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- {
- "nbformat": 4,
- "nbformat_minor": 0,
- "metadata": {
- "colab": {
- "provenance": [],
- "gpuType": "T4",
- "authorship_tag": "ABX9TyOsNL7zeUDPTLklO8UfddKR",
- "include_colab_link": true
- },
- "kernelspec": {
- "name": "python3",
- "display_name": "Python 3"
- },
- "language_info": {
- "name": "python"
- },
- "accelerator": "GPU"
- },
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {
- "id": "view-in-github",
- "colab_type": "text"
- },
- "source": [
- "<a href=\"https://colab.research.google.com/github/ytl0623/monai_wholeBody_ct_segmentation/blob/master/monai_wholeBody_ct_segmentation.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Change Python version 3.10 -> 3.9"
- ],
- "metadata": {
- "id": "_r2WxIAWn6T8"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!sudo apt-get install python3.9\n",
- "!sudo ln -sf /usr/bin/python3.9 /usr/bin/python3\n",
- "!sudo apt-get install python3-pip\n",
- "!sudo apt-get install python3.9-distutils"
- ],
- "metadata": {
- "id": "YmredzKthlTy",
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "outputId": "47d284e1-9318-4888-fb9e-9298301496af"
- },
- "execution_count": 1,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- "Reading package lists... Done\n",
- "Building dependency tree... Done\n",
- "Reading state information... Done\n",
- "The following additional packages will be installed:\n",
- " libpython3.9-minimal libpython3.9-stdlib mailcap mime-support\n",
- " python3.9-minimal\n",
- "Suggested packages:\n",
- " python3.9-venv binfmt-support\n",
- "The following NEW packages will be installed:\n",
- " libpython3.9-minimal libpython3.9-stdlib mailcap mime-support python3.9\n",
- " python3.9-minimal\n",
- "0 upgraded, 6 newly installed, 0 to remove and 16 not upgraded.\n",
- "Need to get 5,278 kB of archives.\n",
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- "Get:2 http://archive.ubuntu.com/ubuntu jammy/main amd64 mime-support all 3.66 [3,696 B]\n",
- "Get:3 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 libpython3.9-minimal amd64 3.9.17-1+jammy1 [835 kB]\n",
- "Get:4 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 python3.9-minimal amd64 3.9.17-1+jammy1 [2,078 kB]\n",
- "Get:5 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 libpython3.9-stdlib amd64 3.9.17-1+jammy1 [1,842 kB]\n",
- "Get:6 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 python3.9 amd64 3.9.17-1+jammy1 [496 kB]\n",
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- "Selecting previously unselected package libpython3.9-minimal:amd64.\n",
- "(Reading database ... 120511 files and directories currently installed.)\n",
- "Preparing to unpack .../0-libpython3.9-minimal_3.9.17-1+jammy1_amd64.deb ...\n",
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- "Unpacking mime-support (3.66) ...\n",
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- "Preparing to unpack .../4-libpython3.9-stdlib_3.9.17-1+jammy1_amd64.deb ...\n",
- "Unpacking libpython3.9-stdlib:amd64 (3.9.17-1+jammy1) ...\n",
- "Selecting previously unselected package python3.9.\n",
- "Preparing to unpack .../5-python3.9_3.9.17-1+jammy1_amd64.deb ...\n",
- "Unpacking python3.9 (3.9.17-1+jammy1) ...\n",
- "Setting up libpython3.9-minimal:amd64 (3.9.17-1+jammy1) ...\n",
- "Setting up python3.9-minimal (3.9.17-1+jammy1) ...\n",
- "Setting up mailcap (3.70+nmu1ubuntu1) ...\n",
- "Setting up mime-support (3.66) ...\n",
- "Setting up libpython3.9-stdlib:amd64 (3.9.17-1+jammy1) ...\n",
- "Setting up python3.9 (3.9.17-1+jammy1) ...\n",
- "Processing triggers for man-db (2.10.2-1) ...\n",
- "Reading package lists... Done\n",
- "Building dependency tree... Done\n",
- "Reading state information... Done\n",
- "The following additional packages will be installed:\n",
- " python3-setuptools python3-wheel\n",
