iNaturalist observations along hiking trails

Overview

iNaturalist observations along hiking trails

This tool reads the route of a hike and generates a table of iNaturalist observations along the trails. It also shows the observations and the route of the hike on a map. Moreover, it saves waypoints of the iNaturalist observations for offline navigation with a GPS device or smartphone.

Usage

This is a command-line tool. It is called with a .gpx file that describes the route. This .gpx file can be either after a hike downloaded from a gps device or smartphone or created before a hike by a mapping tool or website. The gpx files in the examples directory have been created with the free website caltopo.com.

Here is an example. This is the command for Linux and macOS

./inat_trails.py examples/Rancho_Canada_del_Oro.gpx

On Windows the command is:

python.exe .\inat_trails.py examples\Rancho_Canada_del_Oro.gpx

The output looks like this:

Reading 'examples/Rancho_Canada_del_Oro.gpx'...
Loaded 13 named roads and trails: Bald Peaks Trail, Canada Del Oro Cut-Off Trail, Canada Del Oro Trail, Casa Loma Road,
    Catamount Trail, Chisnantuk Peak Trail, Little Llagas Creek Trail, Llagas Creek Loop Trail, Longwall Canyon Trail,
    Mayfair Ranch Trail, Needlegrass Trail, Serpentine Loop Trail.
Loaded 2,708 iNaturalist observations of quality-grade 'research' within bounding box.
Excluded 1,694 observations not along route and 13 with low accuracy.
Loaded 829 taxa.
Waypoints written to './Rancho_Canada_del_Oro_Open_Space_Preserve_all_research_waypoints.gpx'.
Table written to './Rancho_Canada_del_Oro_Open_Space_Preserve_all_research_observations.html'.
Map written to './Rancho_Canada_del_Oro_Open_Space_Preserve_all_research_mapped_observations.html'.

This tools finds named trails along this route. It loads iNaturalist observations from the area of the hike and discards those that are not along the trails. It writes three output files, a waypoints file, a table of observations, and an interactive map. Both the table and the map will pop up in a browser.

The waypoint file can be loaded into the free offline navigation app OsmAnd. This will allow this offline navigation app to display the iNaturalist observations along the hiking trails.

The table of observations lists all the organisms that have been observed along the trails along with the trail names they are on. The table for the mammals seen in this park looks like this:

Scientific Name Common Name Observations
Canidae Canids
Canis latrans Coyote Mayfair Ranch Trail: 38860133, 38860889
Urocyon cinereoargenteus Gray Fox Mayfair Ranch Trail: 39391329
Cervidae Deer
Odocoileus hemionus ssp. columbianus Columbian Black-Tailed Deer Casa Loma Road: 80058758; Little Llagas Creek Trail: 68891936; Mayfair Ranch Trail: 19113219, 21319391, 44158629
Cricetidae Hamsters, Voles, Lemmings, and Allies
Neotoma fuscipes Dusky-Footed Woodrat Mayfair Ranch Trail: 52963985
Felidae Felids
Lynx rufus Bobcat Mayfair Ranch Trail: 15630740, 15689757, 38861135
Geomyidae Pocket Gophers
Thomomys bottae Botta's Pocket Gopher Mayfair Ranch Trail: 38869384, 38875049
Leporidae Hares and Rabbits
Sylvilagus bachmani Brush Rabbit Mayfair Ranch Trail: 73152597, 74462983
Sciuridae Squirrels
Neotamias merriami Merriam's Chipmunk Longwall Canyon Trail: 42605223; Mayfair Ranch Trail: 132863, 46538314
Otospermophilus beecheyi California Ground Squirrel Casa Loma Road: 47200360; Mayfair Ranch Trail: 2328803, 15629491, 53667091
Sciurus griseus Western Gray Squirrel Mayfair Ranch Trail: 73152599

The numbers are the observation ids; a click opens them on the iNaturalist website.

The interactive map shows the route and the iNaturalist observations along the hike. Like the iNaturalist website, the markers on the interactive map have different colors for different iconic taxa, e.g. markers for plants are green. Hoovering the mouse over a marker shows the identification, a click on a marker shows a thumbnail picture, the identification, the observer, the date and a special status like invasive or introduced. A further click on that thumbnail opens the observation in the iNaturalist website in another browser window.

Command-line options

This script is a command-line tool. It is called with options and file names as arguments. These options are supported:

usage: inat_trails.py [-h] [--quality_grade QUALITY_GRADE] [--iconic_taxon ICONIC_TAXON] gpx_file [gpx_file ...]

positional arguments:
  gpx_file              Import GPS track from .gpx file.

optional arguments:
  -h, --help            show this help message and exit
  --quality_grade QUALITY_GRADE
                        Observation quality-grade, values: all, casual, needs_id, research; default research.
  --iconic_taxon ICONIC_TAXON
                        Iconic taxon, values: all, Actinopterygii, Amphibia, Animalia, Arachnida, Aves, Chromista,
                        Fungi, Insecta, Mammalia, Mollusca, Plantae, Protozoa, Reptilia; default all.

Option --quality_grade spcifies the desired quality-grade of the observations to show. By default, only research-grade observations are shown. Alternatively, all quality grades, or only casual and needs_id can be requested.

