-
- variable = self.variables[variableName]
-
- if tindex is not None:
- variable = variable.isel(t=tindex)
-
- if xindex is not None:
- # Extract x slice
- try:
- if "x_u" in dims:
- variable = variable.isel(x_u=xindex)
- else:
- variable = variable.isel(x_r=xindex)
- except Exception:
- pass
-
- if yindex is not None:
- # Extract y slice
- try:
- if "y_v" in dims:
- variable = variable.isel(y_v=yindex)
- else:
- variable = variable.isel(y_r=yindex)
- except Exception:
- pass
-
- if zindex is not None:
- # Extract z slice
- try:
- if "z_w" in dims:
- variable = variable.isel(z_w=zindex)
- else:
- variable = variable.isel(z_r=zindex)
- except Exception:
- pass
-
- return variable
-
- def get_coord(self, variableName, direction=None, timeIndex=None):
- """
- get coordinate corresponding of the variable depending on the direction
- direction : 'x', 'y', 't'
- """
- # If variable is derived variable, return rho point coordinates
- try:
- dims = self.variables[variableName].dims
- except Exception:
- try:
- dims = self.variables['rho'].dims
- except Exception:
- dims = self.variables['temp'].dims
- if direction == 'x':
- if "x_u" in dims:
- return self.wrapper.coords['lon_u']
- elif "y_v" in dims:
- return self.wrapper.coords['lon_v']
- else:
- return self.wrapper.coords['lon_r']
- elif direction == 'y':
- if "x_u" in dims:
- return self.wrapper.coords['lat_u']
- elif "y_v" in dims:
- return self.wrapper.coords['lat_v']
- else:
- return self.wrapper.coords['lat_r']
- elif direction == 'z':
- ssh = self.variables['ssh'].isel(t=timeIndex).values
- if "z_w" in dims:
- z = self.wrapper.scoord2z_w(ssh, alpha=0., beta=0)
- else:
- z = self.wrapper.scoord2z_r(ssh, alpha=0., beta=0)
- if "x_u" in dims:
- z = self.rho2u_3d(z)
- elif "y_v" in dims:
- z = self.rho2v_3d(z)
- return(z)
- elif direction == 't':
- return self.wrapper.coords['time'].values
-
- def create_DataArray(self, data=None, dimstyp='xyzt'):
- '''
- Create a xarrayr DataArray avec les dimensions possible x,y,z et t.
- Par defaut la variable est au point rho.
- '''
-
- # Create dims
- dims = []
- if 't' in dimstyp:
- dims.append('t')
- if 'z' in dimstyp:
- dims.append('z_r')
- if 'y' in dimstyp:
- dims.append('y_r')
- if 'x' in dimstyp:
- dims.append('x_r')
-
- var = xr.DataArray(data=data, dims=dims)
- return var
-
- def zslice(self, var, mask, z, depth, findlev=False):
- """
- #
- #
- # This function interpolate a 3D variable on a horizontal level of constant
- # depth
- #
- # On Input:
- #
- # var Variable to process (3D matrix).
- # z Depths (m) of RHO- or W-points (3D matrix).
- # depth Slice depth (scalar meters, negative).
- #
- # On Output:
- #
- # vnew Horizontal slice (2D matrix).
- #
- #
- """
- [N, Mp, Lp] = z.shape
-
- #
- # Find the grid position of the nearest vertical levels
- #
- a = np.where(z <= depth, 1, 0)
- levs = np.squeeze(np.sum(a, axis=0)) - 1
- levs = np.where(levs == N - 1, N - 2, levs)
- levs = np.where(levs == -1, 0, levs)
- minlev = np.min(levs)
- maxlev = np.max(levs)
- if findlev:
- return minlev, maxlev
-
- # Do the interpolation
- z1 = np.zeros_like(z[0, :, :])
- z2 = np.zeros_like(z[0, :, :])
- v1 = np.zeros_like(z[0, :, :])
- v2 = np.zeros_like(z[0, :, :])
-
- for j in range(Mp):
- for i in range(Lp):
- k = levs[j, i]
- z1[j, i] = z[k + 1, j, i]
- z2[j, i] = z[k, j, i]
- v1[j, i] = var[k + 1, j, i]
- v2[j, i] = var[k, j, i]
- zmask = np.where(z2 > depth, np.nan, 1)
- vnew = mask * zmask * (((v1 - v2) * depth + v2 * z1 - v1 * z2) / (z1 - z2))
- return vnew, minlev, maxlev
-
- def get_run_name(self):
- filename = self.wrapper.keymap_files['variable_file']
- index = filename.find("/CROCO_FILES")
- if index == -1:
- runName = ''
- else:
- runName = os.path.basename(os.path.dirname(filename[:index]))
- return runName
-
-
- def rmask(self):
- return(self.wrapper.masks['mask_r'].values)
-
- def umask(self):
- return(self.wrapper.masks['mask_r'].values[:, 1:] *
- self.wrapper.masks['mask_r'].values[:, :-1])
-
- def vmask(self):
- return(self.wrapper.masks['mask_r'].values[1:, :] *
- self.wrapper.masks['mask_r'].values[:-1, :])
-
- @staticmethod
- def rho2u_2d(rho_in):
- '''
- Convert a 2D field at rho points to a field at u points
- '''
- def _r2u(rho_in, Lp):
- u_out = rho_in[:, :Lp - 1]
- u_out += rho_in[:, 1:Lp]
- u_out *= 0.5
- return u_out.squeeze()
- assert rho_in.ndim == 2, 'rho_in must be 2d'
- Mshp, Lshp = rho_in.shape
- return _r2u(rho_in, Lshp)
-
- @staticmethod
- def rho2u_3d(rho_in):
- '''
- Convert a 3D field at rho points to a field at u points
- Calls rho2u_2d
- '''
- def levloop(rho_in):
- Nlevs, Mshp, Lshp = rho_in.shape
- rho_out = np.zeros((Nlevs, Mshp, Lshp - 1))
- for k in range(Nlevs):
- rho_out[k] = Croco.rho2u_2d(rho_in[k])
- return rho_out
- assert rho_in.ndim == 3, 'rho_in must be 3d'
- return levloop(rho_in)
-
- @staticmethod
- def rho2v_2d(rho_in):
- '''
- Convert a 2D field at rho points to a field at v points
- '''
- def _r2v(rho_in, Mp):
- v_out = rho_in[:Mp - 1]
- v_out += rho_in[1:Mp]
- v_out *= 0.5
- return v_out.squeeze()
- assert rho_in.ndim == 2, 'rho_in must be 2d'
- Mshp, Lshp = rho_in.shape
- return _r2v(rho_in, Mshp)
-
- @staticmethod
- def rho2v_3d(rho_in):
- '''
- Convert a 3D field at rho points to a field at v points
- Calls rho2v_2d
- '''
- def levloop(rho_in):
- Nlevs, Mshp, Lshp = rho_in.shape
- rho_out = np.zeros((Nlevs, Mshp - 1, Lshp))
- for k in range(Nlevs):
- rho_out[k] = Croco.rho2v_2d(rho_in[k])
- return rho_out
- assert rho_in.ndim == 3, 'rho_in must be 3d'
- return levloop(rho_in)
-
- @staticmethod
- def u2rho_2d(u_in):
- '''
- Convert a 2D field at u points to a field at rho points
- '''
- def _uu2ur(uu_in, Mp, Lp):
- L, Lm = Lp - 1, Lp - 2
- u_out = np.zeros((Mp, Lp))
- u_out[:, 1:L] = 0.5 * (u_in[:, 0:Lm] + u_in[:, 1:L])
- u_out[:, 0] = u_out[:, 1]
- u_out[:, L] = u_out[:, Lm]
- return u_out.squeeze()
-
- assert u_in.ndim == 2, 'u_in must be 2d'
- Mp, Lp = u_in.shape
- return _uu2ur(u_in, Mp, Lp + 1)
-
- @staticmethod
- def u2rho_3d(u_in):
- '''
- Convert a 3D field at u points to a field at rho points
- Calls u2rho_2d
- '''
- def _levloop(u_in):
- Nlevs, Mshp, Lshp = u_in.shape
- u_out = np.zeros((Nlevs, Mshp, Lshp + 1))
- for Nlev in range(Nlevs):
- u_out[Nlev] = Croco.u2rho_2d(u_in[Nlev])
- return u_out
- assert u_in.ndim == 3, 'u_in must be 3d'
- return _levloop(u_in)
-
- @staticmethod
- def v2rho_2d(v_in):
- '''
- Convert a 2D field at v points to a field at rho points
- '''
- def _vv2vr(v_in, Mp, Lp):
- M, Mm = Mp - 1, Mp - 2
- v_out = np.zeros((Mp, Lp))
- v_out[1:M] = 0.5 * (v_in[:Mm] + v_in[1:M])
- v_out[0] = v_out[1]
- v_out[M] = v_out[Mm]
- return v_out.squeeze()
-
- assert v_in.ndim == 2, 'v_in must be 2d'
- Mp, Lp = v_in.shape
- return _vv2vr(v_in, Mp + 1, Lp)
-
- @staticmethod
- def v2rho_3d(v_in):
- '''
- Convert a 3D field at v points to a field at rho points
- Calls v2rho_2d
- '''
- def levloop(v_in):
- Nlevs, Mshp, Lshp = v_in.shape
- v_out = np.zeros((Nlevs, Mshp + 1, Lshp))
- for Nlev in range(Nlevs):
- v_out[Nlev] = Croco.v2rho_2d(v_in[Nlev])
- return v_out
- assert v_in.ndim == 3, 'v_in must be 3d'
- return levloop(v_in)
diff --git a/croco_pyvisu/__pycache__/CrocoXarray.cpython-37.pyc b/croco_pyvisu/__pycache__/CrocoXarray.cpython-37.pyc
deleted file mode 100644
index 436734d8f0ef0fa70bf5065b671292becee6e5bb..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/CrocoXarray.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/__pycache__/croco_wrapper.cpython-37.pyc b/croco_pyvisu/__pycache__/croco_wrapper.cpython-37.pyc
deleted file mode 100644
index 9715f1749b4e23b57a2f70b50df40135e3d57899..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/croco_wrapper.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/__pycache__/derived_variables.cpython-37.pyc b/croco_pyvisu/__pycache__/derived_variables.cpython-37.pyc
deleted file mode 100644
index 53768b3a1b3c0cabab7e15c5d1291c2df39472cc..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/derived_variables.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/__pycache__/io_xarray.cpython-37.pyc b/croco_pyvisu/__pycache__/io_xarray.cpython-37.pyc
deleted file mode 100644
index 2b0c83e20c448c49839145943bc3236e04b0ed63..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/io_xarray.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/__pycache__/myplot.cpython-37.pyc b/croco_pyvisu/__pycache__/myplot.cpython-37.pyc
deleted file mode 100644
index 3c8aa6a64362b4367d77d0ef4c050b966e7ed1a3..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/myplot.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/__pycache__/observer.cpython-37.pyc b/croco_pyvisu/__pycache__/observer.cpython-37.pyc
deleted file mode 100644
index beb8c346cff05b6c4e132b9d86c9e43f415fc082..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/__pycache__/observer.cpython-37.pyc and /dev/null differ
diff --git a/croco_pyvisu/croco_gui_xarray.py b/croco_pyvisu/croco_gui_xarray.py
deleted file mode 100755
index 1f08323115d0883464a0471d13825335ef29cc1f..0000000000000000000000000000000000000000
--- a/croco_pyvisu/croco_gui_xarray.py
+++ /dev/null
@@ -1,1375 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: UTF-8 -*-
-#
-
-import sys
-import os
-from time import sleep
-from shutil import copyfile
-from threading import Thread
-import wx
-import xarray as xr
-import numpy as np
-from numpy.matlib import repmat
-import numpy.ma as ma
-from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
-from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as NavigationToolbar
-from matplotlib.figure import Figure
-from CrocoXarray import Croco
-from derived_variables import get_pv, get_zetak, get_dtdz, get_richardson
-from myplot import plotCurv, mypcolor
-from matplotlib.animation import FFMpegWriter
-from observer import Publisher, Subscriber
-
-wildcard = "Netcdf Files (*.nc)|*.nc"
-figsize = [6, 5]
-
-
-########################################################################
-
-class SectionFrame(wx.Frame):
- """
- Window class to plot longitude and latitude sections.
- The window contains a canvas to plot, several buttons (animation, zoom in, zoom out,
- print and reset color) and text control (start time and end time for animation,
- min and max color for the colorbar)
-
- Attributes:
- croco : croco instance to study
- variableName : Name of the variable to plot in the canvas
- variable : 3D dataarray (x,y,t) of the variable to plot
- x : numpy array of x coordinates
- y : numpy array of y coordinates
- typSection: type of slice XZ or YZ
- sliceCoord: coordinate of the slice (latitude for XZ, latitude for YZ)
- timeIndex: current time index to plot
- subscriber: instance of class to which send notification on click event
- """
-
- def __init__(self, croco=None, variableName=None, variable=None,
- x=None, y=None, typSection=None, sliceCoord=None,
- sliceIndex=None, timeIndex=None, subscriber=None):
- """ return a SectioFrame instance """
-
- # Initialize the variables of the class
- self.croco = croco
- self.variable = variable
- self.x = x
- self.y = y
- self.variableName = variableName
- self.typSection = typSection
- self.sliceCoord = sliceCoord
- self.sliceIndex = sliceIndex
- self.timeIndex = timeIndex
-
- # Create the window
- wx.Frame.__init__(self, None, wx.ID_ANY, title='Section')
-
- # Now create the Panel to put the other controls on.
