Merge branch 'somisana_py'

cli.py

@@ -10,18 +10,16 @@
 import argparse
 import sys, os
 from datetime import datetime, timedelta
-<<<<<<< Updated upstream
-from crocotools_py.preprocess import make_tides,reformat_gfs_atm,reformat_saws_atm,make_ini_fcst,make_bry_fcst
-=======
 import calendar
 from crocotools_py.preprocess import make_tides,reformat_gfs_atm,reformat_saws_atm,make_ini,make_bry
->>>>>>> Stashed changes
 from crocotools_py.postprocess import get_ts_multivar
 from crocotools_py.plotting import plot as crocplot
 from crocotools_py.regridding import regrid_tier1, regrid_tier2, regrid_tier3 
 from download.cmems import download_glorys, download_mercator
 from download.gfs import download_gfs_atm
 from download.hycom import download_hycom
+from crocotools_py.regridding_cfc import regrid1_cf_compliant,regrid2_cf_compliant,regrid3_cf_compliant
+
 # functions to help parsing string input to object types needed by python functions
 def parse_datetime(value):
     try:
@@ -38,7 +36,7 @@ def parse_int(value):
         raise argparse.ArgumentTypeError(f"Invalid integer value: {value}")
 
 def parse_list(value):
-    return [x.strip() for x in value.split(',')]
+    return [float(x) for x in value.split(',')]
 
 def parse_bool(s: str) -> bool:
     try:
@@ -251,8 +249,8 @@ def regrid_tier1_handler(args):
             help='tier 2 regridding of a CROCO output: takes the output of regrid-tier1 as input and regrids the sigma levels to constant z levels, including the surface and bottom layers -> output variables are the same as tier 1, only depths is now a dimension with the user specified values')
     parser_regrid_tier2.add_argument('--fname', required=True, type=str, help='input regridded tier1 filename')
     parser_regrid_tier2.add_argument('--fname_out', required=True, help='tier 2 output filename')
-    parser_regrid_tier2.add_argument('--depths', type=parse_list,
-                         default=[0,-5,-10,-20,-50,-100,-200,-500,-1000,-99999],
+    parser_regrid_tier2.add_argument('--depths', type=int, nargs='+',
+                         default=[0,-5,-10,-20,-50,-100,-200,-500,-1000,-99999], # Doesn't work if you do not include zero. See how it is done in regriddding for the CF-complient. 
                          help='list of depths to extract (in metres, negative down). A value of 0 denotes the surface and a value of -99999 denotes the bottom layer)')
     def regrid_tier2_handler(args):
         regrid_tier2(args.fname, args.fname_out, depths = args.depths)
@@ -285,7 +283,7 @@ def regrid_tier3_handler(args):
     parser_get_ts_multivar.add_argument('--vars', type=parse_list, 
                         default=['temp', 'salt'],
                         help='optional list of CROCO variable names')
-    parser_get_ts_multivar.add_argument('--depths', type=parse_list, 
+    parser_get_ts_multivar.add_argument('--depths', type=int, nargs='+',  
                         default=[0,-5,-10,-20,-50,-100,-200,-500,-1000,-99999],
                         help='Depths for time-series extraction (see get_ts_multivar() for description of input)')
     parser_get_ts_multivar.add_argument('--fname_out', required=True, help='output filename')
@@ -307,7 +305,7 @@ def get_ts_multivar_handler(args):
     parser_make_tides_fcst.add_argument('--output_dir', required=True, type=str,
             help='Path to where the forcing file will be saved. This directory also needs a crocotools_param.py file')
     parser_make_tides_fcst.add_argument('--run_date', required=True, type=parse_datetime, 
-            help='datetime of operational workflow initialisation in format i.e. "YYYY-MM-DD HH:MM:SS"')
+            help='operational workflow initialisation time in format "YYYY-MM-DD HH:MM:SS"')
     parser_make_tides_fcst.add_argument('--hdays', required=True, type=int,
             help='Number of days before run_date, corresponding to the run start time')
     parser_make_tides_fcst.add_argument('--Yorig', required=True, type=int,
@@ -360,23 +358,30 @@ def make_tides_inter_handler(args):
 
     parser_make_tides_inter.set_defaults(func=make_tides_inter_handler)
 
