ERDDAP plugin for Intake
Project description
forked from https://github.com/jmunroe/intake-erddap.
Intake-ERDDAP
Copyright 2022 Axiom Data Science
See LICENSE
Copyright 2022 James Munroe
For changes prior to 2022-10-19, all contributions are Copyright James Munroe, see PREV-LICENSE.
Check out our Read The Docs page for additional documentation
Intake is a lightweight set of tools for loading and sharing data in data science projects. Intake ERDDAP provides a set of integrations for ERDDAP.
- Quickly identify all datasets from an ERDDAP service in a geographic region, or containing certain variables.
- Produce a pandas DataFrame for a given dataset or query.
- Get an xarray Dataset for the Gridded datasets.
The key features are:
- Pandas DataFrames for any TableDAP dataset.
- xarray Datasets for any GridDAP datasets.
- Query by any or all:
- bounding box
- time
- CF
standard_name
- variable name
- Plaintext Search term
- Save catalogs locally for future use.
User Installation
In the very near future, we will be offering the project on conda. Currently the
project is available on PyPI, so it can be installed using pip
pip install intake-erddap
Developer Installation
Prerequisites
The following are prerequisites for a developer environment for this project:
Note: if mamba
isn't installed, replace all instances of mamba
in the following instructions with conda
.
-
Create the project environment with:
mamba env update -f environment.yml
-
Install the development environment dependencies:
mamba env update -f dev-environment.yml
-
Activate the new virtual environment:
conda activate intake-erddap
-
Install the project to the virtual environment:
pip install -e .
Note that you need to install with pip install .
once to get the entry_points
correct too.
Examples
To create an intake
catalog for all of the ERDDAP's TableDAP offerings use:
import intake_erddap
catalog = intake_erddap.ERDDAPCatalogReader(
server="https://erddap.sensors.ioos.us/erddap"
).read()
The catalog objects behave like a dictionary with the keys representing the dataset's unique identifier within ERDDAP, and the values being the TableDAPReader
objects. To access a Reader object (for a single dataset, in this case for dataset_id "aoos_204"):
dataset = catalog["aoos_204"]
From the reader object, a pandas DataFrame can be retrieved:
df = dataset.read()
Find other dataset_ids available with
list(catalog)
Consider a case where you need to find all wind data near Florida:
import intake_erddap
from datetime import datetime
bbox = (-87.84, 24.05, -77.11, 31.27)
catalog = intake_erddap.ERDDAPCatalogReader(
server="https://erddap.sensors.ioos.us/erddap",
bbox=bbox,
intersection="union",
start_time=datetime(2022, 1, 1),
end_time=datetime(2023, 1, 1),
standard_names=["wind_speed", "wind_from_direction"],
variables=["wind_speed", "wind_from_direction"],
).read()
dataset_id = list(catalog)[0]
print(dataset_id)
df = catalog[dataset_id].read()
Using the standard_names
input with intersection="union"
searches for datasets that have both "wind_speed" and "wind_from_direction". Using the variables
input subsequently narrows the dataset to only those columns, plus "time", "latitude", "longitude", and "z".
time (UTC) latitude (degrees_north) ... wind_speed (m.s-1) wind_from_direction (degrees)
0 2022-01-01T00:00:00Z 28.508 ... 3.6 126.0
1 2022-01-01T00:10:00Z 28.508 ... 3.8 126.0
2 2022-01-01T00:20:00Z 28.508 ... 3.6 124.0
3 2022-01-01T00:30:00Z 28.508 ... 3.4 125.0
4 2022-01-01T00:40:00Z 28.508 ... 3.5 124.0
... ... ... ... ... ...
52524 2022-12-31T23:20:00Z 28.508 ... 5.9 176.0
52525 2022-12-31T23:30:00Z 28.508 ... 6.8 177.0
52526 2022-12-31T23:40:00Z 28.508 ... 7.2 175.0
52527 2022-12-31T23:50:00Z 28.508 ... 7.4 169.0
52528 2023-01-01T00:00:00Z 28.508 ... 8.1 171.0
[52529 rows x 6 columns]
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