{
"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": [
"
"
]
},
{
"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",
"After this operation, 19.4 MB of additional disk space will be used.\n",
"Get:1 http://archive.ubuntu.com/ubuntu jammy/main amd64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB]\n",
"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",
"Fetched 5,278 kB in 6s (910 kB/s)\n",
"debconf: unable to initialize frontend: Dialog\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 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",
"Unpacking libpython3.9-minimal:amd64 (3.9.17-1+jammy1) ...\n",
"Selecting previously unselected package python3.9-minimal.\n",
"Preparing to unpack .../1-python3.9-minimal_3.9.17-1+jammy1_amd64.deb ...\n",
"Unpacking python3.9-minimal (3.9.17-1+jammy1) ...\n",
"Selecting previously unselected package mailcap.\n",
"Preparing to unpack .../2-mailcap_3.70+nmu1ubuntu1_all.deb ...\n",
"Unpacking mailcap (3.70+nmu1ubuntu1) ...\n",
"Selecting previously unselected package mime-support.\n",
"Preparing to unpack .../3-mime-support_3.66_all.deb ...\n",
"Unpacking mime-support (3.66) ...\n",
"Selecting previously unselected package libpython3.9-stdlib:amd64.\n",
"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",
"debconf: unable to initialize frontend: Dialog\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",
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"dpkg-preconfigure: unable to re-open stdin: \n",
"Selecting previously unselected package python3-setuptools.\n",
"(Reading database ... 121176 files and directories currently installed.)\n",
"Preparing to unpack .../python3-setuptools_59.6.0-1.2ubuntu0.22.04.1_all.deb ...\n",
"Unpacking python3-setuptools (59.6.0-1.2ubuntu0.22.04.1) ...\n",
"Selecting previously unselected package python3-wheel.\n",
"Preparing to unpack .../python3-wheel_0.37.1-2ubuntu0.22.04.1_all.deb ...\n",
"Unpacking python3-wheel (0.37.1-2ubuntu0.22.04.1) ...\n",
"Selecting previously unselected package python3-pip.\n",
"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",
"debconf: unable to initialize frontend: Dialog\n",
"debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 78, <> line 2.)\n",
"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",
"Selecting previously unselected package python3.9-distutils.\n",
"Preparing to unpack .../python3.9-distutils_3.9.17-1+jammy1_all.deb ...\n",
"Unpacking python3.9-distutils (3.9.17-1+jammy1) ...\n",
"Setting up python3.9-lib2to3 (3.9.17-1+jammy1) ...\n",
"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": [
"Collecting flake8>=3.8.1\n",
" Downloading flake8-6.1.0-py2.py3-none-any.whl (58 kB)\n",
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"\u001b[?25hBuilding wheels for collected packages: fire, lit\n",
" Building wheel for fire (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for fire: filename=fire-0.5.0-py2.py3-none-any.whl size=116951 sha256=532122dd1bd434615ee929ed20dad80c3a272be109739d6422d626f266f93f50\n",
" Stored in directory: /root/.cache/pip/wheels/f7/f1/89/b9ea2bf8f80ec027a88fef1d354b3816b4d3d29530988972f6\n",
" Building wheel for lit (pyproject.toml) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for lit: filename=lit-16.0.6-py3-none-any.whl size=93583 sha256=15df868c627dda7845b33112eb0dff5ff5455bcb8a9e34ec161261a3a7ca093c\n",
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"Successfully built fire lit\n",
"Installing collected packages: types-pkg_resources, pytz, ninja, mpmath, lit, distlib, cmake, zipp, wrapt, urllib3, tzdata, typing-extensions, tqdm, tomlkit, tomli, toml, threadpoolctl, termcolor, tensorboard-data-server, tabulate, sympy, soupsieve, rpds-py, pyyaml, python-dateutil, PySocks, pyparsing, pyjwt, pyflakes, pydicom, pycparser, pycodestyle, pyasn1, protobuf, platformdirs, pillow, pathspec, parameterized, packaging, oauthlib, nvidia-nvtx-cu11, nvidia-nccl-cu11, nvidia-cusparse-cu11, nvidia-curand-cu11, nvidia-cufft-cu11, nvidia-cuda-runtime-cu11, nvidia-cuda-nvrtc-cu11, nvidia-cuda-cupti-cu11, nvidia-cublas-cu11, numpy, nodeenv, networkx, natsort, mypy-extensions, mccabe, MarkupSafe, markdown, lazy-object-proxy, lazy_loader, kiwisolver, joblib, isort, idna, identify, grpcio, fonttools, filelock, einops, dill, cycler, click, charset-normalizer, cfgv, certifi, cachetools, attrs, absl-py, werkzeug, virtualenv, typing-inspect, tifffile, scipy, rsa, requests, referencing, PyWavelets, pydot, pyasn1-modules, pandas, opencv-python, nvidia-cusolver-cu11, nvidia-cudnn-cu11, nibabel, mypy, jinja2, itk-core, importlib-resources, importlab, imageio, flake8, fire, deprecated, cucim, contourpy, cffi, black, beautifulsoup4, astroid, scikit-learn, scikit-image, requests-oauthlib, pynacl, pylint, pre-commit, pep8-naming, matplotlib, libcst, jsonschema-specifications, itk-numerics, itk-io, google-auth, flake8-executable, flake8-comprehensions, flake8-bugbear, pytype, PyGithub, jsonschema, itk-filtering, google-auth-oauthlib, gdown, tensorboard, itk-segmentation, itk-registration, itk, triton, torch, pytorch-ignite, monai\n",
" Attempting uninstall: pyjwt\n",
" Found existing installation: PyJWT 2.3.0\n",
" 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 \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-"
}
}
]
}