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Description:

pybioclip 1.0.0

pybioclip

Command line tool and python package to simplify using BioCLIP.
Table of Contents

Installation
Python Package Usage
Command Line Usage
Acknowledgments
License

Requirements

Python compatible with PyTorch

Installation
pip install pybioclip

If you have any issues with installation, please first upgrade pip by running pip install --upgrade pip.
Python Package Usage
Example Notebooks

Predict species for images - examples/PredictImages.ipynb

Predict species for iNaturalist images - examples/iNaturalistPredict.ipynb

Predict species classification
from bioclip import TreeOfLifeClassifier, Rank

classifier = TreeOfLifeClassifier()
predictions = classifier.predict("Ursus-arctos.jpeg", Rank.SPECIES)

for prediction in predictions:
print(prediction["species"], "-", prediction["score"])

Output:
Ursus arctos - 0.9356034994125366
Ursus arctos syriacus - 0.05616999790072441
Ursus arctos bruinosus - 0.004126196261495352
Ursus arctus - 0.0024959812872111797
Ursus americanus - 0.0005009894957765937

Output from the predict() method showing the dictionary structure:
[{
'kingdom': 'Animalia',
'phylum': 'Chordata',
'class': 'Mammalia',
'order': 'Carnivora',
'family': 'Ursidae',
'genus': 'Ursus',
'species_epithet': 'arctos',
'species': 'Ursus arctos',
'common_name': 'Kodiak bear'
'score': 0.9356034994125366
}]

The output from the predict function can be converted into a pandas DataFrame like so:
import pandas as pd
from bioclip import TreeOfLifeClassifier, Rank

classifier = TreeOfLifeClassifier()
predictions = classifier.predict("Ursus-arctos.jpeg", Rank.SPECIES)
df = pd.DataFrame(predictions)

The first argument of the predict() method supports both a single path or a list of paths.
Predict from a list of classes
from bioclip import CustomLabelsClassifier

classifier = CustomLabelsClassifier(["duck","fish","bear"])
predictions = classifier.predict("Ursus-arctos.jpeg")
for prediction in predictions:
print(prediction["classification"], prediction["score"])

Output:
duck 1.0306726583309e-09
fish 2.932403668845507e-12
bear 1.0

Command Line Usage
bioclip predict [-h] [--format {table,csv}] [--output OUTPUT] [--rank {kingdom,phylum,class,order,family,genus,species}] [--k K] [--cls CLS] [--device DEVICE] image_file [image_file ...]
bioclip embed [-h] [--device=DEVICE] [--output=OUTPUT] [IMAGE_FILE...]

Commands:
predict Use BioCLIP to generate predictions for image files.
embed Use BioCLIP to generate embeddings for image files.

Arguments:
IMAGE_FILE input image file

Options:
-h --help
--format=FORMAT format of the output (table or csv) for predict mode [default: csv]
--rank=RANK rank of the classification (kingdom, phylum, class, order, family, genus, species) [default: species]
--k=K number of top predictions to show [default: 5]
--cls=CLS comma separated list of classes to predict, when specified the --rank and --k arguments are not allowed
--device=DEVICE device to use matrix math (cpu or cuda or mps) [default: cpu]
--output=OUTFILE print output to file OUTFILE [default: stdout]

Predict classification
Predict species for an image
The example images used below are Ursus-arctos.jpeg
and Felis-catus.jpeg both from the bioclip-demo.
Predict species for an Ursus-arctos.jpeg file:
bioclip predict Ursus-arctos.jpeg

Output:
bioclip predict Ursus-arctos.jpeg
file_name,kingdom,phylum,class,order,family,genus,species_epithet,species,common_name,score
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos,Ursus arctos,Kodiak bear,0.9356034994125366
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos syriacus,Ursus arctos syriacus,syrian brown bear,0.05616999790072441
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos bruinosus,Ursus arctos bruinosus,,0.004126196261495352
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctus,Ursus arctus,,0.0024959812872111797
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,americanus,Ursus americanus,Louisiana black bear,0.0005009894957765937

Predict species for multiple images saving to a file
To make predictions for files Ursus-arctos.jpeg and Felis-catus.jpeg saving the output to a file named predictions.csv:
bioclip predict --output predictions.csv Ursus-arctos.jpeg Felis-catus.jpeg

The contents of predictions.csv will look like this:
file_name,kingdom,phylum,class,order,family,genus,species_epithet,species,common_name,score
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos,Ursus arctos,Kodiak bear,0.9356034994125366
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos syriacus,Ursus arctos syriacus,syrian brown bear,0.05616999790072441
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctos bruinosus,Ursus arctos bruinosus,,0.004126196261495352
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,arctus,Ursus arctus,,0.0024959812872111797
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Carnivora,Ursidae,Ursus,americanus,Ursus americanus,Louisiana black bear,0.0005009894957765937
Felis-catus.jpeg,Animalia,Chordata,Mammalia,Carnivora,Felidae,Felis,silvestris,Felis silvestris,European Wildcat,0.7221033573150635
Felis-catus.jpeg,Animalia,Chordata,Mammalia,Carnivora,Felidae,Felis,catus,Felis catus,Domestic Cat,0.19810837507247925
Felis-catus.jpeg,Animalia,Chordata,Mammalia,Carnivora,Felidae,Felis,margarita,Felis margarita,Sand Cat,0.02798456884920597
Felis-catus.jpeg,Animalia,Chordata,Mammalia,Carnivora,Felidae,Lynx,felis,Lynx felis,,0.021829601377248764
Felis-catus.jpeg,Animalia,Chordata,Mammalia,Carnivora,Felidae,Felis,bieti,Felis bieti,Chinese desert cat,0.010979168117046356

Predict top 3 genera for an image and display output as a table
bioclip predict --format table --k 3 --rank=genus Ursus-arctos.jpeg

Output:
+-------------------+----------+----------+----------+--------------+----------+--------+------------------------+
| file_name | kingdom | phylum | class | order | family | genus | score |
+-------------------+----------+----------+----------+--------------+----------+--------+------------------------+
| Ursus-arctos.jpeg | Animalia | Chordata | Mammalia | Carnivora | Ursidae | Ursus | 0.9994320273399353 |
| Ursus-arctos.jpeg | Animalia | Chordata | Mammalia | Artiodactyla | Cervidae | Cervus | 0.00032594642834737897 |
| Ursus-arctos.jpeg | Animalia | Chordata | Mammalia | Artiodactyla | Cervidae | Alces | 7.803700282238424e-05 |
+-------------------+----------+----------+----------+--------------+----------+--------+------------------------+

Predict from a list of classes
Create predictions for 3 classes (cat, bird, and bear) for image Ursus-arctos.jpeg:
bioclip predict --cls cat,bird,bear Ursus-arctos.jpeg

Output:
file_name,classification,score
Ursus-arctos.jpeg,cat,4.581644930112816e-08
Ursus-arctos.jpeg,bird,3.051998476166773e-08
Ursus-arctos.jpeg,bear,0.9999998807907104

Create embeddings
Create embedding for an image
bioclip embed Ursus-arctos.jpeg

Output:
{
"model": "hf-hub:imageomics/bioclip",
"embeddings": {
"Ursus-arctos.jpeg": [
-0.23633578419685364,
-0.28467196226119995,
-0.4394485652446747,
...
]
}
}

View command line help
bioclip --help

License
pybioclip is distributed under the terms of the MIT license.
Acknowledgments
The prediction code in this repo is based on work by @samuelstevens in bioclip-demo.