app.py

import gradio as gr
import spaces
import torch
import nibabel as nib
import numpy as np
from huggingface_hub import hf_hub_download
from monai.transforms import (
    Compose,
    LoadImage,
    EnsureChannelFirst,
    ScaleIntensity,
    Resize,
    AsDiscrete,
)
from monai.networks.nets import UNet
import tempfile
import os

# Load the model
model = None
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

def load_model():
    global model
    if model is None:
        # Download model from HuggingFace
        model_path = hf_hub_download(
            repo_id="MONAI/example_spleen_segmentation",
            filename="model.pt"
        )
        
        # Initialize UNet architecture with exact parameters from inference.json
        model = UNet(
            spatial_dims=3,
            in_channels=1,
            out_channels=2,
            channels=(16, 32, 64, 128, 256),
            strides=(2, 2, 2, 2),
            num_res_units=2,
            norm="batch",  # Added: batch normalization as specified in inference.json
        )
        
        # Load weights with strict=False to handle minor key mismatches
        checkpoint = torch.load(model_path, map_location=device)
        model.load_state_dict(checkpoint, strict=False)
        model.to(device)
        model.eval()
    return model


def segment_spleen(input_file):
    """Segment spleen from CT NIfTI file"""
    try:
        # Load model
        net = load_model()
        
        # Load NIfTI file
        img = nib.load(input_file)
        img_data = img.get_fdata()
        
        # Preprocessing
        img_tensor = torch.from_numpy(img_data).float().unsqueeze(0).unsqueeze(0)
        
        # Normalize
        img_tensor = (img_tensor - img_tensor.min()) / (img_tensor.max() - img_tensor.min())
        
        # Resize to model input size (96x96x96)
        img_resized = torch.nn.functional.interpolate(
            img_tensor,
            size=(96, 96, 96),
            mode="trilinear",
            align_corners=True
        )
        
        # Move to device and run inference
        img_resized = img_resized.to(device)
        
        with torch.no_grad():
            output = net(img_resized)
            pred = torch.argmax(output, dim=1)
        
        # Resize back to original size
        pred_resized = torch.nn.functional.interpolate(
            pred.float().unsqueeze(0),
            size=img_data.shape,
            mode="nearest"
        )
        
        pred_np = pred_resized.squeeze().cpu().numpy().astype(np.uint8)
        
        # Save segmentation as NIfTI
        seg_img = nib.Nifti1Image(pred_np, img.affine, img.header)
        output_path = tempfile.mktemp(suffix="_segmentation.nii.gz")
        nib.save(seg_img, output_path)
        
        # Create visualization (middle slice)
        mid_slice = img_data.shape[2] // 2
        img_slice = img_data[:, :, mid_slice]
        seg_slice = pred_np[:, :, mid_slice]
        
        # Normalize image for display
        img_slice = (img_slice - img_slice.min()) / (img_slice.max() - img_slice.min()) * 255
        
        # Create overlay
        overlay = np.stack([img_slice, img_slice, img_slice], axis=-1).astype(np.uint8)
        overlay[seg_slice == 1] = [255, 0, 0]  # Red for spleen
        
        return overlay, output_path, "Segmentation completed successfully!"
        
    except Exception as e:
        return None, None, f"Error: {str(e)}"

# Create Gradio interface
with gr.Blocks(title="Spleen Segmentation") as demo:
    gr.Markdown("# 🏥 CT Spleen Segmentation")
    gr.Markdown(
        """Upload a CT scan in NIfTI format (.nii or .nii.gz) to segment the spleen using the 
        [MONAI/example_spleen_segmentation](https://huggingface.co/MONAI/example_spleen_segmentation) model.

        **Model Info:**
        - Architecture: UNet
        - Input: 3D CT image (96×96×96)
        - Output: Binary segmentation (spleen vs background)
        - Mean Dice Score: 0.96

        **Instructions:**
        1. Upload a NIfTI file (.nii or .nii.gz)
        2. Click Submit
        3. View the segmentation overlay and download the result
        """
    )
    
    with gr.Row():
        with gr.Column():
            input_file = gr.File(
                label="Upload CT Scan (NIfTI format)",
                file_types=[".nii", ".nii.gz"]
            )
            submit_btn = gr.Button("Segment Spleen", variant="primary")
        
        with gr.Column():
            output_image = gr.Image(label="Segmentation Overlay (Middle Slice)", type="numpy")
            output_file = gr.File(label="Download Segmentation")
            status_text = gr.Textbox(label="Status")
    
    submit_btn.click(
        fn=segment_spleen,
        inputs=[input_file],
        outputs=[output_image, output_file, status_text]
    )
    
    gr.Markdown(
        """### Requirements
        - MONAI
        - PyTorch
        - nibabel
        - numpy
        - huggingface_hub

        ### Citation
        If you use this model, please cite:
        ```
        Xia, Yingda, et al. "3D Semi-Supervised Learning with Uncertainty-Aware Multi-View Co-Training." 
        arXiv preprint arXiv:1811.12506 (2018).
        ```
        """
    )

if __name__ == "__main__":
    demo.launch()