app.py

import gradio as gr
import subprocess
import os
import shutil
from huggingface_hub import hf_hub_download
import torch
import nibabel as nib
import matplotlib.pyplot as plt
import spaces  # Import spaces for GPU decoration
import numpy as np
from scipy.ndimage import center_of_mass

# Define paths
MODEL_DIR = "./model"  # Local directory to store the downloaded model
DATASET_DIR = os.path.join(MODEL_DIR, "Dataset004_WML")  # Directory for Dataset004_WML
INPUT_DIR = "/tmp/input"
OUTPUT_DIR = "/tmp/output"

# Hugging Face Model Repository
REPO_ID = "FrancescoLR/FLAMeS-model"  # Replace with your actual model repository ID

# Function to download the Dataset004_WML folder
def download_model():
    if not os.path.exists(DATASET_DIR):
        os.makedirs(DATASET_DIR, exist_ok=True)
        print("Downloading Dataset004_WML.zip...")
        zip_path = hf_hub_download(repo_id=REPO_ID, filename="Dataset004_WML.zip", cache_dir=MODEL_DIR)
        subprocess.run(["unzip", "-o", zip_path, "-d", MODEL_DIR])
        print("Dataset004_WML downloaded and extracted.")

def extract_middle_slices(nifti_path, output_image_path, slice_size=180):
    """
    Extracts slices centered around the center of mass of non-zero voxels in a 3D NIfTI image.
    The slices are taken along axial, coronal, and sagittal planes and saved as a single PNG.
    """
      # Load NIfTI image and get the data
    img = nib.load(nifti_path)
    data = img.get_fdata()

    # Compute the center of mass of non-zero voxels
    com = center_of_mass(data > 0)
    center = np.round(com).astype(int)

    # Define half the slice size to extract regions around the center of mass
    half_size = slice_size // 2

    # Safely extract 2D slices
    def extract_2d_slice(data, center, axis):
        slices = [slice(None)] * 3
        slices[axis] = center[axis]
        extracted_slice = data[tuple(slices)]

        # Crop around the center for the other two dimensions
        other_axes = [i for i in range(3) if i != axis]
        for i in other_axes:
            start = max(center[i] - half_size, 0)
            end = min(center[i] + half_size, data.shape[i])
            extracted_slice = np.take(extracted_slice, range(start, end), axis=i)
        return extracted_slice

    axial_slice = extract_2d_slice(data, center, axis=2)  # Axial (z-axis)
    coronal_slice = extract_2d_slice(data, center, axis=1)  # Coronal (y-axis)
    sagittal_slice = extract_2d_slice(data, center, axis=0)  # Sagittal (x-axis)

    # Create subplots
    fig, axes = plt.subplots(1, 3, figsize=(12, 4))

    # Plot each slice
    axes[0].imshow(axial_slice, cmap="gray", origin="lower")
    axes[0].axis("off")
    axes[0].set_title("Axial")

    axes[1].imshow(coronal_slice, cmap="gray", origin="lower")
    axes[1].axis("off")
    axes[1].set_title("Coronal")

    axes[2].imshow(sagittal_slice, cmap="gray", origin="lower")
    axes[2].axis("off")
    axes[2].set_title("Sagittal")

    # Save the figure
    plt.tight_layout()
    plt.savefig(output_image_path, bbox_inches="tight", pad_inches=0)
    plt.close()

# Function to run nnUNet inference
@spaces.GPU  # Decorate the function to allocate GPU for its execution
def run_nnunet_predict(nifti_file):
    # Prepare directories
    os.makedirs(INPUT_DIR, exist_ok=True)
    os.makedirs(OUTPUT_DIR, exist_ok=True)

    # Extract the original filename without the extension
    original_filename = os.path.basename(nifti_file.name)
    base_filename = original_filename.replace(".nii.gz", "")
    
    # Save the uploaded file to the input directory
    input_path = os.path.join(INPUT_DIR, "image_0000.nii.gz")
    os.rename(nifti_file.name, input_path)  # Move the uploaded file to the expected input location
    
    # Debugging: List files in the /tmp/input directory
    print("Files in /tmp/input:")
    print(os.listdir(INPUT_DIR))

    # Set environment variables for nnUNet
    os.environ["nnUNet_results"] = MODEL_DIR

    # Construct and run the nnUNetv2_predict command
    command = [
        "nnUNetv2_predict",
        "-i", INPUT_DIR,
        "-o", OUTPUT_DIR,
        "-d", "004",                  # Dataset ID
        "-c", "3d_fullres",           # Configuration
        "-tr", "nnUNetTrainer_8000epochs",
        "-device", "cuda"  # Explicitly use GPU
    ]
    print("Files in /tmp/output:")
    print(os.listdir(OUTPUT_DIR))
    try:
        subprocess.run(command, check=True)

        # Rename the output file to match the original input filename
        output_file = os.path.join(OUTPUT_DIR, "image.nii.gz")
        new_output_file = os.path.join(OUTPUT_DIR, f"{base_filename}_LesionMask.nii.gz")
        if os.path.exists(output_file):
            os.rename(output_file, new_output_file)

            # Extract and save 2D slices
            input_slice_path = os.path.join(OUTPUT_DIR, f"{base_filename}_input_slice.png")
            output_slice_path = os.path.join(OUTPUT_DIR, f"{base_filename}_output_slice.png")
            extract_middle_slices(input_path, input_slice_path)
            extract_middle_slices(new_output_file, output_slice_path)

            # Return paths for the Gradio interface
            return new_output_file, input_slice_path, output_slice_path
        else:
            return "Error: Output file not found."
    except subprocess.CalledProcessError as e:
        return f"Error: {e}"

# Gradio Interfaceinterface = gr.Interface(
interface = gr.Interface(
    fn=run_nnunet_predict,
    inputs=gr.File(label="Upload FLAIR Image (.nii.gz)"),
    outputs=[
        gr.File(label="Download Segmentation Mask"),
        gr.Image(label="Input Middle Slice"),
        gr.Image(label="Output Middle Slice")
    ],
    title="FLAMeS: Multiple Sclerosis Lesion Segmentation",
    description="Upload a skull-stripped FLAIR image (.nii.gz) to generate a binary segmentation of MS lesions."
)

# Debugging GPU environment
if torch.cuda.is_available():
    print(f"GPU is available: {torch.cuda.get_device_name(0)}")
else:
    print("No GPU available. Falling back to CPU.")
    os.system("nvidia-smi")  # Check if NVIDIA tools are available

# Download model files before launching the app
download_model()

# Launch the app
if __name__ == "__main__":
    interface.launch(share=True)