- "Suggested packages:\n",
- " python-setuptools-doc\n",
- "The following NEW packages will be installed:\n",
- " python3-pip python3-setuptools python3-wheel\n",
- "0 upgraded, 3 newly installed, 0 to remove and 16 not upgraded.\n",
- "Need to get 1,677 kB of archives.\n",
- "After this operation, 8,965 kB of additional disk space will be used.\n",
- "Get:1 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 python3-setuptools all 59.6.0-1.2ubuntu0.22.04.1 [339 kB]\n",
- "Get:2 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3-wheel all 0.37.1-2ubuntu0.22.04.1 [32.0 kB]\n",
- "Get:3 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3-pip all 22.0.2+dfsg-1ubuntu0.3 [1,305 kB]\n",
- "Fetched 1,677 kB in 1s (2,398 kB/s)\n",
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- "Preparing to unpack .../python3-pip_22.0.2+dfsg-1ubuntu0.3_all.deb ...\n",
- "Unpacking python3-pip (22.0.2+dfsg-1ubuntu0.3) ...\n",
- "Setting up python3-setuptools (59.6.0-1.2ubuntu0.22.04.1) ...\n",
- "Setting up python3-wheel (0.37.1-2ubuntu0.22.04.1) ...\n",
- "Setting up python3-pip (22.0.2+dfsg-1ubuntu0.3) ...\n",
- "Processing triggers for man-db (2.10.2-1) ...\n",
- "Reading package lists... Done\n",
- "Building dependency tree... Done\n",
- "Reading state information... Done\n",
- "The following additional packages will be installed:\n",
- " python3.9-lib2to3\n",
- "The following NEW packages will be installed:\n",
- " python3.9-distutils python3.9-lib2to3\n",
- "0 upgraded, 2 newly installed, 0 to remove and 16 not upgraded.\n",
- "Need to get 319 kB of archives.\n",
- "After this operation, 1,234 kB of additional disk space will be used.\n",
- "Get:1 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 python3.9-lib2to3 all 3.9.17-1+jammy1 [127 kB]\n",
- "Get:2 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu jammy/main amd64 python3.9-distutils all 3.9.17-1+jammy1 [192 kB]\n",
- "Fetched 319 kB in 2s (153 kB/s)\n",
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- "debconf: falling back to frontend: Readline\n",
- "debconf: unable to initialize frontend: Readline\n",
- "debconf: (This frontend requires a controlling tty.)\n",
- "debconf: falling back to frontend: Teletype\n",
- "dpkg-preconfigure: unable to re-open stdin: \n",
- "Selecting previously unselected package python3.9-lib2to3.\n",
- "(Reading database ... 122038 files and directories currently installed.)\n",
- "Preparing to unpack .../python3.9-lib2to3_3.9.17-1+jammy1_all.deb ...\n",
- "Unpacking python3.9-lib2to3 (3.9.17-1+jammy1) ...\n",
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- "Setting up python3.9-distutils (3.9.17-1+jammy1) ...\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Clone Repository"
- ],
- "metadata": {
- "id": "KaymznnwM9BN"
- }
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "SccRcqOXMFKT",
- "outputId": "ac301d5c-c128-4447-d841-9bdefdde376e"
- },
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- "Cloning into 'monai_wholeBody_ct_segmentation'...\n",
- "remote: Enumerating objects: 417, done.\u001b[K\n",
- "remote: Counting objects: 100% (219/219), done.\u001b[K\n",
- "remote: Compressing objects: 100% (212/212), done.\u001b[K\n",
- "remote: Total 417 (delta 22), reused 106 (delta 6), pack-reused 198\u001b[K\n",
- "Receiving objects: 100% (417/417), 223.31 MiB | 21.87 MiB/s, done.\n",
- "Resolving deltas: 100% (28/28), done.\n",
- "Updating files: 100% (199/199), done.\n"
- ]
- }
- ],
- "source": [
- "!git clone https://github.com/ytl0623/monai_wholeBody_ct_segmentation.git"
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Go to the cloned folder"
- ],
- "metadata": {
- "id": "3EAZt1jRNFX0"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "%cd monai_wholeBody_ct_segmentation"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "kOE7W2EoMdvV",
