app.py

import collections
import heapq
import json
import os
import logging

import gradio as gr
import numpy as np
import torch
import torch.nn.functional as F
from open_clip import create_model, get_tokenizer
from torchvision import transforms

from templates import openai_imagenet_template

log_format = "[%(asctime)s] [%(levelname)s] [%(name)s] %(message)s"
logging.basicConfig(level=logging.INFO, format=log_format)
logger = logging.getLogger()


model_str = "hf-hub:imageomics/bioclip"
tokenizer_str = "ViT-B-16"

txt_emb_npy = r"txt_emb_species.npy"
txt_names_json = r"txt_emb_species.json"


min_prob = 1e-9
k = 5

device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")

preprocess_img = transforms.Compose(
    [
        transforms.ToTensor(),
        transforms.Resize((224, 224), antialias=True),
        transforms.Normalize(
            mean=(0.48145466, 0.4578275, 0.40821073),
            std=(0.26862954, 0.26130258, 0.27577711),
        ),
    ]
)

ranks = ("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")

open_domain_examples = [

    ['example1_Pararge_aegeria.jpg', "Species"]

]
zero_shot_examples = [
    ['example1_Pararge_aegeria.jpg', "Pararge aegeria \nPieris brassicae \nSatyrium w-album \nDanaus chrysippus"]
    ]


def indexed(lst, indices):
    return [lst[i] for i in indices]


@torch.no_grad()
def get_txt_features(classnames, templates):
    all_features = []
    for classname in classnames:
        txts = [template(classname) for template in templates]
        txts = tokenizer(txts).to(device)
        txt_features = model.encode_text(txts)
        txt_features = F.normalize(txt_features, dim=-1).mean(dim=0)
        txt_features /= txt_features.norm()
        all_features.append(txt_features)
    all_features = torch.stack(all_features, dim=1)
    return all_features


@torch.no_grad()
def zero_shot_classification(img, cls_str: str) -> dict[str, float]:
    classes = [cls.strip() for cls in cls_str.split("\n") if cls.strip()]
    txt_features = get_txt_features(classes, openai_imagenet_template)

    img = preprocess_img(img).to(device)
    img_features = model.encode_image(img.unsqueeze(0))
    img_features = F.normalize(img_features, dim=-1)

    logits = (model.logit_scale.exp() * img_features @ txt_features).squeeze()
    probs = F.softmax(logits, dim=0).to("cpu").tolist()
    return {cls: prob for cls, prob in zip(classes, probs)}


def format_name(taxon, common):
    taxon = " ".join(taxon)
    if not common:
        return taxon
    return f"{taxon} ({common})"


@torch.no_grad()
def open_domain_classification(img, rank: int) -> dict[str, float]:
    """
    Predicts from the entire tree of life.
    If targeting a higher rank than species, then this function predicts among all
    species, then sums up species-level probabilities for the given rank.
    """
    img = preprocess_img(img).to(device)
    img_features = model.encode_image(img.unsqueeze(0))
    img_features = F.normalize(img_features, dim=-1)

    logits = (model.logit_scale.exp() * img_features @ txt_emb).squeeze()
    probs = F.softmax(logits, dim=0)

    # If predicting species, no need to sum probabilities.
    if rank + 1 == len(ranks):
        topk = probs.topk(k)
        return {
            format_name(*txt_names[i]): prob for i, prob in zip(topk.indices, topk.values)
        }

    # Sum up by the rank
    output = collections.defaultdict(float)
    for i in torch.nonzero(probs > min_prob).squeeze():
        output[" ".join(txt_names[i][0][: rank + 1])] += probs[i]

    topk_names = heapq.nlargest(k, output, key=output.get)

    return {name: output[name] for name in topk_names}


def change_output(choice):
    return gr.Label(num_top_classes=k, label=ranks[choice], show_label=True, value=None)



js = """
function createGradioAnimation() {
    var container = document.createElement('div');
    container.id = 'gradio-animation';
    container.style.fontSize = '2em';
    container.style.fontWeight = 'bold';
    container.style.textAlign = 'center';
    container.style.marginBottom = '20px';