Option --iconic_taxon allows to restrict the observations to an iconic taxon. This can be used to display observations of e.g. only birds or only plants.

Dependencies

A handful of dependencies need to be installed in order for inat_trails.py to run. Besides Python 3.7 or later, a few packages are needed. On Ubuntu or other Debian-based Linux distributions the dependencies can be installed with:

sudo apt install --yes python3-pip python3-aiohttp python3-fiona python3-shapely
pip3 install folium

On other operating systems, Python 3.7 or later and pip need to be installed first and then the dependencies can be installed with:

pip install aiohttp folium shapely
pip install fiona

Note that pip fails to install fiona on Windows. This blogpost has a workaround.

When appropriate pip3 should be called instead of pip to avoid accidentally installing packages for Python 2.

A library to access OpenStreetMap related services

OSMPythonTools The python package OSMPythonTools provides easy access to OpenStreetMap (OSM) related services, among them an Overpass endpoint, Nomina

Franz-Benjamin Mocnik 342 Dec 31, 2022
Python library to visualize circular plasmid maps

Plasmidviewer Plasmidviewer is a Python library to visualize plasmid maps from GenBank. This library provides only the function to visualize circular

Mori Hideto 9 Dec 04, 2022
:earth_asia: Python Geocoder

Python Geocoder Simple and consistent geocoding library written in Python. Table of content Overview A glimpse at the API Forward Multiple results Rev

Denis 1.5k Jan 02, 2023
Histogram matching plugin for rasterio

rio-hist Histogram matching plugin for rasterio. Provides a CLI and python module for adjusting colors based on histogram matching in a variety of col

Mapbox 75 Sep 23, 2022
Starlite-tile38 - Showcase using Tile38 via pyle38 in a Starlite application

Starlite-Tile38 Showcase using Tile38 via pyle38 in a Starlite application. Repo

Ben 8 Aug 07, 2022
Simple CLI for Google Earth Engine Uploads

geeup: Simple CLI for Earth Engine Uploads with Selenium Support This tool came of the simple need to handle batch uploads of both image assets to col

Samapriya Roy 79 Nov 26, 2022
Bacon - Band-limited Coordinate Networks for Multiscale Scene Representation

BACON: Band-limited Coordinate Networks for Multiscale Scene Representation Project Page | Video | Paper Official PyTorch implementation of BACON. BAC

Stanford Computational Imaging Lab 144 Dec 29, 2022
A Python framework for building geospatial web-applications

Hey there, this is Greppo... A Python framework for building geospatial web-applications. Greppo is an open-source Python framework that makes it easy

Greppo 304 Dec 27, 2022
ArcGIS Python Toolbox for WhiteboxTools

WhiteboxTools-ArcGIS ArcGIS Python Toolbox for WhiteboxTools. This repository is related to the ArcGIS Python Toolbox for WhiteboxTools, which is an A

Qiusheng Wu 190 Dec 30, 2022
ESMAC diags - Earth System Model Aerosol-Cloud Diagnostics Package

Earth System Model Aerosol-Cloud Diagnostics Package This Earth System Model (ES

Pacific Northwest National Laboratory 1 Jan 04, 2022
Platform for building statistical models of cities and regions

UrbanSim UrbanSim is a platform for building statistical models of cities and regions. These models help forecast long-range patterns in real estate d

Urban Data Science Toolkit 419 Dec 30, 2022
Open Data Cube analyses continental scale Earth Observation data through time

Open Data Cube Core Overview The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth obse

Open Data Cube 410 Dec 13, 2022
Digital Earth Australia notebooks and tools repository

Repository for Digital Earth Australia Jupyter Notebooks: tools and workflows for geospatial analysis with Open Data Cube and xarray

Geoscience Australia 335 Dec 24, 2022
Ingest and query genomic intervals from multiple BED files

Ingest and query genomic intervals from multiple BED files.

4 May 29, 2021
Satellite imagery for dummies.

felicette Satellite imagery for dummies. What can you do with this tool? TL;DR: Generate JPEG earth imagery from coordinates/location name with public

Shivashis Padhi 1.8k Jan 03, 2023
A python package that extends Google Earth Engine.

A python package that extends Google Earth Engine GitHub: https://github.com/davemlz/eemont Documentation: https://eemont.readthedocs.io/ PyPI: https:

David Montero Loaiza 307 Jan 01, 2023
A trivia questions about Europe

EUROPE TRIVIA QUIZ IN PYTHON Project Outline Ask user if he / she knows more about Europe. If yes show the Trivia main screen, else show the end Trivi

David Danso 1 Nov 17, 2021
WIP: extracting Geometry utilities from datacube-core

odc.geo This is still work in progress. This repository contains geometry related code extracted from Open Datacube. For details and motivation see OD

Open Data Cube 34 Jan 09, 2023
An API built to format given addresses using Python and Flask.

An API built to format given addresses using Python and Flask. About The API returns properly formatted data, i.e. removing duplicate fields, distingu

1 Feb 27, 2022
A package to fetch sentinel 2 Satellite data from Google.

Sentinel 2 Data Fetcher Installation Create a Virtual Environment and activate it. python3 -m venv venv . venv/bin/activate Install the Package via pi

1 Nov 18, 2021