diff --git "a/codes/lungSegmentation.ipynb" "b/codes/lungSegmentation.ipynb" new file mode 100644--- /dev/null +++ "b/codes/lungSegmentation.ipynb" @@ -0,0 +1,2012 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "id": "a_goHaGlBjZf" + }, + "outputs": [], + "source": [ + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Defaulting to user installation because normal site-packages is not writeable\n", + "Requirement already satisfied: opencv-python in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (4.10.0.84)\n", + "Requirement already satisfied: numpy>=1.19.3 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from opencv-python) (1.26.1)\n", + "\u001b[33mWARNING: You are using pip version 21.2.4; however, version 24.3.1 is available.\n", + "You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\n", + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], + "source": [ + "%pip install opencv-python" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "id": "yx4oLfemz4ys" + }, + "outputs": [], + "source": [ + "import cv2" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "id": "Mp2G_NgPBByg" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Defaulting to user installation because normal site-packages is not writeable\n", + "Looking in indexes: https://download.pytorch.org/whl/cpu\n", + "Requirement already satisfied: torch in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (2.5.1)\n", + "Requirement already satisfied: torchvision in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (0.20.1)\n", + "Requirement already satisfied: sympy==1.13.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (1.13.1)\n", + "Requirement already satisfied: fsspec in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (2024.10.0)\n", + "Requirement already satisfied: networkx in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (3.2.1)\n", + "Requirement already satisfied: jinja2 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (3.1.4)\n", + "Requirement already satisfied: filelock in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (3.16.1)\n", + "Requirement already satisfied: typing-extensions>=4.8.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torch) (4.12.2)\n", + "Requirement already satisfied: mpmath<1.4,>=1.1.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from sympy==1.13.1->torch) (1.3.0)\n", + "Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torchvision) (11.0.0)\n", + "Requirement already satisfied: numpy in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from torchvision) (1.26.1)\n", + "Requirement already satisfied: MarkupSafe>=2.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from jinja2->torch) (2.1.3)\n", + "\u001b[33mWARNING: You are using pip version 21.2.4; however, version 24.3.1 is available.\n", + "You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\n", + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], + "source": [ + "%pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "import torch" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Defaulting to user installation because normal site-packages is not writeable\n", + "Requirement already satisfied: albumentations in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (1.4.21)\n", + "Requirement already satisfied: pydantic>=2.7.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (2.10.2)\n", + "Requirement already satisfied: PyYAML in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (6.0.2)\n", + "Requirement already satisfied: albucore==0.0.20 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (0.0.20)\n", + "Requirement already satisfied: numpy>=1.24.4 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (1.26.1)\n", + "Requirement already satisfied: eval-type-backport in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (0.2.0)\n", + "Requirement already satisfied: typing-extensions>=4.9.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (4.12.2)\n", + "Requirement already satisfied: opencv-python-headless>=4.9.0.80 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (4.10.0.84)\n", + "Requirement already satisfied: scipy>=1.10.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albumentations) (1.13.1)\n", + "Requirement already satisfied: stringzilla>=3.10.4 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albucore==0.0.20->albumentations) (3.11.0)\n", + "Requirement already satisfied: simsimd>=5.9.2 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from albucore==0.0.20->albumentations) (6.2.1)\n", + "Requirement already satisfied: pydantic-core==2.27.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from pydantic>=2.7.0->albumentations) (2.27.1)\n", + "Requirement already satisfied: annotated-types>=0.6.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from pydantic>=2.7.0->albumentations) (0.7.0)\n", + "\u001b[33mWARNING: You are using pip version 21.2.4; however, version 24.3.1 is available.\n", + "You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\n", + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], + "source": [ + "%pip install albumentations" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "id": "tC_aZXqr_4np" + }, + "outputs": [], + "source": [ + "import albumentations as A" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + }, + "id": "GvEKb6LlB9FG", + "outputId": "ec6cc734-7673-433a-aed9-c0ed7a25582c" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Defaulting to user installation because normal site-packages is not writeable\n", + "Requirement already satisfied: lungs-segmentation==1.1.