-
     # ----------------
     # make_ini_fcst
     # ----------------
     parser_make_ini_fcst = subparsers.add_parser('make_ini_fcst',
-            help='Make ocean initial conditions for the CROCO operational model.')
             help='Make initial condition file from OGCM data as part of the CROCO operational workflow.')
     parser_make_ini_fcst.add_argument('--input_file', required=True, type=str, 
-            help='Path and filename of input file i.e. "path/to/file/direcory/and/filename.nc"')
+            help='Path and filename of the OGCM input file i.e. "path/to/file/direcory/and/filename.nc"')
     parser_make_ini_fcst.add_argument('--output_dir', required=True, type=str,
-            help='Directory of where the boundary file will be saved i.e. "path/to/save/directory/"')
+            help='Path to where the ini file will be saved. This directory also needs a crocotools_param.py file')
     parser_make_ini_fcst.add_argument('--run_date', required=True, type=parse_datetime, 
-            help='Reference date in datetime format i.e. "YYYY-MM-DD HH:MM:SS"')
+            help='operational workflow initialisation time in format "YYYY-MM-DD HH:MM:SS"')
     parser_make_ini_fcst.add_argument('--hdays', required=True, type=int,
-            help='Number of days to develop the boundary file hindcast')
+            help='Number of days before run_date to initialise model')
+    parser_make_ini_fcst.add_argument('--Yorig', required=True, type=int,
+            help='the Yorig value used in setting up the CROCO model')
     def make_ini_fcst_handler(args):
-        make_ini_fcst(args.input_file,args.output_dir,args.run_date,args.hdays)
+        sys.path.append(args.output_dir)
+        import crocotools_param as params
+
+        fname_out = params.ini_prefix + args.run_date.strftime('_%Y%m%d_%H.nc')
+        ini_date = args.run_date - timedelta(days=args.hdays)
+
+        make_ini(args.input_file,args.output_dir,ini_date,args.Yorig,fname_out)
+
     parser_make_ini_fcst.set_defaults(func=make_ini_fcst_handler)
 
     # ----------------
@@ -409,18 +414,34 @@ def make_ini_inter_handler(args):
     # make_bry_fcst
     # ----------------
     parser_make_bry_fcst = subparsers.add_parser('make_bry_fcst',
-            help='Make ocean boundary conditions for the CROCO operational model.')
+            help='Make ocean boundary conditions as part of the CROCO operational workflow.')
     parser_make_bry_fcst.add_argument('--input_file', required=True, type=str, 
             help='Path and filename of input file i.e. "path/to/file/direcory/and/filename.nc"')
-            help='Path and filename of input OGCM file i.e. "path/to/file/direcory/and/filename.nc"')
     parser_make_bry_fcst.add_argument('--output_dir', required=True, type=str,
-            help='Directory of where the boundary file will be saved i.e. "path/to/save/directory/"')
+            help='Path to where the bry file will be saved. This directory also needs a crocotools_param.py file')
     parser_make_bry_fcst.add_argument('--run_date', required=True, type=parse_datetime, 
-            help='Reference date in datetime format i.e. "YYYY-MM-DD HH:MM:SS"')
+            help='Operational workflow initialisation time in format "YYYY-MM-DD HH:MM:SS"')
     parser_make_bry_fcst.add_argument('--hdays', required=True, type=int,
-            help='Number of days to develop the boundary file hindcast')
+            help='Number of hindcast days to add to the boundary file')
+    parser_make_bry_fcst.add_argument('--fdays', required=True, type=int,
+            help='Number of forecast days to add to the boundary file')
+    parser_make_bry_fcst.add_argument('--Yorig', required=True, type=int,
+                        help='the Yorig value used in setting up the CROCO model')
     def make_bry_fcst_handler(args):
-        make_bry_fcst(args.input_file,args.output_dir,args.run_date,args.hdays)
+        sys.path.append(args.output_dir)
+        import crocotools_param as params
+
+        # create a 2 day buffer around the time span of the CROCO simulation
+        # (2 days is just to be safe - the nearest available times to ini_date and end_date are used in make_bry())
+        hdays = args.hdays + 2
+        fdays = args.fdays + 2
+
+        fname_out = params.bry_prefix + args.run_date.strftime('_%Y%m%d_%H.nc')
+        ini_date = args.run_date - timedelta(days=hdays)
+        end_date = args.run_date + timedelta(days=fdays)
+
+        make_bry(args.input_file,args.output_dir,ini_date,end_date,args.Yorig,fname_out)
+
     parser_make_bry_fcst.set_defaults(func=make_bry_fcst_handler)
 
     # ----------------
@@ -437,7 +458,7 @@ def make_bry_fcst_handler(args):
     parser_make_bry_inter.add_argument('--month_end', required=True, type=str,
             help='last month in the interannual run in format "YYYY-MM"')
     parser_make_bry_inter.add_argument('--Yorig', required=True, type=int,
-                        help='the Yorig value used in setting up the CROCO model')
+            help='the Yorig value used in setting up the CROCO model')
     def make_bry_inter_handler(args):
 
         sys.path.append(args.output_dir)
@@ -461,7 +482,7 @@ def make_bry_inter_handler(args):
             # (to do this I think we'd need to create the input_file list with file names which do exist,
             # and then we'd need a check inside make_bry() where we check that ini_date and end_date are 
             # covered by the OGCM files, and if not we'd pad with the nearest available values)
-            # But I'm in a hurry so for now we'll just make sure that these files exist
+            # But I'm in a hurry so for now we'll just make sure that these files do exist
             if not os.path.exists(fname_month_prev):
                 raise ValueError("Processing of "+month_now.strftime('%Y-%m')+" requires "+fname_month_prev)
             if not os.path.exists(fname_month_now):
@@ -534,6 +555,8 @@ def regrid3_cfc_handler(args):
         regrid3_cf_compliant(args.fname, args.info_dir, args.spacing, args.out_dir)
     parser_regrid3_cfc.set_defaults(func=regrid3_cfc_handler)
 
