import os import h5py import numpy as np import gradio as gr import plotly.graph_objects as go from railnet_model import RailNetSystem from huggingface_hub import hf_hub_download os.environ['KMP_DUPLICATE_LIB_OK'] = 'True' os.environ["CUDA_VISIBLE_DEVICES"] = "0" model = RailNetSystem.from_pretrained("Tournesol-Saturday/railNet-tooth-segmentation-in-CBCT-image").cuda() model.load_weights(from_hub=True, repo_id="Tournesol-Saturday/railNet-tooth-segmentation-in-CBCT-image") def render_plotly_volume(pred, x_eye=1.25, y_eye=1.25, z_eye=1.25): downsample_factor = 2 pred_ds = pred[::downsample_factor, ::downsample_factor, ::downsample_factor] fig = go.Figure(data=go.Volume( x=np.repeat(np.arange(pred_ds.shape[0]), pred_ds.shape[1] * pred_ds.shape[2]), y=np.tile(np.repeat(np.arange(pred_ds.shape[1]), pred_ds.shape[2]), pred_ds.shape[0]), z=np.tile(np.arange(pred_ds.shape[2]), pred_ds.shape[0] * pred_ds.shape[1]), value=pred_ds.flatten(), isomin=0.5, isomax=1.0, opacity=0.1, surface_count=1, colorscale=[[0, 'rgb(255, 0, 0)'], [1, 'rgb(255, 0, 0)']], showscale=False )) fig.update_layout( scene=dict( xaxis=dict(visible=False), yaxis=dict(visible=False), zaxis=dict(visible=False), camera=dict(eye=dict(x=x_eye, y=y_eye, z=z_eye)) ), margin=dict(l=0, r=0, b=0, t=0) ) return fig def handle_example(filename): repo_id = "Tournesol-Saturday/railNet-tooth-segmentation-in-CBCT-image" h5_path = hf_hub_download(repo_id=repo_id, filename=f"example_input_file/{filename}") with h5py.File(h5_path, "r") as f: image = f["image"][:] label = f["label"][:] name = filename.replace(".h5", "") pred, dice, jc, hd, asd = model(image, label, "./output", name) fig = render_plotly_volume(pred) img_path = f"./output/{name}_img.nii.gz" pred_path = f"./output/{name}_pred.nii.gz" metrics = f"Dice: {dice:.4f}, Jaccard: {jc:.4f}, 95HD: {hd:.2f}, ASD: {asd:.2f}" return metrics, pred, fig, img_path, pred_path def clear_all(): return "", None, None, None, None with gr.Blocks() as demo: gr.HTML("
🦷 Demo of RailNet: A CBCT Tooth Segmentation System
") gr.HTML("
βœ… Steps: Select a CBCT example file (.h5) β†’ Automatic inference and metrics display β†’ View 3D segmentation result (Mouse drag and scroll wheel zooming)
") gr.HTML("""
πŸ“‚ Step 1: Select a .h5 example file from the example_input_file folder in our Hugging Face model repository.
""") example_files = ["CBCT_01.h5", "CBCT_02.h5", "CBCT_03.h5", "CBCT_04.h5"] dropdown = gr.Dropdown(choices=example_files, label="Example File", value=example_files[0]) with gr.Row(): clear_btn = gr.Button("清陀", variant="secondary") submit_btn = gr.Button("提亀", variant="primary") gr.HTML("
πŸ“Š Step 2: Metrics (Dice, Jaccard, 95HD, ASD)
") result_text = gr.Textbox() hidden_pred = gr.State(value=None) gr.HTML("
πŸ‘οΈ Step 3: 3D Visualisation
") plot_output = gr.Plot() gr.HTML("
⬇️ Step 4: Download NIfTI files for accurate 1:1 visualization using ITK-SNAP software
") with gr.Row(): hidden_img_file = gr.File(label="Download Original Image", interactive=False) hidden_pred_file = gr.File(label="Download Segmentation Result", interactive=False) submit_btn.click( fn=handle_example, inputs=[dropdown], outputs=[result_text, hidden_pred, plot_output, hidden_img_file, hidden_pred_file] ) clear_btn.click( fn=clear_all, inputs=[], outputs=[result_text, hidden_pred, plot_output, hidden_img_file, hidden_pred_file] ) demo.launch()