search

pyinat / pyinaturalist

Python client for iNaturalist
https://pyinaturalist.readthedocs.io
MIT License
130 stars 17 forks source link
api api-client biodiversity biodiversity-data biodiversity-informatics citizen-science inaturalist python

readme

pyinaturalist

Build Codecov Documentation

PyPI Conda PyPI - Python Versions

Run with Binder Open in VSCode


Introduction

iNaturalist is a community science platform that helps people get involved in the natural world by observing and identifying the living things around them. Collectively, the community produces a rich source of global biodiversity data that can be valuable to anyone from hobbyists to scientists.

pyinaturalist is a client for the iNaturalist API that makes these data easily accessible in the python programming language.

Features

Supported Endpoints

Many of the most relevant API endpoints are supported, including:

Quickstart

Here are usage examples for some of the most commonly used features.

First, install with pip:

pip install pyinaturalist

Then, import the main API functions:

from pyinaturalist import *

Search observations

Let's start by searching for all your own observations. There are numerous fields you can search on, but we'll just use user_id for now:

>>> observations = get_observations(user_id='my_username')

The full response will be in JSON format, but we can use pyinaturalist.pprint() to print out a summary:

>>> for obs in observations['results']:
>>>    pprint(obs)
ID         Taxon                               Observed on   User     Location
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
117585709  Genus: Hyoscyamus (henbanes)        May 18, 2022  niconoe  Calvi, France
117464920  Genus: Omophlus                     May 17, 2022  niconoe  Galéria, France
117464393  Genus: Briza (Rattlesnake Grasses)  May 17, 2022  niconoe  Galéria, France
...

You can also get observation counts by species. On iNaturalist.org, this information can be found on the 'Species' tab of search results. For example, to get species counts of all your own research-grade observations:

>>> counts = get_observation_species_counts(user_id='my_username', quality_grade='research')
>>> pprint(counts)
 ID     Rank      Scientific name               Common name             Count
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
47934   species   🐛 Libellula luctuosa         Widow Skimmer           7
48627   species   🌻 Echinacea purpurea         Purple Coneflower       6
504060  species   🍄 Pleurotus citrinopileatus  Golden Oyster Mushroom  6
...

Another useful format is the observation histogram, which shows the number of observations over a given interval. The default is month_of_year:

>>> histogram = get_observation_histogram(user_id='my_username')
>>> print(histogram)
{
    1: 8,  # January
    2: 1,  # February
    3: 19, # March
    ...,   # etc.
}

Create and update observations

To create or modify observations, you will first need to log in. This requires creating an iNaturalist app, which will be used to get an access token.

token = get_access_token(
    username='my_username',
    password='my_password',
    app_id='my_app_id',
    app_secret='my_app_secret',
)

See Authentication for more options including environment variables, keyrings, and password managers.

Now we can create a new observation:

from datetime import datetime

response = create_observation(
    taxon_id=54327,  # Vespa Crabro
    observed_on_string=datetime.now(),
    time_zone='Brussels',
    description='This is a free text comment for the observation',
    tag_list='wasp, Belgium',
    latitude=50.647143,
    longitude=4.360216,
    positional_accuracy=50,  # GPS accuracy in meters
    access_token=token,
    photos=['~/observations/wasp1.jpg', '~/observations/wasp2.jpg'],
    sounds=['~/observations/recording.mp3'],
)

# Save the new observation ID
new_observation_id = response[0]['id']

We can then update the observation information, photos, or sounds:

update_observation(
    new_observation_id,
    access_token=token,
    description='updated description !',
    photos='~/observations/wasp_nest.jpg',
    sounds='~/observations/wasp_nest.mp3',
)

Search species

Let's say you partially remember either a genus or family name that started with 'vespi'-something. The taxa endpoint can be used to search by name, rank, and several other criteria

>>> response = get_taxa(q='vespi', rank=['genus', 'family'])

As with observations, there is a lot of information in the response, but we'll print just a few basic details:

>>> pprint(response)
[52747] Family: Vespidae (Hornets, Paper Wasps, Potter Wasps, and Allies)
[92786] Genus: Vespicula
[84737] Genus: Vespina
...

Next Steps

For more information, see:

Feedback

If you have any problems, suggestions, or questions about pyinaturalist, you are welcome to create an issue or discussion. Also, PRs are welcome!

Note: pyinaturalist is developed by members of the iNaturalist community, and is not endorsed by iNaturalist.org or the California Academy of Sciences. If you have non-python-specific questions about the iNaturalist API or iNaturalist in general, the iNaturalist Community Forum is the best place to start.

Related Projects

Other python projects related to iNaturalist: