From e1ca3ff41aadbcae8967694cbb509d6810b64b91 Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Fri, 1 Dec 2023 16:35:53 +0100 Subject: [PATCH 01/10] WIP --- pyproject.toml | 5 +- .../AeronetSunTimeseriesReader.py | 170 +- tests/test_AERONETTimeSeriesReader.py | 62 + tests/testdata/aeronetsun_testdata.csv | 10000 ++++++++++++++++ 4 files changed, 10187 insertions(+), 50 deletions(-) create mode 100644 tests/test_AERONETTimeSeriesReader.py create mode 100644 tests/testdata/aeronetsun_testdata.csv diff --git a/pyproject.toml b/pyproject.toml index b850197..1e4e119 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,10 @@ classifiers = [ "Topic :: Scientific/Engineering :: Atmospheric Science", ] requires-python = ">=3.9" -dependencies = ["pyaro@git+https://github.com/metno/pyaro"] +dependencies = [ + "pyaro@git+https://github.com/metno/pyaro", + "requests", +] [project.urls] "Homepage" = "https://github.com/metno/pyaro-readers" diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index da52c7b..2634eaf 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,73 +1,145 @@ import csv import numpy as np from pyaro.timeseries import Data, NpStructuredData, Flag, Reader, Station, Engine +import requests, zipfile, io + +# default URL +BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" +# number of lines to read before the reading is handed to Pythobn's csv reader +HEADER_LINE_NO = 7 +DELIMITER = "," +# main variables to store +LAT_NAME = "Site_Latitude(Degrees)" +LON_NAME = "Site_Longitude(Degrees)" +ALT_NAME = "Site_Elevation(m)" +SITE_NAME = "AERONET_Site_Name" +DATE_NAME = "Date(dd:mm:yyyy)" +TIME_NAME = "Time(hh:mm:ss)" +AOD500_NAME = "AOD_500nm" +ANG4487_NAME = "440-870_Angstrom_Exponent" +AOD440_NAME = "AOD_440nm" +AOD870_NAME = "AOD_870nm" + +# further vars can be added here +VARS_TO_STORE = [ + LAT_NAME, + LON_NAME, + ALT_NAME, + SITE_NAME, + DATE_NAME, + TIME_NAME, + AOD500_NAME, + ANG4487_NAME, + AOD440_NAME, + AOD870_NAME, + "AERONET_Instrument_Number", + "Data_Quality_Level", +] class AeronetSunTimeseriesReader(Reader): def __init__( self, filename, - columns=dict( - variable=0, - station=1, - longitude=2, - latitude=3, - value=4, - units=5, - start_time=6, - end_time=7, - ), - variable_units={"SOx": "Gg", "NOx": "Mg"}, - csvreader_kwargs={"delimiter": ","}, + # columns=dict( + # variable=0, + # station=1, + # longitude=2, + # latitude=3, + # value=4, + # units=5, + # start_time=6, + # end_time=7, + # ), + # variable_units={"SOx": "Gg", "NOx": "Mg"}, + csvreader_kwargs={"delimiter": DELIMITER}, filters=[], ): """open a new csv timeseries-reader - :param filename_or_obj_or_url: path-like object to csv-file + :param filename_or_obj_or_url: path-like object to csv-file + + input file looks like this: + AERONET Version 3; + Cuiaba + Version 3: AOD Level 2.0 + The following data are automatically cloud cleared and quality assured with pre-field and post-field calibration applied. + Contact: PI=Pawan Gupta and Elena Lind; PI Email=Pawan.Gupta@nasa.gov and Elena.Lind@nasa.gov + Daily Averages,UNITS can be found at,,, https://aeronet.gsfc.nasa.gov/new_web/units.html + AERONET_Site,Date(dd:mm:yyyy),Time(hh:mm:ss),Day_of_Year,AOD_1640nm,AOD_1020nm,AOD_870nm,AOD_865nm,AOD_779nm,AOD_675nm,AOD_667nm,AOD_620nm,AOD_560nm,AOD_555nm,AOD_551nm,AOD_532nm,AOD_531nm,AOD_510nm,AOD_500nm,AOD_490nm,AOD_443nm,AOD_440nm,AOD_412nm,AOD_400nm,AOD_380nm,AOD_340nm,Precipitable_Water(cm),AOD_681nm,AOD_709nm,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,440-870_Angstrom_Exponent,380-500_Angstrom_Exponent,440-675_Angstrom_Exponent,500-870_Angstrom_Exponent,340-440_Angstrom_Exponent,440-675_Angstrom_Exponent[Polar],N[AOD_1640nm],N[AOD_1020nm],N[AOD_870nm],N[AOD_865nm],N[AOD_779nm],N[AOD_675nm],N[AOD_667nm],N[AOD_620nm],N[AOD_560nm],N[AOD_555nm],N[AOD_551nm],N[AOD_532nm],N[AOD_531nm],N[AOD_510nm],N[AOD_500nm],N[AOD_490nm],N[AOD_443nm],N[AOD_440nm],N[AOD_412nm],N[AOD_400nm],N[AOD_380nm],N[AOD_340nm],N[Precipitable_Water(cm)],N[AOD_681nm],N[AOD_709nm],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[440-870_Angstrom_Exponent],N[380-500_Angstrom_Exponent],N[440-675_Angstrom_Exponent],N[500-870_Angstrom_Exponent],N[340-440_Angstrom_Exponent],N[440-675_Angstrom_Exponent[Polar]],Data_Quality_Level,AERONET_Instrument_Number,AERONET_Site_Name,Site_Latitude(Degrees),Site_Longitude(Degrees),Site_Elevation(m) + Cuiaba,16:06:1993,12:00:00,167,-999.,0.081800,0.088421,-999.,-999.,0.095266,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.117581,-999.,-999.,-999.,0.149887,2.487799,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.424234,-999.,0.497630,-999.,0.924333,-999.,0,3,3,0,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,3,6,0,0,0,0,0,0,0,3,0,3,0,3,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 + Cuiaba,17:06:1993,12:00:00,168,-999.,0.092246,0.099877,-999.,-999.,0.110915,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.144628,-999.,-999.,-999.,0.187276,2.592902,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.547807,-999.,0.628609,-999.,0.988320,-999.,0,16,16,0,0,16,0,0,0,0,0,0,0,0,0,0,0,16,0,0,0,16,32,0,0,0,0,0,0,0,16,0,16,0,16,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 """ self._filename = filename self._stations = {} self._data = {} # var -> {data-array} self._filters = filters + self._header = [] + _laststatstr = "" with open(self._filename, newline="") as csvfile: - crd = csv.reader(csvfile, **csvreader_kwargs) - for row in crd: - variable = row[columns["variable"]] - value = float(row[columns["value"]]) - station = row[columns["station"]] - lon = float(row[columns["longitude"]]) - lat = float(row[columns["latitude"]]) - start = np.datetime64(row[columns["start_time"]]) - end = np.datetime64(row[columns["end_time"]]) - if "altitude" in columns: - alt = float(row[columns["altitude"]]) - else: - alt = 0 - if "units" in columns: - units = row[columns["units"]] - else: - units = variable_units[variable] + for _hidx in range(HEADER_LINE_NO - 1): + self._header.append(csvfile.readline()) + # get fields from header line although csv can do that as well since we might want to adjust these names + self._fields = csvfile.readline().strip().split(",") - if variable in self._data: - da = self._data[variable] - if da.units != units: - raise Exception(f"unit change from '{da.units}' to 'units'") + crd = csv.DictReader(csvfile, fieldnames=self._fields, **csvreader_kwargs) + for row in crd: + if row[SITE_NAME] != _laststatstr: + print(f"Next station {row[SITE_NAME]}") + _laststatstr = row[SITE_NAME] + # new station + station = row[SITE_NAME] + # lon = float("Site_Longitude(Degrees)") + # lat = float("Site_Latitude(Degrees)") + # start = np.datetime64(row[columns["start_time"]]) + # end = np.datetime64(row[columns["end_time"]]) + # alt = float(row[]) + # if "altitude" in columns: + # else: + # alt = 0 else: - da = NpStructuredData(variable, units) - self._data[variable] = da - da.append(value, station, lat, lon, alt, start, end, Flag.VALID, np.nan) - if not station in self._stations: - self._stations[station] = Station( - { - "station": station, - "longitude": lon, - "latitude": lat, - "altitude": 0, - "country": "NO", - "url": "", - "long_name": station, - } - ) + pass + + print(crd.fieldnames) + + # for row in crd: + # variable = row[columns["variable"]] + # + # value = float(row[columns["value"]]) + # station = row[columns["station"]] + # lon = float(row[columns["longitude"]]) + # lat = float(row[columns["latitude"]]) + # start = np.datetime64(row[columns["start_time"]]) + # end = np.datetime64(row[columns["end_time"]]) + # if "altitude" in columns: + # alt = float(row[columns["altitude"]]) + # else: + # alt = 0 + # if "units" in columns: + # units = row[columns["units"]] + # else: + # units = variable_units[variable] + # + # if variable in self._data: + # da = self._data[variable] + # if da.units != units: + # raise Exception(f"unit change from '{da.units}' to 'units'") + # else: + # da = NpStructuredData(variable, units) + # self._data[variable] = da + # da.append(value, station, lat, lon, alt, start, end, Flag.VALID, np.nan) + # if not station in self._stations: + # self._stations[station] = Station( + # { + # "station": station, + # "longitude": lon, + # "latitude": lat, + # "altitude": 0, + # "country": "NO", + # "url": "", + # "long_name": station, + # } + # ) def _unfiltered_data(self, varname) -> Data: return self._data[varname] diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py new file mode 100644 index 0000000..81ecdea --- /dev/null +++ b/tests/test_AERONETTimeSeriesReader.py @@ -0,0 +1,62 @@ +import unittest +import os + +import numpy as np +import pyaro +import pyaro.timeseries +from pyaro.timeseries.Wrappers import VariableNameChangingReader + + +class TestAERONETTimeSeriesReader(unittest.TestCase): + file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "testdata", + "aeronetsun_testdata.csv", + ) + + def test_init(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") + # just see that it doesn't fail + engine.description() + engine.args() + bla = engine.open(self.file, filters=[]) + # with engine.open(self.file, filters=[]) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertEqual(count, 208) + # self.assertEqual(len(ts.stations()), 4) + + # def test_stationfilter(self): + # engine = pyaro.list_timeseries_engines()["csv_timeseries"] + # sfilter = pyaro.timeseries.filters.get("stations", exclude=["station1"]) + # with engine.open(self.file, filters=[sfilter]) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertEqual(count, 104) + # self.assertEqual(len(ts.stations()), 1) + # + # def test_wrappers(self): + # engine = pyaro.list_timeseries_engines()["csv_timeseries"] + # newsox = "oxidised_sulphur" + # with VariableNameChangingReader( + # engine.open(self.file, filters=[]), {"SOx": newsox} + # ) as ts: + # self.assertEqual(ts.data(newsox).variable, newsox) + # pass + # + # def test_variables_filter(self): + # engine = pyaro.list_timeseries_engines()["csv_timeseries"] + # newsox = "oxidised_sulphur" + # vfilter = pyaro.timeseries.filters.get( + # "variables", reader_to_new={"SOx": newsox} + # ) + # with engine.open(self.file, filters=[vfilter]) as ts: + # self.assertEqual(ts.data(newsox).variable, newsox) + # pass + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/testdata/aeronetsun_testdata.csv b/tests/testdata/aeronetsun_testdata.csv new file mode 100644 index 0000000..24b3b6c --- /dev/null +++ b/tests/testdata/aeronetsun_testdata.csv @@ -0,0 +1,10000 @@ +AERONET Version 3; +Cuiaba +Version 3: AOD Level 2.0 +The following data are automatically cloud cleared and quality assured with pre-field and post-field calibration applied. +Contact: PI=Pawan Gupta and Elena Lind; PI Email=Pawan.Gupta@nasa.gov and Elena.Lind@nasa.gov +Daily Averages,UNITS can be found at,,, https://aeronet.gsfc.nasa.gov/new_web/units.html +AERONET_Site,Date(dd:mm:yyyy),Time(hh:mm:ss),Day_of_Year,AOD_1640nm,AOD_1020nm,AOD_870nm,AOD_865nm,AOD_779nm,AOD_675nm,AOD_667nm,AOD_620nm,AOD_560nm,AOD_555nm,AOD_551nm,AOD_532nm,AOD_531nm,AOD_510nm,AOD_500nm,AOD_490nm,AOD_443nm,AOD_440nm,AOD_412nm,AOD_400nm,AOD_380nm,AOD_340nm,Precipitable_Water(cm),AOD_681nm,AOD_709nm,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,440-870_Angstrom_Exponent,380-500_Angstrom_Exponent,440-675_Angstrom_Exponent,500-870_Angstrom_Exponent,340-440_Angstrom_Exponent,440-675_Angstrom_Exponent[Polar],N[AOD_1640nm],N[AOD_1020nm],N[AOD_870nm],N[AOD_865nm],N[AOD_779nm],N[AOD_675nm],N[AOD_667nm],N[AOD_620nm],N[AOD_560nm],N[AOD_555nm],N[AOD_551nm],N[AOD_532nm],N[AOD_531nm],N[AOD_510nm],N[AOD_500nm],N[AOD_490nm],N[AOD_443nm],N[AOD_440nm],N[AOD_412nm],N[AOD_400nm],N[AOD_380nm],N[AOD_340nm],N[Precipitable_Water(cm)],N[AOD_681nm],N[AOD_709nm],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[440-870_Angstrom_Exponent],N[380-500_Angstrom_Exponent],N[440-675_Angstrom_Exponent],N[500-870_Angstrom_Exponent],N[340-440_Angstrom_Exponent],N[440-675_Angstrom_Exponent[Polar]],Data_Quality_Level,AERONET_Instrument_Number,AERONET_Site_Name,Site_Latitude(Degrees),Site_Longitude(Degrees),Site_Elevation(m) +Cuiaba,16:06:1993,12:00:00,167,-999.,0.081800,0.088421,-999.,-999.,0.095266,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.117581,-999.,-999.,-999.,0.149887,2.487799,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.424234,-999.,0.497630,-999.,0.924333,-999.,0,3,3,0,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,3,6,0,0,0,0,0,0,0,3,0,3,0,3,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 +Cuiaba,17:06:1993,12:00:00,168,-999.,0.092246,0.099877,-999.,-999.,0.110915,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.144628,-999.,-999.,-999.,0.187276,2.592902,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.547807,-999.,0.628609,-999.,0.988320,-999.,0,16,16,0,0,16,0,0,0,0,0,0,0,0,0,0,0,16,0,0,0,16,32,0,0,0,0,0,0,0,16,0,16,0,16,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 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+GSFC,27:11:2003,12:00:00,331,-999.,-999.,0.040393,-999.,-999.,0.058782,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.105077,-999.,-999.,0.127420,-999.,-999.,0.157968,0.178062,1.716771,-999.,-999.,-999.,-999.,-999.,-999.,-999.,1.731670,1.519388,1.842991,1.748310,1.352567,-999.,0,0,16,0,0,16,0,0,0,0,0,0,0,0,16,0,0,16,0,0,15,15,16,0,0,0,0,0,0,0,16,16,16,16,15,0,lev20,89,GSFC,38.992500,-76.839833,87.000000 From c5d92812d83f07d6a36d04c2b6ad706c897acb2b Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Mon, 4 Dec 2023 14:16:26 +0100 Subject: [PATCH 02/10] 1st version that reads actual Aeronet data --- .../AeronetSunTimeseriesReader.py | 115 ++++++++---------- tests/test_AERONETTimeSeriesReader.py | 14 +-- 2 files changed, 60 insertions(+), 69 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 2634eaf..b99f499 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -2,6 +2,8 @@ import numpy as np from pyaro.timeseries import Data, NpStructuredData, Flag, Reader, Station, Engine import requests, zipfile, io +import geocoder +from tqdm import tqdm # default URL BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" @@ -14,12 +16,15 @@ ALT_NAME = "Site_Elevation(m)" SITE_NAME = "AERONET_Site_Name" DATE_NAME = "Date(dd:mm:yyyy)" -TIME_NAME = "Time(hh:mm:ss)" +TIME_NAME: str = "Time(hh:mm:ss)" AOD500_NAME = "AOD_500nm" ANG4487_NAME = "440-870_Angstrom_Exponent" AOD440_NAME = "AOD_440nm" AOD870_NAME = "AOD_870nm" +DATA_VARS = [AOD500_NAME, ANG4487_NAME, AOD440_NAME, AOD870_NAME] +FILL_COUNTRY_FLAG = False + # further vars can be added here VARS_TO_STORE = [ LAT_NAME, @@ -41,17 +46,6 @@ class AeronetSunTimeseriesReader(Reader): def __init__( self, filename, - # columns=dict( - # variable=0, - # station=1, - # longitude=2, - # latitude=3, - # value=4, - # units=5, - # start_time=6, - # end_time=7, - # ), - # variable_units={"SOx": "Gg", "NOx": "Mg"}, csvreader_kwargs={"delimiter": DELIMITER}, filters=[], ): @@ -83,63 +77,60 @@ def __init__( self._fields = csvfile.readline().strip().split(",") crd = csv.DictReader(csvfile, fieldnames=self._fields, **csvreader_kwargs) - for row in crd: + for _ridx, row in enumerate(crd): + # for _ridx in tqdm(range(len(crd))): + # row = crd[_ridx] if row[SITE_NAME] != _laststatstr: print(f"Next station {row[SITE_NAME]}") _laststatstr = row[SITE_NAME] # new station station = row[SITE_NAME] - # lon = float("Site_Longitude(Degrees)") - # lat = float("Site_Latitude(Degrees)") - # start = np.datetime64(row[columns["start_time"]]) - # end = np.datetime64(row[columns["end_time"]]) - # alt = float(row[]) - # if "altitude" in columns: - # else: - # alt = 0 - else: - pass + lon = float(row[LON_NAME]) + lat = float(row[LAT_NAME]) + alt = float(row["Site_Elevation(m)"]) + if FILL_COUNTRY_FLAG: + try: + country = geocoder.osm([lat, lon], method='reverse').json['country_code'] + except: + country = "NN" + else: + country = "NN" + # units of Aeronet data are always 1 + units = "1" + if not station in self._stations: + self._stations[station] = Station( + { + "station": station, + "longitude": lon, + "latitude": lat, + "altitude": alt, + "country": country, + "url": "", + "long_name": station, + } + ) + # every line contains all variables, sometimes filled with NaNs though + if _ridx == 0: + for variable in DATA_VARS: + if variable in self._data: + da = self._data[variable] + if da.units != units: + raise Exception(f"unit change from '{da.units}' to 'units'") + else: + da = NpStructuredData(variable, units) + self._data[variable] = da + for variable in DATA_VARS: + day, month, year = row[DATE_NAME].split(":") + datestring = "-".join([year, month, day]) + datestring = "T".join([datestring, row[TIME_NAME]]) + start = np.datetime64(datestring) + end = start + value = float(row[variable]) + self._data[variable].append(value, station, lat, lon, alt, start, end, Flag.VALID, np.nan) - print(crd.fieldnames) - # for row in crd: - # variable = row[columns["variable"]] - # - # value = float(row[columns["value"]]) - # station = row[columns["station"]] - # lon = float(row[columns["longitude"]]) - # lat = float(row[columns["latitude"]]) - # start = np.datetime64(row[columns["start_time"]]) - # end = np.datetime64(row[columns["end_time"]]) - # if "altitude" in columns: - # alt = float(row[columns["altitude"]]) - # else: - # alt = 0 - # if "units" in columns: - # units = row[columns["units"]] - # else: - # units = variable_units[variable] - # - # if variable in self._data: - # da = self._data[variable] - # if da.units != units: - # raise Exception(f"unit change from '{da.units}' to 'units'") - # else: - # da = NpStructuredData(variable, units) - # self._data[variable] = da - # da.append(value, station, lat, lon, alt, start, end, Flag.VALID, np.nan) - # if not station in self._stations: - # self._stations[station] = Station( - # { - # "station": station, - # "longitude": lon, - # "latitude": lat, - # "altitude": 0, - # "country": "NO", - # "url": "", - # "long_name": station, - # } - # ) + + print(crd.fieldnames) def _unfiltered_data(self, varname) -> Data: return self._data[varname] diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index 81ecdea..7cdd000 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -20,13 +20,13 @@ def test_init(self): # just see that it doesn't fail engine.description() engine.args() - bla = engine.open(self.file, filters=[]) - # with engine.open(self.file, filters=[]) as ts: - # count = 0 - # for var in ts.variables(): - # count += len(ts.data(var)) - # self.assertEqual(count, 208) - # self.assertEqual(len(ts.stations()), 4) + # bla = engine.open(self.file, filters=[]) + with engine.open(self.file, filters=[]) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 39972) + self.assertEqual(len(ts.stations()), 4) # def test_stationfilter(self): # engine = pyaro.list_timeseries_engines()["csv_timeseries"] From bf0c82a0f7f8755a8b5c9e7ef93282d95d1fd4db Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Mon, 4 Dec 2023 14:54:49 +0100 Subject: [PATCH 03/10] 1st version with all original tests passing --- .../AeronetSunTimeseriesReader.py | 46 +++++---------- tests/test_AERONETTimeSeriesReader.py | 57 +++++++++---------- 2 files changed, 42 insertions(+), 61 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index b99f499..7ebbaa2 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,6 +1,6 @@ import csv import numpy as np -from pyaro.timeseries import Data, NpStructuredData, Flag, Reader, Station, Engine +from pyaro.timeseries import Data, NpStructuredData, Flag, AutoFilterReaderEngine, Station, Engine import requests, zipfile, io import geocoder from tqdm import tqdm @@ -42,7 +42,9 @@ ] -class AeronetSunTimeseriesReader(Reader): +class AeronetSunTimeseriesReader( + AutoFilterReaderEngine.AutoFilterReader +): def __init__( self, filename, @@ -78,10 +80,8 @@ def __init__( crd = csv.DictReader(csvfile, fieldnames=self._fields, **csvreader_kwargs) for _ridx, row in enumerate(crd): - # for _ridx in tqdm(range(len(crd))): - # row = crd[_ridx] if row[SITE_NAME] != _laststatstr: - print(f"Next station {row[SITE_NAME]}") + print(f"reading station {row[SITE_NAME]}...") _laststatstr = row[SITE_NAME] # new station station = row[SITE_NAME] @@ -90,7 +90,9 @@ def __init__( alt = float(row["Site_Elevation(m)"]) if FILL_COUNTRY_FLAG: try: - country = geocoder.osm([lat, lon], method='reverse').json['country_code'] + country = geocoder.osm([lat, lon], method="reverse").json[ + "country_code" + ] except: country = "NN" else: @@ -115,7 +117,9 @@ def __init__( if variable in self._data: da = self._data[variable] if da.units != units: - raise Exception(f"unit change from '{da.units}' to 'units'") + raise Exception( + f"unit change from '{da.units}' to 'units'" + ) else: da = NpStructuredData(variable, units) self._data[variable] = da @@ -126,11 +130,9 @@ def __init__( start = np.datetime64(datestring) end = start value = float(row[variable]) - self._data[variable].append(value, station, lat, lon, alt, start, end, Flag.VALID, np.nan) - - - - print(crd.fieldnames) + self._data[variable].append( + value, station, lat, lon, alt, start, end, Flag.VALID, np.nan + ) def _unfiltered_data(self, varname) -> Data: return self._data[varname] @@ -141,26 +143,6 @@ def _unfiltered_stations(self) -> dict[str, Station]: def _unfiltered_variables(self) -> list[str]: return list(self._data.keys()) - def variables(self) -> list[str]: - vars = self._unfiltered_variables() - for fi in self._filters: - vars = fi.filter_variables(vars) - return vars - - def stations(self) -> dict[str, Station]: - stats = self._unfiltered_stations() - for fi in self._filters: - stats = fi.filter_stations(stats) - return stats - - def data(self, varname) -> Data: - dat = self._unfiltered_data(varname) - stats = self._unfiltered_stations() - vars = self._unfiltered_variables() - for fi in self._filters: - dat = fi.filter_data(dat, stats, vars) - return dat - def close(self): pass diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index 7cdd000..e7dbb4c 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -20,7 +20,6 @@ def test_init(self): # just see that it doesn't fail engine.description() engine.args() - # bla = engine.open(self.file, filters=[]) with engine.open(self.file, filters=[]) as ts: count = 0 for var in ts.variables(): @@ -28,34 +27,34 @@ def test_init(self): self.assertEqual(count, 39972) self.assertEqual(len(ts.stations()), 4) - # def test_stationfilter(self): - # engine = pyaro.list_timeseries_engines()["csv_timeseries"] - # sfilter = pyaro.timeseries.filters.get("stations", exclude=["station1"]) - # with engine.open(self.file, filters=[sfilter]) as ts: - # count = 0 - # for var in ts.variables(): - # count += len(ts.data(var)) - # self.assertEqual(count, 104) - # self.assertEqual(len(ts.stations()), 1) - # - # def test_wrappers(self): - # engine = pyaro.list_timeseries_engines()["csv_timeseries"] - # newsox = "oxidised_sulphur" - # with VariableNameChangingReader( - # engine.open(self.file, filters=[]), {"SOx": newsox} - # ) as ts: - # self.assertEqual(ts.data(newsox).variable, newsox) - # pass - # - # def test_variables_filter(self): - # engine = pyaro.list_timeseries_engines()["csv_timeseries"] - # newsox = "oxidised_sulphur" - # vfilter = pyaro.timeseries.filters.get( - # "variables", reader_to_new={"SOx": newsox} - # ) - # with engine.open(self.file, filters=[vfilter]) as ts: - # self.assertEqual(ts.data(newsox).variable, newsox) - # pass + def test_stationfilter(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) + with