glider2ioda.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
import numpy as np
import numpy.matlib
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 = [
    "sea_water_temperature",
    "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)
        dpth = (ncd.variables['ctd_depth'][:])
        time = ncd.variables['ctd_time'][:]
        lons = np.float32(ncd.variables['longitude'][:])
        lats = np.float32(ncd.variables['latitude'][:])
        with np.errstate(invalid='ignore'):
            temperature = np.float32(ncd.variables['temperature'][:])
        with np.errstate(invalid='ignore'):
            salinity = np.float32(ncd.variables['salinity'][:])
        errs = np.float32(np.matlib.repmat(0.2, len(lons), 1))
        Tqcs = ncd.variables['temperature_qc'][:]-1
        Sqcs = ncd.variables['salinity_qc'][:]-1
        errs = np.squeeze(errs)
        ncd.close()
        base_date = datetime(1970, 1, 1)
        for i in range(len(time)-1):
            for j in [0, 1]:
                valKey = vName[j], self.writerwriter.OvalName()
                errKey = vName[j], self.writerwriter.OerrName()
                qcKey = vName[j], self.writerwriter.OqcName()
                dt = base_date + timedelta(seconds=int(time[i]))
                locKey = lats[i], lons[i], dpth[i], dt.strftime(
                    "%Y-%m-%dT%H:%M:%SZ")
                if j == 0:
                    self.datadata[0][locKey][valKey] = temperature[i]
                    self.datadata[0][locKey][errKey] = errs[i]
                    self.datadata[0][locKey][qcKey] = Tqcs[i]
                else:
                    self.datadata[0][locKey][valKey] = salinity[i]
                    self.datadata[0][locKey][errKey] = errs[i]
                    self.datadata[0][locKey][qcKey] = Sqcs[i]
 
 
def main():
 
    parser = argparse.ArgumentParser(
        description=(
            'Read NOAA AOML Hurricane Glider Temperature and Salinity profile observation file(s) '
        )
    )
 
    required = parser.add_argument_group(title='required arguments')
    required.add_argument(
        '-i', '--input',
        help="name of Glider 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)
 
    prof = Profile(args.input, fdate, writer)
    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()