- self.panel = wx.Panel(self, wx.ID_ANY)
-
- # and a few controls
- self.figure = Figure()
- self.axes = self.figure.add_axes([0, 0, 1, 1])
- self.canvas = FigureCanvas(self.panel, -1, self.figure)
- self.toolbar = NavigationToolbar(self.canvas)
- self.toolbar.Hide()
-
- self.TimeLabel = wx.StaticText(self.panel, -1, label="Time", style=wx.ALIGN_CENTER)
- self.TimeMinusBtn = wx.Button(self.panel, wx.ID_ANY, "<")
- self.TimeTxt = wx.TextCtrl(self.panel, wx.ID_ANY, " ", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.TimePlusBtn = wx.Button(self.panel, wx.ID_ANY, ">")
- self.ZoomBtn = wx.Button(self.panel, wx.ID_ANY, "Zoom")
- self.PanBtn = wx.Button(self.panel, wx.ID_ANY, "Pan")
- self.HomeBtn = wx.Button(self.panel, wx.ID_ANY, "Home")
- self.SavePlotBtn = wx.Button(self.panel, wx.ID_ANY, "Save Plot")
-
- self.AnimationBtn = wx.Button(self.panel, wx.ID_ANY, "Animation")
- self.startTimeTxt = wx.TextCtrl(self.panel, wx.ID_ANY, "1", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.endTimeTxt = wx.TextCtrl(self.panel, wx.ID_ANY, "1", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.AbortBtn = wx.Button(self.panel, wx.ID_ANY, "Abort")
- self.SaveAnimBtn = wx.Button(self.panel, wx.ID_ANY, "Save Anim")
-
- self.ResetColorBtn = wx.Button(self.panel, wx.ID_ANY, "Reset Color")
- self.MinColorTxt = wx.TextCtrl(self.panel, wx.ID_ANY, "Min Color", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.MaxColorTxt = wx.TextCtrl(self.panel, wx.ID_ANY, "Max Color", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
-
- if self.typSection == "XY":
- self.TopoBtn = wx.ToggleButton(self.panel, wx.ID_ANY, "Topo", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.TopoTxt = wx.TextCtrl(self.panel, wx.ID_ANY, "10", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
-
- # bind the menu event to an event handler
- self.canvas.mpl_connect('button_press_event', self.onFigureClick)
- self.AnimationBtn.Bind(wx.EVT_BUTTON, self.onAnimationBtn)
- self.AbortBtn.Bind(wx.EVT_BUTTON, self.onAbortBtn)
- self.startTimeTxt.Bind(wx.EVT_TEXT_ENTER, self.onstartTimeTxt)
- self.endTimeTxt.Bind(wx.EVT_TEXT_ENTER, self.onendTimeTxt)
- self.ZoomBtn.Bind(wx.EVT_BUTTON, self.onZoomBtn)
- self.PanBtn.Bind(wx.EVT_BUTTON, self.onPanBtn)
- self.HomeBtn.Bind(wx.EVT_BUTTON, self.onHomeBtn)
- self.SavePlotBtn.Bind(wx.EVT_BUTTON, self.onSavePlotBtn)
- self.ResetColorBtn.Bind(wx.EVT_BUTTON, self.onResetColorBtn)
- self.MinColorTxt.Bind(wx.EVT_TEXT_ENTER, self.onMinColorTxt)
- self.MaxColorTxt.Bind(wx.EVT_TEXT_ENTER, self.onMaxColorTxt)
- self.AbortBtn.Bind(wx.EVT_BUTTON, self.onAbortBtn)
- self.SaveAnimBtn.Bind(wx.EVT_BUTTON, self.onSaveAnimBtn)
- self.TimeMinusBtn.Bind(wx.EVT_BUTTON, self.onTimeMinusBtn)
- self.TimeTxt.Bind(wx.EVT_TEXT_ENTER, self.onTimeTxt)
- self.TimePlusBtn.Bind(wx.EVT_BUTTON, self.onTimePlusBtn)
-
- if self.typSection == "XY":
- self.TopoBtn.Bind(wx.EVT_TOGGLEBUTTON, self.onTopoBtn)
- self.TopoTxt.Bind(wx.EVT_TEXT_ENTER, self.onTopoTxt)
-
- self.showPosition = self.CreateStatusBar(2)
- self.showPosition.SetStatusText("x= , y= ", 1)
- self.showPosition.SetStatusWidths([-1, 150])
-
- self.__do_layout()
-
- # Register main window subscriber to send new location level/latitude/longitude
- # on window click
- self.sub = subscriber
- self.pub = Publisher()
- self.pub.register(self.sub, self.sub.update)
-
- # Set variables of the class
- if croco is not None:
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
- if typSection == "XY":
- self.xlabel = "Longitude"
- self.ylabel = "Latitude"
- elif typSection == "XZ":
- self.xlabel = "Longitude"
- self.ylabel = "Depth"
- self.slice = "Latitude"
- elif typSection == "YZ":
- self.xlabel = "Latitude"
- self.ylabel = "Depth"
- self.slice = "Longitude"
- if croco is not None:
- timeMin = self.croco.wrapper._get_date(0)
- timeMax = self.croco.wrapper._get_date(self.croco.wrapper.ntimes - 1)
- self.startTimeTxt.SetValue(str(timeMin))
- self.startTime = timeMin
- self.startTimeIndex = 0
- self.endTimeTxt.SetValue(str(timeMax))
- self.endTime = timeMax
- self.endTimeIndex = self.croco.wrapper.ntimes - 1
-
- def __do_layout(self):
- """
- Use a sizer to layout the controls, stacked vertically or horizontally
- """
- topSizer = wx.BoxSizer(wx.VERTICAL)
- canvasSizer = wx.BoxSizer(wx.VERTICAL)
- timeSizer = wx.BoxSizer(wx.HORIZONTAL)
- buttonsSizer = wx.BoxSizer(wx.HORIZONTAL)
- colorSizer = wx.BoxSizer(wx.HORIZONTAL)
-
- canvasSizer.Add(self.canvas, 0, wx.ALL, 5)
-
- timeSizer.Add(self.TimeLabel, 0, wx.ALL, 5)
- timeSizer.Add(self.TimeMinusBtn, 0, wx.ALL, 5)
- timeSizer.Add(self.TimeTxt, 0, wx.ALL, 5)
- timeSizer.Add(self.TimePlusBtn, 0, wx.ALL, 5)
- timeSizer.Add(self.ZoomBtn, 0, wx.ALL, 5)
- timeSizer.Add(self.PanBtn, 0, wx.ALL, 5)
- timeSizer.Add(self.HomeBtn, 0, wx.ALL, 5)
- timeSizer.Add(self.SavePlotBtn, 0, wx.ALL, 5)
-
- buttonsSizer.Add(self.AnimationBtn, 0, wx.ALL, 5)
- buttonsSizer.Add(self.startTimeTxt, 0, wx.ALL, 5)
- buttonsSizer.Add(self.endTimeTxt, 0, wx.ALL, 5)
- buttonsSizer.Add(self.AbortBtn, 0, wx.ALL, 5)
- buttonsSizer.Add(self.SaveAnimBtn, 0, wx.ALL, 5)
-
- colorSizer.Add(self.ResetColorBtn, 0, wx.ALL, 5)
- colorSizer.Add(self.MinColorTxt, 0, wx.ALL, 5)
- colorSizer.Add(self.MaxColorTxt, 0, wx.ALL, 5)
-
- if self.typSection == "XY":
- colorSizer.Add(self.TopoBtn, 0, wx.ALL, 5)
- colorSizer.Add(self.TopoTxt, 0, wx.ALL, 5)
-
- topSizer.Add(canvasSizer, 0, wx.CENTER)
- topSizer.Add(timeSizer, 0, wx.ALL | wx.EXPAND, 5)
- topSizer.Add(buttonsSizer, 0, wx.ALL | wx.EXPAND, 5)
- topSizer.Add(colorSizer, 0, wx.ALL | wx.EXPAND, 5)
-
- self.panel.SetSizer(topSizer)
- topSizer.Fit(self)
-
- self.Layout()
-
- if self.typSection == "XY":
- self.toggletopo = self.TopoBtn.GetValue()
- self.nbtopo = int(self.TopoTxt.GetValue())
- else:
- self.toggletopo = None
- self.nbtopo = None
-
- # Event handler
-
- # Event handler on plot canvas
- def onFigureClick(self, event):
- """
- Event handler for the button click on plot
- send new location to main window
- """
- # Retreive new location on canvas click
- self.xPress, self.yPress = event.xdata, event.ydata
- level = longitude = latitude = None
- if self.typSection == "XY":
- longitude = self.xPress
- latitude = self.yPress
- elif self.typSection == "XZ":
- longitude = self.xPress
- level = self.yPress
- elif self.typSection == "YZ":
- latitude = self.xPress
- level = self.yPress
- # send new location to main window
- self.pub.dispatch(level, longitude, latitude)
-
- def ShowPosition(self, event):
- """Show the current cursor position at the bottom right of the window """
- if event.inaxes:
- self.showPosition.SetStatusText(
- "x={:5.1f} y={:5.1f}".format(event.xdata, event.ydata), 1)
-
- def onAnimationBtn(self, event):
- """
- Launch the animation in a separate thread to keep the GUI alive
- Prepare tools to save the movie
- """
- # Initialize creation of movie
- self.movie = FFMpegWriter()
- self.movie.setup(self.figure, 'moviez.mp4', dpi=100)
-
- self.shouldAbort = False
-
- # Launch animate in a thread
- self.thread = Thread(target=self.animate)
- self.thread.start()
-
- def onAbortBtn(self, event):
- self.shouldAbort = True
-
- def animate(self):
- """
- Calculate and draw the variable from start Time to end Time
- """
- for i in range(self.startTimeIndex, self.endTimeIndex + 1):
- sleep(0.5)
- self.timeIndex = i
- # Get the variable at the new timeIndex
- self.updateVariableZ(setlim=False)
- # Draw the variable in the main thread
- wx.CallAfter(self.drawz, setlim=False, setcol=False, anim=True)
- if self.shouldAbort:
- break
- # Go to animateDone after aborting or ending the animation
- wx.CallAfter(self.animateDone, self.shouldAbort)
-
- def animateDone(self, abort):
- """
- method called at the end of the animation or after aborting it
- """
- # Close the movie
- self.movie.finish()
-
- # Remove the movie if aborting
- if self.shouldAbort:
- os.system('rm -rf ' + 'moviez.mp4')
- self.shouldAbort = False
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
-
- # Event handler for Save animation
- def onSaveAnimBtn(self, event):
- """
- Copy file movie*.mp4 in the right place with the right name
- """
- if os.path.isfile('moviez.mp4'):
- printDir = self.croco.startDir + "/Figures_" + self.croco.get_run_name() + "/"
- if not os.path.isdir(printDir):
- os.mkdir(printDir)
- time1 = str(self.croco.wrapper._get_date(self.startTimeIndex))
- time2 = str(self.croco.wrapper._get_date(self.endTimeIndex))
- filename = "{:s}_{:s}{:4.1f}_Time{:s}-{:s}.mp4".format(self.variableName, self.slice, self.sliceCoord,
- time1, time2).replace(" ", "")
- copyfile('moviez.mp4', printDir + filename)
- os.system('rm -rf ' + 'moviez.mp4')
-
- def onstartTimeTxt(self, event):
- """Event handler for Enter key in start time text """
- self.startTime = float(self.startTimeTxt.GetValue())
- times = self.croco.get_coord(self.variableName, direction='t')
- # find nearest index corresponding to instant time to plot
- self.startTimeIndex = min(range(len(times)), key=lambda j: abs(self.startTime - times[j]))
- self.startTime = self.croco.wrapper._get_date(self.startTimeIndex)
- self.startTimeTxt.SetValue(str(self.startTime))
-
- # Event handler for Time dialog
- def onendTimeTxt(self, event):
- """Event handler for Enter key in end time text """
- self.endTime = float(self.endTimeTxt.GetValue())
- times = self.croco.get_coord(self.variableName, direction='t')
- # find nearest index corresponding to instant time to plot
- self.endTimeIndex = min(range(len(times)), key=lambda j: abs(self.endTime - times[j]))
- self.endTime = self.croco.wrapper._get_date(self.endTimeIndex)
- self.endTimeTxt.SetValue(str(self.endTime))
-
- def onTimeTxt(self, event):
- """Event handler for Enter key in end time text """
- time = float(self.TimeTxt.GetValue())
- times = self.croco.get_coord(self.variableName, direction='t')
- # find index corresponding to the nearest instant time to plot
- self.timeIndex = min(range(len(times)), key=lambda j: abs(time - times[j]))
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
- self.updateVariableZ(setlim=False)
- self.drawz(setlim=False)
-
- def onTimeMinusBtn(self, event):
- self.timeIndex = max(self.timeIndex - 1, 0)
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
- self.updateVariableZ()
- self.drawz(setlim=False)
-
- def onTimePlusBtn(self, event):
- self.timeIndex = min(self.timeIndex + 1, self.croco.wrapper.ntimes - 1)
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
- self.updateVariableZ()
- self.drawz(setlim=False)
-
- def notify(self, ax):
- self.xlim = ax.get_xlim()
- self.ylim = ax.get_ylim()
- # print("notify:",ax.get_xlim(),ax.get_ylim())
-
- # Event handler for zoom
- def onZoomBtn(self, event):
- """
- Event handler for the button click Zoom in button
- """
- # self.figure.RS.set_active(True)
- self.toolbar.zoom()
-
- # Event handler for zoom
- def onPanBtn(self, event):
- """
- Event handler for the button click Zoom in button
- """
- self.toolbar.pan()
-
- def onHomeBtn(self, event):
- """
- Event handler for the button click Zoom out button
- """
- self.drawz(setlim=True, setcol=False)
- # self.toolbar.home()
-
- # Event handler for Print
- def onSavePlotBtn(self, event):
- """
- Event handler for the button click Print button
- """
- printDir = self.croco.startDir + "/Figures_" + self.croco.get_run_name() + "/"
- if not os.path.isdir(printDir):
- os.mkdir(printDir)
- filename = self.title.replace(',', '_').replace(" ", "") + ".png"
- os.system('rm -rf ' + printDir + filename)
- self.figure.savefig(printDir + filename, dpi=self.figure.dpi)
- # self.toolbar.save_figure(None)
-
- # Event handler for Color setup
- def onResetColorBtn(self, event):
- """
- Event handler for the button click Reset Color button
- """
- self.drawz(setlim=False, setcol=True)
-
- def onMinColorTxt(self, event):
- """Event handler for Enter key in Min Color text """
- self.clim[0] = float(self.MinColorTxt.GetValue())
- self.drawz(setlim=False, setcol=False)
-
- def onMaxColorTxt(self, event):
- """Event handler for Enter key in Max Color text """
- self.clim[1] = float(self.MaxColorTxt.GetValue())
- self.drawz(setlim=False, setcol=False)
-
- # Event handler for topography toggle button
- def onTopoBtn(self, evnet):
- self.toggletopo = self.TopoBtn.GetValue()
- self.drawz(setlim=False, setcol=False)
-
- def onTopoTxt(self, evnet):
- self.nbtopo = int(self.TopoTxt.GetValue())
- self.drawz(setlim=False, setcol=False)
-
- # Methods of class
-
- def updateVariableZ(self, setlim=True):
- """ reload current variable depending on the time and plot it """
-
- # Level section
- if self.typSection == "XY":
-
- try:
- dims = self.croco.variables[self.variableName].dims
- except Exception:
- dims = []
-
- if "x_u" in dims:
- mask = self.croco.umask()
- self.topo = self.croco.rho2u_2d(self.croco.wrapper.metrics["h"].values)
- elif "y_v" in dims:
- mask = self.croco.vmask()
- self.topo = self.croco.rho2v_2d(self.croco.wrapper.metrics["h"].values)
- else:
- mask = self.croco.rmask()
- self.topo = self.croco.wrapper.metrics["h"]
- mask = np.where(mask == 0., np.nan, mask)
-
- # Level plot
- if self.sliceCoord > 0:
- self.slice = "Level"
- if self.variableName in self.croco.ListOfVariables:
- # 3D variable rho level
- try:
- self.variableZ = self.croco.variables[self.variableName]\
- .isel(t=self.timeIndex, z_r=self.sliceIndex)
- except Exception:
- # 3D variable w level
- try:
- self.variableZ = self.croco.variables[self.variableName]\
- .isel(t=self.timeIndex, z_w=self.sliceIndex)
- # 2D variable
- except Exception:
- self.variableZ = self.croco.variables[self.variableName].isel(t=self.timeIndex)
-
- elif self.variableName in self.croco.ListOfDerived:
- if 'pv' in self.variableName:
- var = get_pv(self.croco, self.timeIndex, depth=self.sliceCoord, typ=self.variableName)
- self.variableZ = xr.DataArray(data=var)
- elif self.variableName == 'zeta_k':
- var = get_zetak(self.croco, self.timeIndex, depth=self.sliceCoord)
- self.variableZ = xr.DataArray(data=var)
- elif self.variableName == 'dtdz':
- try:
- self.croco.variables['temp']
- var = get_dtdz(self.croco, self.timeIndex, depth=self.sliceCoord)
- self.variableZ = xr.DataArray(data=var)
- except Exception:
- print("No variable temp")
- return
- elif self.variableName == 'log(Ri)':
- var = get_richardson(self.croco, self.timeIndex, depth=self.sliceCoord)
- self.variableZ = xr.DataArray(data=var)
- else:
- print("unknown variable ", self.variableName)
- return
-
- # Depth plot
- elif self.sliceCoord <= 0:
- self.slice = "Depth"
- # Calculate depths
- z = self.croco.get_coord(self.variableName, direction='z', timeIndex=self.timeIndex)
- minlev, maxlev = self.croco.zslice(None, mask, z, self.sliceCoord, findlev=True)
- # Variable from croco file
- if self.variableName in self.croco.ListOfVariables:
- try:
- var = self.croco.variables[self.variableName]\
- .isel(t=self.timeIndex, z_r=slice(minlev, maxlev + 1))
- except Exception:
- var = self.croco.variables[self.variableName]\
- .isel(t=self.timeIndex, z_w=slice(minlev, maxlev + 1))
- try:
- zslice = self.croco.zslice(var.values, mask, z[minlev:maxlev + 1, :, :], self.sliceCoord)[0]
- self.variableZ = xr.DataArray(data=zslice)
- except Exception:
- print("Not enough points")
-
- # Derived variable
- elif self.variableName in self.croco.ListOfDerived:
- if 'pv' in self.variableName:
- var = get_pv(self.croco, self.timeIndex, depth=self.sliceCoord, minlev=minlev,
- maxlev=maxlev, typ=self.variableName)
- try:
- zslice = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], self.sliceCoord)[0]
- self.variableZ = xr.DataArray(data=zslice)
- except Exception:
- print("Not enough points")
- pass
-
- elif self.variableName == 'zeta_k':
- var = get_zetak(self.croco, self.timeIndex, depth=self.sliceCoord, minlev=minlev, maxlev=maxlev)
- try:
- zslice = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], self.sliceCoord)[0]
- self.variableZ = xr.DataArray(data=zslice)
- except Exception:
- print("Not enough points")
- pass
-
- elif self.variableName == 'dtdz':
- var = get_dtdz(self.croco, self.timeIndex, depth=self.sliceCoord, minlev=minlev, maxlev=maxlev)
- try:
- zslice = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], self.sliceCoord)[0]
- self.variableZ = xr.DataArray(data=zslice)
- except Exception:
- print("Not enough points")
- pass
-
- elif self.variableName == 'log(Ri)':
- var = get_richardson(self.croco, self.timeIndex, depth=self.sliceCoord, minlev=minlev, maxlev=maxlev)
- try:
- zslice = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], self.sliceCoord)[0]
- self.variableZ = xr.DataArray(data=zslice)
- except Exception:
- print("Not enough points")
- pass
- # Draw the new self.variableZ
- self.variableZ.values = mask * self.variableZ.values
-
- # Latitude section
- elif self.typSection == "XZ":
-
- # Variable from croco file
- if self.variableName in self.croco.ListOfVariables:
- self.variableZ = self.croco.get_variable(self.variableName,
- tindex=self.timeIndex,
- yindex=self.sliceIndex)
- # Derived Variable
- elif self.variableName in self.croco.ListOfDerived:
- # ntimes = self.croco.wrapper.ntimes
- N = self.croco.wrapper.N
- L = self.croco.wrapper.L
- self.variableZ = self.croco.create_DataArray(data=np.full((N, L),np.nan),
- dimstyp='xz')
- if 'pv' in self.variableName:
- self.variableZ[1:, :] = get_pv(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- latindex=self.sliceIndex,
- typ=self.variableName)
-
- elif self.variableName == 'zeta_k':
- self.variableZ[1:, :] = get_zetak(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- latindex=self.sliceIndex)
-
- elif self.variableName == 'dtdz':
- self.variableZ[1:, :] = get_dtdz(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- latindex=self.sliceIndex)
-
- elif self.variableName == 'log(Ri)':
- self.variableZ[1:, :] = get_richardson(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- latindex=self.sliceIndex)
-
- # Longitude section
- elif self.typSection == "YZ":
-
- # Variable from croco file
- if self.variableName in self.croco.ListOfVariables:
- self.variableZ = self.croco.get_variable(self.variableName,
- tindex=self.timeIndex,
- xindex=self.sliceIndex)
- # Derived Variable
- elif self.variableName in self.croco.ListOfDerived:
- # ntimes = self.croco.wrapper.ntimes
- N = self.croco.wrapper.N
- M = self.croco.wrapper.M
- self.variableZ = self.croco.create_DataArray(data=np.full((N, M),np.nan),
- dimstyp='yz')
- if 'pv' in self.variableName:
- self.variableZ[1:, :] = get_pv(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- lonindex=self.sliceIndex,
- typ=self.variableName)
-
- elif self.variableName == 'zeta_k':
- self.variableZ[1:, :] = get_zetak(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- lonindex=self.sliceIndex)
-
- elif self.variableName == 'dtdz':
- self.variableZ[1:, :] = get_dtdz(self.croco, self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- lonindex=self.sliceIndex)
-
- elif self.variableName == 'log(Ri)':
- self.variableZ[1:, :] = get_richardson(self.croco,
- self.timeIndex,
- minlev=0,
- maxlev=self.croco.wrapper.N - 1,
- lonindex=self.sliceIndex)
-
- def drawz(self, setlim=False, setcol=False, anim=False):
- """ plot the current variable in the canvas """
-
- # Don't plot if variable full of Nan
- if np.count_nonzero(~np.isnan(self.variableZ.values)) == 0: return
-
- self.figure.clf()
- self.canvas.mpl_connect('button_press_event', self.onFigureClick)
- self.canvas.mpl_connect('motion_notify_event', self.ShowPosition)
-
- # if self.variableZ.values is None: return
- variableZ = ma.masked_invalid(self.variableZ.values)
- if setcol:
- if self.variableName == 'log(Ri)':
- self.mincolor = -3.2
- self.maxcolor = 2.
