EBAS file query and database browser

The previous tutorial showed how to read EBAS NASA Ames files and gave insights into the structure of these files. However, this did not include the specification of an actual data request (for instance: get data from all stations in the arctic that contain measurements of the AOD between 2010 and 2016).

In this tutorial, we show, how such requests can be specified easily in pyaerocom and how the database can be browsed for instance by variable name, type of instrument, location or other relevant parameters.

The notebook is categorised as follows:

  • Defining a request

  • Retrieve all files for a request

  • Browse the database

Specifying a request

Request parameters can be specified using the EbasSQLRequest class. E.g.:

[1]:
import pyaerocom as pya

request = pya.io.ebas_file_index.EbasSQLRequest(variables=('aerosol_light_scattering_coefficient',
                                                             'aerosol_light_backscattering_coefficient',
                                                             'pressure'),
                                                  start_date="2010-01-01",
                                                  stop_date="2011-01-01")
print(request)
Initating pyaerocom configuration
Checking database access...
Checking access to: /lustre/storeA
Access to lustre database: True
Init data paths for lustre
Expired time: 0.016 s

Pyaerocom EbasSQLRequest
------------------------
variables: ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure')
start_date: 2010-01-01
stop_date: 2011-01-01
station_names: None
matrices: None
altitude_range: None
lon_range: None
lat_range: None
instrument_types: None
statistics: None
datalevel: None
Filename request string:
select distinct filename from variable join station on station.station_code=variable.station_code where comp_name in ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure') and first_end < '2011-01-01' and last_start > '2010-01-01';

You can also output the actual SQL query string:

[2]:
print(request.make_query_str())
select distinct filename from variable join station on station.station_code=variable.station_code where comp_name in ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure') and first_end < '2011-01-01' and last_start > '2010-01-01';

The request class is an extended dictionary and can thus be used like a dictionary:

[3]:
request.update(instrument_types=("nephelometer"))
print(request)

Pyaerocom EbasSQLRequest
------------------------
variables: ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure')
start_date: 2010-01-01
stop_date: 2011-01-01
station_names: None
matrices: None
altitude_range: None
lon_range: None
lat_range: None
instrument_types: nephelometer
statistics: None
datalevel: None
Filename request string:
select distinct filename from variable join station on station.station_code=variable.station_code where instr_type in ('nephelometer') and comp_name in ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure') and first_end < '2011-01-01' and last_start > '2010-01-01';

Execution of file request query

Now that we have defined which files we would like to look into, we can execute the query and retrieve all files that match our specifications. This can be done with the EbasFileIndex class:

[4]:
db = pya.io.EbasFileIndex()
files = db.execute_request(request)
[5]:
print("Total number of files found:{}\nRequest:\n{}".format(len(files), request))
Total number of files found:78
Request:

Pyaerocom EbasSQLRequest
------------------------
variables: ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure')
start_date: 2010-01-01
stop_date: 2011-01-01
station_names: None
matrices: None
altitude_range: None
lon_range: None
lat_range: None
instrument_types: nephelometer
statistics: None
datalevel: None
Filename request string:
select distinct filename from variable join station on station.station_code=variable.station_code where instr_type in ('nephelometer') and comp_name in ('aerosol_light_scattering_coefficient', 'aerosol_light_backscattering_coefficient', 'pressure') and first_end < '2011-01-01' and last_start > '2010-01-01';

Browsing the database

The EbasFileIndex class provides some convenience function that allow to browse meta information for a given request. These are illustrated in the following:

For instance, we can check, what variables could actually be retrieved in the request:

[6]:
print(db.contains_variables(request))
[('pressure',), ('aerosol_light_backscattering_coefficient',), ('aerosol_light_scattering_coefficient',)]

Or what matrices the data contains:

[7]:
print(db.contains_matrices(request))
[('instrument',), ('aerosol',), ('pm10',), ('pm1',)]

Or which station coordinates (lon, lat) the dataset contains:

