diff --git a/src/gnssro/CMakeLists.txt b/src/gnssro/CMakeLists.txt index 77dda978..899fcfd5 100644 --- a/src/gnssro/CMakeLists.txt +++ b/src/gnssro/CMakeLists.txt @@ -14,9 +14,10 @@ ecbuild_add_executable( TARGET gnssro_gsidiag2ioda # config for scripts list(APPEND scripts - gnssro_bufr2ioda.py + gnss_tec_ground_based.py gnssaro_netcdf2ioda.py gnssro_AWSopendataNetcdf2ioda.py + gnssro_bufr2ioda.py ) file( RELATIVE_PATH SCRIPT_LIB_PATH ${CMAKE_BINARY_DIR}/bin ${PYIODACONV_BUILD_LIBDIR} ) diff --git a/src/gnssro/gnss_tec_ground_based.py b/src/gnssro/gnss_tec_ground_based.py new file mode 100755 index 00000000..9d2c18d8 --- /dev/null +++ b/src/gnssro/gnss_tec_ground_based.py @@ -0,0 +1,469 @@ +#!/usr/bin/env python3 + +# +# (C) Copyright 2019-2024 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. +# + +# +# decode TENET formatted ground-based GNSS Total Electron Content (TEC) +# + +import sys +import os +import time +from datetime import datetime, timezone +import numpy as np +import logging + +# These modules need the path to lib-python modules +import pyiodaconv.ioda_conv_engines as iconv +from pyiodaconv.orddicts import DefaultOrderedDict +from pyiodaconv.def_jedi_utils import iso8601_string, epoch + +os.environ["TZ"] = "UTC" + +# these are the unique values in the raw input file +varDict = { + 'totalElectronContent': ['totalElectronContent', "integer", 'TECU'], +} + +# these are the MetaData common to each input +locationKeyList = [ + ('latitude', 'float', 'degrees_north'), + ('longitude', 'float', 'degrees_east'), + ('satelliteTransmitterId', 'integer', 'GNSS transmitter ID constellation pseudoRandomNoise PRN code'), + ('elevationAngleGNSS', 'float', 'GNSS transmitter satellite elevation angle in degrees'), + ('sensorAzimuthAngle', 'float', 'aziumuth angle viewing GNSS transmitter in degrees west'), + ('xECEFPosition', 'float', 'receiving station Earth Centered Earth Fixed X-coordinate in meters'), + ('yECEFPosition', 'float', 'receiving station Earth Centered Earth Fixed Y-coordinate in meters'), + ('zECEFPosition', 'float', 'receiving station Earth Centered Earth Fixed Z-coordinate in meters'), + ('xECEFPositionGNSS', 'float', 'GNSS transmitting satellite Earth Centered Earth Fixed X-coordinate in meters'), + ('yECEFPositionGNSS', 'float', 'GNSS transmitting satellite Earth Centered Earth Fixed Y-coordinate in meters'), + ('zECEFPositionGNSS', 'float', 'GNSS transmitting satellite Earth Centered Earth Fixed Z-coordinate in meters'), + ('latitudeIPP', 'float', 'latitude of Ionospheric Pierce Point in degrees_north'), + ('longitudeIPP', 'float', 'longitude of Ionospheric Pierce Point in degrees_east'), + ('dateTime', 'long', iso8601_string), + ('stationIdentifierWMO', 'integer', 'WMO assigned number for the site'), + ('stationIdentifier', 'string', 'GNSS ground-based receiving station name'), +] + +meta_keys = [m_item[0] for m_item in locationKeyList] + +GlobalAttrs = { + 'converter': os.path.basename(__file__), + 'ioda_version': 3, + 'description': 'Ground-based Total Electron Content', + 'source': 'TENET Network', +} + +metaDataName = iconv.MetaDataName() +obsValName = iconv.OvalName() +obsErrName = iconv.OerrName() +qcName = iconv.OqcName() + +float_missing_value = iconv.get_default_fill_val(np.float32) +int_missing_value = iconv.get_default_fill_val(np.int32) +long_missing_value = iconv.get_default_fill_val(np.int64) +string_missing_value = '_' + +missing_vals = {'string': string_missing_value, + 'integer': int_missing_value, + 'long': long_missing_value, + 