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (1.1.1)\n", + "\u001b[33mWARNING: You are using pip version 21.2.4; however, version 24.3.1 is available.\n", + "You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\n", + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], + "source": [ + "%pip install lungs-segmentation==1.1.1 --no-deps" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 150, + "referenced_widgets": [ + "b7b94541cad54b3186c4ee205af0c21f", + "5e8c6ed7a4c44c839308ad74d43049cf", + "5dbfabd623ee42df8ddf74c28f568caf", + "cf9014584f2542b6b46d5ab3b8dc68f5", + "455588147e894c91afa8bd7eebc9208f", + "66440c840c9f486ebee81f0e170ae501", + "5c19b2d580d44d4fbb99eee0764937d9", + "5230b5a9b0ed45bdb2b7caec5d96c2c4", + "c99fad2216b04e3594b864e1bbe1ee90", + "51e9326730de437f96ef679fd8ca655e", + "a6434f4cc3fa42ef9ded133ab17fc093", + "421a1c2059164d3aa7c756f05106cece", + "0153f368dd7d44e9ac9dc86847c317b8", + "3ba0284726284053a5a983ad423bdc24", + "4d4b894b7e2442c19349eea410173a49", + "32cf01248b0b45bca7e8a7226de51463" + ] + }, + "id": "-X9O3-sACCHi", + "outputId": "e3fad8c4-9dad-4b75-d524-7028a81929db" + }, + "outputs": [], + "source": [ + "from lungs_segmentation.pre_trained_models import create_model" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 84, + "referenced_widgets": [ + "a3e86e0f38cb42199129f239c5182f7d", + "01d9285bbb8a498fb0141dbf32e16c0b", + "41882823b0cf481283798c9d5c7c1a09", + "f1f5c36cd9b54e25b2ba89642d607c3e", + "cfa6397bacbd43cba5f58c08097aceae", + "559be0e998db425bbc67a3a850832cdd", + "4661621481e340718dd40b162ad45084", + "341b9d230d70400f9629fc940342ba5a" + ] + }, + "id": "He9OLLi1CX57", + "outputId": "9608d088-8a7e-4686-949e-da3c65573bc1" + }, + "outputs": [], + "source": [ + "model = create_model(\"resnet34\")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": { + "id": "DZr-dHypKNOB" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "cpu\n" + ] + } + ], + "source": [ + "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n", + "model = model.to(device)\n", + "print(device)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Defaulting to user installation because normal site-packages is not writeable\n", + "Requirement already satisfied: matplotlib in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (3.9.3)\n", + "Requirement already satisfied: contourpy>=1.0.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (1.3.0)\n", + "Requirement already satisfied: kiwisolver>=1.3.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (1.4.7)\n", + "Requirement already satisfied: fonttools>=4.22.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (4.55.0)\n", + "Requirement already satisfied: pillow>=8 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (11.0.0)\n", + "Requirement already satisfied: packaging>=20.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (24.2)\n", + "Requirement already satisfied: numpy>=1.23 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (1.26.1)\n", + "Requirement already satisfied: importlib-resources>=3.2.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (6.4.5)\n", + "Requirement already satisfied: pyparsing>=2.3.1 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (3.2.0)\n", + "Requirement already satisfied: cycler>=0.10 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (0.12.1)\n", + "Requirement already satisfied: python-dateutil>=2.7 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from matplotlib) (2.8.2)\n", + "Requirement already satisfied: zipp>=3.1.0 in /Users/bennychan/Library/Python/3.9/lib/python/site-packages (from importlib-resources>=3.2.0->matplotlib) (3.17.0)\n", + "Requirement already satisfied: six>=1.5 in /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib) (1.15.0)\n", + "\u001b[33mWARNING: You are using pip version 21.2.4; however, version 24.3.1 is available.\n", + "You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.\u001b[0m\n", + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], + "source": [ + "%pip install matplotlib" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "id": "UgVNWEKgHD8i" + }, + "outputs": [], + "source": [ + "import lungs_segmentation.inference as inference" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "sQ1WVclcHJFx", + "outputId": "6834e134-ac4f-4c32-87c2-0dc2454ca93f" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "zsh:1: command not found: wget\n" + ] + } + ], + "source": [ + "!wget https://upload.wikimedia.org/wikipedia/commons/thumb/c/c8/Chest_Xray_PA_3-8-2010.png/739px-Chest_Xray_PA_3-8-2010.png" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": { + "id": "9kNOo5rNHtV5" + }, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "import matplotlib" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 1000 + }, + "id": "lR3-DXKtHZyx", + "outputId": "02316111-3dfb-49a0-b8d0-861a353b75fa" + }, + "outputs": [], + "source": [ + "import os\n", + "\n", + "# # 强制将模型加载到 CPU\n", + "# model = model.cpu()\n", + "# # 调用推理函数\n", + "# image, mask = inference.inference(model, '/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/CXR/0.png', thresh=0.2)\n", + "\n", + "# Resize the result image to 1024x1024 before saving\n", + "\n", + "# result_img = inference.img_with_masks(image, [mask[0], mask[1]])\n", + "\n", + "# # 