- else:
- self.mincolor = np.min(variableZ)
- self.maxcolor = np.max(variableZ)
- self.MinColorTxt.SetValue('%.2E' % self.mincolor)
- self.MaxColorTxt.SetValue('%.2E' % self.maxcolor)
- self.clim = [self.mincolor, self.maxcolor]
- if setlim:
- self.xlim = [np.min(self.x), np.max(self.x)]
- self.ylim = [np.min(self.y), np.max(self.y)]
- if self.typSection == "XY" and self.toggletopo == True:
- topo = self.topo
- else:
- topo = None
- time = str(self.croco.wrapper._get_date(self.timeIndex))
- self.title = "{:s}, {:s}={:4.1f}, Time={:s}".\
- format(self.variableName, self.slice, self.sliceCoord, time)
- mypcolor(self, self.x, self.y, variableZ,
- title=self.title,
- xlabel=self.xlabel,
- ylabel=self.ylabel,
- xlim=self.xlim,
- ylim=self.ylim,
- clim=self.clim,
- topo=topo,
- nbtopo=self.nbtopo)
-
- if anim:
- self.movie.grab_frame()
-
- self.canvas.draw()
- self.canvas.Refresh()
- self.Show()
-
-# end of SectionFrame Class
-########################################################################
-
-
-class ProfileFrame(wx.Frame):
- """
- Window class to plot time series or depth profile.
- The window contains a canvas to plot, several buttons (zoom in, zoom out
- and print )
-
- Attributes:
- croco : croco instance to study
- x : numpy array of x coordinates
- y : numpy array of y coordinates
- variableName : Name of the variable to plot in the canvas
- title : title of the plot
- xlabel : label of x axis
- ylabel : label of y axis
- """
-
- def __init__(self, croco=None, x=None, y=None,
- variableName=None, title=None, xlabel=None, ylabel=None):
-
- # Create the window
- wx.Frame.__init__(self, None, wx.ID_ANY, title='Profile')
-
- # Now create the Panel to put the other controls on.
- self.panel = wx.Panel(self, wx.ID_ANY)
-
- # and a few controls
- self.figure = Figure()
- self.canvas = FigureCanvas(self.panel, -1, self.figure)
- self.toolbar = NavigationToolbar(self.canvas)
- self.toolbar.Hide()
-
- self.ZoomBtn = wx.Button(self.panel, wx.ID_ANY, "Zoom")
- self.HomeBtn = wx.Button(self.panel, wx.ID_ANY, "Home")
- self.PanBtn = wx.Button(self.panel, wx.ID_ANY, "Pan")
- self.SavePlotBtn = wx.Button(self.panel, wx.ID_ANY, "Save Plot")
-
- # bind the menu event to an event handler
- self.ZoomBtn.Bind(wx.EVT_BUTTON, self.onZoomBtn)
- self.HomeBtn.Bind(wx.EVT_BUTTON, self.onHomeBtn)
- self.PanBtn.Bind(wx.EVT_BUTTON, self.onPanBtn)
- self.SavePlotBtn.Bind(wx.EVT_BUTTON, self.onSavePlotBtn)
-
- self.showPosition = self.CreateStatusBar(2)
- self.showPosition.SetStatusText("x= , y= ", 1)
- self.showPosition.SetStatusWidths([-1, 150])
-
- self.__do_layout()
-
- # Initialize the variables of the class
- self.croco = croco
- self.x = x
- self.y = y
- self.variableName = variableName
- self.title = title
- self.xlabel = xlabel
- self.ylabel = ylabel
-
- def __do_layout(self):
-
- """
- Use a sizer to layout the controls, stacked vertically or horizontally
- """
- topSizer = wx.BoxSizer(wx.VERTICAL)
- canvasSizer = wx.BoxSizer(wx.VERTICAL)
- buttonsSizer = wx.BoxSizer(wx.HORIZONTAL)
-
- canvasSizer.Add(self.canvas, 0, wx.ALL, 5)
- buttonsSizer.Add(self.ZoomBtn, 0, wx.ALL, 5)
- buttonsSizer.Add(self.PanBtn, 0, wx.ALL, 5)
- buttonsSizer.Add(self.HomeBtn, 0, wx.ALL, 5)
- buttonsSizer.Add(self.SavePlotBtn, 0, wx.ALL, 5)
-
- topSizer.Add(canvasSizer, 0, wx.CENTER)
- topSizer.Add(buttonsSizer, 0, wx.ALL | wx.EXPAND, 5)
-
- self.panel.SetSizer(topSizer)
- topSizer.Fit(self)
-
- self.Layout()
-
- # ------------ Event handler
-
- def rect_select_callback(self, eclick, erelease):
- """Event handler for rectangle selector on plot"""
- self.xPress, self.yPress = eclick.xdata, eclick.ydata
- self.xRelease, self.yRelease = erelease.xdata, erelease.ydata
- self.xlim = [min(self.xPress, self.xRelease), max(self.xPress, self.xRelease)]
- self.ylim = [min(self.yPress, self.yRelease), max(self.yPress, self.yRelease)]
- self.draw(setlim=False)
-
- def ShowPosition(self, event):
- if event.inaxes:
- self.showPosition.SetStatusText(
- "x={:5.1f} y={:5.1f}".format(event.xdata, event.ydata), 1)
-
- def onZoomBtn(self, event):
- """
- Event handler for the button click Zoom in button
- """
- # self.figure.RS.set_active(True)
- self.toolbar.zoom()
-
- def onHomeBtn(self, event):
- """
- Event handler for the button click Zoom out button
- """
- # self.draw()
- self.toolbar.home()
-
- def onPanBtn(self, event):
- """
- Event handler for the button click Zoom out button
- """
- # self.draw()
- self.toolbar.pan()
-
- def onSavePlotBtn(self, event):
- """
- Event handler for the button click Print button
- """
- printDir = self.croco.startDir + "/Figures_" \
- + self.croco.get_run_name() + "/"
- if not os.path.isdir(printDir):
- os.mkdir(printDir)
- filename = self.title.replace(",", "_").replace(" ", "") + ".png"
- os.system('rm -Rf ' + printDir + filename)
- self.figure.savefig(printDir + filename, dpi=self.figure.dpi)
- # self.toolbar.save_figure(None)
-
- # Methods of class
-
- def draw(self, setlim=True):
- """ plot the current variable in the canvas """
-
- # Don't plot if variable full of Nan
- if np.count_nonzero(~np.isnan(self.x)) == 0 or \
- np.count_nonzero(~np.isnan(self.y)) == 0: return
-
- self.canvas.mpl_connect('motion_notify_event', self.ShowPosition)
-
- self.x = ma.masked_invalid(self.x)
- self.y = ma.masked_invalid(self.y)
- if setlim:
- self.xlim = [np.min(self.x), np.max(self.x)]
- self.ylim = [np.min(self.y), np.max(self.y)]
- title = self.title
- plotCurv(self, x=self.x, y=self.y, title=title, xlabel=self.xlabel,
- ylabel=self.ylabel, xlim=self.xlim, ylim=self.ylim)
- self.canvas.draw()
- self.canvas.Refresh()
- self.Show()
-
-# end of ProfileFrame Class
-########################################################################
-
-
-class CrocoGui(wx.Frame):
- """
- Window class to plot the XY sections, manage variables, times, levels and
- create other windows for vertical sections and profiles
-
- Attributes:
- title : name of the window
- """
-
- def __init__(self):
-
- # Create the window
- wx.Frame.__init__(self, None, wx.ID_ANY, title='Main Window')
- self.Bind(wx.EVT_CLOSE, self.OnClose)
-
- # Now create the Panel to put the other controls on.
- self.Panel = wx.Panel(self, wx.ID_ANY)
-
- # and a few controls
- self.CrocoVariableChoice = wx.Choice(self.Panel, wx.ID_ANY,
- choices=["Croco Variables ..."])
- self.CrocoVariableChoice.SetSelection(0)
-
- self.DerivedVariableChoice = wx.Choice(self.Panel, wx.ID_ANY,
- choices=["Derived Variables ..."])
- self.DerivedVariableChoice.SetSelection(0)
-
- self.LabelTime = wx.StaticText(self.Panel, -1, label="Choose Time",
- style=wx.ALIGN_CENTER)
- self.LabelMinMaxTime = wx.StaticText(self.Panel, wx.ID_ANY, " ", style=wx.ALIGN_LEFT)
- self.TimeTxt = wx.TextCtrl(self.Panel, wx.ID_ANY, "Time", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
-
- self.LabelLevel = wx.StaticText(self.Panel, -1, label="Choose level (level>0, depth<0)",
- style=wx.ALIGN_CENTER)
- self.LabelMinMaxLevel = wx.StaticText(self.Panel, wx.ID_ANY, " ", style=wx.ALIGN_LEFT)
- self.LabelMinMaxDepth = wx.StaticText(self.Panel, wx.ID_ANY, " ", style=wx.ALIGN_LEFT)
- self.LevSectionBtn = wx.Button(self.Panel, wx.ID_ANY, "Level/Depth Section")
- self.LevSectionTxt = wx.TextCtrl(self.Panel, wx.ID_ANY, "Level", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.LonSectionBtn = wx.Button(self.Panel, wx.ID_ANY, "Longitude Section")
- self.LonSectionTxt = wx.TextCtrl(self.Panel, wx.ID_ANY, "Longitude", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.LatSectionBtn = wx.Button(self.Panel, wx.ID_ANY, "Latitude Section")
- self.LatSectionTxt = wx.TextCtrl(self.Panel, wx.ID_ANY, "Latitude", style=wx.TE_CENTRE | wx.TE_PROCESS_ENTER)
- self.TimeSeriesBtn = wx.Button(self.Panel, wx.ID_ANY, "Time Series")
- self.VerticalProfileBtn = wx.Button(self.Panel, wx.ID_ANY, "Vertical Profile")
-
- # bind the menu event to an event handler
- self.CrocoVariableChoice.Bind(wx.EVT_CHOICE, self.onCrocoVariableChoice)
- self.DerivedVariableChoice.Bind(wx.EVT_CHOICE, self.onDerivedVariableChoice)
- self.TimeTxt.Bind(wx.EVT_TEXT_ENTER, self.onTimeTxt)
- self.LevSectionBtn.Bind(wx.EVT_BUTTON, self.onLevSectionBtn)
- self.LonSectionBtn.Bind(wx.EVT_BUTTON, self.onLonSectionBtn)
- self.LatSectionBtn.Bind(wx.EVT_BUTTON, self.onLatSectionBtn)
- self.TimeSeriesBtn.Bind(wx.EVT_BUTTON, self.onTimeSeriesBtn)
- self.VerticalProfileBtn.Bind(wx.EVT_BUTTON, self.onVerticalProfileBtn)
-
- # self.__set_properties()
- self.__do_layout()
-
- # Subscribe for future publication of sections. To retrieve notifications
- # when location (level/longitude/latitude) change after a click on a plot
- self.sub = Subscriber(self)
-
- # Initialize the croco instance
- self.openCroco()
-
- def __do_layout(self):
-
- """
- Use a sizer to layout the controls, stacked vertically or horizontally
- """
-
- topSizer = wx.BoxSizer(wx.HORIZONTAL)
- leftSizer = wx.BoxSizer(wx.VERTICAL)
- rightSizer = wx.BoxSizer(wx.VERTICAL)
- chooseVariablesSizer = wx.BoxSizer(wx.HORIZONTAL)
- labelTimeSizer = wx.BoxSizer(wx.HORIZONTAL)
- timeSizer = wx.BoxSizer(wx.HORIZONTAL)
- labelLevelSizer = wx.BoxSizer(wx.HORIZONTAL)
- labelMinMaxLevelSizer = wx.BoxSizer(wx.HORIZONTAL)
- labelMinMaxDepthSizer = wx.BoxSizer(wx.HORIZONTAL)
- levelSizer = wx.BoxSizer(wx.HORIZONTAL)
- longitudeSizer = wx.BoxSizer(wx.HORIZONTAL)
- latitudeSizer = wx.BoxSizer(wx.HORIZONTAL)
- timeSeriesSizer = wx.BoxSizer(wx.HORIZONTAL)
- profileSizer = wx.BoxSizer(wx.HORIZONTAL)
-
- chooseVariablesSizer.Add(self.CrocoVariableChoice, 0, wx.ALL, 5)
- chooseVariablesSizer.Add(self.DerivedVariableChoice, 0, wx.ALL, 5)
-
- labelTimeSizer.Add(self.LabelMinMaxTime, 0, wx.ALL | wx.EXPAND, 5)
- timeSizer.Add(self.LabelTime, 0, wx.ALL, 5)
- timeSizer.Add(self.TimeTxt, 0, wx.ALL, 5)
-
- labelLevelSizer.Add(self.LabelLevel, 0, wx.ALL | wx.EXPAND, 5)
- labelMinMaxLevelSizer.Add(self.LabelMinMaxLevel, 0, wx.ALL | wx.EXPAND, 5)
- labelMinMaxDepthSizer.Add(self.LabelMinMaxDepth, 0, wx.ALL | wx.EXPAND, 5)
-
- levelSizer.Add(self.LevSectionBtn, 0, wx.ALL, 5)
- levelSizer.Add(self.LevSectionTxt, 0, wx.ALL, 5)
-
- longitudeSizer.Add(self.LonSectionBtn, 0, wx.ALL, 5)
- longitudeSizer.Add(self.LonSectionTxt, 0, wx.ALL, 5)
-
- latitudeSizer.Add(self.LatSectionBtn, 0, wx.ALL, 5)
- latitudeSizer.Add(self.LatSectionTxt, 0, wx.ALL, 5)
-
- timeSeriesSizer.Add(self.TimeSeriesBtn, 0, wx.ALL, 5)
-
- profileSizer.Add(self.VerticalProfileBtn, 0, wx.ALL, 5)
-
- leftSizer.Add(chooseVariablesSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(labelTimeSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(timeSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(labelLevelSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(labelMinMaxLevelSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(labelMinMaxDepthSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(levelSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(longitudeSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(latitudeSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(timeSeriesSizer, 0, wx.ALL | wx.EXPAND, 5)
- leftSizer.Add(profileSizer, 0, wx.ALL | wx.EXPAND, 5)
-
- topSizer.Add(leftSizer, 0, wx.ALL | wx.EXPAND, 5)
-
- self.Panel.SetSizer(topSizer)
- self.Panel.SetAutoLayout(True)
- topSizer.Fit(self)
-
- self.Layout()
-
- # ------------ Event handler
-
- def update(self, level=None, longitude=None, latitude=None):
- """
- method to be applied when a section publisher send a new location
- (level/longitude/latitude) after a mouse click the plot
- """
- if level is not None:
- if level > 0:
- self.LevSectionTxt.SetValue('%d' % level)
- else:
- self.LevSectionTxt.SetValue('%.1F' % level)
- if longitude is not None:
- self.LonSectionTxt.SetValue('%.2F' % longitude)
- if latitude is not None:
- self.LatSectionTxt.SetValue('%.2F' % latitude)
-
- def OnClose(self, event):
- self.Destroy()
- sys.exit()
-
- def openCroco(self):
- """
- Create and show the Open FileDialog to select file name
- Initialize few outputs
- """
-
- startDir = os.getcwd()
- self.croco = Croco()
- self.croco.startDir = startDir
-
- # Fill the different text of the main window
- timeMin = self.croco.wrapper._get_date(0)
- timeMax = self.croco.wrapper._get_date(self.croco.wrapper.ntimes - 1)
- self.LabelMinMaxTime.SetLabel("Min/Max Time = " + str(timeMin) + " ... " +
- str(timeMax) + " days")
- self.TimeTxt.SetValue(str(timeMin))
- self.timeIndex = 0
- self.time = timeMin
- # minLevel = 1
- maxLevel = int(self.croco.wrapper.N)
- minDepth = - int(self.croco.wrapper.metrics['h'].max())
- maxDepth = 0
- self.LabelMinMaxLevel.SetLabel("Min/Max Level = 1 ... " + str(maxLevel))
- self.LabelMinMaxDepth.SetLabel("Min/Max Depth = " + str(minDepth) + " ... " + str(maxDepth))
- self.levelIndex = self.croco.wrapper.N - 1
- self.LevSectionTxt.SetValue(str(self.levelIndex + 1))
- self.depth = self.levelIndex + 1
- self.CrocoVariableChoice.AppendItems(self.croco.ListOfVariables)
- self.DerivedVariableChoice.AppendItems(self.croco.ListOfDerived)
-
- lon = self.croco.get_coord('ssh', direction='x')
- self.lon = lon[int(0.5 * self.croco.wrapper.M), int(0.5 * self.croco.wrapper.L)]
- lat = self.croco.get_coord('ssh', direction='y')
- self.lat = lat[int(0.5 * self.croco.wrapper.M), int(0.5 * self.croco.wrapper.L)]
- self.latIndex, self.lonIndex = self.findLatLonIndex(self.lon, self.lat)
- self.LonSectionTxt.SetValue('%.2F' % self.lon)
- self.LatSectionTxt.SetValue('%.2F' % self.lat)
-
- def onCrocoVariableChoice(self, event):
- ''' Choose variable from croco file to plot '''
- self.variableName = self.CrocoVariableChoice.GetString(self.CrocoVariableChoice.GetSelection())
- self.DerivedVariableChoice.SetSelection(0)
-
- def onDerivedVariableChoice(self, event):
- ''' Choose a computed variable to plot '''
- self.variableName = self.DerivedVariableChoice.GetString(self.DerivedVariableChoice.GetSelection())
- self.CrocoVariableChoice.SetSelection(0)
-
- def onTimeTxt(self, event):
- time = float(self.TimeTxt.GetValue())
- times = self.croco.get_coord(self.variableName, direction='t')
- # find index corresponding to the nearest instant time to plot
- self.timeIndex = min(range(len(times)), key=lambda j: abs(time - times[j]))
- self.time = self.croco.wrapper._get_date(self.timeIndex)
- self.TimeTxt.SetValue(str(self.time))
-
- def onLevSectionBtn(self, event):
-
- # if 2D variable, reset level to N
- try:
- dims = self.croco.variables[self.variableName].dims
- except Exception:
- dims = []
- if len(dims) == 3:
- self.level = self.croco.wrapper.N
- self.LevSectionTxt.SetValue('%d' % self.level)
-
- self.level = float(self.LevSectionTxt.GetValue())
- if self.level > 0:
- self.levelIndex = min(int(self.level - 1), self.croco.wrapper.N - 1)
- # self.LevSectionTxt.SetValue(str(self.levelIndex + 1))
- else:
- z = self.croco.get_coord(self.variableName, direction='z', timeIndex=self.timeIndex)
- self.levelIndex = np.argmax(z[:, self.latIndex, self.lonIndex] >= self.level)
