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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"authorship_tag": "ABX9TyPtBCPwRr46IKKbW1mJHhmU",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/andreped/f83e53b120ddc2f6930f1dd66a16f248/neukit-demo-example.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"source": [
"# Setup Python 3.7\n",
"!sudo apt-get install python3.7\n",
"!sudo apt-get install python3.7-distutils\n",
"!sudo apt-get install python3-apt\n",
"!sudo apt-get install python3-pip\n",
"\n",
"!python3.7 -V\n",
"!python3.7 -m pip -V"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "li1rmocnKcb9",
"outputId": "59d5c28a-082b-4b99-8488-a7d1e683cae1"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"The following additional packages will be installed:\n",
" libpython3.7-minimal libpython3.7-stdlib python3.7-minimal\n",
"Suggested packages:\n",
" python3.7-venv binfmt-support\n",
"The following NEW packages will be installed:\n",
" libpython3.7-minimal libpython3.7-stdlib python3.7 python3.7-minimal\n",
"0 upgraded, 4 newly installed, 0 to remove and 15 not upgraded.\n",
"Need to get 4,531 kB of archives.\n",
"After this operation, 23.3 MB of additional disk space will be used.\n",
"Get:1 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 libpython3.7-minimal amd64 3.7.17-1+focal1 [589 kB]\n",
"Get:2 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 python3.7-minimal amd64 3.7.17-1+focal1 [1,808 kB]\n",
"Get:3 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 libpython3.7-stdlib amd64 3.7.17-1+focal1 [1,774 kB]\n",
"Get:4 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 python3.7 amd64 3.7.17-1+focal1 [361 kB]\n",
"Fetched 4,531 kB in 3s (1,569 kB/s)\n",
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"dpkg-preconfigure: unable to re-open stdin: \n",
"Selecting previously unselected package libpython3.7-minimal:amd64.\n",
"(Reading database ... 123069 files and directories currently installed.)\n",
"Preparing to unpack .../libpython3.7-minimal_3.7.17-1+focal1_amd64.deb ...\n",
"Unpacking libpython3.7-minimal:amd64 (3.7.17-1+focal1) ...\n",
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"Preparing to unpack .../python3.7-minimal_3.7.17-1+focal1_amd64.deb ...\n",
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"Preparing to unpack .../libpython3.7-stdlib_3.7.17-1+focal1_amd64.deb ...\n",
"Unpacking libpython3.7-stdlib:amd64 (3.7.17-1+focal1) ...\n",
"Selecting previously unselected package python3.7.\n",
"Preparing to unpack .../python3.7_3.7.17-1+focal1_amd64.deb ...\n",
"Unpacking python3.7 (3.7.17-1+focal1) ...\n",
"Setting up libpython3.7-minimal:amd64 (3.7.17-1+focal1) ...\n",
"Setting up python3.7-minimal (3.7.17-1+focal1) ...\n",
"Setting up libpython3.7-stdlib:amd64 (3.7.17-1+focal1) ...\n",
"Setting up python3.7 (3.7.17-1+focal1) ...\n",
"Processing triggers for man-db (2.9.1-1) ...\n",
"Processing triggers for mime-support (3.64ubuntu1) ...\n",
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"The following additional packages will be installed:\n",
" python3.7-lib2to3\n",
"The following NEW packages will be installed:\n",
" python3.7-distutils python3.7-lib2to3\n",
"0 upgraded, 2 newly installed, 0 to remove and 15 not upgraded.\n",
"Need to get 309 kB of archives.\n",
"After this operation, 1,229 kB of additional disk space will be used.\n",
"Get:1 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 python3.7-lib2to3 all 3.7.17-1+focal1 [122 kB]\n",
"Get:2 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 python3.7-distutils all 3.7.17-1+focal1 [187 kB]\n",
"Fetched 309 kB in 1s (332 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 76, <> 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",
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"dpkg-preconfigure: unable to re-open stdin: \n",
"Selecting previously unselected package python3.7-lib2to3.\n",
"(Reading database ... 123689 files and directories currently installed.)\n",
"Preparing to unpack .../python3.7-lib2to3_3.7.17-1+focal1_all.deb ...\n",
"Unpacking python3.7-lib2to3 (3.7.17-1+focal1) ...\n",
"Selecting previously unselected package python3.7-distutils.\n",
"Preparing to unpack .../python3.7-distutils_3.7.17-1+focal1_all.deb ...\n",
"Unpacking python3.7-distutils (3.7.17-1+focal1) ...\n",
"Setting up python3.7-lib2to3 (3.7.17-1+focal1) ...\n",