engine.open(self.file, filters=[sfilter]) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 39020) + self.assertEqual(len(ts.stations()), 3) + + def test_wrappers(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + new_var_name = "od500aer" + with VariableNameChangingReader( + engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} + ) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + pass + + def test_variables_filter(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + new_var_name = "od500aer" + vfilter = pyaro.timeseries.filters.get( + "variables", reader_to_new={"AOD_500nm": new_var_name} + ) + with engine.open(self.file, filters=[vfilter]) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + pass if __name__ == "__main__": From bcfb05d9a2f4dc01b541bd429b9c6d02ddcdf1dc Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Mon, 4 Dec 2023 15:42:09 +0100 Subject: [PATCH 04/10] added the computation of AOD@550nm (based on AOD@440nm) --- .../AeronetSunTimeseriesReader.py | 90 ++++++++++++++++--- tests/test_AERONETTimeSeriesReader.py | 8 +- 2 files changed, 84 insertions(+), 14 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 7ebbaa2..61d32ec 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,6 +1,13 @@ import csv import numpy as np -from pyaro.timeseries import Data, NpStructuredData, Flag, AutoFilterReaderEngine, Station, Engine +from pyaro.timeseries import ( + Data, + NpStructuredData, + Flag, + AutoFilterReaderEngine, + Station, + Engine, +) import requests, zipfile, io import geocoder from tqdm import tqdm @@ -10,6 +17,8 @@ # number of lines to read before the reading is handed to Pythobn's csv reader HEADER_LINE_NO = 7 DELIMITER = "," +# +NAN_VAL = -999.0 # main variables to store LAT_NAME = "Site_Latitude(Degrees)" LON_NAME = "Site_Longitude(Degrees)" @@ -21,8 +30,13 @@ ANG4487_NAME = "440-870_Angstrom_Exponent" AOD440_NAME = "AOD_440nm" AOD870_NAME = "AOD_870nm" +AOD550_NAME = "AOD_550nm" DATA_VARS = [AOD500_NAME, ANG4487_NAME, AOD440_NAME, AOD870_NAME] +COMPUTED_VARS = [AOD550_NAME] +# The computed variables have to be named after the read ones, otherwise the calculation will fail! +DATA_VARS.extend(COMPUTED_VARS) + FILL_COUNTRY_FLAG = False # further vars can be added here @@ -42,9 +56,7 @@ ] -class AeronetSunTimeseriesReader( - AutoFilterReaderEngine.AutoFilterReader -): +class AeronetSunTimeseriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, filename, @@ -123,16 +135,33 @@ def __init__( else: da = NpStructuredData(variable, units) self._data[variable] = da + + day, month, year = row[DATE_NAME].split(":") + datestring = "-".join([year, month, day]) + datestring = "T".join([datestring, row[TIME_NAME]]) + start = np.datetime64(datestring) + end = start + + ts_dummy_data = {} for variable in DATA_VARS: - day, month, year = row[DATE_NAME].split(":") - datestring = "-".join([year, month, day]) - datestring = "T".join([datestring, row[TIME_NAME]]) - start = np.datetime64(datestring) - end = start - value = float(row[variable]) + try: + value = float(row[variable]) + if value == NAN_VAL: + value = np.nan + ts_dummy_data[variable] = value + except KeyError: + # computed variable + if variable == AOD550_NAME: + value = self.compute_od_from_angstromexp( + 0.55, + ts_dummy_data[AOD440_NAME], + 0.44, + ts_dummy_data[ANG4487_NAME], + ) self._data[variable].append( value, station, lat, lon, alt, start, end, Flag.VALID, np.nan ) + # add computed variables def _unfiltered_data(self, varname) -> Data: return self._data[varname] @@ -146,6 +175,47 @@ def _unfiltered_variables(self) -> list[str]: def close(self): pass + def compute_od_from_angstromexp( + self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float + ) -> float: + """Compute AOD at specified wavelength + + Uses Angstrom coefficient and reference AOD to compute the + corresponding wavelength shifted AOD + + Parameters + ---------- + to_lambda : :obj:`float` or :obj:`ndarray` + wavelength for which AOD is calculated + od_ref : :obj:`float` or :obj:`ndarray` + reference AOD + lambda_ref : :obj:`float` or :obj:`ndarray` + wavelength corresponding to reference AOD + angstrom_coeff : :obj:`float` or :obj:`ndarray` + Angstrom coefficient + + Returns + ------- + :obj:`float` or :obj:`ndarray` + AOD(s) at shifted wavelength + + """ + return od_ref * (lambda_ref / to_lambda) ** angstrom_coeff + + def calc_angstroem_coeff( + self, od1: float, od2: float, wl1: float, wl2: float + ) -> float: + """ + small helper method to calculate angstroem coefficient + + :param od1: + :param od2: + :param wl1: + :param wl2: + :return: + """ + return -np.log(od1 / od2) / np.log(wl1 / wl2) + class AeronetSunTimeseriesEngine(Engine): def open(self, filename, *args, **kwargs) -> AeronetSunTimeseriesReader: diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index e7dbb4c..c6937b1 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -24,7 +24,7 @@ def test_init(self): count = 0 for var in ts.variables(): count += len(ts.data(var)) - self.assertEqual(count, 39972) + self.assertEqual(count, 49965) self.assertEqual(len(ts.stations()), 4) def test_stationfilter(self): @@ -34,7 +34,7 @@ def test_stationfilter(self): count = 0 for var in ts.variables(): count += len(ts.data(var)) - self.assertEqual(count, 39020) + self.assertEqual(count, 48775) self.assertEqual(len(ts.stations()), 3) def test_wrappers(self): @@ -48,9 +48,9 @@ def test_wrappers(self): def test_variables_filter(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - new_var_name = "od500aer" + new_var_name = "od550aer" vfilter = pyaro.timeseries.filters.get( - "variables", reader_to_new={"AOD_500nm": new_var_name} + "variables", reader_to_new={"AOD_550nm": new_var_name} ) with engine.open(self.file, filters=[vfilter]) as ts: self.assertEqual(ts.data(new_var_name).variable, new_var_name) From 956bc7e41057b4f4cfbebecb49eb8863a092f5fd Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Mon, 