app.py

import os
import numpy as np
import torch
import SimpleITK as sitk
import torch.nn.functional as F
import cv2
from PIL import Image, ImageDraw, ImageOps
import tempfile
import gradio as gr
from segment_anything.build_sam3D import sam_model_registry3D
from utils.click_method import get_next_click3D_torch_ritm, get_next_click3D_torch_2


def build_model():
    checkpoint_path = 'ckpt\\BoSAM.pth'
    
    checkpoint = torch.load(checkpoint_path, map_location='cuda', weights_only=False)
    
    state_dict = checkpoint['model_state_dict']
    
    sam_model = sam_model_registry3D['vit_b_ori'](checkpoint=None).to('cuda')
    sam_model.load_state_dict(state_dict)
    
    return sam_model


def center_crop_or_pad(image_array, target_shape=(128, 128, 128)):
    """中心裁剪或填充图像到目标尺寸"""
    current_shape = image_array.shape
    
    start = [(c - t) // 2 if c > t else 0 for c, t in zip(current_shape, target_shape)]
    end = [s + t if c > t else c for s, t, c in zip(start, target_shape, current_shape)]
    
    result = np.zeros(target_shape, dtype=image_array.dtype)
    
    target_start = [0 if c > t else (t - c) // 2 for c, t in zip(current_shape, target_shape)]
    target_end = [t if c > t else ts + c for ts, c, t in zip(target_start, current_shape, target_shape)]
    
    if all(c >= t for c, t in zip(current_shape, target_shape)):
        cropped = image_array[
            start[0]:start[0]+target_shape[0],
            start[1]:start[1]+target_shape[1],
            start[2]:start[2]+target_shape[2]
        ]
        return cropped
    else:
        source_slices = tuple(slice(0 if c <= t else s, c if c <= t else e) 
                            for s, e, c, t in zip(start, end, current_shape, target_shape))
        target_slices = tuple(slice(ts, te) 
                             for ts, te in zip(target_start, target_end))
        
        result[target_slices] = image_array[source_slices]
        return result


def preprocess_image(image_path):
    """预处理图像为128x128x128"""
    image = sitk.ReadImage(image_path)
    image_array = sitk.GetArrayFromImage(image)
    
    processed_array = center_crop_or_pad(image_array, (128, 128, 128))
    
    image_tensor = torch.tensor(processed_array).float().unsqueeze(0).unsqueeze(0)
    
    return image_tensor.to('cuda')


def load_gt3d(image3d_path):
    """加载并预处理GT标签为128x128x128"""
    gt3d_path = r'examples\labels\1.3.6.1.4.1.9328.50.4.0357.nii.gz'  # 使用固定的GT
    if not os.path.exists(gt3d_path):
        raise FileNotFoundError(f"The file {gt3d_path} does not exist.")
    
    image = sitk.ReadImage(gt3d_path)
    image_array = sitk.GetArrayFromImage(image)
    
    processed_array = center_crop_or_pad(image_array, (128, 128, 128))
    
    gt_tensor = torch.tensor(processed_array).float().unsqueeze(0).unsqueeze(0)
    
    return gt_tensor.to('cuda')


def overlay_mask_on_image(image_slice, mask_slice, alpha=0.6):
    """在图像切片上叠加掩码，增强视觉效果"""
    # 增强对比度
    p2, p98 = np.percentile(image_slice, (2, 98))
    image_contrast = np.clip((image_slice - p2) / (p98 - p2), 0, 1)
    image_contrast = (image_contrast * 255).astype(np.uint8)
    
    # 创建彩色图像
    image_rgb = Image.fromarray(image_contrast).convert("RGB")
    
    # 应用轻微的锐化和增强
    enhancer = ImageOps.autocontrast(image_rgb, cutoff=0.5)
    image_rgba = enhancer.convert("RGBA")

    # 创建更鲜明的掩码颜色
    mask_image = Image.new('RGBA', image_rgba.size, (0, 0, 0, 0))
    mask_draw = ImageDraw.Draw(mask_image)

    mask = (mask_slice > 0).astype(np.uint8) * 255
    mask_pil = Image.fromarray(mask, mode='L')
    