'float': float_missing_value} +dtypes = {'string': object, + 'integer': np.int32, + 'long': np.int64, + 'float': np.float32} + + +def main(args): + + file_names = args.input + output_file = args.output + + start_time = time.time() + + data = None + any_data = False + for fname in file_names: + logging.info(f"Reading file: {fname}") + file_data, any_data = read_file(fname, any_data, qc_strict=args.qc_strict) + # if there is data do something + if file_data: + # first successful read + if not data: + data = file_data + # subsequent successful read + else: + for key in set(varDict.keys()).union(meta_keys): + # data[key] = np.concatenate(data[key], file_data[key]) # why not and gotta be much better way + data[key] = np.append(data[key], file_data[key]) + + # if all files have no data + if not any_data: + logging.error("No data to write, stopping execution.") + sys.exit() + + dtg = datetime.fromtimestamp(data['dateTime'][0]) + datetimeRef = dtg.isoformat() + "Z" + + # prepare global attributes we want to output in the file, + # in addition to the ones already loaded in from the input file + GlobalAttrs = { + 'sourceFiles': ", ".join(file_names), + 'datetimeReference': datetimeRef + } + + nlocs = len(data['dateTime']) + logging.info(f" found a total of {nlocs} observations") + DimDict = {'Location': nlocs} + + varDims = {} + for key in varDict.keys(): + variable = varDict[key][0] + varDims[variable] = ['Location'] + + varAttrs = DefaultOrderedDict(lambda: DefaultOrderedDict(dict)) + + # Set units of the MetaData variables and all _FillValues. + for key in meta_keys: + dtype = locationKeyList[meta_keys.index(key)][1] + if locationKeyList[meta_keys.index(key)][2]: + varAttrs[(key, metaDataName)]['units'] = locationKeyList[meta_keys.index(key)][2] + varAttrs[(key, metaDataName)]['_FillValue'] = missing_vals[dtype] + for key in varDict.keys(): + if 'totalElectronContent' in key: + continue + dtype = varDict[key][1] + units = varDict[key][2] + if units: + varAttrs[(key, metaDataName)]['units'] = units + varAttrs[(key, metaDataName)]['_FillValue'] = missing_vals[dtype] + + # Set units and FillValue attributes for groups associated with observed variable. + for key in varDict.keys(): + variable = varDict[key][0] + dtype = varDict[key][1] + units = varDict[key][2] + varAttrs[(variable, obsValName)]['units'] = units + varAttrs[(variable, obsErrName)]['units'] = units + varAttrs[(variable, obsValName)]['coordinates'] = 'longitude latitude' + varAttrs[(variable, obsErrName)]['coordinates'] = 'longitude latitude' + varAttrs[(variable, qcName)]['coordinates'] = 'longitude latitude' + varAttrs[(variable, obsValName)]['_FillValue'] = missing_vals[dtype] + varAttrs[(variable, obsErrName)]['_FillValue'] = missing_vals[dtype] + varAttrs[(variable, qcName)]['_FillValue'] = int_missing_value + + # Fill the final IODA data: MetaData then ObsValues, ObsErrors, and QC + ioda_data = {} + +# should populate ioda_data directly rather than creating another copy + for key in meta_keys: + dtype = locationKeyList[meta_keys.index(key)][1] + ioda_data[(key, metaDataName)] = np.array(data[key], dtype=dtypes[dtype]) + for key in varDict.keys(): + variable = varDict[key][0] + dtype = varDict[key][1] + if 'totalElectronContent' not in key: + logging.info(f" the variable: {variable} will be placed into MetaData of ioda_data") + # these MetaData are arrays nlocs long already + ioda_data[(key, metaDataName)] = np.array(data[variable], dtype=dtypes[dtype]) + else: + # what should be used as ObsError (10% or a fixed value) + variable = varDict[key][0] + logging.info(f" the variable: {variable} will be placed into ObsValue of ioda_data") + ioda_data[(variable, obsValName)] = np.array(data[variable], dtype=np.float32) + ioda_data[(variable, obsErrName)] = np.array(data[variable]*0.1, dtype=np.float32) + # ioda_data[(variable, obsErrName)] = np.full((nlocs), errValue, dtype=np.float32) + qc_array_hack = apply_gross_quality_control(data, qc_strict=args.qc_strict) + ioda_data[(variable, qcName)] = np.array(qc_array_hack, dtype=np.int32) # how to interpret AQI ? + + logging.debug("Writing file: " + output_file) + + # setup the IODA writer and write everything out. + writer = iconv.IodaWriter(output_file, locationKeyList, DimDict) + writer.BuildIoda(ioda_data, varDims, varAttrs, GlobalAttrs) + + logging.info("--- {:9.4g} total seconds ---".format(time.time() - start_time)) + + +def read_file(file_name, any_data, qc_strict=True): + + local_data = init_data_dict() + + # Open the file + with open(file_name, 'r') as file: + # Create an iterator from the file object + file_iterator = iter(file) + + while True: + try: + + local_data, header_read = get_header(file_iterator, local_data) + logging.debug(f'header was read w/o error: {header_read}') + + while header_read: + # Get the next line from the iterator + line = next(file_iterator) + local_data, endReport = populate_obsValue(line, local_data) + if endReport: + header_read = False + break + + except StopIteration: + # If StopIteration is raised, break from the loop + break + + any_data = True + # repeat all the metaData values + nlocs = len(local_data['dateTime']) + if nlocs == 0: + # if the header was not sucessfully read return nothing + local_data = None + return local_data, any_data + + +def get_header(file_iterator, local_data): + ##################################################### + # get header (3 lines) + ##################################################### + + # Line #1: HIUS1 KJPL 080213 + # This line is standard in all TENET files the only thing that changes is the numeric value 080213 + # This value indicates the Coordinated Universal Time (UTC) JPL produces the TENET file + # The format is: DDHHMM (where DD = day, HH = UTC hour, and MM = minutes) + + # Line #2: TENET + # This line is standard in all TENET files and never changes. It indicates the nature of the file – TENET + + # Line #3: 23074 0694/ 271608 NRIL 000064539804 002253881156 005946178085 + # WMO number, latitude (N), longitude (W), station name, ECEF station coordinates + + header_read = False + # read first line + line = next(file_iterator) + try: + _, _, report_time = line.split() + except ValueError: + return local_data, header_read + + # read second line + line = next(file_iterator) + if 'TENET' not in line: + return local_data, header_read # not necessarily needed could try to continue + + # read third line + line = next(file_iterator) + try: + WMOid, lat, lon, stationName, xECEFPosition, yECEFPosition, zECEFPosition = line.split() + except ValueError: + return local_data, header_read + + xECEFPosition = convert_ECEF_string(xECEFPosition) + yECEFPosition = convert_ECEF_string(yECEFPosition) + zECEFPosition = convert_ECEF_string(zECEFPosition) + + lat = parse_latitude(lat) + + try: + local_data['latitude'] = np.append(local_data['latitude'], float(lat)) + local_data['longitude'] = np.append(local_data['longitude'], float(lon)/1000.) + local_data['stationIdentifier'] = np.append(local_data['stationIdentifier'], stationName) + local_data['stationIdentifierWMO'] = np.append(local_data['stationIdentifierWMO'], int(WMOid)) + local_data['xECEFPosition'] = np.append(local_data['xECEFPosition'], xECEFPosition) + local_data['yECEFPosition'] = np.append(local_data['yECEFPosition'], yECEFPosition) + local_data['zECEFPosition'] = np.append(local_data['zECEFPosition'], zECEFPosition) + except