app.py

import os
import numpy as np
import gradio as gr
from glob import glob
from functools import partial
from dataclasses import dataclass

import torch
import torch.nn.functional as F
import torchvision.transforms as TF
from transformers import SegformerForSemanticSegmentation


@dataclass
class Configs:
    NUM_CLASSES: int = 4  # including background.
    CLASSES: tuple = ("Large bowel", "Small bowel", "Stomach")
    IMAGE_SIZE: tuple[int, int] = (288, 288)  # W, H
    MEAN: tuple = (0.485, 0.456, 0.406)
    STD: tuple = (0.229, 0.224, 0.225)
    MODEL_PATH: str = os.path.join(os.getcwd(), "segformer_trained_weights")


def get_model(*, model_path, num_classes):
    model = SegformerForSemanticSegmentation.from_pretrained(model_path, num_labels=num_classes, ignore_mismatched_sizes=True)
    return model


@torch.inference_mode()
def predict(input_image, model=None, preprocess_fn=None, device="cpu"):
    shape_H_W = input_image.size[::-1]
    input_tensor = preprocess_fn(input_image)
    input_tensor = input_tensor.unsqueeze(0).to(device)

    # Generate predictions
    outputs = model(pixel_values=input_tensor.to(device), return_dict=True)
    predictions = F.interpolate(outputs["logits"], size=shape_H_W, mode="bilinear", align_corners=False)

    preds_argmax = predictions.argmax(dim=1).cpu().squeeze().numpy()

    seg_info = [(preds_argmax == idx, class_name) for idx, class_name in enumerate(Configs.CLASSES, 1)]

    return (input_image, seg_info)


if __name__ == "__main__":
    class2hexcolor = {"Stomach": "#007fff", "Small bowel": "#009A17", "Large bowel": "#FF0000"}

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

    model = get_model(model_path=Configs.MODEL_PATH, num_classes=Configs.NUM_CLASSES)
    model.to(DEVICE)
    model.eval()
    _ = model(torch.randn(1, 3, *Configs.IMAGE_SIZE[::-1], device=DEVICE))

    preprocess = TF.Compose(
        [
            TF.Resize(size=Configs.IMAGE_SIZE[::-1]),
            TF.ToTensor(),
            TF.Normalize(Configs.MEAN, Configs.STD, inplace=True),
        ]
    )

    with gr.Blocks(title="Medical Image Segmentation") as demo:
        gr.Markdown("""<h1><center>Medical Image Segmentation with UW-Madison GI Tract Dataset</center></h1>""")
        with gr.Row():
            img_input = gr.Image(type="pil", height=300, width=300, label="Input image")
            img_output = gr.AnnotatedImage(label="Predictions", height=300, width=300, color_map=class2hexcolor)

        section_btn = gr.Button("Generate Predictions")
        section_btn.click(partial(predict, model=model, preprocess_fn=preprocess, device=DEVICE), img_input, img_output)

        images_dir = glob(os.path.join(os.getcwd(), "samples") + os.sep + "*.png")
        examples = [i for i in np.random.choice(images_dir, size=8, replace=False)]
        gr.Examples(examples=examples, inputs=img_input, outputs=img_output)

    demo.launch()