    var text = 'Global Species Identifier: Powered by Artificial Intelligence';
    for (var i = 0; i < text.length; i++) {
        (function(i){
            setTimeout(function(){
                var letter = document.createElement('span');
                letter.style.opacity = '0';
                letter.style.transition = 'opacity 0.5s';
                letter.innerText = text[i];

                container.appendChild(letter);

                setTimeout(function() {
                    letter.style.opacity = '1';
                }, 50);
            }, i * 50);
        })(i);
    }

    var gradioContainer = document.querySelector('.gradio-container');
    gradioContainer.insertBefore(container, gradioContainer.firstChild);

    return 'Animation created';
}
"""

if __name__ == "__main__":
    logger.info("Starting.")
    model = create_model(model_str, output_dict=True, require_pretrained=True)
    model = model.to(device)
    logger.info("Created model.")

   # model = torch.compile(model)
    logger.info("Compiled model.")

    tokenizer = get_tokenizer(tokenizer_str)

    txt_emb = torch.from_numpy(np.load(txt_emb_npy, mmap_mode="r")).to(device)
    with open(txt_names_json) as fd:
        txt_names = json.load(fd)

    done = txt_emb.any(axis=0).sum().item()
    total = txt_emb.shape[1]
    status_msg = ""
    if done != total:
        status_msg = f"{done}/{total} ({done / total * 100:.1f}%) indexed"

    with gr.Blocks(title='Global Species Identifier: Powered by Artificial Intelligence', css="footer {visibility: hidden}", js=js) as app:

        gr.Markdown(
        """
        Upload an image of any plant, animal, or other organism, and our Artificial Intelligence-powered tool will identify the species. Our database covers species from around the world, aiming to support biodiversity awareness and conservation efforts.

Features include:
- **Instant identification** of plants, animals, and other organisms.
- **Detailed information** on species, including habitat, distribution, and conservation status.
- An **interactive, user-friendly interface** designed for both experts and enthusiasts.
- **Continuous learning and improvement** of AI models to expand the app's knowledge base and accuracy.

Join us in exploring the diversity of life on Earth, powered by the intelligence of technology. Start your journey of discovery today!

""")
        img_input = gr.Image()

        with gr.Tab("Open-Ended"):
            with gr.Row():
                with gr.Column():
                    rank_dropdown = gr.Dropdown(
                        label="Taxonomic Rank",
                        info="Which taxonomic rank to predict. Fine-grained ranks (genus, species) are more challenging.",
                        choices=ranks,
                        value="Species",
                        type="index",
                    )
                    open_domain_btn = gr.Button("Submit", variant="primary")
                with gr.Column():
                    open_domain_output = gr.Label(
                        num_top_classes=k,
                        label="Prediction",
                        show_label=True,
                        value=None,
                    )

            with gr.Row():
                gr.Examples(
                    examples=open_domain_examples,
                    inputs=[img_input, rank_dropdown],
                    cache_examples=True,
                    fn=open_domain_classification,
                    outputs=[open_domain_output],
                )


        with gr.Tab("Zero-Shot"):
            with gr.Row():
                with gr.Column():
                    classes_txt = gr.Textbox(
                        placeholder= "Pararge aegeria \nPieris brassicae \nSatyrium w-album \nDanaus chrysippus\n...",
                        lines=3,
                        label="Classes",
                        show_label=True,
                        info="Use taxonomic names where possible; include common names if possible.",
                    )
                    zero_shot_btn = gr.Button("Submit", variant="primary")

                with gr.Column():
                    zero_shot_output = gr.Label(
                        num_top_classes=k, label="Prediction", show_label=True
                    )

            with gr.Row():
                gr.Examples(
                    examples=zero_shot_examples,
                    inputs=[img_input, classes_txt],
                    cache_examples=True,
                    fn=zero_shot_classification,
                    outputs=[zero_shot_output],
                )


        rank_dropdown.change(
            fn=change_output, inputs=rank_dropdown, outputs=[open_domain_output]
        )

        open_domain_btn.click(
            fn=open_domain_classification,
            inputs=[img_input, rank_dropdown],
            outputs=[open_domain_output],
        )

        zero_shot_btn.click(
            fn=zero_shot_classification,
            inputs=[img_input, classes_txt],
            outputs=zero_shot_output,
        )

    app.queue(max_size=20)
    app.launch(show_api=False)