ValueError: + return local_data, header_read + + header_read = True + + return local_data, header_read + + +def populate_obsValue(line, local_data): + + # get the electron content retrieved from GNSS transmitter + # if can correctly parse all fields populate local_data otherwise do nothing + + # ObsValue data row (example) + # Line #4: 11111 180208 021000 280771 26911 2165166150 4210322950 0233/ 3558/ 102029725204 114864753823 022550194624 + # unknown, YYMMDD, HHMMSS, PRN/LatitudeIPP, LongitudeIPP, VOBS, SOBS, satelite elevation angle, azimuth angle, GNSS ECEF coordinates + + # for all ECEF coordinates 0 in front indicates positive, and 1 indicates negative. + # IPP = Ionospheric Pierce Point + + endReport = False + if '99999' in line[0:5]: + # reset for next record + endReport = True + return local_data, endReport + + # read data lines beginning at fourth line + try: + _, yymmdd, hhmmss, PRNlatitudeIPP, longitudeIPP, vobs, sobs, elevationAngle, azimuthAngle, \ + xECEFPositionGNSS, yECEFPositionGNSS, zECEFPositionGNSS = line.split() + except ValueError: + return local_data, endReport + + dateTime = convert_string_to_dateTime(yymmdd, hhmmss) + PRN, latitudeIPP = parse_station_and_latitude(PRNlatitudeIPP) + + xECEFPositionGNSS = convert_ECEF_string(xECEFPositionGNSS) + yECEFPositionGNSS = convert_ECEF_string(yECEFPositionGNSS) + zECEFPositionGNSS = convert_ECEF_string(zECEFPositionGNSS) + + try: + local_data['dateTime'] = np.append(local_data['dateTime'], dateTime) + local_data['satelliteTransmitterId'] = np.append(local_data['satelliteTransmitterId'], PRN) + local_data['latitudeIPP'] = np.append(local_data['latitudeIPP'], latitudeIPP) + local_data['longitudeIPP'] = np.append(local_data['longitudeIPP'], float(longitudeIPP)/100.) + local_data['elevationAngleGNSS'] = np.append(local_data['elevationAngleGNSS'], float(elevationAngle.rstrip('/'))/10.) + local_data['sensorAzimuthAngle'] = np.append(local_data['sensorAzimuthAngle'], float(azimuthAngle.rstrip('/'))/10.) + local_data['totalElectronContent'] = np.append(local_data['totalElectronContent'], int(sobs.lstrip('/'))) + local_data['xECEFPositionGNSS'] = np.append(local_data['xECEFPositionGNSS'], xECEFPositionGNSS) + local_data['yECEFPositionGNSS'] = np.append(local_data['yECEFPositionGNSS'], yECEFPositionGNSS) + local_data['zECEFPositionGNSS'] = np.append(local_data['zECEFPositionGNSS'], zECEFPositionGNSS) + except ValueError: + return local_data, endReport + + # repeat the metaData + if len(local_data['latitude']) < len(local_data['latitudeIPP']): + for key in ['latitude', 'longitude', 'stationIdentifier', 'stationIdentifierWMO', 'xECEFPosition', 'yECEFPosition', 'zECEFPosition']: + local_data[key] = np.append(local_data[key], local_data[key][-1]) + + return local_data, endReport + + +def convert_ECEF_string(c): + # for all ECEF coordinates 0 in front indicates positive, and 1 indicates negative. + try: + # Attempt the conversion logic + result = -int(c[1:]) if c[0] == '1' else int(c[1:]) if c[0] == '0' else int(c) + return result + except (IndexError, ValueError) as e: + # Raise an exception with a descriptive message + raise ValueError(f"Invalid input string '{c}': {e}") + + +def convert_string_to_dateTime(yymmdd, hhmmss): + + # convert strings of time into python