Mapping YAML and Python script for ADPUPA prepBUFR

dump/mapping/bufr2ioda_adpupa_prepbufr.py

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+import os
+import sys
+sys.path.append('/work2/noaa/da/pkumar/HERCULES/EMC-bufr-query/bufr-query/build/lib')
+sys.path.append('/work2/noaa/da/pkumar/HERCULES/EMC-bufr-query/bufr-query/build/lib/python3.10')
+sys.path.append('/work2/noaa/da/pkumar/HERCULES/EMC-bufr-query/bufr-query/build/lib/python3.10/site-packages')
+
+import bufr
+from bufr.encoders import netcdf
+import copy
+import numpy as np
+import numpy.ma as ma
+import math
+import calendar
+import time
+from datetime import datetime
+import argparse
+
+
+def Mask_typ_for_var(typ, var):
+
+    typ_var = copy.deepcopy(typ)
+    for i in range(len(typ_var)):
+        if ma.is_masked(var[i]):
+            typ_var[i] = typ_var.fill_value
+
+    return typ_var
+
+
+def create_obs_group(input_path, output_path, mapping_path):
+
+    container = bufr.Parser(input_path, mapping_path).parse()
+
+    print("Get the Variables/Paths")
+    lat_path = container.get_paths('variables/latitude')
+    typ_path = container.get_paths('variables/observationType')
+    typ = container.get('variables/observationType')
+    cat = container.get('variables/prepbufrDataLevelCategory')
+    tpc = container.get('variables/temperatureEventProgramCode')
+    tob = container.get('variables/airTemperature')
+    pob = container.get('variables/pressure')
+    #tvo = container.get('variables/virtualTemperature')
+    uob = container.get('variables/windEastward')
+    vob = container.get('variables/windNorthward')
+    qob = container.get('variables/specificHumidity')
+    pqm = container.get('variables/pressureQualityMarker')
+    tqm = container.get('variables/airTemperatureQualityMarker')
+    poe = container.get('variables/pressureError')
+    toe = container.get('variables/airTemperatureError')
+
+    print("ObsValue- Derived Variable Calculation")
+    ps = np.full(pob.shape[0], pob.fill_value)
+    ps = np.where(cat == 0, pob, ps)
+
+    tsen = np.full(tob.shape[0], tob.fill_value)
+    tsen = np.where(((tpc >= 1) & (tpc < 8)), tob, tsen)
+
+    tvo = np.full(tob.shape[0], tob.fill_value)
+    tvo = np.where((tpc == 8), tob, tvo)
+
+    print("QualityMarker- Derived Variable Calculation")
+    psqm = np.full(pqm.shape[0], pqm.fill_value)
+    psqm = np.where(cat == 0, pqm, psqm)
+
+    tsenqm = np.full(tqm.shape[0], tqm.fill_value)
+    tsenqm = np.where(((tpc >= 1) & (tpc < 8)), tqm, tsenqm)
+
+    tvoqm = np.full(tqm.shape[0], tqm.fill_value)
+    tvoqm = np.where((tpc == 8), tqm, tvoqm)
+
+    print("ObsError- Derived Variable Calculation")
+    psoe = ma.array(np.full(poe.shape[0], poe.fill_value))
+    psoe = ma.where(cat == 0, poe, psoe)
+
+    tsenoe = np.full(toe.shape[0], toe.fill_value)
+    tsenoe = np.where(((tpc >= 1) & (tpc < 8)), toe, tsenoe)
+
+    tvooe = np.full(toe.shape[0], toe.fill_value)
+    tvooe = np.where((tpc == 8), toe, tvooe)
+
+    print("Add Variables to Container")
+    container.add('variables/stationPressure', ps, lat_path)
+    container.add('variables/stationPressureQualityMarker', psqm, lat_path)
+    container.add('variables/stationPressureError', psoe, lat_path)
+
+    container.add('variables/sensibleTemperature', tsen, lat_path)
+    container.add('variables/sensibleTemperatureQualityMarker', tsenqm, lat_path)
+    container.add('variables/sensibleTemperatureError', tsenoe, lat_path)
+
+    #container.add('variables/virtualTemperature', tvo, lat_path)
+    container.add('variables/virtualTemperatureQualityMarker', tvoqm, lat_path)
+    container.add('variables/virtualTemperatureError', tvooe, lat_path)
+
+    print("Create ObsType Variables")
+    typ_pob = Mask_typ_for_var(typ, pob)
+    typ_ps  = Mask_typ_for_var(typ, ps)
+    typ_tob = Mask_typ_for_var(typ, tob)
+    typ_tvo = Mask_typ_for_var(typ, tvo)
+    typ_uob = Mask_typ_for_var(typ, uob)
+    typ_vob = Mask_typ_for_var(typ, vob)
+    typ_qob = Mask_typ_for_var(typ, qob)
+
+    print("Add ObsType Variables to Container")
+    container.add('variables/pressureObsType', typ_pob, typ_path)
+    container.add('variables/stationPressureObsType', typ_ps, typ_path)
+    container.add('variables/airTemperatureObsType', typ_tob, typ_path)
+    container.add('variables/virtualTemperatureObsType', typ_tvo, typ_path)
+    container.add('variables/windEastwardObsType', typ_uob, typ_path)
+    container.add('variables/windNorthwardObsType', typ_vob, typ_path)
+    container.add('variables/specificHumidityObsType', typ_qob, typ_path)
+
+    netcdf.Encoder(mapping_path).encode(container, output_path)
+
+
+if __name__ == '__main__':
+
+    start_time = time.time()
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input', type=str, help='Input BUFR', required=True)
+    parser.add_argument('-o', '--output', type=str, help='Output NetCDF', required=True)
+    parser.add_argument('-m', '--mapping', type=str, help='Mapping YAML', required=True)
+    args = parser.parse_args()
+
+    infile = args.input
+    outfile = args.output
+    mappingfile = args.mapping
+
+    create_obs_group(infile, outfile, mappingfile)
+
+    end_time = time.time()
+    running_time = end_time - start_time
+    print("Total running time: ", running_time)