- self.drawz(typSection="XY")
-
- def onLonSectionBtn(self, event):
- # if variable without z dimension
- try:
- ndims = len(self.croco.variables[self.variableName].dims)
- except Exception:
- ndims = 4
- if ndims < 4:
- print("Not 3D variable")
- return
- self.lon = float(self.LonSectionTxt.GetValue())
- # Find nearest indices of selected point
- self.latIndex, self.lonIndex = self.findLatLonIndex(self.lon, self.lat)
- self.drawz(typSection="YZ")
-
- def onLatSectionBtn(self, event):
- # if variable without z dimension
- try:
- ndims = len(self.croco.variables[self.variableName].dims)
- except Exception:
- ndims = 4
- if ndims < 4:
- print("Not 3D variable")
- return
- self.lat = float(self.LatSectionTxt.GetValue())
- # Find nearest indices of selected point
- self.latIndex, self.lonIndex = self.findLatLonIndex(self.lon, self.lat)
- self.drawz(typSection="XZ")
-
- def onTimeSeriesBtn(self, event):
- depth = float(self.LevSectionTxt.GetValue())
-
- # Get the mask at the rigth point
- try:
- dims = self.croco.variables[self.variableName].dims
- except Exception:
- dims = []
-
- if "x_u" in dims:
- mask = self.croco.umask()
- elif "y_v" in dims:
- mask = self.croco.vmask()
- else:
- mask = self.croco.rmask()
- # mask = np.where(mask == 0., np.nan, mask)
-
- # Get x coordinate: time
- x = self.croco.get_coord(self.variableName, direction='t').astype('timedelta64[D]').astype('float')
-
- # Time series on level
- if depth > 0:
- # Variable from croco file
- if self.variableName in self.croco.ListOfVariables:
- y = self.croco.get_variable(self.variableName, xindex=self.lonIndex,
- yindex=self.latIndex, zindex=self.levelIndex).values
-
- # Derived variable
- elif self.variableName in self.croco.ListOfDerived:
- y = np.full_like(x, np.nan)
- for it in range(len(x)):
- if 'pv' in self.variableName:
- y[it] = get_pv(self.croco, it, depth=self.levelIndex,
- typ=self.variableName)[self.latIndex, self.lonIndex]
- elif self.variableName == 'zeta_k':
- y[it] = get_zetak(self.croco, it, depth=self.levelIndex)[self.latIndex, self.lonIndex]
- elif self.variableName == 'dtdz':
- y[it] = get_dtdz(self.croco, it, depth=self.levelIndex)[self.latIndex, self.lonIndex]
- elif self.variableName == 'log(Ri)':
- y[it] = get_richardson(self.croco, it, depth=self.levelIndex)[self.latIndex, self.lonIndex]
-
- title = "{:s}, Lon={:4.1f}, Lat={:4.1f}, Level={:4.0f}".\
- format(self.variableName, self.lon, self.lat, self.depth)
-
- # Time series on depth
- else:
-
- y = np.zeros_like(x)
- # recalculate the depth slice at each time step
- for it in range(len(x)):
- # Calculate z
- z = self.croco. get_coord(self.variableName, direction='z', timeIndex=self.timeIndex)
-
- if self.variableName in self.croco.ListOfVariables:
- # Find levels around depth
- maxlev = np.argmax(z[:, self.latIndex, self.lonIndex] >= depth)
- minlev = maxlev - 1
- z1 = z[minlev, self.latIndex, self.lonIndex]
- z2 = z[maxlev, self.latIndex, self.lonIndex]
- # read variable and do interpolation
- try:
- var = self.croco.variables[self.variableName].isel(t=it,
- z_r=slice(minlev, maxlev + 1))[:, self.latIndex, self.lonIndex]
- except Exception:
- var = self.croco.variables[self.variableName].isel(t=it,
- z_w=slice(minlev,maxlev+1))[:,self.latIndex,self.lonIndex]
- y[it] = ((var[0] - var[1]) * depth + var[1] * z1 - var[0] * z2) / (z1 - z2)
-
- elif self.variableName in self.croco.ListOfDerived:
- # Find all the level corresponding to depth
- minlev, maxlev = self.croco.zslice(None, mask, z, depth, findlev=True)
- if 'pv' in self.variableName:
- # Compute pv between these levels
- var = get_pv(self.croco, it, depth=depth, minlev=minlev, maxlev=maxlev,
- typ=self.variableName)
- # Extract the slice of pv corresponding at the depth
- try:
- varz = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], depth)[0]
- except Exception:
- print("Not enough points")
- pass
- y[it] = varz[self.latIndex, self.lonIndex]
-
- elif self.variableName == 'zeta_k':
- # Compute pv between these levels
- var = get_zetak(self.croco, it, depth=depth, minlev=minlev, maxlev=maxlev)
- # Extract the slice of pv corresponding at the depth
- try:
- varz = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], depth)[0]
- except Exception:
- print("Not enough points")
- pass
- y[it] = varz[self.latIndex, self.lonIndex]
-
- elif self.variableName == 'dtdz':
- # Compute pv between these levels
- var = get_dtdz(self.croco, it, depth=depth, minlev=minlev, maxlev=maxlev)
- # Extract the slice of pv corresponding at the depth
- try:
- varz = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], depth)[0]
- except Exception:
- print("Not enough points")
- pass
- y[it] = varz[self.latIndex, self.lonIndex]
-
- elif self.variableName == 'log(Ri)':
- # Compute pv between these levels
- var = get_richardson(self.croco, it, depth=depth, minlev=minlev, maxlev=maxlev)
- # Extract the slice of pv corresponding at the depth
- try:
- varz = self.croco.zslice(var, mask, z[minlev:maxlev, :, :], depth)[0]
- except Exception:
- print("Not enough points")
- pass
- y[it] = varz[self.latIndex, self.lonIndex]
-
- title = "{:s}, Lon={:4.1f}, Lat={:4.1f}, depth={:4.1f}".format(self.variableName, self.lon, self.lat, depth)
-
- # Plot the time series
- self.timeFrame = ProfileFrame(croco=self.croco,
- x=x, y=y,
- variableName=self.variableName,
- title=title,
- xlabel="Time (days)")
- self.timeFrame.draw()
-
- def onVerticalProfileBtn(self, event):
- # Dimension must have z coordinate
- try:
- ndims = len(self.croco.variables[self.variableName].dims)
- except Exception:
- ndims = 4
- if ndims < 4:
- print("Not 3D variable")
- return
-
- time = str(self.croco.wrapper._get_date(self.timeIndex))
- title = "{:s}, Lon={:4.1f}, Lat={:4.1f}, Time={:s}".\
- format(self.variableName, self.lon, self.lat, time)
- # Get depths coordinate
- z = self.croco. get_coord(self.variableName, direction='z',
- timeIndex=self.timeIndex)[:, self.latIndex, self.lonIndex]
-
- # Get variable profile
- if self.variableName in self.croco.ListOfVariables:
- x = self.croco.get_variable(self.variableName,
- xindex=self.lonIndex, yindex=self.latIndex,
- tindex=self.timeIndex).values
-
- elif self.variableName in self.croco.ListOfDerived:
- if 'pv' in self.variableName:
- x = np.full_like(z, np.nan)
- var = get_pv(self.croco, self.timeIndex,
- minlev=0, maxlev=self.croco.wrapper.N - 1,
- lonindex=self.lonIndex, typ=self.variableName)
- x[1:] = var[:, self.latIndex]
-
- elif self.variableName == 'zeta_k':
- x = np.full_like(z, np.nan)
- var = get_zetak(self.croco, self.timeIndex,
- minlev=0, maxlev=self.croco.wrapper.N - 1,
- lonindex=self.lonIndex,)
- x[1:] = var[:, self.latIndex]
-
- elif self.variableName == 'dtdz':
- x = np.full_like(z, np.nan)
- var = get_dtdz(self.croco, self.timeIndex,
- minlev=0, maxlev=self.croco.wrapper.N - 1,
- lonindex=self.lonIndex,)
- x[1:] = var[:, self.latIndex]
-
- elif self.variableName == 'log(Ri)':
- x = np.full_like(z, np.nan)
- var = get_richardson(self.croco, self.timeIndex,
- minlev=0, maxlev=self.croco.wrapper.N - 1,
- lonindex=self.lonIndex,)
- x[1:] = var[:, self.latIndex]
-
- # Plot the profile
- self.profileFrame = ProfileFrame(croco=self.croco,
- x=x, y=z,
- variableName=self.variableName,
- title=title,
- ylabel="Depth (m)")
- self.profileFrame.draw()
-
- def notify(self, ax):
- self.xlim = ax.get_xlim()
- self.ylim = ax.get_ylim()
-
- def findLatLonIndex(self, lonValue, latValue):
- ''' Find nearest grid point of click value '''
- a = abs(self.croco.wrapper.coords['lon_r'] - lonValue) + \
- abs(self.croco.wrapper.coords['lat_r'] - latValue)
- return np.unravel_index(a.argmin(), a.shape)
-
- def drawz(self, typSection=None):
- '''
- Extract the rigth section for the current variable and
- plot in a new window
- '''
- # Level/Depth section
- if typSection == "XY":
-
- # Get Latitude coordinates
- y = self.croco.get_coord(self.variableName, direction='y')
-
- # Get Longitude coordinates
- x = self.croco.get_coord(self.variableName, direction='x')
- # x = repmat(x[self.latIndex, :].squeeze(), y.shape[0], 1)
-
- # Create new window
- self.sectionXY = SectionFrame(croco=self.croco,
- variableName=self.variableName,
- # variable=variable,
- x=x, y=y,
- typSection="XY",
- sliceCoord=self.level,
- sliceIndex=self.levelIndex,
- timeIndex=self.timeIndex,
- subscriber=self.sub)
- # Draw the plot
- self.sectionXY.updateVariableZ()
- self.sectionXY.drawz(setlim=True, setcol=True)
-
- # Latitude section
- elif typSection == "XZ":
-
- # Get depths coordinates
- y = self.croco.get_coord(self.variableName, direction='z',
- timeIndex=self.timeIndex)[:, self.latIndex, :]
- # Get Longitude coordinates
- x = self.croco.get_coord(self.variableName, direction='x')
- x = repmat(x[self.latIndex, :].squeeze(), y.shape[0], 1)
-
- # Create new window
- self.sectionXZ = SectionFrame(croco=self.croco,
- variableName=self.variableName,
- # variable=variable,
- x=x, y=y,
- typSection="XZ",
- sliceCoord=self.lat,
- sliceIndex=self.latIndex,
- timeIndex=self.timeIndex,
- subscriber=self.sub)
- # Draw the plot
- self.sectionXZ.updateVariableZ()
- self.sectionXZ.drawz(setlim=True, setcol=True)
-
- # Longitude section
- elif typSection == "YZ":
-
- # Get depths coordinates
- y = self.croco.get_coord(self.variableName, direction='z',
- timeIndex=self.timeIndex)[:, :, self.lonIndex]
- # Get Latitude coordinates
- x = self.croco.get_coord(self.variableName, direction='y')
- x = repmat(x[:, self.lonIndex].squeeze(), y.shape[0], 1)
- # Create new window
- self.sectionYZ = SectionFrame(croco=self.croco,
- variableName=self.variableName,
- # variable=variable,
- x=x, y=y,
- typSection="YZ",
- sliceCoord=self.lon,
- sliceIndex=self.lonIndex,
- timeIndex=self.timeIndex,
- subscriber=self.sub)
- # Draw the plot
- self.sectionYZ.updateVariableZ()
- self.sectionYZ.drawz(setlim=True, setcol=True)
-
-
-# end of class CrocoGui
-
-
-# Run the program
-if __name__ == "__main__":
- import ctypes
- if sys.platform.startswith('linux'):
- try:
- print(ctypes.x)
- sys.exit()
- x11 = ctypes.cdll.LoadLibrary('libX11.so')
- x11.XInitThreads()
- except Exception:
- print("Warning: failed to XInitThreads()")
- app = wx.App(False)
- frame = CrocoGui()
- frame.Show()
- app.MainLoop()
diff --git a/croco_pyvisu/croco_wrapper.py b/croco_pyvisu/croco_wrapper.py
deleted file mode 100644
index 132902be914c7b349d9b638597a28e9b408c53bd..0000000000000000000000000000000000000000
--- a/croco_pyvisu/croco_wrapper.py
+++ /dev/null
@@ -1,408 +0,0 @@
-# -*- coding: UTF-8 -*-
-#
-
-import numpy as np
-import xarray as xr
-from io_xarray import return_xarray_dataarray, return_xarray_dataset
-
-second2hour = 1. / 3600.
-second2day = 1. / 86400.
-
-# Benguela resolution (169x172x32)
-path = "/home/datawork-croco/datarmor-only/TRAININGS/TRAINING_2019/DATA/DATASETS_PYVISU/"
-keymap_files = {
- 'coordinate_file': path + "croco_his_Y2008.nc",
- 'metric_file': path + "croco_his_Y2008.nc",
- 'mask_file': path + "croco_his_Y2008.nc",
- 'variable_file': path + "croco_his_Y2008.nc"
-}
-
-keymap_dimensions = {
- 'xi_rho': 'x_r',
- 'eta_rho': 'y_r',
- 'xi_u': 'x_u',
- 'y_u': 'y_r',
- 'x_v': 'x_r',
- 'eta_v': 'y_v',
- 'x_w': 'x_r',
- 'y_w': 'y_r',
- 's_rho': 'z_r',
- 's_w': 'z_w',
- 'time': 't'
-}
-
-
-keymap_coordinates = {
- 'lon_rho': 'lon_r',
- 'lat_rho': 'lat_r',
- 'lon_u': 'lon_u',
- 'lat_u': 'lat_u',
- 'lon_v': 'lon_v',
- 'lat_v': 'lat_v',
- 'scrum_time': 'time'
-}
-
-
-keymap_variables = {
- 'zeta': 'ssh',
- 'u': 'u',
- 'v': 'v',
- 'w': 'w',
- 'temp': 'temp',
- 'salt': 'salt',
- 'rho': 'rho'
-}
-
-keymap_metrics = {
- 'pm': 'dx_r',
- 'pn': 'dy_r',
- 'theta_s': 'theta_s',
- 'theta_b': 'theta_b',
- 'Vtransform': 'scoord',
- 'hc': 'hc',
- 'h': 'h',
- 'f': 'f'
-}
-
-keymap_masks = {
- 'mask_rho': 'mask_r'
-}
-
-# Variables holders for croco
-
-
-class CrocoWrapper(object):
- """This class create the dictionnary of variables used for creating a
- generic grid from xios croco output files.
- """
- def __init__(self, chunks=None, mask_level=0):
-
- self.keymap_files = keymap_files
- self.keymap_dimensions = keymap_dimensions
- self.keymap_coordinates = keymap_coordinates
- self.keymap_variables = keymap_variables
- self.keymap_metrics = keymap_metrics
- self.keymap_masks = keymap_masks
-
- self.chunks = chunks
- self.mask_level = mask_level
- self.coords = {}
- self.metrics = {}
- self.masks = {}
-
- self.define_coordinates()
- self.define_dimensions(self.dscoord)
- self.define_metrics()
- self.define_masks()
- self.define_variables()
- self.parameters = {}
- self.parameters['chunks'] = chunks
-
- def _get(self, *args, **kwargs):
- return return_xarray_dataarray(*args, **kwargs)
-
- def _get_date(self, tindex):
- return self.coords['time'].values[tindex]
-
- def change_dimensions(self, ds):
- for key, val in self.keymap_dimensions.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_coords(self, ds):
- for key, val in self.keymap_coordinates.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_variables(self, ds):
- for key, val in self.keymap_variables.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_metrics(self, ds):
- for key, val in self.keymap_metrics.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_mask(self, ds):
- for key, val in self.keymap_masks.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def define_dimensions(self, ds):
- self.L = ds.dims['x_r']
- self.M = ds.dims['y_r']
- self.N = ds.dims['z_r']
- self.ntimes = ds.dims['t']
-
- def define_coordinates(self):
- ds = return_xarray_dataset(self.keymap_files['coordinate_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- self.dscoord = ds
- lon_r = self._get(self.dscoord, 'lon_r', chunks=self.chunks, decode_times=False).values
- lat_r = self._get(self.dscoord, 'lat_r', chunks=self.chunks, decode_times=False).values
- self.coords['lon_r'] = lon_r
- self.coords['lat_r'] = lat_r
- self.coords['lon_u'] = 0.5 * (lon_r[:, :-1] + lon_r[:, 1:])
- self.coords['lat_u'] = 0.5 * (lat_r[:, :-1] + lat_r[:, 1:])
- self.coords['lon_v'] = 0.5 * (lon_r[:-1, :] + lon_r[1:, :])
- self.coords['lat_v'] = 0.5 * (lat_r[:-1, :] + lat_r[1:, :])
- self.coords['lon_w'] = lon_r
- self.coords['lat_w'] = lat_r
-
- # time = time - time_origin
- self.coords['time'] = self._get(self.dscoord, 'time', chunks=self.chunks, decode_times=False)
- self.coords['time'] = self.coords['time'] * second2day
- # self.coords['time'].values = np.array(self.coords['time'], dtype='datetime64[D]') - \
- # np.array(self.coords['time'].time_origin, dtype='datetime64[D]')
- # self.coords['time'].values = self.coords['time'].values / np.timedelta64(1, 'D')
-
- def define_metrics(self):
- ds = return_xarray_dataset(self.keymap_files['metric_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_metrics(ds)
- self.dsmetrics = ds
- for key, val in self.keymap_metrics.items():
- self.metrics[val] = self._get(self.dsmetrics, val, chunks=self.chunks)
- # Add missing metrics
- # self.metrics['theta_s'] = xr.DataArray(data=[5.])
