More ways to access with variables¶

The stream-lined way to input variables to ocean_data_gateway is demonstrated in the “Details” section. However, it is still possible to input variables individually by reader. That is demonstrated here.

[1]:

from cf_xarray.units import units  # isort:skip
import pint_xarray  # isort:skip

pint_xarray.unit_registry = units  # isort:skip
import ocean_data_gateway as odg
import pandas as pd
import xarray as xr
import numpy as np
pd.set_option('display.max_rows', 5)

[2]:

kw = {
    "min_lon": -124.0,
    "max_lon": -123.0,
    "min_lat": 39.0,
    "max_lat": 40.0,
    "min_time": '2021-4-1',
    "max_time": '2021-4-2',
}

All variables¶

Don’t input anything with the variables keyword, or use 'variables': None:

[3]:

kwargs = {
          'kw': kw,
          'approach': 'region',
          'readers': [odg.erddap,
                      odg.axds],
          'variables': None
}
data = odg.Gateway(**kwargs)

By variables(s)¶

If no variables are specified for a given reader (for a region search), datasets with any variables will be returned from a search.

However, if you want to specify a variable or variables, keep in mind that different readers have different names for variables, which is why you can’t just input a variable name for all the readers.

This is only relevant for the ERDDAP and Axiom readers currently (it will retain all variables in local files). The Axiom reader of type platform2 will search by variable where the available variable names are specified, and of type layer_group, the query method will be used for variable searching.

Let’s say you want to search for salinity. You can input the base of the word as variables (“sal” or “salinity” but not “salt” since the checker searches for matches with the whole input variable name and “salt” isn’t used for any variable names) and the code will make sure it exactly matches a known variable name. If it cannot match, it will throw an error with suggestions. This is not done automatically since for example “soil_salinity” matches for “salinity”. You need to do this for each known_server for the erddap reader separately, and specific variables will only be used to filter for the axds reader for axds_type='platform2'. Any variable names can be input for the axds reader for axds_type='layer_group'.

You can first check each reader/server individually to determine the variable names you want to use:

[4]:

# IOOS ERDDAP
server = 'http://erddap.sensors.ioos.us/erddap'
odg.search_variables(server, 'sal')

[4]:

	count
variable
salinity	954
salinity_qc	954
...	...
sea_water_practical_salinity_4161sc_a_qc_agg	1
sea_water_practical_salinity_10091sc_a	1

1148 rows × 1 columns

[5]:

# Coastwatch ERDDAP
server = 'http://coastwatch.pfeg.noaa.gov/erddap'
odg.search_variables(server, 'sal')

[5]:

	count
variable
salinity	73
salt	4
...	...
stop_salinity	1
ts_salinity	1

14 rows × 1 columns

[6]:

# axds 'platform2'
odg.search_variables('axds', 'sal')

[6]:

	count
variable
Salinity	3204
Soil Salinity	622

Once you have selected variables that match, the code won’t complain anymore.

[7]:

kwargs = {
          'kw': kw,
          'approach': 'region',
          'readers': [odg.erddap,
                      odg.axds],

          'erddap': {
                          'known_server': ['coastwatch','ioos'],
                           'variables': [['salinity', 'sea_water_salinity'],
                                         ['salinity', 'sea_water_practical_salinity']]
          },
          'axds': {
                          'axds_type': ['platform2','layer_group'],
                         'variables': ['Salinity',
                                       'salinity'  # this one can be called anything that might make a match
                                      ]},
}

data = odg.Gateway(**kwargs)

[8]:

data.dataset_ids

[8]:

['d359748a-fe78-11e7-8128-0023aeec7b98',
 '5104d464-8a30-4720-aeb7-57e801844e6e',
 '3261285c-e3c9-45fd-b777-e6d681a3eaad']

Other actions with variables¶

Demonstrated here are the available functions to work with variables. Currently the ways to call the individiual libraries aren’t pretty but they’ll work. Note that the number of times a variable is used in the system is also included under “count” to see what the popular names are (many are not widely used).

All available variables¶

Return all variables for the two ERDDAP known_servers, then for the Axiom reader axds_type='platform2'.

[9]:

# IOOS ERDDAP
server = 'http://erddap.sensors.ioos.us/erddap'
odg.all_variables(server)

[9]:

	count
variable
air_pressure	4028
air_pressure_10011met_a	2
...	...
wmo_id	954
z	37377

20246 rows × 1 columns

[10]:

# Coastwatch ERDDAP
server = 'http://coastwatch.pfeg.noaa.gov/erddap'
odg.all_variables(server)

[10]:

	count
variable
abund_m3	2
ac_line	1
...	...
z_mean	2
zlev	6

1451 rows × 1 columns

The Axiom reader variables are for axds_type='platform2' not axds_type='layer_group since the latter are more unique grid products that don’t conform well.

[11]:

# axds 'platform2'
odg.all_variables('axds')

[11]:

	count
variable
Ammonium	23
Atmospheric Pressure: Air Pressure at Sea Level	362
...	...
Winds: at 10 m	18
pH	965

200 rows × 1 columns

All available variables, sorted by count¶

[12]:

# IOOS ERDDAP
server = 'http://erddap.sensors.ioos.us/erddap'
odg.search_variables(server, '')

[12]:

	count
variable
time	38331
longitude	38331
...	...
sea_surface_wave_from_direction_elw11b2t01wv_qc_tests	1
sea_water_pressure_7263arc_a	1

20246 rows × 1 columns

[13]:

# Coastwatch ERDDAP
server = 'http://coastwatch.pfeg.noaa.gov/erddap'
odg.search_variables(server, '')

[13]:

	count
variable
time	1637
longitude	1352
...	...
haliotis_fulgens_stderr	1
observationuri	1

1451 rows × 1 columns

[14]:

# axds 'platform2'
odg.search_variables('axds', '')

[14]:

	count
variable
Stream Height	19758
Water Surface above Datum	19489
...	...
CO2: PPM of Carbon Dioxide in Air in Dry Gas	1
Evaporation Rate	1

200 rows × 1 columns

Variables search, sorted by count¶

[15]:

# IOOS ERDDAP
server = 'http://erddap.sensors.ioos.us/erddap'
odg.search_variables(server, 'sal')

[15]:

	count
variable
salinity	954
salinity_qc	954
...	...
sea_water_practical_salinity_4161sc_a_qc_agg	1
sea_water_practical_salinity_10091sc_a	1

1148 rows × 1 columns

[16]:

# Coastwatch ERDDAP
server = 'http://coastwatch.pfeg.noaa.gov/erddap'
odg.search_variables(server, 'sal')

[16]:

	count
variable
salinity	73
salt	4
...	...
stop_salinity	1
ts_salinity	1

14 rows × 1 columns

[17]:

# axds 'platform2'
odg.search_variables('axds', 'sal')

[17]:

	count
variable
Salinity	3204
Soil Salinity	622

Check variables¶

And finally you can check to make sure you have good variables. No news is good news in this. Reminder that you don’t check for axds reader for axds_type=‘layer_group’ because that is searched for in the database just by name as a query.

[18]:

# IOOS ERDDAP
server = 'http://erddap.sensors.ioos.us/erddap'
odg.check_variables(server, ['salinity', 'sea_water_practical_salinity'])

[19]:

# Coastwatch ERDDAP
server = 'http://coastwatch.pfeg.noaa.gov/erddap'
odg.check_variables(server, ['salinity', 'sea_water_salinity'])

[20]:

# axds 'platform2'
odg.check_variables('axds', 'Salinity')