- "outputId": "f773a61d-6446-4b65-b7ed-80e4b0e7dbee"
- },
- "execution_count": 3,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- "/content/monai_wholeBody_ct_segmentation\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Install the dependencies"
- ],
- "metadata": {
- "id": "H2-H_2rcNGlT"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!pip install -r requirements.txt"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/",
- "height": 1000
- },
- "id": "jn25fz1CMfMs",
- "outputId": "175e368f-993d-44ee-8c30-87bb67a3532e"
- },
- "execution_count": 4,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
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- " Not uninstalling pyjwt at /usr/lib/python3/dist-packages, outside environment /usr\n",
- " Can't uninstall 'PyJWT'. No files were found to uninstall.\n",
- "Successfully installed MarkupSafe-2.1.3 PyGithub-1.59.1 PySocks-1.7.1 PyWavelets-1.4.1 absl-py-1.4.0 astroid-2.15.6 attrs-23.1.0 beautifulsoup4-4.12.2 black-23.7.0 cachetools-5.3.1 certifi-2023.7.22 cffi-1.15.1 cfgv-3.3.1 charset-normalizer-3.2.0 click-8.1.6 cmake-3.27.1 contourpy-1.1.0 cucim-22.8.1 cycler-0.11.0 deprecated-1.2.14 dill-0.3.7 distlib-0.3.7 einops-0.6.1 filelock-3.12.2 fire-0.5.0 flake8-6.1.0 flake8-bugbear-23.7.10 flake8-comprehensions-3.14.0 flake8-executable-2.1.3 fonttools-4.42.0 gdown-4.7.1 google-auth-2.22.0 google-auth-oauthlib-1.0.0 grpcio-1.56.2 identify-2.5.26 idna-3.4 imageio-2.31.1 importlab-0.8 importlib-resources-6.0.1 isort-5.12.0 itk-5.3.0 itk-core-5.3.0 itk-filtering-5.3.0 itk-io-5.3.0 itk-numerics-5.3.0 itk-registration-5.3.0 itk-segmentation-5.3.0 jinja2-3.1.2 joblib-1.3.1 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 kiwisolver-1.4.4 lazy-object-proxy-1.9.0 lazy_loader-0.3 libcst-1.0.1 lit-16.0.6 markdown-3.4.4 matplotlib-3.7.2 mccabe-0.7.0 monai-1.2.0 mpmath-1.3.0 mypy-1.4.1 mypy-extensions-1.0.0 natsort-8.4.0 networkx-3.1 nibabel-5.1.0 ninja-1.11.1 nodeenv-1.8.0 numpy-1.25.2 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-cupti-cu11-11.7.101 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 nvidia-cufft-cu11-10.9.0.58 nvidia-curand-cu11-10.2.10.91 nvidia-cusolver-cu11-11.4.0.1 nvidia-cusparse-cu11-11.7.4.91 nvidia-nccl-cu11-2.14.3 nvidia-nvtx-cu11-11.7.91 oauthlib-3.2.2 opencv-python-4.8.0.74 packaging-23.1 pandas-2.0.3 parameterized-0.9.0 pathspec-0.11.2 pep8-naming-0.13.3 pillow-10.0.0 platformdirs-3.10.0 pre-commit-3.3.3 protobuf-4.23.4 pyasn1-0.5.0 pyasn1-modules-0.3.0 pycodestyle-2.11.0 pycparser-2.21 pydicom-2.4.2 pydot-1.4.2 pyflakes-3.1.0 pyjwt-2.8.0 pylint-2.17.5 pynacl-1.5.0 pyparsing-3.0.9 python-dateutil-2.8.2 pytorch-ignite-0.4.12 pytype-2023.7.28 pytz-2023.3 pyyaml-6.0.1 referencing-0.30.2 requests-2.31.0 requests-oauthlib-1.3.1 rpds-py-0.9.2 rsa-4.9 scikit-image-0.21.0 scikit-learn-1.3.0 scipy-1.11.1 soupsieve-2.4.1 sympy-1.12 tabulate-0.9.0 tensorboard-2.13.0 tensorboard-data-server-0.7.1 termcolor-2.3.0 threadpoolctl-3.2.0 tifffile-2023.7.18 toml-0.10.2 tomli-2.0.1 tomlkit-0.12.1 torch-2.0.1 tqdm-4.65.0 triton-2.0.0 types-pkg_resources-0.1.3 typing-extensions-4.7.1 typing-inspect-0.9.0 tzdata-2023.3 urllib3-1.26.16 virtualenv-20.24.2 werkzeug-2.3.6 wrapt-1.15.0 zipp-3.16.2\n",
- "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
- "\u001b[0m"
- ]
- },
- {
- "output_type": "display_data",
- "data": {
- "application/vnd.colab-display-data+json": {
- "pip_warning": {
- "packages": [
- "certifi",
- "cffi",
- "cycler",
- "dateutil",
- "kiwisolver",
- "socks"
- ]
- }
- }
- },
- "metadata": {}
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Execute inference"
- ],
- "metadata": {
- "id": "5MUQJU2WNn40"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "\n",
- "It will cost about three minutes. Check NIFTI directory after run done."