- # self.metrics['theta_b'] = xr.DataArray(data=[0.])
- # self.metrics['scoord'] = xr.DataArray(data=[2])
- # rad = np.pi/180
- # Rearth = 6.3708e6
- # dx_r = np.zeros_like(self.coords['lon_r'])
- # dx_r[:,:-1] = np.diff(self.coords['lon_r'],axis=1) * rad * Rearth
- # dx_r[:,-1] = dx_r[:,0]
- # dx_r = 1./dx_r
- # dy_r = np.zeros_like(self.coords['lat_r'])
- # dy_r[:-1,:] = np.diff(self.coords['lat_r'],axis=0) * rad * Rearth
- # dy_r[-1,:] = dy_r[0,:]
- # dy_r = 1./dy_r
- # self.metrics['dx_r'] = xr.DataArray(data=dx_r)
- # self.metrics['dy_r'] = xr.DataArray(data=dy_r)
-
- def define_masks(self):
- ds = return_xarray_dataset(self.keymap_files['mask_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_mask(ds)
- self.dsmask = ds
- for key, val in self.keymap_masks.items():
- try:
- self.masks[val] = self._get(self.dsmask, val, chunks=self.chunks)
- except Exception:
- mask_rho = np.ones_like(self.coords['lon_r'])
- self.masks[val] = xr.DataArray(data=mask_rho)
-
- def define_variables(self):
- ds = return_xarray_dataset(self.keymap_files['variable_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_variables(ds)
- # Add ssh as variable
- # ds = ds.assign(ssh = xr.DataArray(data=np.zeros((self.ntimes,self.M,self.L)),dims=('t','y_r','x_r')))
- self.dsvar = ds
-
- def chunk(self, chunks=None):
- """
- Chunk all the variables.
- Parameters
- ----------
- chunks : dict-like
- dictionnary of sizes of chunk along xarray dimensions.
- """
- for dataname in self.variables:
- data = self.variables[dataname]
- if isinstance(data, xr.DataArray):
- self.variables[dataname] = data.chunk(chunks)
-
- def _scoord2z(self, point_type, ssh, alpha, beta, lonindex=None, latindex=None):
- """
- scoord2z finds z at either rho or w points (positive up, zero at rest surface)
- h = array of depths (e.g., from grd file)
- theta_s = surface focusing parameter
- theta_b = bottom focusing parameter
- hc = critical depth
- N = number of vertical rho-points
- point_type = 'r' or 'w'
- scoord = 'new2008' :new scoord 2008, 'new2006' : new scoord 2006,
- or 'old1994' for Song scoord
- ssh = sea surface height
- message = set to False if don't want message
- """
- def CSF(sc, theta_s, theta_b):
- '''
- Allows use of theta_b > 0 (July 2009)
- '''
- one64 = np.float64(1)
-
- if theta_s > 0.:
- csrf = ((one64 - np.cosh(theta_s * sc)) /
- (np.cosh(theta_s) - one64))
- else:
- csrf = -sc ** 2
- sc1 = csrf + one64
- if theta_b > 0.:
- Cs = ((np.exp(theta_b * sc1) - one64) /
- (np.exp(theta_b) - one64) - one64)
- else:
- Cs = csrf
- return Cs
- #
- try:
- self.scoord
- except Exception:
- self.scoord = 2
- N = np.float64(self.N)
- try:
- theta_s = self.metrics['theta_s'].values
- except Exception:
- theta_s = self.metrics['theta_s']
- try:
- theta_b = self.metrics['theta_b'].values
- except Exception:
- theta_b = self.metrics['theta_b']
- try:
- hc = self.metrics['hc'].values
- except Exception:
- hc = self.metrics['hc']
-
- if lonindex is not None:
- h = self.metrics['h'].values[:, lonindex - 1:lonindex + 2]
- elif latindex is not None:
- h = self.metrics['h'].values[latindex - 1:latindex + 2, :]
- else:
- h = self.metrics['h'].values
- scoord = self.metrics['scoord'].values
-
- sc_w = (np.arange(N + 1, dtype=np.float64) - N) / N
- sc_r = ((np.arange(1, N + 1, dtype=np.float64)) - N - 0.5) / N
-
- if 'w' in point_type:
- sc = sc_w
- # add a level
- N += 1.
- else:
- sc = sc_r
-
- z = np.empty((int(N),) + h.shape, dtype=np.float64)
- if scoord == 2:
- Cs = CSF(sc, theta_s, theta_b)
- else:
- try:
- cff1 = 1. / np.sinh(theta_s)
- cff2 = 0.5 / np.tanh(0.5 * theta_s)
- except Exception:
- cff1 = 0.
- cff2 = 0.
- Cs = (1. - theta_b) * cff1 * np.sinh(theta_s * sc) +\
- theta_b * (cff2 * np.tanh(theta_s * (sc + 0.5)) - 0.5)
-
- if scoord == 2:
- hinv = 1. / (h + hc)
- cff = (hc * sc).squeeze()
- cff1 = (Cs).squeeze()
- for k in np.arange(N, dtype=int):
- z[k] = ssh + (ssh + h) * (cff[k] + cff1[k] * h) * hinv
- elif scoord == 1:
- hinv = 1. / h
- cff = (hc * (sc - Cs)).squeeze()
- cff1 = Cs.squeeze()
- cff2 = (sc + 1).squeeze()
- for k in np.arange(N) + 1:
- z0 = cff[k - 1] + cff1[k - 1] * h
- z[k - 1, :] = z0 + ssh * (1. + z0 * hinv)
- else:
- raise Exception("Unknown scoord, should be 1 or 2")
- return z.squeeze(), np.float32(Cs)
-
- def scoord2z_r(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at rho point
- '''
- return self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
-
- def scoord2z_w(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at rho point
- '''
- return self._scoord2z('w', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
-
- def scoord2z_u(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at u point
- '''
- depth = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta)[0]
- if lonindex is not None:
- return np.squeeze(0.5 * (depth[:, :, lonindex] + depth[:, :, lonindex - 1]))
- elif latindex is not None:
- return np.squeeze(0.5 * (depth[:, latindex, 1:] + depth[:, latindex, :-1]))
- else:
- return np.squeeze(0.5 * (depth[:, :, :-1] + depth[:, :, 1:]))
-
- def scoord2z_v(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at v point
- '''
- depth = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta)[0]
- if lonindex is not None:
- return np.squeeze(0.5 * (depth[:, 1:, lonindex] + depth[:, :-1, lonindex]))
- elif latindex is not None:
- return np.squeeze(0.5 * (depth[:, latindex, :] + depth[:, latindex - 1, :]))
- else:
- return np.squeeze(0.5 * (depth[:, :-1, :] + depth[:, 1:, :]))
-
- def scoord2dz_r(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- """
- dz at rho points, 3d matrix
- """
- dz = self._scoord2z('w', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
- return dz[1:] - dz[:-1]
-
- def scoord2dz_w(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- """
- dz at rho points, 3d matrix
- """
- dz = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
- return dz[1:] - dz[:-1]
-
- def scoord2dz_u(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- dz at u points, 3d matrix
- '''
- dz = self.scoord2z_u(ssh=ssh, alpha=0., beta=1., lonindex=None, latindex=latindex)
- return dz[1:] - dz[:-1]
-
- def scoord2dz_v(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- dz at v points
- '''
- dz = self.scoord2z_v(ssh=ssh, alpha=0., beta=1., lonindex=lonindex, latindex=latindex)
- return dz[1:] + dz[:-1]
-
-
-# Run the program
-
-if __name__ == '__main__':
- croco = CrocoWrapper(coordinate_file="moz_his.nc", mask_file="moz_his.nc")
diff --git a/croco_pyvisu/croco_wrapper.xios.py b/croco_pyvisu/croco_wrapper.xios.py
deleted file mode 100644
index 65319fff0c598f4e3da444af4ac085dad063fd4a..0000000000000000000000000000000000000000
--- a/croco_pyvisu/croco_wrapper.xios.py
+++ /dev/null
@@ -1,407 +0,0 @@
-# -*- coding: UTF-8 -*-
-#
-
-import numpy as np
-import xarray as xr
-from io_xarray import return_xarray_dataarray, return_xarray_dataset
-
-second2day = 1. / 86400.
-
-# path = "./"
-path = "/home/datawork-lops-osi/cmenesg/moz/moz_256x120_ts5_tb0_hc10_new_skpp_bkpp/t1/CROCO_FILES/"
-# path = "/home/datawork-lops-osi/cmenesg/moz/moz_512x240_ts5_tb0_hc10_new/t1/CROCO_FILES/"
-keymap_files = {
- 'coordinate_file': path + "moz_his.nc",
- 'metric_file': path + "moz_his.nc",
- 'mask_file': path + "moz_his.nc",
- 'variable_file': path + "moz_his.nc"
-}
-
-keymap_dimensions = {
- 'x_rho': 'x_r',
- 'y_rho': 'y_r',
- 'x_u': 'x_u',
- 'y_u': 'y_r',
- 'x_v': 'x_r',
- 'y_v': 'y_v',
- 'x_w': 'x_r',
- 'y_w': 'y_r',
- 's_rho': 'z_r',
- 's_w': 'z_w',
- 'time_counter': 't'
-}
-
-
-keymap_coordinates = {
- 'nav_lon_rho': 'lon_r',
- 'nav_lat_rho': 'lat_r',
- 'nav_lon_u': 'lon_u',
- 'nav_lat_u': 'lat_u',
- 'nav_lon_v': 'lon_v',
- 'nav_lat_v': 'lat_v',
- 'time_instant': 'time'
-}
-
-
-keymap_variables = {
- 'ssh': 'ssh',
- 'u': 'u',
- 'v': 'v',
- 'w': 'w',
- 'temp': 'temp',
- 'salt': 'salt',
- 'rho': 'rho'
-}
-
-keymap_metrics = {
- 'pm': 'dx_r',
- 'pn': 'dy_r',
- 'theta_s': 'theta_s',
- 'theta_b': 'theta_b',
- 'Vtransform': 'scoord',
- 'hc': 'hc',
- 'h': 'h',
- 'f': 'f'
-}
-
-keymap_masks = {
- 'mask_rho': 'mask_r'
-}
-
-# Variables holders for croco
-
-
-class CrocoWrapper(object):
- """This class create the dictionnary of variables used for creating a
- generic grid from xios croco output files.
- """
- def __init__(self, chunks=None, mask_level=0):
-
- self.keymap_files = keymap_files
- self.keymap_dimensions = keymap_dimensions
- self.keymap_coordinates = keymap_coordinates
- self.keymap_variables = keymap_variables
- self.keymap_metrics = keymap_metrics
- self.keymap_masks = keymap_masks
-
- self.chunks = chunks
- self.mask_level = mask_level
- self.coords = {}
- self.metrics = {}
- self.masks = {}
-
- self.define_coordinates()
- self.define_dimensions(self.dscoord)
- self.define_metrics()
- self.define_masks()
- self.define_variables()
- self.parameters = {}
- self.parameters['chunks'] = chunks
-
- def _get(self, *args, **kwargs):
- return return_xarray_dataarray(*args, **kwargs)
-
- def _get_date(self, tindex):
- return self.coords['time'].values[tindex]
-
- def change_dimensions(self, ds):
- for key, val in self.keymap_dimensions.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_coords(self, ds):
- for key, val in self.keymap_coordinates.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_variables(self, ds):
- for key, val in self.keymap_variables.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_metrics(self, ds):
- for key, val in self.keymap_metrics.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def change_mask(self, ds):
- for key, val in self.keymap_masks.items():
- try:
- ds = ds.rename({key: val})
- except Exception:
- pass
- return ds
-
- def define_dimensions(self, ds):
- self.L = ds.dims['x_r']
- self.M = ds.dims['y_r']
- self.N = ds.dims['z_r']
- self.ntimes = ds.dims['t']
-
- def define_coordinates(self):
- ds = return_xarray_dataset(self.keymap_files['coordinate_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- self.dscoord = ds
- lon_r = self._get(self.dscoord, 'lon_r', chunks=self.chunks, decode_times=False).values
- lat_r = self._get(self.dscoord, 'lat_r', chunks=self.chunks, decode_times=False).values
- self.coords['lon_r'] = lon_r
- self.coords['lat_r'] = lat_r
- self.coords['lon_u'] = 0.5 * (lon_r[:, :-1] + lon_r[:, 1:])
- self.coords['lat_u'] = 0.5 * (lat_r[:, :-1] + lat_r[:, 1:])
- self.coords['lon_v'] = 0.5 * (lon_r[:-1, :] + lon_r[1:, :])
- self.coords['lat_v'] = 0.5 * (lat_r[:-1, :] + lat_r[1:, :])
- self.coords['lon_w'] = lon_r
- self.coords['lat_w'] = lat_r
-
- # time = time - time_origin
- self.coords['time'] = self._get(self.dscoord, 'time', chunks=self.chunks, decode_times=False)
- self.coords['time'].values = np.array(self.coords['time'], dtype='datetime64[D]') - \
- np.array(self.coords['time'].time_origin, dtype='datetime64[D]')
- self.coords['time'].values = self.coords['time'].values / np.timedelta64(1, 'D')
-
- def define_metrics(self):
- ds = return_xarray_dataset(self.keymap_files['metric_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_metrics(ds)
- self.dsmetrics = ds
- for key, val in self.keymap_metrics.items():
- self.metrics[val] = self._get(self.dsmetrics, val, chunks=self.chunks)
- # Add missing metrics
- # self.metrics['theta_s'] = xr.DataArray(data=[5.])
- # self.metrics['theta_b'] = xr.DataArray(data=[0.])
- # self.metrics['scoord'] = xr.DataArray(data=[2])
- # rad = np.pi/180
- # Rearth = 6.3708e6
- # dx_r = np.zeros_like(self.coords['lon_r'])
- # dx_r[:,:-1] = np.diff(self.coords['lon_r'],axis=1) * rad * Rearth
- # dx_r[:,-1] = dx_r[:,0]
- # dx_r = 1./dx_r
- # dy_r = np.zeros_like(self.coords['lat_r'])
- # dy_r[:-1,:] = np.diff(self.coords['lat_r'],axis=0) * rad * Rearth
- # dy_r[-1,:] = dy_r[0,:]
- # dy_r = 1./dy_r
- # self.metrics['dx_r'] = xr.DataArray(data=dx_r)
- # self.metrics['dy_r'] = xr.DataArray(data=dy_r)
-
- def define_masks(self):
- ds = return_xarray_dataset(self.keymap_files['mask_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_mask(ds)
- self.dsmask = ds
- for key, val in self.keymap_masks.items():
- try:
- self.masks[val] = self._get(self.dsmask, val, chunks=self.chunks)
- except Exception:
- mask_rho = np.ones_like(self.coords['lon_r'])
- self.masks[val] = xr.DataArray(data=mask_rho)
-
- def define_variables(self):
- ds = return_xarray_dataset(self.keymap_files['variable_file'])
- ds = self.change_dimensions(ds)
- ds = self.change_coords(ds)
- ds = self.change_variables(ds)
- # Add ssh as variable
- # ds = ds.assign(ssh = xr.DataArray(data=np.zeros((self.ntimes,self.M,self.L)),dims=('t','y_r','x_r')))
- self.dsvar = ds
-
- def chunk(self, chunks=None):
- """
- Chunk all the variables.
- Parameters
- ----------
- chunks : dict-like
- dictionnary of sizes of chunk along xarray dimensions.
- """
- for dataname in self.variables:
- data = self.variables[dataname]
- if isinstance(data, xr.DataArray):
- self.variables[dataname] = data.chunk(chunks)
-
- def _scoord2z(self, point_type, ssh, alpha, beta, lonindex=None, latindex=None):
- """
- scoord2z finds z at either rho or w points (positive up, zero at rest surface)
- h = array of depths (e.g., from grd file)
- theta_s = surface focusing parameter
- theta_b = bottom focusing parameter
- hc = critical depth
- N = number of vertical rho-points
- point_type = 'r' or 'w'
- scoord = 'new2008' :new scoord 2008, 'new2006' : new scoord 2006,
- or 'old1994' for Song scoord
- ssh = sea surface height
- message = set to False if don't want message
- """
- def CSF(sc, theta_s, theta_b):
- '''
- Allows use of theta_b > 0 (July 2009)
- '''
- one64 = np.float64(1)
-
- if theta_s > 0.:
- csrf = ((one64 - np.cosh(theta_s * sc)) /
- (np.cosh(theta_s) - one64))
- else:
- csrf = -sc ** 2
- sc1 = csrf + one64
- if theta_b > 0.:
- Cs = ((np.exp(theta_b * sc1) - one64) /
- (np.exp(theta_b) - one64) - one64)
- else:
- Cs = csrf
- return Cs
- #
- try:
- self.scoord
- except Exception:
- self.scoord = 2
- N = np.float64(self.N)
- try:
- theta_s = self.metrics['theta_s'].values
- except Exception:
- theta_s = self.metrics['theta_s']
- try:
- theta_b = self.metrics['theta_b'].values
- except Exception:
- theta_b = self.metrics['theta_b']
- try:
- hc = self.metrics['hc'].values
- except Exception:
- hc = self.metrics['hc']
-
- if lonindex is not None:
- h = self.metrics['h'].values[:, lonindex - 1:lonindex + 2]
- elif latindex is not None:
- h = self.metrics['h'].values[latindex - 1:latindex + 2, :]
- else:
- h = self.metrics['h'].values
- scoord = self.metrics['scoord'].values
-
- sc_w = (np.arange(N + 1, dtype=np.float64) - N) / N
- sc_r = ((np.arange(1, N + 1, dtype=np.float64)) - N - 0.5) / N
-
- if 'w' in point_type:
- sc = sc_w
- # add a level
- N += 1.
