hgodas_insitu2ioda.py

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#!/usr/bin/env python3
 
#
# (C) Copyright 2019 UCAR
#
# This software is licensed under the terms of the Apache Licence Version 2.0
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
#
 
from __future__ import print_function
import sys
import argparse
import netCDF4 as nc
from datetime import datetime, timedelta
from pathlib import Path
 
IODA_CONV_PATH = Path(__file__).parent/"@SCRIPT_LIB_PATH@"
if not IODA_CONV_PATH.is_dir():
    IODA_CONV_PATH = Path(__file__).parent/'..'/'lib-python'
sys.path.append(str(IODA_CONV_PATH.resolve()))
 
import ioda_conv_ncio as iconv
from orddicts import DefaultOrderedDict
 
 
vName = {
    2210: "sea_water_temperature",
    2220: "sea_water_salinity",
}
 
locationKeyList = [
    ("latitude", "float"),
    ("longitude", "float"),
    ("depth", "float"),
    ("datetime", "string")
]
 
AttrData = {
    'odb_version': 1,
}
 
 
class Profile(object):
 
    def __init__(self, filename, date, writer):
        self.filenamefilename = filename
        self.datedate = date
        self.datadata = DefaultOrderedDict(lambda: DefaultOrderedDict(dict))
        self.writerwriter = writer
        self._read_read()
 
    def _read(self):
        ncd = nc.Dataset(self.filenamefilename)
        time = ncd.variables['time'][:]
        obid = ncd.variables['obid'][:]
        dpth = ncd.variables['depth'][:]
        lons = ncd.variables['lon'][:]
        lats = ncd.variables['lat'][:]
        hrs = ncd.variables['hr'][:]
        vals = ncd.variables['val'][:]
        errs = ncd.variables['err'][:]
        qcs = ncd.variables['qc'][:]
        ncd.close()
 
        base_date = datetime(1970, 1, 1) + timedelta(seconds=int(time[0]))
 
        for i in range(len(hrs)):
            # there shouldn't be any bad obs, but just in case remove them all
            if qcs[i] != 0:
                continue
 
            valKey = vName[obid[i]], self.writerwriter.OvalName()
            errKey = vName[obid[i]], self.writerwriter.OerrName()
            qcKey = vName[obid[i]], self.writerwriter.OqcName()
 
            dt = base_date + timedelta(hours=float(hrs[i]))
            locKey = lats[i], lons[i], dpth[i], dt.strftime(
                "%Y-%m-%dT%H:%M:%SZ")
            self.datadata[0][locKey][valKey] = vals[i]
            self.datadata[0][locKey][errKey] = errs[i]
            self.datadata[0][locKey][qcKey] = qcs[i]
 
 
def main():
 
    parser = argparse.ArgumentParser(
        description=(
            'Read insitu T/S profile observation file(s) that have already'
            ' been QCd and thinned for use in Hybrid-GODAS system.')
    )
 
    required = parser.add_argument_group(title='required arguments')
    required.add_argument(
        '-i', '--input',
        help="name of HGODAS observation input file(s)",
        type=str, required=True)
    required.add_argument(
        '-o', '--output',
        help="path of ioda output file",
        type=str, required=True)
    required.add_argument(
        '-d', '--date',
        help="base date for the center of the window",
        metavar="YYYYMMDDHH", type=str, required=True)
    args = parser.parse_args()
    fdate = datetime.strptime(args.date, '%Y%m%d%H')
 
    writer = iconv.NcWriter(args.output, locationKeyList)
 
    # Read in the profiles
    prof = Profile(args.input, fdate, writer)
 
    # write them out
    AttrData['date_time_string'] = fdate.strftime("%Y-%m-%dT%H:%M:%SZ")
    (ObsVars, LocMdata, VarMdata) = writer.ExtractObsData(prof.data)
    writer.BuildNetcdf(ObsVars, LocMdata, VarMdata, AttrData)
 
 
if __name__ == '__main__':
    main()