dateTime object + try: + # Combine and parse the string as a datetime object + dtg = datetime.strptime(f"{yymmdd}{hhmmss}", '%y%m%d%H%M%S') + # Set timezone to UTC + dtg = dtg.replace(tzinfo=timezone.utc) + # Convert to Unix time in seconds since epoch + dateTime = np.int64(round((dtg - epoch).total_seconds())) + + return dateTime + + except ValueError as e: + # Raise an informative error if parsing fails + raise ValueError(f"Invalid date or time format in inputs '{yymmdd}' and '{hhmmss}': {e}") + + +def parse_station_and_latitude(code): + try: + # Extract the station code (first two digits) + station_code = int(code[:2]) + + # Determine latitude sign based on the third digit + latitude_sign = 1 if code[2] == '0' else -1 if code[2] == '1' else None + if latitude_sign is None: + raise ValueError(f"Invalid latitude sign indicator '{code[2]}'; expected '0' for positive or '1' for negative.") + + # Extract the latitude (remaining digits) and apply sign and scale + latitude = latitude_sign * int(code[3:]) / 10.0 + + return station_code, latitude + + except ValueError as e: + raise ValueError(f"Invalid input '{code}': {e}") + + +def parse_latitude(lat_str): + try: + # Determine the latitude sign based on the first digit + latitude_sign = 1 if lat_str[0] == '0' else -1 if lat_str[0] == '1' else None + if latitude_sign is None: + raise ValueError(f"Invalid latitude sign indicator '{lat_str[0]}'; expected '0' for positive or '1' for negative.") + + # Convert the remaining digits to latitude, apply the sign, and divide by 10 + latitude = latitude_sign * float(lat_str[1:-1]) / 10.0 + + return latitude + + except ValueError as e: + raise ValueError(f"Invalid latitude input '{lat_str}': {e}") + + +def apply_gross_quality_control(data, qc_strict=False): + # if strict quality-control is requested + # apply using simple physical reality check on variables + + # initialize returned variable + qc_array_hack = np.zeros_like(data['totalElectronContent'], dtype=np.int32) + # is requested apply check + if qc_strict: + qc_array_hack = np.where( + (data['totalElectronContentSlant'].astype(float) < 0) + | (data['latitude'].astype(float) > 90) + | (data['longitude'].astype(float) > 360) + | (data['elevationAngleGNSS'].astype(float) < 0), + 1, + 0) + return qc_array_hack + + +def init_data_dict(): + local_data = {} # Before assigning the output types into the above. + for key in set(varDict.keys()).union(meta_keys): + local_data[key] = [] + return local_data + + +if __name__ == "__main__": + + from argparse import ArgumentParser + + parser = ArgumentParser( + description=('Read a satwind AMV ascii/csv file from SSEC' + ' and convert into IODA output file') + ) + + required = parser.add_argument_group(title='required arguments') + required.add_argument('-i', '--input', nargs='+', + action='store', default=None, required=True, + help='input files') + required.add_argument('-o', '--output', + action='store', default=None, required=True, + help='output file') + + optional = parser.add_argument_group(title='optional arguments') + optional.add_argument('--debug', action='store_true', default=False, + help='enable debug messages') + optional.add_argument('--quality-control', action='store_true', + default=False, dest='qc_strict', + help='add PreQC values') + optional.add_argument('--verbose', action='store_true', default=False, + help='enable verbose debug messages') + + args = parser.parse_args() + + if args.debug: + logging.basicConfig(level=logging.INFO) + elif args.verbose: + logging.basicConfig(level=logging.DEBUG) + else: + logging.basicConfig(level=logging.ERROR) + + for file_name in args.input: + if not os.path.isfile(file_name): + parser.error('Input (-i option) file: ', file_name, ' does not exist') + + main(args) diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 5ec3c26f..ca7e22f9 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -102,6 +102,7 @@ list( APPEND test_input testinput/Pandora57s1_BoulderCO_L2_rnvs3p1-8.txt testinput/pandora_site_classification.csv testinput/balloonsonde_sample_20241001T00Z_PT15M.json + testinput/tec_groundBased_TENET_20201001T00Z.tec ) list( APPEND test_output @@ -196,6 +197,7 @@ list( APPEND test_output testoutput/20240401T105230_PT1M_dpr_gpm.nc testoutput/Pandora57s1_BoulderCO_L2_rnvs3p1-8.nc testoutput/obs.20241001T000000Z_PT15M_balloonsonde.nc4 + testoutput/obs.20201001T000000Z_PT1M_tec_groundbased.nc4 ) if( iodaconv_gnssro_ENABLED ) @@ -2176,7 +2178,18 @@ endif() --sort" obs.20241001T000000Z_PT15M_balloonsonde.nc4 ${IODA_CONV_COMP_TOL}) - ecbuild_add_test( TARGET test_${PROJECT_NAME}_osw_cygnss + ecbuild_add_test( TARGET test_${PROJECT_NAME}_tec_groundbased + TYPE SCRIPT + ENVIRONMENT "PYTHONPATH=${IODACONV_PYTHONPATH}" + COMMAND bash + ARGS ${CMAKE_BINARY_DIR}/bin/iodaconv_comp.sh + netcdf + "${Python3_EXECUTABLE} ${CMAKE_BINARY_DIR}/bin/gnss_tec_ground_based.py + -i testinput/tec_groundBased_TENET_20201001T00Z.tec + -o testrun/obs.20201001T000000Z_PT1M_tec_groundbased.nc4" + obs.20201001T000000Z_PT1M_tec_groundbased.nc4 ${IODA_CONV_COMP_TOL}) + +ecbuild_add_test( TARGET test_${PROJECT_NAME}_osw_cygnss TYPE SCRIPT ENVIRONMENT "PYTHONPATH=${IODACONV_PYTHONPATH}" COMMAND bash diff --git a/test/testinput/tec_groundBased_TENET_20201001T00Z.tec b/test/testinput/tec_groundBased_TENET_20201001T00Z.tec new file mode 100644 index 00000000..ef59a7e7 --- /dev/null +++ b/test/testinput/tec_groundBased_TENET_20201001T00Z.tec @@ -0,0 +1,683 @@ +HIUS1 KJPL 010002 +TENET +00000 1210/ 242907 KARR 102713875465 005304018101 102269379877 +11111 201001 000000 131265 24771 4714133950 8820250550 0252/ 1435/ 007025345077 013882442942 121666885863 +11111 201001 000000 281205 24271 6769134750 6810135550 0833/ 3350/ 112447865917 022145344610 107435220803 +11111 201001 000000 071260 23611 5985061550 1200012360 0219/ 2294/ 118798737186 000534235495 118615910088 +11111 201001 000000 051216 24641 7272119950 9350154150 0477/ 1038/ 003590034578 023803544329 111165607124 +11111 201001 000000 171119 23961 8554141450 1884031160 0175/ 3400/ 116353457832 014638871711 015357454224 +11111 201001 000000 301245 24141 ////124460 ////169260 0435/ 2011/ 111727010619 010455564137 121367744783 +11111 201001 000000 091182 23631 8336068450 1512012460 0267/ 2916/ 125427069453 007618409242 001104167821 +99999 +HIUS1 KJPL 010002 +TENET +08512 0377/ 025704 PDEL 004551708955 102186947293 003883216988 +11111 201001 000000 310402 03121 3590060650 5530093350 0355/ 0567/ 001707173343 117587766017 019632680518 +11111 201001 000000 290347 02331 6674063050 8640081550 0472/ 2134/ 026052853499 103562016877 003888966888 +11111 201001 000000 120412 02031 4414042450 7080068150 0332/ 3125/ 012271346259 009418316979 021377484549 +11111 201001 000000 250389 02491 4882062050 5190065950 0687/ 3351/ 015684634010 104098219502 020750406448 +99999 +HIUS1 KJPL 010002 +TENET +80222 0046/ 074106 BOGT 001744418322 106116105149 000512699203 +11111 201001 000000 210002 08111 1535009060 3138018560 0210/ 1216/ 113641769971 120173542274 110268527561 +11111 201001 000000 201035 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