- else:
- sc = sc_r
-
- z = np.empty((int(N),) + h.shape, dtype=np.float64)
- if scoord == 2:
- Cs = CSF(sc, theta_s, theta_b)
- else:
- try:
- cff1 = 1. / np.sinh(theta_s)
- cff2 = 0.5 / np.tanh(0.5 * theta_s)
- except Exception:
- cff1 = 0.
- cff2 = 0.
- Cs = (1. - theta_b) * cff1 * np.sinh(theta_s * sc) +\
- theta_b * (cff2 * np.tanh(theta_s * (sc + 0.5)) - 0.5)
-
- if scoord == 2:
- hinv = 1. / (h + hc)
- cff = (hc * sc).squeeze()
- cff1 = (Cs).squeeze()
- for k in np.arange(N, dtype=int):
- z[k] = ssh + (ssh + h) * (cff[k] + cff1[k] * h) * hinv
- elif scoord == 1:
- hinv = 1. / h
- cff = (hc * (sc - Cs)).squeeze()
- cff1 = Cs.squeeze()
- cff2 = (sc + 1).squeeze()
- for k in np.arange(N) + 1:
- z0 = cff[k - 1] + cff1[k - 1] * h
- z[k - 1, :] = z0 + ssh * (1. + z0 * hinv)
- else:
- raise Exception("Unknown scoord, should be 1 or 2")
- return z.squeeze(), np.float32(Cs)
-
- def scoord2z_r(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at rho point
- '''
- return self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
-
- def scoord2z_w(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at rho point
- '''
- return self._scoord2z('w', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
-
- def scoord2z_u(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at u point
- '''
- depth = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta)[0]
- if lonindex is not None:
- return np.squeeze(0.5 * (depth[:, :, lonindex] + depth[:, :, lonindex - 1]))
- elif latindex is not None:
- return np.squeeze(0.5 * (depth[:, latindex, 1:] + depth[:, latindex, :-1]))
- else:
- return np.squeeze(0.5 * (depth[:, :, :-1] + depth[:, :, 1:]))
-
- def scoord2z_v(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- Depths at v point
- '''
- depth = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta)[0]
- if lonindex is not None:
- return np.squeeze(0.5 * (depth[:, 1:, lonindex] + depth[:, :-1, lonindex]))
- elif latindex is not None:
- return np.squeeze(0.5 * (depth[:, latindex, :] + depth[:, latindex - 1, :]))
- else:
- return np.squeeze(0.5 * (depth[:, :-1, :] + depth[:, 1:, :]))
-
- def scoord2dz_r(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- """
- dz at rho points, 3d matrix
- """
- dz = self._scoord2z('w', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
- return dz[1:] - dz[:-1]
-
- def scoord2dz_w(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- """
- dz at rho points, 3d matrix
- """
- dz = self._scoord2z('r', ssh=ssh, alpha=alpha, beta=beta,
- lonindex=lonindex, latindex=latindex)[0]
- return dz[1:] - dz[:-1]
-
- def scoord2dz_u(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- dz at u points, 3d matrix
- '''
- dz = self.scoord2z_u(ssh=ssh, alpha=0., beta=1., lonindex=None, latindex=latindex)
- return dz[1:] - dz[:-1]
-
- def scoord2dz_v(self, ssh=0., alpha=0., beta=1., lonindex=None, latindex=None):
- '''
- dz at v points
- '''
- dz = self.scoord2z_v(ssh=ssh, alpha=0., beta=1., lonindex=lonindex, latindex=latindex)
- return dz[1:] + dz[:-1]
-
-
-# Run the program
-
-if __name__ == '__main__':
- croco = CrocoWrapper(coordinate_file="moz_his.nc", mask_file="moz_his.nc")
diff --git a/croco_pyvisu/derived_variables.py b/croco_pyvisu/derived_variables.py
deleted file mode 100644
index 5992167418b06d8bcaefefb4c34889019ee5c242..0000000000000000000000000000000000000000
--- a/croco_pyvisu/derived_variables.py
+++ /dev/null
@@ -1,459 +0,0 @@
-# -*- coding: UTF-8 -*-
-#
-# generated by wxGlade 0.8.0b3 on Tue Jan 30 13:49:27 2018
-#
-
-import numpy as np
-
-
-###############################################################
-# Ertel Potential vorticity
-
-
-def get_pv(croco, tindex, depth=None, minlev=None, maxlev=None,
- lonindex=None, latindex=None, typ='ijk'):
-
- # mask = croco.wrapper.masks['mask_r']
- # pv = np.full_like(mask,np.nan)
-
- # pv from minlev to maxlev
- if depth is None:
- if lonindex is not None:
- var = np.full((maxlev - minlev, croco.wrapper.M), np.nan)
- else:
- var = np.full((maxlev - minlev, croco.wrapper.L), np.nan)
- var[:, 1:-1] = calc_ertel(croco, tindex, minlev=minlev, maxlev=maxlev,
- lonindex=lonindex, latindex=latindex, typ=typ)
-
- # pv on a depth
- elif depth <= 0:
- var = np.full((maxlev - minlev, croco.wrapper.M, croco.wrapper.L), np.nan)
- # pv = np.tile(pv,(maxlev-minlev,1,1))
- var[:, 1:-1, 1:-1] = calc_ertel(croco, tindex, minlev=minlev, maxlev=maxlev,
- lonindex=lonindex, latindex=latindex, typ=typ)
-
- # pv on a level
- elif depth > 0:
- var = np.full((croco.wrapper.M, croco.wrapper.L), np.nan)
- var[1:-1, 1:-1] = calc_ertel(croco, tindex,
- minlev=int(depth) - 2, maxlev=int(depth - 1),
- lonindex=lonindex, latindex=latindex, typ=typ)
- return var
-
-
-def calc_ertel(croco, tindex, minlev=None, maxlev=None, lonindex=None, latindex=None, typ='ijk'):
- """
- #
- # epv - The ertel potential vorticity with respect to property 'lambda'
- #
- # [ curl(u) + f ]
- # - epv is given by: EPV = --------------- . del(lambda)
- # rho
- #
- # - pvi,pvj,pvk - the x, y, and z components of the potential vorticity.
- #
- # - Ertel PV is calculated on horizontal rho-points, vertical w-points.
- #
- #
- # tindex - The time index at which to calculate the potential vorticity.
- # depth - depth
- #
- # Adapted from rob hetland.
- #
- """
-
- # Grid parameters
-
- minlon = 0 if lonindex is None else lonindex - 1
- maxlon = croco.wrapper.L - 1 if lonindex is None else lonindex + 1
- minlat = 0 if latindex is None else latindex - 1
- maxlat = croco.wrapper.M - 1 if latindex is None else latindex + 1
-
- pm = croco.wrapper.metrics['dx_r'][minlat:maxlat + 1, minlon:maxlon + 1]
- pm = np.tile(pm, (maxlev - minlev + 1, 1, 1))
- pn = croco.wrapper.metrics['dy_r'][minlat:maxlat + 1, minlon:maxlon + 1]
- pn = np.tile(pn, (maxlev - minlev + 1, 1, 1))
- f = croco.wrapper.metrics['f'][minlat:maxlat + 1, minlon:maxlon + 1]
- f = np.tile(f, (maxlev - minlev + 1, 1, 1))
- rho0 = croco.rho0
- #
- # 3D variables
- #
-
- ssh = croco.variables['ssh'].isel(t=tindex, y_r=slice(minlat, maxlat + 1),
- x_r=slice(minlon, maxlon + 1)).values
- dz = croco.wrapper.scoord2dz_r(ssh, alpha=0., beta=0, lonindex=lonindex,
- latindex=latindex)[minlev:maxlev + 1, :]
- u = croco.variables['u'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_r=slice(minlat, maxlat + 1), x_u=slice(minlon, maxlon)).values
- v = croco.variables['v'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_v=slice(minlat, maxlat), x_r=slice(minlon, maxlon + 1)).values
- w = croco.variables['w'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_r=slice(minlat, maxlat + 1), x_r=slice(minlon, maxlon + 1))
-
- try:
- rho = croco.variables['rho'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_r=slice(minlat, maxlat + 1), x_r=slice(minlon, maxlon + 1))
- except Exception:
- # temp = croco.variables['temp'].isel(t=tindex, z_r=slice(minlev,maxlev+1),\
- # y_r=slice(minlat,maxlat+1), x_r=slice(minlon,m axlon + 1))
- # salt = croco.variables['salt'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),\
- # y_r=slice(minlat,maxlat+1),x_r=slice(minlon,maxlon+1))
- # rho = croco.rho_eos(temp,salt,0)
- print('rho not in history file')
- return
-
- if 'k' in typ:
- #
- #
- # Ertel potential vorticity, term 1: [f + (dv/dx - du/dy)]*drho/dz
- #
- # Compute d(v)/d(xi) at PSI-points.
- #
- dxm1 = 0.25 * (pm[:, :-1, 1:] + pm[:, 1:, 1:] + pm[:, :-1, :-1] + pm[:, 1:, :-1])
- dvdxi = np.diff(v, n=1, axis=2) * dxm1
- #
- # Compute d(u)/d(eta) at PSI-points.
- #
- dym1 = 0.25 * (pn[:, :-1, 1:] + pn[:, 1:, 1:] + pn[:, :-1, :-1] + pn[:, 1:, :-1])
- dudeta = np.diff(u, n=1, axis=1) * dym1
- #
- # Compute d(rho)/d(z) at horizontal RHO-points and vertical W-points
- #
- dz_w = 0.5 * (dz[:-1, :, :] + dz[1:, :, :])
- drhodz = np.diff(rho, n=1, axis=0) / dz_w
- #
- # Compute Ertel potential vorticity <k hat> at horizontal RHO-points and
- # vertical W-points.
- omega = dvdxi - dudeta
- omega = f[:, 1:-1, 1:-1] + 0.25 * (omega[:, :-1, 1:] + omega[:, 1:, 1:] +
- omega[:, :-1, :-1] + omega[:, 1:, :-1])
- pvk = 0.5 * (omega[:-1, :, :] + omega[1:, :, :]) * drhodz[:, 1:-1, 1:-1]
- else:
- pvk = 0.
-
- if 'i' in typ:
- #
- #
- # Ertel potential vorticity, term 2: (dw/dy - dv/dz)*(drho/dx)
- #
- # Compute d(w)/d(y) at horizontal V-points and vertical RHO-points
- #
- dym1 = 0.5 * (pn[:, :-1, :] + pn[:, 1:, :])
- dwdy = np.diff(w, axis=1) * dym1
- #
- # Compute d(v)/d(z) at horizontal V-points and vertical W-points
- #
- dz_v = 0.5 * (dz[:, 1:, :] + dz[:, :-1, :])
- # dz_v = croco.crocoGrid.scoord2dz_v(zeta, alpha=0., beta=0.)
- dvdz = np.diff(v, axis=0) / (0.5 * (dz_v[:-1, :, :] + dz_v[1:, :, :]))
- #
- # Compute d(rho)/d(xi) at horizontal U-points and vertical RHO-points
- #
- dxm1 = 0.5 * (pm[:, :, 1:] + pm[:, :, :-1])
- drhodx = np.diff(rho, axis=2) * dxm1
- #
- # Add in term 2 contribution to Ertel potential vorticity at horizontal RHO-points and
- # vertical W-points.
- #
- pvi = (0.25 * (dwdy[1:, :-1, 1:-1] + dwdy[1:, 1:, 1:-1] + dwdy[:-1, :-1, 1:-1] + dwdy[:-1, 1:, 1:-1]) -
- 0.5 * (dvdz[:, :-1, 1:-1] + dvdz[:, 1:, 1:-1])) *\
- 0.25 * (drhodx[1:, 1:-1, :-1] + drhodx[1:, 1:-1, 1:] +
- drhodx[:-1, 1:-1, :-1] + drhodx[:-1, 1:-1, 1:])
- else:
- pvi = 0.
-
- if 'j' in typ:
- #
- #
- # Ertel potential vorticity, term 3: (du/dz - dw/dx)*(drho/dy)
- #
- # Compute d(u)/d(z) at horizontal U-points and vertical W-points
- #
- dz_u = 0.5 * (dz[:, :, 1:] + dz[:, :, :-1])
- dudz = np.diff(u, axis=0) / (0.5 * (dz_u[:-1, :, :] + dz_u[1:, :, :]))
- #
- # Compute d(w)/d(x) at horizontal U-points and vertical RHO-points
- #
- dxm1 = 0.5 * (pm[:, :, 1:] + pm[:, :, :-1])
- dwdx = np.diff(w, axis=2) * dxm1
- #
- # Compute d(rho)/d(eta) at horizontal V-points and vertical RHO-points
- #
- dym1 = 0.5 * (pn[:, 1:, :] + pn[:, :-1, :])
- drhodeta = np.diff(rho, axis=1) * dym1
- #
- # Add in term 3 contribution to Ertel potential vorticity at horizontal RHO-points and
- # vertical W-points..
- #
- pvj = (0.5 * (dudz[:, 1:-1, 1:] + dudz[:, 1:-1, :-1]) -
- 0.25 * (dwdx[1:, 1:-1, 1:] + dwdx[1:, 1:-1, :-1] + dwdx[:-1, 1:-1, 1:] + dwdx[:-1, 1:-1, :-1])) * \
- 0.25 * (drhodeta[1:, :-1, 1:-1] + drhodeta[1:, 1:, 1:-1] +
- drhodeta[:-1, :-1, 1:-1] + drhodeta[:-1, 1:, 1:-1])
- else:
- pvj = 0.
-
- #
- #
- # Sum potential vorticity components, and divide by rho0
- #
- pvi = pvi / rho0
- pvj = pvj / rho0
- pvk = pvk / rho0
- #
- return(np.squeeze(pvi + pvj + pvk))
- #
- #
- ####################################################################################
-
-
-###############################################################
-# Zeta_k term
-
-def get_zetak(croco, tindex, depth=None, minlev=None, maxlev=None,
- lonindex=None, latindex=None):
-
- # mask = croco.wrapper.masks['mask_r']
- # pv = np.full_like(mask,np.nan)
-
- # pv from level 0 to N at latitude or longitude index
- if depth is None:
- if lonindex is not None:
- var = np.full((maxlev - minlev, croco.wrapper.M), np.nan)
- else:
- var = np.full((maxlev - minlev, croco.wrapper.L), np.nan)
- var[:, 1:-1] = calc_zetak(croco, tindex, minlev=minlev, maxlev=maxlev - 1,
- lonindex=lonindex, latindex=latindex)
- elif depth <= 0:
- var = np.full((maxlev - minlev, croco.wrapper.M, croco.wrapper.L), np.nan)
- var[:, 1:-1, 1:-1] = calc_zetak(croco, tindex, minlev=minlev, maxlev=maxlev - 1,
- lonindex=lonindex, latindex=latindex)
- # pv on a level
- elif depth > 0:
- var = np.full((croco.wrapper.M, croco.wrapper.L), np.nan)
- var[1:-1, 1:-1] = calc_zetak(croco, tindex,
- minlev=int(depth) - 1, maxlev=int(depth - 1),
- lonindex=lonindex, latindex=latindex)
- return var
-
-
-def calc_zetak(croco, tindex, minlev=None, maxlev=None, lonindex=None, latindex=None):
- """
- # - zetak is given by: (dv/dx - du/dy)/f
- #
- # - zetak is calculated at RHO-points
- #
- #
- # tindex - The time index at which to calculate the potential vorticity.
- # depth - depth
- #
- # Adapted from rob hetland.
- #
- """
- #
- # Grid parameters
- #
- minlon = 0 if lonindex is None else lonindex - 1
- maxlon = croco.wrapper.L - 1 if lonindex is None else lonindex + 1
- minlat = 0 if latindex is None else latindex - 1
- maxlat = croco.wrapper.M - 1 if latindex is None else latindex + 1
-
- pm = croco.wrapper.metrics['dx_r'][minlat:maxlat + 1, minlon:maxlon + 1]
- pm = np.tile(pm, (maxlev - minlev + 1, 1, 1))
- pn = croco.wrapper.metrics['dy_r'][minlat:maxlat + 1, minlon:maxlon + 1]
- pn = np.tile(pn, (maxlev - minlev + 1, 1, 1))
- f = croco.wrapper.metrics['f'][minlat:maxlat + 1, minlon:maxlon + 1]
- f = np.tile(f, (maxlev - minlev + 1, 1, 1))
- #
- # 3D variables
- #
-
- u = croco.variables['u'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_r=slice(minlat, maxlat + 1), x_u=slice(minlon, maxlon)).values
- v = croco.variables['v'].isel(t=tindex, z_r=slice(minlev, maxlev + 1),
- y_v=slice(minlat, maxlat), x_r=slice(minlon, maxlon + 1)).values
-
- #
- #
- # Ertel potential vorticity, term 1: (dv/dx - du/dy)/f
- #
- # Compute d(v)/d(xi) at PSI-points.
- #
- dxm1 = 0.25 * (pm[:, :-1, 1:] + pm[:, 1:, 1:] + pm[:, :-1, :-1] + pm[:, 1:, :-1])
- dvdxi = np.diff(v, n=1, axis=2) * dxm1
- #
- # Compute d(u)/d(eta) at PSI-points.
- #
- dym1 = 0.25 * (pn[:, :-1, 1:] + pn[:, 1:, 1:] + pn[:, :-1, :-1] + pn[:, 1:, :-1])
- dudeta = np.diff(u, n=1, axis=1) * dym1
- #
- # Compute Ertel potential vorticity <k hat> at horizontal RHO-points and
- # vertical RHO-points.