- ],
- "metadata": {
- "id": "9x7qRnttNuPu"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!python -m monai.bundle run --config_file configs/inference.json"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "HbDBe8jANMpY",
- "outputId": "d26f8fa1-7dfc-473b-8817-48d871fc1413"
- },
- "execution_count": 5,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- "2023-08-08 01:02:00,317 - INFO - --- input summary of monai.bundle.scripts.run ---\n",
- "2023-08-08 01:02:00,317 - INFO - > config_file: 'configs/inference.json'\n",
- "2023-08-08 01:02:00,317 - INFO - ---\n",
- "\n",
- "\n",
- "2023-08-08 01:02:00,317 - INFO - Setting logging properties based on config: configs/logging.conf.\n",
- "monai.transforms.io.dictionary LoadImaged.__init__:image_only: Current default value of argument `image_only=False` has been deprecated since version 1.1. It will be changed to `image_only=True` in version 1.3.\n",
- "monai.transforms.io.dictionary SaveImaged.__init__:resample: Current default value of argument `resample=True` has been deprecated since version 1.1. It will be changed to `resample=False` in version 1.3.\n",
- "monai.handlers.stats_handler StatsHandler.__init__:name: Current default value of argument `name=None` has been deprecated since version 1.1. It will be changed to `name=StatsHandler` in version 1.3.\n",
- "2023-08-08 01:02:00,562 - ignite.engine.engine.SupervisedEvaluator - INFO - Engine run resuming from iteration 0, epoch 0 until 1 epochs\n",
- "2023-08-08 01:02:02,723 - ignite.engine.engine.SupervisedEvaluator - INFO - Restored all variables from ./models/model_lowres.pt\n",
- "^C\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Unzip inference file"
- ],
- "metadata": {
- "id": "zlHCcB4rQMS5"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!gzip -d NIFTI/DLCSI033/DLCSI033_trans.nii.gz"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "jd_5gJdRVlZF",
- "outputId": "1d0e159d-a86c-4410-92fd-cf6572d204ff"
- },
- "execution_count": 6,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- "gzip: NIFTI/DLCSI033/DLCSI033_trans.nii.gz: No such file or directory\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Convert NIFTI file to mask file"
- ],
- "metadata": {
- "id": "KokHjc9zaUXm"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "It will cost about three minutes. Check MONAI directory after run done."
- ],
- "metadata": {
- "id": "rRb-NTzoaXTm"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!python nii2png.py"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "VP2O7ECYaVxu",
- "outputId": "a0b263bd-4faa-42a6-f672-70f90e2e79fe"
- },
- "execution_count": 7,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- ".gitignore ==================================================\n",
- "Label's shape:\n",
- " (105, 0)\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Generate DICOM-RT file"
- ],
- "metadata": {
- "id": "MzjEOxCCabPF"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "It will cost about two minutes. Check DICOM directory after run done."
- ],
- "metadata": {
- "id": "F7tWolcQad7u"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "!python main.py"
- ],
- "metadata": {
- "colab": {
- "base_uri": "https://localhost:8080/"
- },
- "id": "--GWn5vOacXk",
- "outputId": "9be6e087-b3ca-4d2a-d9c1-c0c70bca5847"
- },
- "execution_count": 8,
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": [
- ".gitignore ==================================================\n",
- "DICOM/.gitignore/ MONAI/.gitignore/\n",
- "get Contour Sequence from Images.Traceback (most recent call last):\n",
- " File \"/content/monai_wholeBody_ct_segmentation/main.py\", line 22, in <module>\n",
- " spacingDatabase, DICOMInformation = SegmentiontoImageData(dcm_file_path, label_path)()\n",
- " File \"/content/monai_wholeBody_ct_segmentation/SegmentiontoImageData.py\", line 29, in __call__\n",
- " self.getDICOMinformation()\n",
- " File \"/content/monai_wholeBody_ct_segmentation/SegmentiontoImageData.py\", line 43, in getDICOMinformation\n",
- " DICOMdir = os.listdir(self.DICOM_File_PATH)\n",
- "FileNotFoundError: [Errno 2] No such file or directory: 'DICOM/.gitignore/'\n"
- ]
- }
- ]
- },
- {
- "cell_type": "markdown",
- "source": [
- "Download DICOM directory"
- ],
- "metadata": {
- "id": "5FC-8olzagBm"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "There are two DICOM-RT files. (Original and MONAI)"
- ],
- "metadata": {
- "id": "38eTIn_Cai3W"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- ""
- ],
- "metadata": {
- "id": "vuKqblW9bCH-"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "Download [Dicompyler](https://github.com/bastula/dicompyler/releases/download/release-0.4.2/dicompyler_setup-0.4.2.win32.exe)"
- ],
- "metadata": {
- "id": "eBhwQg3cam_e"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- ""
- ],
- "metadata": {
- "id": "K2hKyLSabEeW"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "Show results with Dicompyler"
- ],
- "metadata": {
- "id": "RwDs61JhbGpO"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "Pay attention to the Chinese path."
- ],
- "metadata": {
- "id": "VBDUHhTnbK1e"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- ""
- ],
- "metadata": {
- "id": "D15tjOn_bNP2"
- }
- },
- {
- "cell_type": "markdown",
- "source": [
- "Reference\n",
- "- https://github.com/Kiragroh/Kira_DICOM-RT-Anonymizer-MG\n",
- "- https://github.com/Project-MONAI/model-zoo\n",
- "- https://monai.io/model-zoo.html"
- ],
- "metadata": {
- "id": "cFLRp9zDbRE-"
- }
- }
- ]
- }
|