4 Dec 2023 16:15:43 +0100 Subject: [PATCH 05/10] make country code upper case, add test where the country code is set --- .../AeronetSunTimeseriesReader.py | 26 +++++-------------- tests/test_AERONETTimeSeriesReader.py | 2 +- 2 files changed, 8 insertions(+), 20 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 61d32ec..53efdc9 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -39,29 +39,13 @@ FILL_COUNTRY_FLAG = False -# further vars can be added here -VARS_TO_STORE = [ - LAT_NAME, - LON_NAME, - ALT_NAME, - SITE_NAME, - DATE_NAME, - TIME_NAME, - AOD500_NAME, - ANG4487_NAME, - AOD440_NAME, - AOD870_NAME, - "AERONET_Instrument_Number", - "Data_Quality_Level", -] - - class AeronetSunTimeseriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, filename, csvreader_kwargs={"delimiter": DELIMITER}, filters=[], + fill_country_flag:bool = FILL_COUNTRY_FLAG, ): """open a new csv timeseries-reader @@ -84,6 +68,7 @@ def __init__( self._filters = filters self._header = [] _laststatstr = "" + with open(self._filename, newline="") as csvfile: for _hidx in range(HEADER_LINE_NO - 1): self._header.append(csvfile.readline()) @@ -100,15 +85,17 @@ def __init__( lon = float(row[LON_NAME]) lat = float(row[LAT_NAME]) alt = float(row["Site_Elevation(m)"]) - if FILL_COUNTRY_FLAG: + if fill_country_flag: try: country = geocoder.osm([lat, lon], method="reverse").json[ "country_code" ] + country = country.upper() except: country = "NN" else: country = "NN" + # print(country) # units of Aeronet data are always 1 units = "1" if not station in self._stations: @@ -148,6 +135,8 @@ def __init__( value = float(row[variable]) if value == NAN_VAL: value = np.nan + # store value in ts_dummy_data, so we don't need to perform the nan check + # for each component of calculated values again ts_dummy_data[variable] = value except KeyError: # computed variable @@ -161,7 +150,6 @@ def __init__( self._data[variable].append( value, station, lat, lon, alt, start, end, Flag.VALID, np.nan ) - # add computed variables def _unfiltered_data(self, varname) -> Data: return self._data[varname] diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index c6937b1..b077bc4 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -20,7 +20,7 @@ def test_init(self): # just see that it doesn't fail engine.description() engine.args() - with engine.open(self.file, filters=[]) as ts: + with engine.open(self.file, filters=[], fill_country_flag=True) as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) From bdc043e29166caa5ed03ba912f0e38576814b7fa Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Wed, 6 Dec 2023 11:15:45 +0100 Subject: [PATCH 06/10] add tests to CI --- .github/workflows/CI.yml | 35 +++++++++++++++++++ pyproject.toml | 4 +-- .../AeronetSunTimeseriesReader.py | 9 +++-- tests/test_AERONETTimeSeriesReader.py | 2 ++ 4 files changed, 44 insertions(+), 6 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index fd5e46f..58e11c7 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -28,3 +28,38 @@ jobs: - name: Run linters continue-on-error: true run: tox -e lint + + venv: + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + python-version: [ '3.11' ] + experimental: [ false ] + os: [ ubuntu-22.04 ] + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Python info + run: | + which python + python --version + - name: Cache pip and tox + uses: actions/cache@v3 + if: ${{ ! matrix.experimental }} + with: + path: | + ~/.cache/pip + ~/.cache/srtm + .tox + key: ${{ matrix.os }}-tox-${{ matrix.python-version }}-${{ hashFiles('setup.cfg', 'pyproject.toml') }} + - name: Install Tox + run: | + python -m pip install --upgrade pip + python -m pip install tox + - name: Run test + continue-on-error: ${{ matrix.experimental }} + run: tox -e py diff --git a/pyproject.toml b/pyproject.toml index 1e4e119..3097e94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,6 +24,7 @@ requires-python = ">=3.9" dependencies = [ "pyaro@git+https://github.com/metno/pyaro", "requests", + "geocoder", ] [project.urls] @@ -52,9 +53,6 @@ skip_missing_interpreters = True isolated_build = True envlist = - py39 - - py310 py311 format diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 53efdc9..3ef9c8e 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -8,9 +8,11 @@ Station, Engine, ) -import requests, zipfile, io + +# import requests, zipfile, io import geocoder -from tqdm import tqdm + +# from tqdm import tqdm # default URL BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" @@ -39,13 +41,14 @@ FILL_COUNTRY_FLAG = False + class AeronetSunTimeseriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, filename, csvreader_kwargs={"delimiter": DELIMITER}, filters=[], - fill_country_flag:bool = FILL_COUNTRY_FLAG, + fill_country_flag: bool = FILL_COUNTRY_FLAG, ): """open a new csv timeseries-reader diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index b077bc4..4c025fb 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -54,6 +54,8 @@ def test_variables_filter(self): ) with engine.open(self.file, filters=[vfilter]) as ts: self.assertEqual(ts.data(new_var_name).variable, new_var_name) + + def test_downloaded_file(self): pass From 46c15ebd50eb943d7e32e4470e150a2a42d5e77a Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Wed, 6 Dec 2023 15:49:56 +0100 Subject: [PATCH 07/10] add tests including downloading --- .../AeronetSunTimeseriesReader.py | 192 ++++++++++-------- tests/test_AERONETTimeSeriesReader.py | 27 ++- 2 files changed, 135 insertions(+), 84 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 3ef9c8e..ce5429b 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -9,9 +9,12 @@ Engine, ) -# import requests, zipfile, io +import requests, zipfile, io import geocoder +from urllib.parse import urlparse + + # from tqdm import tqdm # default URL @@ -72,87 +75,109 @@ def __init__( self._header = [] _laststatstr = "" - with open(self._filename, newline="") as csvfile: - for _hidx in range(HEADER_LINE_NO - 1): - self._header.append(csvfile.readline()) - # get fields from header line although csv can do that as well since we might want to adjust these names - self._fields = csvfile.readline().strip().split(",") - - crd = csv.DictReader(csvfile, fieldnames=self._fields, **csvreader_kwargs) - for _ridx, row in enumerate(crd): - if row[SITE_NAME] != _laststatstr: - print(f"reading station {row[SITE_NAME]}...") - _laststatstr = row[SITE_NAME] - # new station - station = row[SITE_NAME] - lon = float(row[LON_NAME]) - lat = float(row[LAT_NAME]) - alt = float(row["Site_Elevation(m)"]) - if fill_country_flag: - try: - country = geocoder.osm([lat, lon], method="reverse").json[ - "country_code" - ] - country = country.upper() - except: - country = "NN" - else: - country = "NN" - # print(country) - # units of Aeronet data are always 1 - units = "1" - if not station in self._stations: - self._stations[station] = Station( - { - "station": station, - "longitude": lon, - "latitude": lat, - "altitude": alt, - "country": country, - "url": "", - "long_name": station, - } - ) - # every line contains all variables, sometimes filled with NaNs though - if _ridx == 0: - for variable in DATA_VARS: - if variable in self._data: - da = self._data[variable] - if da.units != units: - raise Exception( - f"unit change from '{da.units}' to 'units'" - ) - else: - da = NpStructuredData(variable, units) - self._data[variable] = da - - day, month, year = row[DATE_NAME].split(":") - datestring = "-".join([year, month, day]) - datestring = "T".join([datestring, row[TIME_NAME]]) - start = np.datetime64(datestring) - end = start - - ts_dummy_data = {} - for variable in DATA_VARS: + # check if file is a URL + if self.is_valid_url(self._filename): + from urllib.request import urlopen + from io import BytesIO + from zipfile import ZipFile + + # try to open as zipfile + try: + r = requests.get(self._filename) + zip_ref = ZipFile(BytesIO(r.content)) + for file in zip_ref.namelist(): + with zip_ref.open(file) as response: + lines = [line.decode("utf-8") for line in response.readlines()] + # read only 1st file here + break + except: + response = urlopen(self._filename) + lines = [line.decode("utf-8") for line in response.readlines()] + + else: + with open(self._filename, newline="") as csvfile: + lines = csvfile.readlines() + + for _hidx in range(HEADER_LINE_NO - 1): + self._header.append(lines.pop(0)) + # get fields from header line although csv can do that as well since we might want to adjust these names + self._fields = lines.pop(0).strip().split(",") + + crd = csv.DictReader(lines, fieldnames=self._fields, **csvreader_kwargs) + for _ridx, row in enumerate(crd): + if row[SITE_NAME] != _laststatstr: + print(f"reading station {row[SITE_NAME]}...") + _laststatstr = row[SITE_NAME] + # new station + station = row[SITE_NAME] + lon = float(row[LON_NAME]) + lat = float(row[LAT_NAME]) + alt = float(row["Site_Elevation(m)"]) + if fill_country_flag: try: - value = float(row[variable]) - if value == NAN_VAL: - value = np.nan - # store value in ts_dummy_data, so we don't need to perform the nan check - # for each component of calculated values again - ts_dummy_data[variable] = value - except KeyError: - # computed variable - if variable == AOD550_NAME: - value = self.compute_od_from_angstromexp( - 0.55, - ts_dummy_data[AOD440_NAME], - 0.44, - ts_dummy_data[ANG4487_NAME], - ) - self._data[variable].append( - value, station, lat, lon, alt, start, end, Flag.VALID, np.nan + country = geocoder.osm([lat, lon], method="reverse").json[ + "country_code" + ] + country = country.upper() + except: + country = "NN" + else: + country = "NN" + + # units of Aeronet data are always 1 + units = "1" + if not station in self._stations: + self._stations[station] = Station( + { + "station": station, + "longitude": lon, + "latitude": lat, + "altitude": alt, + "country": country, + "url": "", + "long_name": station, + } ) + # every line contains all variables, sometimes filled with NaNs though + if _ridx == 0: + for variable in DATA_VARS: + if variable in self._data: + da = self._data[variable] + if da.units != units: + raise Exception( + f"unit change from '{da.units}' to 'units'" + ) + else: + da = NpStructuredData(variable, units) + self._data[variable] = da + + day, month, year = row[DATE_NAME].split(":") + datestring = "-".join([year, month, day]) + datestring = "T".join([datestring, row[TIME_NAME]]) + start = np.datetime64(datestring) + end = start + + ts_dummy_data = {} + for variable in DATA_VARS: + try: + value = float(row[variable]) + if value == NAN_VAL: + value = np.nan + # store value in ts_dummy_data, so we don't need to perform the nan check + # for each component of calculated values again + ts_dummy_data[variable] = value + except KeyError: + # computed variable + if variable == AOD550_NAME: + value = self.compute_od_from_angstromexp( + 0.55, + ts_dummy_data[AOD440_NAME], + 0.44, + ts_dummy_data[ANG4487_NAME], + ) + self._data[variable].append( + value, station, lat, lon, alt, start, end, Flag.VALID, np.nan + ) def _unfiltered_data(self, varname) -> Data: return self._data[varname] @@ -207,6 +232,13 @@ def calc_angstroem_coeff( """ return -np.log(od1 / od2) / np.log(wl1 / wl2) + def is_valid_url(self, url): + try: + result = urlparse(url) + return all([result.scheme, result.netloc]) + except ValueError: + return False + class AeronetSunTimeseriesEngine(Engine): def open(self, filename, *args, **kwargs) -> AeronetSunTimeseriesReader: diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index 4c025fb..2b4f242 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -1,11 +1,15 @@ import unittest import os -import numpy as np import pyaro import pyaro.timeseries from pyaro.timeseries.Wrappers import VariableNameChangingReader +TEST_URL = "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv" +TEST_ZIP_URL = ( + "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv.zip" +) + class TestAERONETTimeSeriesReader(unittest.TestCase): file = os.path.join( @@ -14,6 +18,24 @@ class TestAERONETTimeSeriesReader(unittest.TestCase): "aeronetsun_testdata.csv", ) + def test_dl_data_unzipped(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + with engine.open(TEST_URL, filters=[], fill_country_flag=False) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 49965) + self.assertEqual(len(ts.stations()), 4) + + def test_dl_data_zipped(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + with engine.open(TEST_ZIP_URL, filters=[], fill_country_flag=False) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 49965) + self.assertEqual(len(ts.stations()), 4) + def test_init(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") @@ -55,9 +77,6 @@ def test_variables_filter(self): with engine.open(self.file, filters=[vfilter]) as ts: self.assertEqual(ts.data(new_var_name).variable, new_var_name) - def test_downloaded_file(self): - pass - if __name__ == "__main__": unittest.main() From 08eeb5314b92bd001a5b8535d03f396fcd30041e Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Wed, 6 Dec 2023 16:27:56 +0100 Subject: [PATCH 08/10] add progressbar using tqdm --- pyproject.toml | 1 + .../AeronetSunTimeseriesReader.py | 29 ++++++++++--------- 2 files changed, 17 insertions(+), 13 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3097e94..84ea44b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,6 +25,7 @@ dependencies = [ "pyaro@git+https://github.com/metno/pyaro", "requests", "geocoder", + "tqdm", ] [project.urls] diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index ce5429b..8b93729 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,21 +1,18 @@ import csv +from urllib.parse import urlparse + +import geocoder import numpy as np +import requests from pyaro.timeseries import ( + AutoFilterReaderEngine, Data, - NpStructuredData, + Engine, Flag, - AutoFilterReaderEngine, + NpStructuredData, Station, - Engine, ) - -import requests, zipfile, io -import geocoder - -from urllib.parse import urlparse - - -# from tqdm import tqdm +from tqdm import tqdm # default URL BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" @@ -24,6 +21,8 @@ DELIMITER = "," # NAN_VAL = -999.0 +# update progress bar every N lines... +PG_UPDATE_LINES = 100 # main variables to store LAT_NAME = "Site_Latitude(Degrees)" LON_NAME = "Site_Longitude(Degrees)" @@ -77,8 +76,8 @@ def __init__( # check if file is a URL if self.is_valid_url(self._filename): - from urllib.request import urlopen from io import BytesIO + from urllib.request import urlopen from zipfile import ZipFile # try to open as zipfile @@ -104,9 +103,12 @@ def __init__( self._fields = lines.pop(0).strip().split(",") crd = csv.DictReader(lines, fieldnames=self._fields, **csvreader_kwargs) + bar = tqdm(total=len(lines)) for _ridx, row in enumerate(crd): + # if _ridx % PG_UPDATE_LINES == 0: + bar.update(1) if row[SITE_NAME] != _laststatstr: - print(f"reading station {row[SITE_NAME]}...") + # print(f"reading station {row[SITE_NAME]}...") _laststatstr = row[SITE_NAME] # new station station = row[SITE_NAME] @@ -178,6 +180,7 @@ def __init__( self._data[variable].append( value, station, lat, lon, alt, start, end, Flag.VALID, np.nan ) + bar.close() def _unfiltered_data(self, varname) -> Data: return self._data[varname] From c05cd95db44a48a08fde74ea9f26a4bb20c12293 Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Wed, 6 Dec 2023 16:42:09 +0100 Subject: [PATCH 09/10] remove clutter, reorganise imports --- .../AeronetSunTimeseriesReader.py | 21 ++++++------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 8b93729..2d6fdbc 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,17 +1,14 @@ import csv +from io import BytesIO from urllib.parse import urlparse +from urllib.request import urlopen +from zipfile import BadZipFile, ZipFile import geocoder import numpy as np import requests -from pyaro.timeseries import ( - AutoFilterReaderEngine, - Data, - Engine, - Flag, - NpStructuredData, - Station, -) +from pyaro.timeseries import (AutoFilterReaderEngine, Data, Engine, Flag, + NpStructuredData, Station) from tqdm import tqdm # default URL @@ -76,10 +73,6 @@ def __init__( # check if file is a URL if self.is_valid_url(self._filename): - from io import BytesIO - from urllib.request import urlopen - from zipfile import ZipFile - # try to open as zipfile try: r = requests.get(self._filename) @@ -89,7 +82,7 @@ def __init__( lines = [line.decode("utf-8") for line in response.readlines()] # read only 1st file here break - except: + except BadZipFile: response = urlopen(self._filename) lines = [line.decode("utf-8") for line in response.readlines()] @@ -105,10 +98,8 @@ def __init__( crd = csv.DictReader(lines, fieldnames=self._fields, **csvreader_kwargs) bar = tqdm(total=len(lines)) for _ridx, row in enumerate(crd): - # if _ridx % PG_UPDATE_LINES == 0: bar.update(1) if row[SITE_NAME] != _laststatstr: - # print(f"reading station {row[SITE_NAME]}...") _laststatstr = row[SITE_NAME] # new station station = row[SITE_NAME] From 5e455597e2d87c7f9648455092c05b949d413c0b Mon Sep 17 00:00:00 2001 From: Jan Jurgen Griesfeller Date: Wed, 6 Dec 2023 16:44:04 +0100 Subject: [PATCH 10/10] linting --- .../aeronetsunreader/AeronetSunTimeseriesReader.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 2d6fdbc..6f93bdd 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -7,8 +7,14 @@ import geocoder import numpy as np import requests -from pyaro.timeseries import (AutoFilterReaderEngine, Data, Engine, Flag, - NpStructuredData, Station) +from pyaro.timeseries import ( + AutoFilterReaderEngine, + Data, + Engine, + Flag, + NpStructuredData, + Station, +) from tqdm import tqdm # default URL