- omega = dvdxi - dudeta
- return(np.squeeze(0.25 * (omega[:, :-1, 1:] + omega[:, 1:, 1:] +
- omega[:, :-1, :-1] + omega[:, 1:, :-1]) / f[:, 1:-1, 1:-1]))
-
-###############################################################
-# dtdz term
-
-def get_dtdz(croco, tindex, depth=None, minlev=None, maxlev=None, lonindex=None, latindex=None):
-
- # dtdz from levels 1 to N at a given longitude or latitude
- if depth is None:
- if lonindex is not None:
- dtdz = np.full((maxlev - minlev, croco.wrapper.M), np.nan)
- else:
- dtdz = np.full((maxlev - minlev, croco.wrapper.L), np.nan)
- dtdz[:] = calc_dtdz(croco, tindex, minlev=minlev, maxlev=maxlev,
- lonindex=lonindex, latindex=latindex)
- # dtdz from levels minlev to maxlev
- elif depth <= 0:
- dtdz = np.full((maxlev - minlev, croco.wrapper.M, croco.wrapper.L), np.nan)
- dtdz[:] = calc_dtdz(croco, tindex, minlev=minlev, maxlev=maxlev)
- # dtdz on a level
- elif depth > 0:
- dtdz = np.full((croco.wrapper.M, croco.wrapper.L), np.nan)
- dtdz[:] = calc_dtdz(croco, tindex, minlev=int(depth) - 2, maxlev=int(depth) - 1)
- return dtdz
-
-
-def calc_dtdz(croco, tindex, minlev=None, maxlev=None, lonindex=None, latindex=None):
-
- #
- # 3D variables
- #
- if lonindex is not None:
- ssh = croco.variables['ssh'].isel(t=tindex,
- x_r=slice(lonindex - 1, lonindex + 2)).values
- dz = np.squeeze(croco.wrapper.scoord2dz_r(ssh, alpha=0., beta=0, lonindex=lonindex)
- [minlev:maxlev + 1, :, 1:-1])
- t = croco.variables['temp'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), x_r=lonindex)
- elif latindex is not None:
- ssh = croco.variables['ssh'].isel(t=tindex,
- y_r=slice(latindex - 1, latindex + 2)).values
- dz = np.squeeze(croco.wrapper.scoord2dz_r(ssh, alpha=0., beta=0, latindex=latindex)
- [minlev:maxlev + 1, 1:-1, :])
- t = croco.variables['temp'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), y_r=latindex)
- else:
- ssh = croco.variables['ssh'].isel(t=tindex).values
- dz = croco.wrapper.scoord2dz_r(ssh, alpha=0., beta=0)[minlev:maxlev + 1, :, :]
- t = croco.variables['temp'].isel(t=tindex, z_r=slice(minlev, maxlev + 1))
- dtdz = np.diff(t, axis=0) / (0.5 * (dz[:-1, :] + dz[1:, :]))
- return(dtdz)
-
-
-###############################################################
-# Richardson Number
-
-def get_richardson(croco, tindex, depth=None, minlev=None, maxlev=None,
- lonindex=None, latindex=None):
-
- # mask = croco.wrapper.masks['mask_r']
- # pv = np.full_like(mask,np.nan)
-
- # Ri from level 0 to N at latitude or longitude index
- if depth is None:
- if lonindex is not None:
- var = np.full((maxlev - minlev, croco.wrapper.M), np.nan)
- else:
- var = np.full((maxlev - minlev, croco.wrapper.L), np.nan)
- var[:, 1:-1] = calc_richardson(croco, tindex, minlev=minlev, maxlev=maxlev,
- lonindex=lonindex, latindex=latindex)
- # pv at depth
- elif depth <= 0:
- var = np.full((maxlev - minlev, croco.wrapper.M, croco.wrapper.L), np.nan)
- var[:, 1:-1, 1:-1] = calc_richardson(croco, tindex, minlev=minlev, maxlev=maxlev)
- # pv on a level
- elif depth > 0:
- var = np.full((croco.wrapper.M, croco.wrapper.L), np.nan)
- var[1:-1, 1:-1] = calc_richardson(croco, tindex,
- minlev=int(depth) - 2, maxlev=int(depth) - 1)
- return var
-
-
-def calc_richardson(croco, tindex, minlev=None, maxlev=None, lonindex=None, latindex=None):
- """
- - Ri is given by: N²/((du/dz)² - (dv/dz)²)
- with N = sqrt(-g/rho0 * drho/dz)
-
- - Ri is calculated at RHO-points and w level
-
-
- tindex - The time index at which to calculate the potential vorticity.
- depth - depth
-
- """
-
- # If u or v or rho not in netcdf file, abort
- try:
- croco.variables['rho']
- croco.variables['u']
- croco.variables['v']
- except Exception:
- print("Variable rho, u or v missing in the netcdf file")
- return
-
- # Longitude section
- if lonindex is not None:
- ssh = croco.variables['ssh'].isel(t=tindex,
- x_r=slice(lonindex - 1, lonindex + 2)).values
- z_r = np.squeeze(croco. get_coord("rho", direction='z', timeIndex=tindex)
- [:, :, lonindex])
- z_u = np.squeeze(croco. get_coord("u", direction='z', timeIndex=tindex)
- [:, :, lonindex])
- z_v = np.squeeze(croco. get_coord("v", direction='z', timeIndex=tindex)
- [:, :, lonindex])
- rho = croco.variables['rho'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), x_r=lonindex)
- u = croco.variables['u'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), x_u=lonindex)
- v = croco.variables['v'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), x_r=lonindex)
- drhodz = np.diff(rho, axis=0) / np.diff(z_r, axis=0)
- N2 = (-croco.g / croco.rho0) * (drhodz)
- dudz = np.diff(u, axis=0) / np.diff(z_u, axis=0)
- dvdz = np.diff(v, axis=0) / np.diff(z_v, axis=0)
- Ri = np.squeeze(np.log10(N2[:, 1:-1] / (
- (0.5 * (dudz[:, 1:-1] + dudz[:, 1:-1]))**2 +
- (0.5 * (dvdz[:, :-1] + dvdz[:, 1:]))**2)))
-
- # Latitude section
- elif latindex is not None:
- ssh = croco.variables['ssh'].isel(t=tindex,
- y_r=slice(latindex - 1, latindex + 2)).values
- z_r = np.squeeze(croco. get_coord("rho", direction='z', timeIndex=tindex)
- [:, latindex, :])
- z_u = np.squeeze(croco. get_coord("u", direction='z', timeIndex=tindex)
- [:, latindex, :])
- z_v = np.squeeze(croco. get_coord("v", direction='z', timeIndex=tindex)
- [:, latindex, :])
- rho = croco.variables['rho'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), y_r=latindex)
- u = croco.variables['u'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), y_r=latindex)
- v = croco.variables['v'].isel(t=tindex, z_r=slice(minlev, maxlev + 1), y_v=latindex)
- drhodz = np.diff(rho, axis=0) / np.diff(z_r, axis=0)
- N2 = (-croco.g / croco.rho0) * (drhodz)
- dudz = np.diff(u, axis=0) / np.diff(z_u, axis=0)
- dvdz = np.diff(v, axis=0) / np.diff(z_v, axis=0)
- Ri = np.squeeze(np.log10(N2[:, 1:-1] / (
- (0.5 * (dudz[:, 1:] + dudz[:, :-1]))**2 +
- (0.5 * (dvdz[:, 1:-1] + dvdz[:, 1:-1]))**2)))
-
- # Level or depth section
- else:
- ssh = croco.variables['ssh'].isel(t=tindex).values
- dz = croco.wrapper.scoord2dz_r(ssh, alpha=0., beta=0)[minlev:maxlev + 1, :, :]
- z_r = np.squeeze(croco. get_coord("rho", direction='z', timeIndex=tindex)
- [minlev:maxlev + 1, :, :])
- z_u = np.squeeze(croco. get_coord("u", direction='z', timeIndex=tindex)
- [minlev:maxlev + 1, :, :])
- z_v = np.squeeze(croco. get_coord("v", direction='z', timeIndex=tindex)
- [minlev:maxlev + 1, :, :])
- rho = croco.variables['rho'].isel(t=tindex, z_r=slice(minlev, maxlev + 1))
- u = croco.variables['u'].isel(t=tindex, z_r=slice(minlev, maxlev + 1))
- v = croco.variables['v'].isel(t=tindex, z_r=slice(minlev, maxlev + 1))
- drhodz = np.diff(rho, axis=0) / np.diff(z_r, axis=0)
- N2 = (-croco.g / croco.rho0) * (drhodz)
- dudz = np.diff(u, axis=0) / np.diff(z_u, axis=0)
- dvdz = np.diff(v, axis=0) / np.diff(z_v, axis=0)
- Ri = np.squeeze(np.log10(N2[:, 1:-1, 1:-1] / (
- (0.5 * (dudz[:, 1:-1, 1:] + dudz[:, 1:-1, :-1]))**2 +
- (0.5 * (dvdz[:, :-1, 1:-1] + dvdz[:, 1:, 1:-1]))**2)))
-
- return(Ri)
diff --git a/croco_pyvisu/doc/CONDA.md b/croco_pyvisu/doc/CONDA.md
deleted file mode 100644
index dd74c9ad6cf3155c881e79658f7e0642d0ffb438..0000000000000000000000000000000000000000
--- a/croco_pyvisu/doc/CONDA.md
+++ /dev/null
@@ -1,86 +0,0 @@
-
-# General information about miniconda:
-
-## Overview
-
-Miniconda installers contain the conda package manager and Python.
-Once miniconda is installed, you can use the conda command to install any other packages and create environments.
-
-After downloading `Miniconda3-latest-Linux-x86_64.sh` or `Miniconda3-latest-MacOSX-x86_64.sh` you need to run it with: `sh Miniconda3-latest-MacOSX-x86_64.sh`
-
-Add in your .cshrc
-```
-# Conda environment
-source /pathto/.miniconda/etc/profile.d/conda.csh
-```
-## Main commands:
-What version, update conda
-```
-conda --version
-conda update conda
-```
-Create new environment myenv
-```
-conda create --name myenv python
-```
-Switch to another environment
-```
-conda activate myenv
-```
-To change your path from the current environment back to the root (or source_deactivate in csh)
-```
-conda deactivate
-```
-List all environments
-```
-conda info --envs
-```
-Delete an environment
-```
-conda remove --name myenv --all
-```
-View a list of packages and versions installed in an environmentSearch for a package
-```
-conda list
-```
-Check to see if a package is available for conda to install
-```
-conda search packagename
-```
-Install a new package
-```
-conda install packagename
-```
-Remove conda
-```
-rm -rf /pathto/miniconda3
-```
-where machine is the name of your computer and username is your username.
-
-
-## Install a package from Anaconda.org
-
-For packages that are not available using conda install, we can next look on Anaconda.org. Anaconda.org is a package management service for both public and private package repositories. Anaconda.org is a Continuum Analytics product, just like Anaconda and Miniconda.
-
-In a browser, go to http://anaconda.org. We are looking for a package named “pestc4pyâ€
-There are more than a dozen copies of petsc4py available on Anaconda.org, first select your platform, then you can sort by number of downloads by clicking the “Downloads†heading.
-
-Select the version that has the most downloads by clicking the package name. This brings you to the Anaconda.org detail page that shows the exact command to use to download it:
-
-Check to see that the package downloaded
-```
-conda list
-```
-
-## Install a package with pip
-
-For packages that are not available from conda or Anaconda.org, we can often install the package with pip (short for “pip installs packagesâ€).
-
-## Exporting environment
-
-```
-conda env export > environment.yml on a machine
-conda env create -f environment.yml -n $ENV_NAME on the new machine
-```
-
-
diff --git a/croco_pyvisu/doc/GIT.md b/croco_pyvisu/doc/GIT.md
deleted file mode 100644
index e4652db4f4db91e2e4f0a2ffd5be6d7c77a11c0f..0000000000000000000000000000000000000000
--- a/croco_pyvisu/doc/GIT.md
+++ /dev/null
@@ -1,44 +0,0 @@
-
-Reference:
-
-https://git-scm.com/book/en/v2/Git-Branching-Remote-Branches
-
-Bring data from remote server
-```
-git clone https://apatlpo@bitbucket.org/apatlpo/natl60_dimup.git
-git log --oneline --decorate --graph --all
-```
-
-Create local branch from remote ones
-```
-git checkout -b ap_changes origin/ap_changes
-git checkout -b sf_changes origin/sf_changes
-```
-
-Merge sf_changes into master
-```
-git checkout master
-git merge sf_changes
-git branch -d sf_changes
-```
-
-Now merge ap_changes into master
-```
-git merge ap_changes
-(CONFLICT (content): Merge conflict in overview/plot_snapshot_2d_noproj.py)
-vim overview/plot_snapshot_2d_noproj.py
-git add overview/plot_snapshot_2d_noproj.py
-git commit
-```
-
-Delete ap_changes branch
-```
-git branch -d ap_changes
-```
-
-Checkout a file from another branch
-```
-git checkout mybranch
-git checkout otherbranch -- dev/file.py
-```
-
diff --git a/croco_pyvisu/io_xarray.py b/croco_pyvisu/io_xarray.py
deleted file mode 100644
index c03ed347c790582bd5641bf2922edc5d214d009c..0000000000000000000000000000000000000000
--- a/croco_pyvisu/io_xarray.py
+++ /dev/null
@@ -1,61 +0,0 @@
-import xarray as xr
-
-# Creation of xarray objects
-
-
-def return_xarray_dataset(filename, chunks=None, decode_times=True, **kwargs):
- """Return an xarray dataset corresponding to filename.
- Parameters
- ----------
- filename : str
- path to the netcdf file from which to create a xarray dataset
- chunks : dict-like
- dictionnary of sizes of chunk for creating xarray.Dataset.
- Returns
- -------
- ds : xarray.Dataset
- """
- return xr.open_dataset(filename, chunks=chunks, **kwargs)
-
-
-def return_xarray_mfdataset(filename, chunks=None, **kwargs):
- """Return an xarray dataset corresponding to filename which may include
- wildcards (e.g. file_*.nc).
- Parameters
- ----------
- filename : str
- path to a netcdf file or several netcdf files from which to create a
- xarray dataset
- chunks : dict-like
- dictionnary of sizes of chunk for creating xarray.Dataset.
- Returns
- ------
- ds : xarray.Dataset
- """
- return xr.open_mfdataset(filename, chunks=chunks, **kwargs)
-
-
-def return_xarray_dataarray(ds, varname, chunks=None, **extra_kwargs):
- """Return a xarray dataarray corresponding to varname in filename.
- Parameters
- ----------
- filename : str
- path to the netcdf file from which to create a xarray.DataArray
- varname : str
- name of the variable from which to create a xarray.DataArray
- chunks : dict-like
- dictionnary of sizes of chunk for creating a xarray.DataArray.
- **extra_kwargs
- not used
- Returns
- -------
- da : xarray.DataArray
- """
- # ds = return_xarray_dataset(filename,chunks=chunks)
- try:
- dataarray = ds[varname]
- except Exception:
- dataarray = ds.attrs[varname]
- for kwargs in extra_kwargs:
- dataarray.attrs[kwargs] = extra_kwargs[kwargs]
- return dataarray
diff --git a/croco_pyvisu/map_64_wc.mat b/croco_pyvisu/map_64_wc.mat
deleted file mode 100644
index c09dea491785ed60d9e65a8beeb8b89609d0d6c7..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/map_64_wc.mat and /dev/null differ
diff --git a/croco_pyvisu/moviez.mp4 b/croco_pyvisu/moviez.mp4
deleted file mode 100644
index f6f7b1e99318f5e0fdcfabad2411061bce4ca77d..0000000000000000000000000000000000000000
Binary files a/croco_pyvisu/moviez.mp4 and /dev/null differ
diff --git a/croco_pyvisu/myplot.py b/croco_pyvisu/myplot.py
deleted file mode 100644
index 5cfbf62d055bf90bf153ab0638404a62f3c03ad9..0000000000000000000000000000000000000000
--- a/croco_pyvisu/myplot.py
+++ /dev/null
@@ -1,183 +0,0 @@
-# -*- coding: UTF-8 -*-
-#
-# generated by wxGlade 0.8.0b3 on Tue Jan 30 13:49:27 2018
-#
-
-import os
-import numpy as np
-import numpy.ma as ma
-import scipy.io
-from matplotlib import colors
-
-# -------------------------------------------------------------------------
-def plotCurv(frame,
- x=None, y=None,
- xlabel=None, ylabel=None,
- legend=None, title=None,
- xlim=None, ylim=None,
- xlog=False, ylog=False):
-
- # and the axes for the figure
-
- fig = frame.figure
- fig.clf()
- # axes = fig.add_axes([0.07,0.05,0.98,0.90])
- axes = fig.add_axes([0.08, 0.1, 0.85, 0.85])
-
- xm = ma.masked_invalid(x)
- ym = ma.masked_invalid(y)
-
- # axes = self.axes
- if xlim:
- axes.set_xlim((xlim[0], xlim[1]))
- if ylim:
- axes.set_ylim((ylim[0], ylim[1]))
-
- if y is None:
- if legend is None:
- axes.plot(xm, linewidth=2.0)
- else:
- axes.plot(xm, label=legend, linewidth=2.0)
- elif y.ndim == 1:
- if legend is None:
- axes.plot(xm, ym, linewidth=2.0)
- else:
- axes.plot(xm, ym, label=legend, linewidth=2.0)
- else:
- NbCurv = ym.shape[1]
- for i in range(0, NbCurv):
- if legend is None:
- axes.plot(xm, ym[:, i], linewidth=2.0)
- else:
- axes.plot(xm, ym[:, i], label=legend[i], linewidth=2.0)
-
- axes.figure.set_facecolor('white')
- axes.grid('on')
- axes.legend()
- if xlabel is not None:
- axes.set_xlabel(xlabel)
- if ylabel is not None:
- axes.set_ylabel(ylabel)
- if xlog:
- axes.set_xscale('log')
- if ylog:
- axes.set_yscale('log')
- if title is not None:
- axes.set_title(title)
-
-
-# -------------------------------------------------------------------------
-def mypcolor(frame, x, y, z,
- x2=None, xlabel2=None,
- xlim=None, ylim=None,
- clim=None, cformat=None,
- norm=None,
- xlabel=None, ylabel=None, title=None,
- cmap=None, xlog=False, ylog=False,
- z1=None, z2=None,
- topo=None, nbtopo=None,
- winsize=None, dpi=80):
-
- zm = ma.masked_invalid(z)
- # # plt.rc('text', usetex=True)
-
- # # default size if 8 x 6 inch, 80 DPI (640x480 pixels)
- # if winsize is None:
- # winsize=[8., 6.]