显示结果\n", + "# plt.figure(figsize=(20, 40))\n", + "# plt.imshow(result_img, cmap=\"gray\")\n", + "# Ensure the saved image has the same resolution as the original image\n", + "# plt.show()\n", + "# Define the directory containing the images\n", + "image_dir = '/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/CXR/'\n", + "\n", + "# Iterate over all files in the directory\n", + "for filename in os.listdir(image_dir):\n", + " if filename.endswith('.png') or filename.endswith('.jpg'):\n", + " # Create a new directory to save the results\n", + " result_dir = '/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/Mask-ResNet34/'\n", + " os.makedirs(result_dir, exist_ok=True)\n", + " \n", + " # Construct the full file path\n", + " file_path = os.path.join(image_dir, filename)\n", + " \n", + " # Perform inference\n", + " image, mask = inference.inference(model, file_path, thresh=0.2)\n", + " \n", + " # Generate result image with segmentation mask\n", + " result_img = inference.img_with_masks(image, [mask[0], mask[1]])\n", + " result_img = cv2.resize(result_img, (1024, 1024))\n", + " \n", + " # Save the result image in the new directory with the same name as the original image\n", + " result_filepath = os.path.join(result_dir, filename)\n", + " plt.imsave(result_filepath, result_img, cmap=\"gray\")" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/348.png\n", + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/412.png\n", + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/374.png\n", + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/360.png\n", + "Processed and saved: 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Evaluation/MaskBS-DenseNet121/345.png\n", + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/351.png\n", + "Processed and saved: /Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121/437.png\n" + ] + } + ], + "source": [ + "import os\n", + "import cv2\n", + "import numpy as np\n", + "import albumentations as A\n", + "\n", + "# 设置图像大小和预处理\n", + "img_size = 1024\n", + "aug = A.Compose([A.Resize(img_size, img_size, interpolation=1, p=1)], p=1)\n", + "\n", + "# 读取图片和mask\n", + "def preprocess_image(img_path, mask_path):\n", + " # 读取去骨的 CXR 图像\n", + " cxr_image = cv2.imread(img_path, cv2.IMREAD_GRAYSCALE)\n", + " if cxr_image is None:\n", + " raise FileNotFoundError(f\"Image not found at {img_path}\")\n", + " \n", + " cxr_image = cv2.normalize(cxr_image, None, 0, 255, cv2.NORM_MINMAX) # 归一化到0-255范围\n", + " cxr_image = np.array(cxr_image, dtype=np.uint8) # 确保是 NumPy 数组\n", + " cxr_image_aug = aug(image=cxr_image)[\"image\"]\n", + "\n", + " # 读取 mask\n", + " mask = cv2.imread(mask_path, cv2.IMREAD_GRAYSCALE)\n", + " if mask is None:\n", + " raise FileNotFoundError(f\"Mask not found at {mask_path}\")\n", + " \n", + " mask = np.array(mask, dtype=np.uint8) # 确保是 NumPy 数组\n", + " mask_aug = aug(image=mask)[\"image\"]\n", + "\n", + " # 转换 mask 为二值\n", + " binary_mask = (mask_aug > 128).astype(np.uint8) # 二值化 (0 或 1)\n", + " \n", + " return cxr_image_aug, binary_mask\n", + "\n", + "# 应用 mask 到去骨的胸片上\n", + "def apply_mask_to_cxr(cxr_image, binary_mask):\n", + " # 按位与操作，仅保留 mask 中为 1 的区域\n", + " masked_image = cv2.bitwise_and(cxr_image, cxr_image, mask=binary_mask)\n", + " return masked_image\n", + "\n", + "# 文件夹处理函数\n", + "def process_folder(bs_folder, mask_folder, output_folder):\n", + " # 确保输出文件夹存在\n", + " os.makedirs(output_folder, exist_ok=True)\n", + " \n", + " # 遍历去骨胸片图像文件夹\n", + " for filename in os.listdir(bs_folder):\n", + " # 过滤非图像文件\n", + " if not filename.lower().endswith(('.png', '.jpg', '.jpeg')):\n", + " print(f\"Skipping non-image file: {filename}\")\n", + " continue\n", + "\n", + " # 构造去骨图像和 mask 的完整路径\n", + " cxr_path = os.path.join(bs_folder, filename)\n", + " mask_path = os.path.join(mask_folder, filename)\n", + " \n", + " # 检查去骨图像和 mask 文件是否存在\n", + " if not os.path.exists(cxr_path):\n", + " print(f\"BS image not found for {filename}, skipping...\")\n", + " continue\n", + " if not os.path.exists(mask_path):\n", + " print(f\"Mask not found for {filename}, skipping...\")\n", + " continue\n", + " \n", + " try:\n", + " # 预处理图像和 mask\n", + " cxr_image, binary_mask = preprocess_image(cxr_path, mask_path)\n", + "\n", + " # 应用 mask\n", + " masked_cxr = apply_mask_to_cxr(cxr_image, binary_mask)\n", + "\n", + " # 保存结果到输出文件夹\n", + " output_path = os.path.join(output_folder, filename)\n", + " cv2.imwrite(output_path, masked_cxr)\n", + " print(f\"Processed and saved: {output_path}\")\n", + " \n", + " except FileNotFoundError as e:\n", + " print(f\"File error for {filename}: {e}\")\n", + " except Exception as e:\n", + " print(f\"Unexpected error for {filename}: {e}\")\n", + "\n", + "# 主函数\n", + "if __name__ == \"__main__\":\n", + " # 输入文件夹路径（替换为你的路径）\n", + " bs_folder = \"/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/BS\" # 去骨胸片图像文件夹路径\n", + " mask_folder = \"/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/Mask-DenseNet121\" # mask 文件夹路径\n", + " output_folder = \"/Users/bennychan/Desktop/SZCH-X-Rays - Clinical Evaluation/MaskBS-DenseNet121\" # 输出文件夹路径\n", + "\n", + " # 对整个文件夹进行处理\n", + " process_folder(bs_folder, mask_folder, output_folder)" + ] + } + ], + "metadata": { + "accelerator": "GPU", + "colab": { + "provenance": [] + }, + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + 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