app.py

import zipfile
import nibabel as nib
import numpy as np
import gradio as gr
import Segformer3DBRATS2021  # Giả sử bạn đã định nghĩa mô hình này ở đâu đó.
import torch 
import torch.nn.functional as F
from io import BytesIO
import tempfile

def predict_segmentation(zip_file):
    """
    Hàm xử lý file zip chứa dữ liệu MRI, gọi mô hình Segformer3D để dự đoán và trả về file .nii kết quả.
    """
    try:
        # Giải nén file zip
        with zipfile.ZipFile(zip_file) as zip_ref:
            
            overlay = Segformer3DBRATS2021.__call__(zip_ref)
        overlay_all_slices = np.transpose(overlay,(3,2,1,0))
        overlay_tensor = torch.tensor(overlay_all_slices, dtype=torch.float32).unsqueeze(0)
        target_shape = (240, 240, 155)
        # Tính toán padding (thêm padding để đạt được kích thước mong muốn)
        z_pad_before = (target_shape[0] - overlay_tensor.shape[2]) // 2
        z_pad_after = target_shape[0] - overlay_tensor.shape[2] - z_pad_before

        y_pad_before = (target_shape[1] - overlay_tensor.shape[3]) // 2
        y_pad_after = target_shape[1] - overlay_tensor.shape[3] - y_pad_before

        x_pad_before = (target_shape[2] - overlay_tensor.shape[4]) // 2
        x_pad_after = target_shape[2] - overlay_tensor.shape[4] - x_pad_before

        # Tạo padding (đệm đen)
        padded_tensor = F.pad(overlay_tensor, (x_pad_before, x_pad_after, y_pad_before, y_pad_after, z_pad_before, z_pad_after), value=0)
        assert padded_tensor.shape[2:] == target_shape, f"Expected shape {target_shape}, got {padded_tensor.shape[2:]}"
        padded_tensor = padded_tensor.permute(0,2,3,4,1)
        padded_slices = padded_tensor.squeeze(0).numpy()

        for i in range(padded_slices.shape[2]):
            padded_slices[:, :, i, :] = np.flipud(np.fliplr(padded_slices[:, :, i, :]))
        padded_slices = padded_slices.astype(np.uint8)
        affine = np.eye(4)  
        nii_image = nib.Nifti1Image(padded_slices, affine)
        with tempfile.NamedTemporaryFile(delete=False, suffix='.nii') as temp_file:
            nii_file_path = temp_file.name
            nib.save(nii_image, nii_file_path)

        # Trả về đường dẫn đến file NIfTI đã lưu
        return nii_file_path

    except Exception as e:
        return str(e)

def main():
    # Định nghĩa giao diện Gradio
    inputs = gr.File(label="Upload a ZIP file containing MRI modalities (flair, t1, t1ce, t2)")
    outputs = gr.File(label="Segmentation Result (.nii)")

    gr.Interface(
        fn=predict_segmentation,
        inputs=inputs,
        outputs=outputs,
        title="3D Brain Tumor Segmentation",
        description="Upload a ZIP file containing MRI modalities (flair, t1, t1ce, t2).",
        allow_flagging="never",
    ).launch(show_error=True)

if __name__ == '__main__':
    main()