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Command Line Tutorial

Before beginning this tutorial you need to install pybioclip and download two example images: Ursus-arctos.jpeg and Felis-catus.jpeg.

Tree Of Life Predictions

The bioclip predict command, when not supplying a custom list of labels, will create a prediction based on the BioCLIP tree of life embeddings.

Predict species for an image

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

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

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

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

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  |
+-------------------+----------+----------+----------+--------------+----------+--------+------------------------+

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

Predict using a TOL subset

The predict command has support for a --subset <csv-path> argument. The first column in the CSV file must be named kingdom, phylum, class, order, family, genus, or species. The values must match the TOL labels otherwise an error occurs. See the bioclip list-tol-taxa command to create a CSV of TOL labels.

In this example we create a CSV to subset TOL to two orders. Create a CSV named orders.csv with the following content: 

order
Artiodactyla
Rodentia


bioclip predict --subset orders.csv Ursus-arctos.jpeg

Output: 

file_name,kingdom,phylum,class,order,family,genus,species_epithet,species,common_name,score
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Artiodactyla,Cervidae,Cervus,canadensis sibericus,Cervus canadensis sibericus,,0.7347981333732605
Ursus-arctos.jpeg,Animalia,Chordata,Mammalia,Artiodactyla,Cervidae,Alces,alces,Alces alces,European elk,0.17302176356315613
...

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

Custom Label Predictions

To predict with custom labels using the bioclip predict command the --cls or --bins arguments must be used.

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,bear,0.9999998807907104
Ursus-arctos.jpeg,cat,4.581697155003894e-08
Ursus-arctos.jpeg,bird,3.052039332374079e-08

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

Predict from a binning CSV

Create predictions for 3 classes (cat, bird, and bear) with 2 bins (one, two) for image Ursus-arctos.jpeg:

Create a CSV file named bins.csv with the following contents: 

cls,bin
cat,one
bird,one
bear,two
The names of the columns do not matter. The first column values will be used as the classes. The second column values will be used for bin names.

Run predict command: 

bioclip predict --bins bins.csv Ursus-arctos.jpeg

Output: 

Ursus-arctos.jpeg,two,0.9999998807907104
Ursus-arctos.jpeg,one,7.633736487377973e-08

Documentation

The bioclip predict documentation describes all arguments supported by bioclip predict command.

Predict using a custom model

List available models: 

bioclip list-models
Output: 
...
ViT-B-16
ViT-B-16-plus
...
List pretrained models for a model: 
bioclip list-models --model  ViT-B-16
Output: 
...
laion2b_s34b_b88k
...
Create a prediction: 
bioclip predict --cls duck,fish,bear --model ViT-B-16 --pretrained laion2b_s34b_b88k Ursus-arctos.jpeg
Output: 
file_name,classification,score
Ursus-arctos.jpeg,bear,0.9999988079071045
Ursus-arctos.jpeg,fish,1.1098603636128246e-06
Ursus-arctos.jpeg,duck,2.7479762465532076e-08

Create embeddings

The bioclip embed command creates an embedding for one or more image files.

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,
            ...
        ]
    }
}

Documentation

The bioclip embed documentation describes all arguments supported by bioclip embed command.

View command line help

bioclip -h
bioclip <command> -h