[8]:
print(db.contains_coordinates(request))
[(23.583333, 42.166667), (-79.783839, 44.231006), (-122.9576034546, 50.059299469), (-104.986864, 54.353743), (-62.3415260315, 82.4991455078), (7.985, 46.5475), (11.0096197128, 47.8014984131), (12.93386, 51.53014), (10.97964, 47.4165), (-8.266, -70.666), (-16.4994, 28.309), (-3.605, 37.164), (-6.733333, 37.1), (2.35, 41.766667), (24.283333, 61.85), (24.116111111, 67.973333333), (2.964886, 45.772223), (25.666667, 35.316667), (19.583333, 46.966667), (-9.89944, 53.32583), (77.151389, 28.427778), (8.633333, 45.8), (10.7, 44.183333), (126.3300018311, 36.5383338928), (126.17, 33.28), (4.926389, 51.970278), (8.252, 58.38853), (11.88668, 78.90715), (2.533333, -72.016667), (-65.618, 18.381), (13.15, 56.016667), (120.87, 23.47), (-156.6114654541, 71.3230133057), (-111.9841, 35.9731), (-112.1288, 36.0778), (-111.6832, 34.3405), (-88.36667, 40.05), (-83.9416, 35.6334), (-112.8, 31.9506), (-109.3889, 32.0097), (-155.5761566162, 19.5362300873), (-86.148, 37.1317), (-68.2608, 44.3772), (-113.9958, 48.5103), (-114.2158, 39.005), (-81.7, 36.2), (-103.1772, 29.3022), (-78.4358, 38.5225), (-122.1243, 46.7582), (-97.484999, 36.605), (-24.7999992371, -89.9969482422), (-124.1510009766, 41.0541000366), (-105.5457, 40.2783), (-111.9692, 35.1406), (-77.04, 38.9), (-109.7958, 34.9139), (18.48968, -34.35348)]

Now, let’s narrow this down:

[9]:
request.update(lat_range=(60, 90))
print(db.contains_coordinates(request))
[(-62.3415260315, 82.4991455078), (24.283333, 61.85), (24.116111111, 67.973333333), (11.88668, 78.90715), (-156.6114654541, 71.3230133057)]

Print all station names:

[10]:
print(db.contains_station_names(request))
[('Alert',), ('Hyytiälä',), ('Pallas (Sammaltunturi)',), ('Zeppelin mountain (Ny-Ålesund)',), ('Barrow',)]

Custom browsing

The previous browsing methods (e.g. contains_coordinates(), contains_matrices, contains_variables) are all just simple wrappers for the general query method make_query_str of the EbasSQLRequest class, that is then called by the EbasFileIndex class using the method execute_request). Thus, if needed, you may define your own request simply by using the provided interface. Here an example using the request constraints specified above. Let’s say we want to retrieve a list of station names and their coordinates (lon, lat, alt). This can be done by calling (we store the results in a list named station_info):

[11]:
query_str = request.make_query_str(what=("station_name",
                                         "station_longitude",
                                         "station_latitude",
                                         "station_altitude"))

station_info = db.execute_request(query_str)

for item in station_info:
    print(item)
('Alert', -62.3415260315, 82.4991455078, 210.0)
('Hyytiälä', 24.283333, 61.85, 181.0)
('Pallas (Sammaltunturi)', 24.116111111, 67.973333333, 565.0)
('Zeppelin mountain (Ny-Ålesund)', 11.88668, 78.90715, 474.0)
('Barrow', -156.6114654541, 71.3230133057, 11.0)

You can see that the results for each station are stored in tuples in the order of the request.

Read all files

Let’s update the file list and read all files.

[12]:
files = db.execute_request(request)
print("Total number of files found: {}".format(len(files)))
Total number of files found: 5

Let’s read the files:

[13]:
import os
data = []
data_dir = os.path.join(pya.const.OBSCONFIG["EBASMC"]["PATH"], 'data')
for f in files:
    data.append(pya.io.EbasNasaAmesFile(os.path.join(data_dir, f[0])))
[14]:
len(data)
[14]:
5