+
+
     args = parser.parse_args()
     if hasattr(args, 'func'):
         args.func(args)
@@ -542,4 +565,3 @@ def regrid3_cfc_handler(args):
 
 if __name__ == "__main__":
     main()
-

configs/sa_west_02/croco_v1.3.1/MERCATOR/crocotools_param.py

@@ -1,8 +1,6 @@
-# params required by make_ini() and make_bry()
-
-# Dates
-# starting date
-Yorig, Morig, Dorig = '2000','01','01' # Month and days need to be 2-digits format
+'''
+params required by make_ini() and make_bry()
+'''
 
 # Input data information and formating
 inputdata = 'mercator' # Input data dictionnary as defined in the Readers/ibc_reader.py
@@ -16,15 +14,16 @@
 # tracers
 tracers = ['temp','salt']
 
-# CROCO grid information
-croco_dir = '/home/rautenbach/SOMISANA/croco/somisana-croco/configs/sa_west_02/croco_v1.3.1/GRID/'
-croco_grd = croco_dir+'croco_grd.nc'
+# relative path to the CROCO grid
+croco_grd = '../GRID/croco_grd.nc'
 sigma_params = dict(theta_s=5, theta_b=7, N=30, hc=200) # Vertical streching, sig_surf/sig_bot/ nb level/critical depth
 
-# Ini file information
-ini_filename = 'croco_ini.nc'
+# Ini filename prefix
+ini_prefix = 'croco_ini_MERCATOR'
 
-# Bry file informations
-bry_filename = 'croco_bry.nc' # output will be put in croco_dir by default
+# Bry filename prefinformations
+bry_prefix = 'croco_bry_MERCATOR' 
 obc_dict = dict(south=1, west=1, east=0, north=1) # open boundaries (1=open , [S W E N])
 cycle_bry=0
+
+

configs/sa_west_02/croco_v1.3.1/croco_cf_compliance.py

@@ -0,0 +1,29 @@
+title = "sa_southeast"
+institution = "South African Observation Network (SAEON)"
+source = "Ocean Simulation"
+references = "DOI: ###"
+comment = ""
+conventions = "NetCDF"
+summary = """This realistic ocean simulation was run using the Coastal and Regional Ocean COmmunity model (CROCO). The variables of the CROCO model are originally aranged on a Arakawa C-grid. Here the variables have been interpolated onto the rho point of the grid cell (center of the grid cell), to ensure that all the variables have the same shape. It has 30 terrain-following vertical levels and encompasses the entire Algoa Bay, from 24.82° to 27.77° E and -34.85° to -33.07° S. The variable grid resolution (0.35 – 4 km) is due to the curvilinear grid setup. At the coast, the resolution is greatest which decreases offshore. Monthly outputs of GLORYS ocean reanalysis is used to force the boundaries (grid resolution of ~9 km). The surface forcing for this model is provided by a bulk formulation using WASA3 atmospheric reanalysis (grid resolution of ~3 km). The model output are saved as daily averages. Model output includes: averaged free-surface (zeta), averaged vertically integrated u-momentum component (ubar), averaged vertically integrated v-momentum component (vbar), averaged u-momentum component (u), averaged v-momentum component (v),averaged potential temperature (temp), averaged salinity (salt), averaged vertical momentum component (w)."""    
+# add link to github repo -  https://github.com/SAEON/somisana-croco/tree/main/configs/sa_southeast_01/croco_v1.3.1 & explain the compile options, inputs, 
+keywords = "Algoa Bay, Ocean Model, CROCO, Ocean Currents"
+license = "Open source"
+license_url = "https://creativecommons.org/licenses/by-sa/4.0/legalcode"
+date_created = ""
+creator_name = "Giles Fearon"
+creator_email = "[email protected]"
+project = "Sustainable Ocean Modelling Initiative: a South african approach (SOMISANA)"
+publisher_name = "South African Observation Network (SAEON)"
+publisher_email = "[email protected]"
+geospatial_lat_units = "degrees North"
+geospatial_lon_units = "degrees East"
+geospatial_vertical_min = "5"
+geospatial_vertical_max = "2171.9214"
+geospatial_vertical_units = "m"
+geospatial_vertical_positive = "down"
+time_coverage_start = "2009-01-01T00:00:00Z"
+time_coverage_end = "2019-12-31T00:00:00Z"
+date_modified = ""
+date_metadata_modified = ""  
+instrument = "Coastal and Regional Ocean Community (CROCO) modelling system"
+lineage = "Ocean simulation"