- # fig.set_size_inches( (winsize[0], winsize[1]) )
- fig = frame.figure
- ax = fig.add_axes([0.15, 0.1, 0.85, 0.85])
- ax.callbacks.connect("xlim_changed", frame.notify)
- ax.callbacks.connect("ylim_changed", frame.notify)
-
- if xlim is None:
- ax.set_xlim((np.min(x), np.max(x)))
- else:
- ax.set_xlim((xlim[0], xlim[1]))
- if ylim is None:
- ax.set_ylim((np.min(y), np.max(y)))
- else:
- ax.set_ylim((ylim[0], ylim[1]))
- if xlabel is not None:
- ax.set_xlabel(xlabel)
- if ylabel is not None:
- ax.set_ylabel(ylabel)
- if title is not None:
- ax.set_title(title)
-
- if cmap is None:
- cmap = DefCmap()
-
- if clim is not None:
- mesh = ax.pcolormesh(x, y, zm, cmap=cmap, norm=norm, vmin=clim[0], vmax=clim[1])
- else:
- mesh = ax.pcolormesh(x, y, zm, cmap=cmap, norm=norm)
-
- if z1 is not None:
- # level1 = (z1.min() + z1.max())*0.8
- level1 = (z1.min() + 0) * 0.8
- cp1 = ax.contour(x, y, z1, [level1], colors='b', linewidths=2)
- if z2 is not None:
- # level2 = (z2.min() + z2.max())*0.8
- level2 = (z2.min() + 0) * 0.8
- cp2 = ax.contour(x, y, z2, [level2], colors='r', linewidths=2)
- if topo is not None:
- # Show isocontour of the topography
- cp3 = ax.contour(x, y, topo, nbtopo, colors='grey', linewidths=0.5)
- # Show labels
- # ax.clabel(cp3)
-
- # Add colorbar
- if cformat == 'sci':
- # make sure to specify tick locations to match desired ticklabels
- cb = fig.colorbar(mesh, ax=ax, format='%.0e', ticks=[clim[0], clim[0] / 10,
- clim[0] / 100, 0, clim[1] / 100, clim[1] / 10, clim[1]])
- # plt.colorbar(mesh, ax=ax, format='%.0e')
- else:
- cb = fig.colorbar(mesh, ax=ax)
-
- if xlog:
- ax.set_xscale('log')
- if ylog:
- ax.set_yscale('log')
-
- if x2 is not None:
- ax2 = ax.twiny()
- mn, mx = ax.get_xlim()
- ax2.set_xlim(2 * np.pi / mn * 1e-3, 2 * np.pi / mx * 1e-3)
- # ax2.set_xlim(2*np.pi/mx, 2*np.pi/mn)
- if xlabel2 is not None:
- ax2.set_xlabel(xlabel2)
- if xlabel2 is not None and xlog:
- ax2.set_xscale('log')
-
- # font = {'family' : 'normal',
- # 'weight' : 'bold',
- # 'size' : 18}
- # plt.rc('font', **font)
-
-
-def DefCmap():
-
- # get path of launch script croco_gui.py
- script_path = os.path.dirname(os.path.realpath(__file__))
- matfile = scipy.io.loadmat(script_path + '/map_64_wc.mat')
- return array2cmap(np.array(matfile['cm']))
-
-
-def array2cmap(X):
- N = X.shape[0]
-
- r = np.linspace(0., 1., N + 1)
- r = np.sort(np.concatenate((r, r)))[1:-1]
-
- rd = np.concatenate([[X[i, 0], X[i, 0]] for i in range(N)])
- gr = np.concatenate([[X[i, 1], X[i, 1]] for i in range(N)])
- bl = np.concatenate([[X[i, 2], X[i, 2]] for i in range(N)])
-
- rd = tuple([(r[i], rd[i], rd[i]) for i in range(2 * N)])
- gr = tuple([(r[i], gr[i], gr[i]) for i in range(2 * N)])
- bl = tuple([(r[i], bl[i], bl[i]) for i in range(2 * N)])
-
- cdict = {'red': rd, 'green': gr, 'blue': bl}
- return colors.LinearSegmentedColormap('my_colormap', cdict, N)
diff --git a/croco_pyvisu/observer.py b/croco_pyvisu/observer.py
deleted file mode 100644
index 63859fb8f7f38302f4831ae2856274694b8169b3..0000000000000000000000000000000000000000
--- a/croco_pyvisu/observer.py
+++ /dev/null
@@ -1,19 +0,0 @@
-class Subscriber:
- def __init__(self, who):
- self.who = who
- def update(self, level, longitude, latitude):
- self.who.update(level, longitude, latitude)
-
-
-class Publisher:
- def __init__(self):
- self.subscribers = dict()
- def register(self, who, callback=None):
- if callback == None:
- callback = getattr(who, 'update')
- self.subscribers[who] = callback
- def unregister(self, who):
- del self.subscribers[who]
- def dispatch(self, level, longitude, latitude):
- for subscriber, callback in self.subscribers.items():
- callback(level, longitude, latitude)
diff --git a/crocotools_param.m b/crocotools_param.m
index 3cd89505822980b050118dcedf15b45c769dea2c..a3538d7ae055db755bcde8c6918ff5fc644d4624 100644
--- a/crocotools_param.m
+++ b/crocotools_param.m
@@ -5,7 +5,7 @@
%
% This file is used by make_grid.m, make_forcing.m,
% make_clim.m, make_biol.m, make_bry.m, make_tides.m,
-% make_NCEP.m, make_OGCM.m, make_...
+% make_NCEP.m, make_OGCM_*.m, make_...
%
% Further Information:
% http://www.croco-ocean.org
@@ -92,7 +92,7 @@ hmax_coast = 500;
% Maximum depth [m] (cut the topography to prevent
% extrapolations below WOA data)
%
-hmax = 5000;
+hmax = 6000;
%
% Slope parameter (r=grad(h)/h) maximum value for topography smoothing
%
@@ -150,7 +150,7 @@ CROCO_files_dir=[RUN_dir,'CROCO_FILES/'];
%
% Global data directory (etopo, coads, datasets download from ftp, etc..)
%
-DATADIR='../../croco_tools/';
+DATADIR='../../croco_tools/';
%
% Forcing data directory (ncep, quikscat, datasets download with opendap, etc..)
%
@@ -221,7 +221,7 @@ pathfinder_sst_name=[DATADIR,...
%
% 4 - Open boundaries and initial conditions parameters
% used by make_clim.m, make_biol.m, make_bry.m
-% make_OGCM.m and make_OGCM_frcst.m
+% make_OGCM_*.m and make_OGCM_frcst.m
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
@@ -235,7 +235,7 @@ zref = -1000;
%
% initial/boundary data options (1 = process)
% (used in make_clim, make_biol, make_bry,
-% make_OGCM.m and make_OGCM_frcst.m)
+% make_OGCM_*.m and make_OGCM_*frcst.m)
%
makeini = 1; % initial data
makeclim = 1; % climatological data (for boundaries and nudging layers)
@@ -322,7 +322,7 @@ Z0 = 1; % Mean depth of tide gauge
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 6 - Reference date and simulation times
-% (used for make_tides, make_CFSR (or make_NCEP), make_OGCM)
+% (used for make_tides, make_CFSR (or make_NCEP), make_OGCM_*)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
@@ -345,7 +345,7 @@ Mth_format = '%02d'; % Number of digit for month on input files
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% 7 - Parameters for Interannual forcing (SODA, ECCO, CFSR, NCEP, ...)
+% 7 - Parameters for Interannual forcing (SODA, mercator, CFSR, ERA5 ...)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
@@ -353,7 +353,7 @@ Download_data = 1; % Get data from OPENDAP sites
level = 0; % AGRIF level; 0 = parent grid
%
NCEP_version = 3; % NCEP version:
- % [ CFSR up-to-date product are recommandated ]
+ % [ CFSR up-to-date product are recommended ]
% 1: NCEP/NCAR Reanalysis, 1/1/1948 - present
% 2: NCEP-DOE Reanalysis, 1/1/1979 - present
% 3: CFSR (Climate Forecast System Reanalysis),
@@ -401,9 +401,9 @@ QSCAT_clim_file = [DATADIR,'QuikSCAT_clim/',... % QSCAT climatolog
%
Reformat_ECMWF = 1;
ECMWF_dir = [FORC_DATA_DIR,'ECMWF_',CROCO_config,'/']; % ERA-I data dir. [croco format]
-My_ECMWF_dir = [FORC_DATA_DIR,'ERAI/']; % ERA-I native data downloaded
- % with python script
-itolap_ecmwf = 3; % 3 records for daily ECMWF
+My_ECMWF_dir = [FORC_DATA_DIR,'ERAI/']; % ERA-I native data downloaded
+ % with python script
+itolap_ecmwf = 3; % 3 records for daily ECMWF
%
%--------------------------------------------------
% Options for make_ERA5
@@ -417,10 +417,10 @@ itolap_era5 = 2; % 2 records = 2 h
%
%
%--------------------------------------------
-% Options for make_OGCM or make_OGCM_mercator
+% Options for make_OGCM_SODA or make_OGCM_mercator
%--------------------------------------------
%
-OGCM = 'SODA'; % Select OGCM: SODA, ECCO, mercator
+OGCM = 'SODA'; % Select OGCM: SODA or mercator
%
OGCM_dir = [FORC_DATA_DIR,OGCM,'_',CROCO_config,'/']; % OGCM data dir. [croco format]
%
@@ -429,21 +429,52 @@ clm_prefix = [CROCO_files_dir,'croco_clm_',OGCM,'_']; % generic climatology
ini_prefix = [CROCO_files_dir,'croco_ini_',OGCM,'_']; % generic initial file name
OGCM_prefix = [OGCM,'_']; % generic OGCM file name
+
+mercator_type=1; % 1 --> 1/12 deg Mercator global reanalysis
+ % 2 --> 1/12 deg Mercator global analysis
+ % 3 --> 1/12 deg Mercator global forecast (See Section 8.)
+ % 4 --> 1/24 deg Mercator Mediterranean analysis/forecast (See Section 8.)
+ % 5 --> the same than 4 but with detiding postprocessing on current and ssh
+
+% =============
+% To download CMEMS data: set login/password (http://marine.copernicus.eu)
+% and path to copernicusmarine executable
+% see Oforc_OGCM/Copernicus_Marine_Toolbox_installation.md
+%
+% Various sets of data are proposed in the Copernicus web site
+%
if strcmp(OGCM,'mercator')
+ %
+ pathCMC='/path/to/home/copernicusmarine'; % copernicusmarine client
+ %
+ user = 'XXXX';
+ password = 'XXXX';
+ %
+ if mercator_type==1
% ========================
- % For GLORYS 12 reanalysis extraction + download using python motuclient
+ % For GLORYS 12 reanalysis extraction
% ========================
- raw_mercator_name = 'mercator';
- kdata='MONTHLY' ; % or DAILY
- motu_url_reana='http://my.cmems-du.eu/motu-web/Motu';
- service_id_reana='GLOBAL_MULTIYEAR_PHY_001_030-TDS';
+ kdata='MONTHLY' ; % DAILY or MONTHLY
if strcmp(kdata,'DAILY')
- product_id_reana='cmems_mod_glo_phy_my_0.083_P1D-m';
+ product_id='cmems_mod_glo_phy_my_0.083_P1D-m';
elseif strcmp(kdata,'MONTHLY')
- product_id_reana='cmems_mod_glo_phy_my_0.083_P1M-m'
+ product_id='cmems_mod_glo_phy_my_0.083_P1M-m';
else
- disp('Please specify what reanalysis frequency you want (DAILY or MONTHLY)')
+ disp('Please specify what kind of data you want (DAILY or MONTHLY)')
end
+ %
+ elseif mercator_type==2
+ % ========================
+ % 2 -> For analysis PSY4
+ % ========================
+ product_id={'cmems_mod_glo_phy_anfc_0.083deg_P1D-m' ...
+ 'cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m', ...
+ 'cmems_mod_glo_phy-thetao_anfc_0.083deg_P1D-m', ...
+ 'cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m'};
+ %
+ else
+ end
+%
end
%
% Number of OGCM bottom levels to remove
@@ -451,14 +482,14 @@ end
%
rmdepth = 2;
%
-% Overlap parameters : nb of records around each monthly sequence
+% Overlap parameters : nb of records around each sequence
%
itolap_a = 1; % before
itolap_p = 1; % after
- %
-%--------------------------
-% Options for make_bry_WKB
-%--------------------------
+%
+%----------------------------------------------------
+% Options for make_bry_WKB_ECMWF or make_bry_WKB_ERA5
+%----------------------------------------------------
%
wkb_prefix=[CROCO_files_dir,'croco_wkb'];
wkb_obc= [1 1 1 1];
@@ -468,25 +499,21 @@ wkb_obc= [1 1 1 1];
% 8 - Parameters for the forecast system
%
% --> select OGCM name above (mercator ...)
+% --> select Aforc name (GFS)
% --> don't forget to define in cppdefs.h:
-% - ROBUST_DIAG
-% - CLIMATOLOGY
-% - BULK_FLUX
-% - TIDES if you choose so, but without TIDERAMP
+% - ROBUST_DIAG
+% - CLIMATOLOGY
+% - BULK_FLUX
+% - TIDES if you choose so, but without TIDERAMP
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
FRCST_dir = [FORC_DATA_DIR,'Forecast/']; % path to local OGCM data directory
%
-% Number of hindcast/forecast days
+% Number of hindcast / forecast days
%
-if strcmp(OGCM,'ECCO')
- hdays=1;
- fdays=6;
-elseif strcmp(OGCM,'mercator')
- hdays=1;
- fdays=3;
-end
+hdays=1;
+fdays=3;
%
% Local time= UTC + timezone
%
@@ -496,36 +523,38 @@ timezone = +2;
%
add_tides_fcst = 1; % 1: add tides
%
-% MERCATOR case:
+% MERCATOR cases (See Section 7):
% =============
-% To download CMEMS data: set login/password (http://marine.copernicus.eu)
-% and path to croco's motuclient python package;
-% or set pathMotu='' (empty) to use your own motuclient
-%
-% Various sets of data are proposed in the Copernicus web site
%
if strcmp(OGCM,'mercator')
- user = 'XXX';
- password = 'XXX';
-
- pathMotu =[CROCOTOOLS_dir,'Forecast_tools/'];
-
- mercator_type=1; % 1 --> 1/12 deg Mercator forecast
- % 2 --> high-resolution regional grids
- if mercator_type==1
- motu_url_fcst='http://nrt.cmems-du.eu/motu-web/Motu';
- service_id_fcst='GLOBAL_ANALYSISFORECAST_PHY_001_024-TDS';
- product_id_fcst={'cmems_mod_glo_phy_anfc_0.083deg_P1D-m', ...
- 'cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m', ...
- 'cmems_mod_glo_phy-thetao_anfc_0.083deg_P1D-m', ...
- 'cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m'};
- elseif mercator_type==2
- motu_url_fcst='http://nrt.cmems-du.eu/motu-web/Motu';
- service_id_fcst='MEDSEA_ANALYSISFORECAST_PHY_006_013-TDS';
- product_id_fcst={'cmems_mod_med_phy-ssh_anfc_4.2km_P1D-m', ...
- 'cmems_mod_med_phy-cur_anfc_4.2km_P1D-m', ...
- 'cmems_mod_med_phy-tem_anfc_4.2km_P1D-m', ...
- 'cmems_mod_med_phy-sal_anfc_4.2km_P1D-m'};
+ if mercator_type==3
+ % ========================
+ % 3 -> For Global Forecast PSY4
+ % ========================
+ product_id={'cmems_mod_glo_phy_anfc_0.083deg_P1D-m' ...
+ 'cmems_mod_glo_phy-cur_anfc_0.083deg_P1D-m', ...
+ 'cmems_mod_glo_phy-thetao_anfc_0.083deg_P1D-m', ...
+ 'cmems_mod_glo_phy-so_anfc_0.083deg_P1D-m'};
+ %
+ elseif mercator_type==4
+ % ========================
+ % 4 -> For Mediterannean Forecast PSY4 4.2km
+ % ========================
+ product_id={'cmems_mod_med_phy-ssh_anfc_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-cur_anfc_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-tem_anfc_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-sal_anfc_4.2km_P1D-m'};
+ %
+ elseif mercator_type==5
+ % ========================
+ % 5 -> For Mediterannean Forecast PSY4 4.2km (ssh detided)
+ % ========================
+ product_id={'cmems_mod_med_phy-ssh_anfc_detided_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-cur_anfc_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-tem_anfc_4.2km_P1D-m', ...
+ 'cmems_mod_med_phy-sal_anfc_4.2km_P1D-m'};
+ %
+ else
end
end
%
diff --git a/start.m b/start.m
index cb94c5cbe0cee11b5a7a8c4e30f5537ce9314a96..525096190278e93fb908f3a95ef5a0ed6eb57e0a 100644
--- a/start.m
+++ b/start.m
@@ -41,6 +41,7 @@ myutilpath=[tools_path,'UTILITIES/'];
addpath([myutilpath,'m_map1.4h'])
addpath([myutilpath,'air_sea'])
addpath([myutilpath,'mask'])
+addpath([myutilpath,'export_fig'])
%
% CROCOTOOLS directories
%