    # 使用高饱和度的蓝色
    mask_draw.bitmap((0, 0), mask_pil, fill=(41, 128, 255, int(255 * alpha)))

    # 叠加并添加轻微的发光效果
    combined_image = Image.alpha_composite(image_rgba, mask_image)
    
    return combined_image


def predict(image3D, sam_model, points=None, prev_masks=None, num_clicks=5):
    """使用SAM模型预测掩码"""
    sam_model.eval()
    
    image3D = (image3D - image3D.mean()) / image3D.std()
    
    gt3D = load_gt3d(None)
    
    if prev_masks is None:
        prev_masks = torch.zeros_like(image3D).to('cuda')
    
    low_res_masks = F.interpolate(prev_masks.float(), size=(32, 32, 32))
    
    with torch.no_grad():
        image_embedding = sam_model.image_encoder(image3D)
    
    for num_click in range(num_clicks):
        with torch.no_grad():
            batch_points, batch_labels = get_next_click3D_torch_2(prev_masks.to('cuda'), gt3D.to('cuda'))
            
            points_co = torch.cat(batch_points, dim=0).to('cuda')  
            points_la = torch.cat(batch_labels, dim=0).to('cuda')  
            
            sparse_embeddings, dense_embeddings = sam_model.prompt_encoder(
                points=[points_co, points_la],
                boxes=None,
                masks=low_res_masks.to('cuda'),
            )
            
            low_res_masks, iou_predictions = sam_model.mask_decoder(
                image_embeddings=image_embedding.to('cuda'),
                image_pe=sam_model.prompt_encoder.get_dense_pe(),
                sparse_prompt_embeddings=sparse_embeddings,
                dense_prompt_embeddings=dense_embeddings,
                multimask_output=False,
            )
            
            prev_masks = F.interpolate(low_res_masks, size=[128, 128, 128], mode='trilinear', align_corners=False)
            
            medsam_seg_prob = torch.sigmoid(prev_masks)
            medsam_seg_prob = medsam_seg_prob.cpu().numpy().squeeze()
            medsam_seg = (medsam_seg_prob > 0.5).astype(np.uint8)
    
    return medsam_seg, medsam_seg_prob


def normalize_image(image):
    """增强图像对比度"""
    # 使用百分位数来增强对比度
    p2, p98 = np.percentile(image, (2, 98))
    if p98 - p2 != 0:
        image = np.clip((image - p2) / (p98 - p2), 0, 1)
    else:
        image = np.zeros_like(image)
    image = (image * 255).astype(np.uint8)
    return image


def predicts(img_path, sam_model):
    """预处理图像并预测"""
    img = preprocess_image(img_path)
    prediction, prediction_prob = predict(img, sam_model)
    return prediction, prediction_prob


def save_nifti(prediction, original_image_path):
    """保存预测结果为NIFTI文件"""
    original_image = sitk.ReadImage(original_image_path)
    
    output_image = sitk.GetImageFromArray(prediction.astype(np.uint8))
    
    output_image.SetDirection(original_image.GetDirection())
    output_image.SetOrigin(original_image.GetOrigin())
    
    original_size = original_image.GetSize()
    original_spacing = original_image.GetSpacing()
    
    new_spacing = [
        original_spacing[0] * (original_size[0] / 128),
        original_spacing[1] * (original_size[1] / 128),
        original_spacing[2] * (original_size[2] / 128)
    ]
    output_image.SetSpacing(new_spacing)
    
    temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".nii.gz")
    temp_filename = temp_file.name
    
    sitk.WriteImage(output_image, temp_filename)
    
    return temp_filename


def gr_interface(img_path, sam_model=None):
    """增强的Gradio界面函数"""
    if sam_model is None:
        sam_model = build_model()
    
    # 显示进度信息    
    yield None, gr.update(value="正在加载数据..."), None, None, None
    
    processed_img = preprocess_image(img_path)
    
    yield None, gr.update(value="正在分割..."), None, None, None
    
    prediction, prediction_prob = predicts(img_path, sam_model)
    
    yield None, gr.update(value="正在生成可视化..."), None, None, None
    
    processed_slices = []
    combined_slices = []
    predicted_slices = []
    
    nifti_file_path = save_nifti(prediction, img_path)
    
    # 计算中心32张切片的索引
    start_idx = (128 - 32) // 2  # 48
    end_idx = start_idx + 32     # 80
    
    for i in range(start_idx, end_idx):
        # 处理原始图像切片
        processed_slice = processed_img[0, 0, i].cpu().numpy()
        processed_slices.append(normalize_image(processed_slice))
        
        # 处理预测掩码切片
        mask_slice = prediction[i]
        normalized_mask = normalize_image(mask_slice)
        
        # 叠加掩码到图像上 - 使用更醒目的视觉效果
        combined_image = overlay_mask_on_image(processed_slices[-1], mask_slice)
        combined_slices.append(combined_image)
        
        # 添加预测切片
        predicted_slices.append(normalized_mask)
    
    yield processed_slices, gr.update(value="分割完成!"), combined_slices, predicted_slices, nifti_file_path


# 使用示例文件路径作为常量
DEFAULT_EXAMPLE = "examples\\1.3.6.1.4.1.9328.50.4.0327.nii.gz"
EXAMPLES = [
    ["examples\\1.3.6.1.4.1.9328.50.4.0327.nii.gz"],
    ["examples\\1.3.6.1.4.1.9328.50.4.0357.nii.gz"],
    ["examples\\1.3.6.1.4.1.9328.50.4.0477.nii.gz"],
    ["examples\\1.3.6.1.4.1.9328.50.4.0491.nii.gz"],
    ["examples\\1.3.6.1.4.1.9328.50.4.0708.nii.gz"],
    ["examples\\1.3.6.1.4.1.9328.50.4.0719.nii.gz"]
]

