app.py

from PIL import Image
import gradio as gr
import numpy as np
from datasets import load_dataset
import os
import tempfile


dataset = load_dataset("erceguder/histocan-test", token=os.environ["HF_TOKEN"])


COLOR_PALETTE = {
    'others': (0, 0, 0),
    't-g1': (0, 192, 0),
    't-g2': (255, 224, 32),
    't-g3': (255, 0, 0),
    'normal-mucosa': (0, 32, 255)
}


def files_uploaded(paths):
    if len(paths) != 16:
        raise gr.Error("16 segmentation masks are needed.")

    uploaded_file_names = [paths[i].name.split('/')[-1] for i in range(16)]
    for i in range(16):
        if f"test{i:04d}.png" not in uploaded_file_names:
            raise gr.Error(f"Uploaded file names are not recognized.")


def evaluate(paths):
    if len(dataset["test"]) != 16:
        raise gr.Error("Could not read ground truth data from the server.")

    if paths == None:
        raise gr.Error("Upload segmentation masks first!")

    # Init dicts for accumulating image metrics and calculating per-class scores
    metrics = {}
    for class_ in COLOR_PALETTE.keys():
        idict = {
            "tp": 0.0,
            "fp": 0.0,
            "tn": 0.0,
            "fn": 0.0,
        }
        metrics[class_] = idict

    scores = {}
    for class_ in COLOR_PALETTE.keys():
        idict = {
            "recall": 0.0,
            "precision": 0.0,
            "f1": 0.0
        }
        scores[class_] = idict

    tmpdir = tempfile.TemporaryDirectory()
    for path in paths:
        os.rename(path.name, os.path.join(tmpdir.name, path.name.split('/')[-1]))

    for item in dataset["test"]:
        pred_path = os.path.join(tmpdir.name, item["name"])
        pred = np.array(Image.open(pred_path))
        gt = np.array(item["annotation"])

        assert gt.ndim == 2
        assert pred.ndim == 3 and pred.shape[-1] == 3
        assert gt.shape == pred.shape[:-1]

        # Get predictions for all classes
        out = [(pred == color).all(axis=-1) for color in COLOR_PALETTE.values()]
        maps = np.stack(out)

        # Calculate confusion matrix and metrics
        for i, class_ in enumerate(COLOR_PALETTE.keys()):
            class_pred = maps[i]
            class_gt = (gt == i)

            tp = np.sum(class_pred[class_gt==True])
            fp = np.sum(class_pred[class_gt==False])
            tn = np.sum(np.logical_not(class_pred)[class_gt==False])
            fn = np.sum(np.logical_not(class_pred)[class_gt==True])

            # Accumulate metrics for each class
            metrics[class_]['tp'] += tp
            metrics[class_]['fp'] += fp
            metrics[class_]['tn'] += tn
            metrics[class_]['fn'] += fn

    # Init mean recall, precision and F1 score
    mRecall = 0.0
    mPrecision = 0.0
    mF1 = 0.0

    # Calculate recall, precision and f1 scores for each class
    for i, class_ in enumerate(COLOR_PALETTE.keys()):
        scores[class_]['recall'] = metrics[class_]['tp'] / (metrics[class_]['tp'] + metrics[class_]['fn']) if metrics[class_]['tp'] > 0 else 0.0
        scores[class_]['precision'] = metrics[class_]['tp'] / (metrics[class_]['tp'] + metrics[class_]['fp']) if metrics[class_]['tp'] > 0 else 0.0
        scores[class_]['f1'] = 2 * scores[class_]['precision'] * scores[class_]['recall'] / (scores[class_]['precision'] + scores[class_]['recall']) if (scores[class_]['precision'] != 0 and scores[class_]['recall'] != 0) else 0.0

        mRecall += scores[class_]['recall']
        mPrecision += scores[class_]['precision']
        mF1 += scores[class_]['f1']

    # Calculate mean recall, precision and F1 score over all classes
    class_count = len(COLOR_PALETTE)
    mRecall /= class_count
    mPrecision /= class_count
    mF1 /= class_count

    tmpdir.cleanup()

    result = """
    <div align="center">

    # Results

    |           | Others | T-G1 | T-G2 | T-G3 | Normal mucosa |
    |-----------|--------|------|------|------|---------------|
    | Precision | {:.2f} |{:.2f}|{:.2f}|{:.2f}|    {:.2f}     |
    | Recall    | {:.2f} |{:.2f}|{:.2f}|{:.2f}|    {:.2f}     |
    | Dice      | {:.2f} |{:.2f}|{:.2f}|{:.2f}|    {:.2f}     |

    ### mPrecision: {:.4f}
    ### mRecall: {:.4f}
    ### mDice: {:.4f}

    </div>
    """

    result = result.format(
        scores["others"]["precision"],
        scores["t-g1"]["precision"],
        scores["t-g2"]["precision"],
        scores["t-g3"]["precision"],
        scores["normal-mucosa"]["precision"],
        scores["others"]["recall"],
        scores["t-g1"]["recall"],
        scores["t-g2"]["recall"],
        scores["t-g3"]["recall"],
        scores["normal-mucosa"]["recall"],
        scores["others"]["f1"],
        scores["t-g1"]["f1"],
        scores["t-g2"]["f1"],
        scores["t-g3"]["f1"],
        scores["normal-mucosa"]["f1"],
        mPrecision,
        mRecall,
        mF1
    )
    return gr.Markdown(value=result)


if __name__ == "__main__":
    with gr.Blocks() as demo:
        gr.Markdown("# Histocan Test Set Evaluation Page")
        files = gr.File(label="Upload your segmentation masks for the test set", file_count="multiple", file_types=["image"])
        run = gr.Button(value="Evaluate!")
        output = gr.Markdown(value="")

        files.upload(files_uploaded, files, [])
        run.click(evaluate, files, [output])

        demo.queue(max_size=1)
        demo.launch()