# 自定义CSS样式以美化界面
css = """
body {
    background-color: #f8fafc;
}

.container {
    max-width: 1200px;
    margin: 0 auto;
}

.main-title {
    text-align: center;
    color: #2563eb;
    font-size: 2.5rem;
    margin-bottom: 1rem;
    font-weight: bold;
    animation: fadeIn 1.5s ease-in-out;
}

.sub-title {
    text-align: center;
    color: #1e293b;
    margin-bottom: 2rem;
    animation: fadeIn 2s ease-in-out;
}

.custom-button {
    background-color: #2563eb !important;
    color: white !important;
    transition: transform 0.3s, box-shadow 0.3s;
}

.custom-button:hover {
    transform: translateY(-2px);
    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
}

.gallery-item {
    border-radius: 8px;
    overflow: hidden;
    box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);
    transition: transform 0.3s;
}

.gallery-item:hover {
    transform: scale(1.02);
    box-shadow: 0 6px 12px rgba(0, 0, 0, 0.15);
}

@keyframes fadeIn {
    from { opacity: 0; transform: translateY(20px); }
    to { opacity: 1; transform: translateY(0); }
}
"""

# 加载模型（全局变量）
sam_model = build_model()

# 创建更美观的Gradio界面，使用兼容的组件
with gr.Blocks(title="3D医学影像智能分割系统", css=css) as demo:
    gr.HTML("<h1 class='main-title'>3D医学影像智能分割系统</h1>")
    gr.HTML("<p class='sub-title'>基于BoSAM的前沿人工智能自动分割技术，为医学影像分析提供高精度解决方案</p>")
    
    with gr.Row():
        with gr.Column(scale=1):
            # 输入区域
            gr.Markdown("### 上传/选择影像")
            input_file = gr.File(label="上传NIfTI文件", value=DEFAULT_EXAMPLE)
            
            status = gr.Textbox(label="处理状态", value="准备就绪")
            process_btn = gr.Button("开始智能分割", elem_classes=["custom-button"])
            
            # 示例区域
            gr.Markdown("### 示例数据")
            examples = gr.Examples(
                examples=EXAMPLES,
                inputs=[input_file]
            )
            
            gr.HTML("""
            <div style="margin-top: 2rem; padding: 1rem; background-color: rgba(16, 185, 129, 0.1); border-radius: 8px;">
                <h3 style="color: #10b981; margin-bottom: 0.5rem;">技术亮点</h3>
                <ul style="margin-left: 1.5rem;">
                    <li>基于最新的Segment Anything Model (SAM) 技术</li>
                    <li>专为3D医学影像优化的深度学习模型</li>
                    <li>智能识别解剖结构，无需手动绘制边界</li>
                    <li>高精度分割结果，提升诊断效率</li>
                </ul>
            </div>
            """)

        with gr.Column(scale=2):
            # 输出区域
            with gr.Row():
                gr.Markdown("## 原始医学影像")
                output_original = gr.Gallery(label="", show_label=False, columns=4, rows=8, height="600px", elem_classes=["gallery-item"])
            
            with gr.Row():
                with gr.Column():
                    gr.Markdown("## 分割叠加结果")
                    output_combined = gr.Gallery(label="", show_label=False, columns=4, rows=4, height="400px", elem_classes=["gallery-item"])
                
                with gr.Column():
                    gr.Markdown("## 分割掩码")
                    output_mask = gr.Gallery(label="", show_label=False, columns=4, rows=4, height="400px", elem_classes=["gallery-item"])
            
            gr.Markdown("## 分割结果下载")
            output_file = gr.File(label="下载完整3D分割结果 (NIFTI格式)")
    
    gr.HTML("""
    <div style="text-align: center; margin-top: 2rem; padding: 1rem; border-top: 1px solid rgba(0, 0, 0, 0.1);">
        <p>© 2025 3D医学影像智能分割系统 | 人工智能辅助医学影像分析平台</p>
        <p>基于最新的BoaSAM模型，为医疗影像分析提供高精度自动分割解决方案</p>
    </div>
    """)
    
    # 处理事件
    process_btn.click(
        fn=gr_interface,
        inputs=[input_file],
        outputs=[output_original, status, output_combined, output_mask, output_file]
    )
    
    examples.dataset.click(
        fn=gr_interface,
        inputs=[input_file],
        outputs=[output_original, status, output_combined, output_mask, output_file]
    )
    
    demo.load(
        fn=gr_interface,
        inputs=[input_file],
        outputs=[output_original, status, output_combined, output_mask, output_file]
    )

if __name__ == "__main__":
    demo.launch(debug=True, share = True)