"Setting up python3.7-distutils (3.7.17-1+focal1) ...\n",
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"python3-apt is already the newest version (2.0.1ubuntu0.20.04.1).\n",
"python3-apt set to manually installed.\n",
"0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.\n",
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"The following additional packages will be installed:\n",
" python-pip-whl python3-setuptools python3-wheel\n",
"Suggested packages:\n",
" python-setuptools-doc\n",
"The following NEW packages will be installed:\n",
" python-pip-whl python3-pip python3-setuptools python3-wheel\n",
"0 upgraded, 4 newly installed, 0 to remove and 15 not upgraded.\n",
"Need to get 2,389 kB of archives.\n",
"After this operation, 4,933 kB of additional disk space will be used.\n",
"Get:1 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-pip-whl all 20.0.2-5ubuntu1.9 [1,805 kB]\n",
"Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-setuptools all 45.2.0-1ubuntu0.1 [330 kB]\n",
"Get:3 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 python3-wheel all 0.34.2-1ubuntu0.1 [23.9 kB]\n",
"Get:4 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 python3-pip all 20.0.2-5ubuntu1.9 [231 kB]\n",
"Fetched 2,389 kB in 0s (5,756 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",
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"dpkg-preconfigure: unable to re-open stdin: \n",
"Selecting previously unselected package python-pip-whl.\n",
"(Reading database ... 123828 files and directories currently installed.)\n",
"Preparing to unpack .../python-pip-whl_20.0.2-5ubuntu1.9_all.deb ...\n",
"Unpacking python-pip-whl (20.0.2-5ubuntu1.9) ...\n",
"Selecting previously unselected package python3-setuptools.\n",
"Preparing to unpack .../python3-setuptools_45.2.0-1ubuntu0.1_all.deb ...\n",
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"Selecting previously unselected package python3-wheel.\n",
"Preparing to unpack .../python3-wheel_0.34.2-1ubuntu0.1_all.deb ...\n",
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"Selecting previously unselected package python3-pip.\n",
"Preparing to unpack .../python3-pip_20.0.2-5ubuntu1.9_all.deb ...\n",
"Unpacking python3-pip (20.0.2-5ubuntu1.9) ...\n",
"Setting up python3-setuptools (45.2.0-1ubuntu0.1) ...\n",
"Setting up python3-wheel (0.34.2-1ubuntu0.1) ...\n",
"Setting up python-pip-whl (20.0.2-5ubuntu1.9) ...\n",
"Setting up python3-pip (20.0.2-5ubuntu1.9) ...\n",
"Processing triggers for man-db (2.9.1-1) ...\n",
"Python 3.7.17\n",
"pip 20.0.2 from /usr/lib/python3/dist-packages/pip (python 3.7)\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"# Install dependencies\n",
"!python3.7 -m pip install virtualenv"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "3Ga-vm6oLazz",
"outputId": "b4f94ed6-7c65-4fc9-91cd-9f7f0b0c4ab8"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Collecting virtualenv\n",
" Downloading virtualenv-20.23.1-py3-none-any.whl (3.3 MB)\n",
"\u001b[K |████████████████████████████████| 3.3 MB 4.0 MB/s \n",
"\u001b[?25hCollecting platformdirs<4,>=3.5.1\n",
" Downloading platformdirs-3.6.0-py3-none-any.whl (16 kB)\n",
"Collecting filelock<4,>=3.12\n",
" Downloading filelock-3.12.2-py3-none-any.whl (10 kB)\n",
"Collecting distlib<1,>=0.3.6\n",
" Downloading distlib-0.3.6-py2.py3-none-any.whl (468 kB)\n",
"\u001b[K |████████████████████████████████| 468 kB 44.7 MB/s \n",
"\u001b[?25hCollecting importlib-metadata>=6.6; python_version < \"3.8\"\n",
" Downloading importlib_metadata-6.6.0-py3-none-any.whl (22 kB)\n",
"Collecting typing-extensions>=4.6.3; python_version < \"3.8\"\n",
" Downloading typing_extensions-4.6.3-py3-none-any.whl (31 kB)\n",
"Collecting zipp>=0.5\n",
" Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB)\n",
"Installing collected packages: typing-extensions, platformdirs, filelock, distlib, zipp, importlib-metadata, virtualenv\n",
"Successfully installed distlib-0.3.6 filelock-3.12.2 importlib-metadata-6.6.0 platformdirs-3.6.0 typing-extensions-4.6.3 virtualenv-20.23.1 zipp-3.15.0\n"
]
}
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "nuxfs4GZKGRy",
"outputId": "12a47064-54a8-4baf-8e10-ae3f40c393bb"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Cloning into 'neukit'...\n",
"remote: Enumerating objects: 179, done.\u001b[K\n",
"remote: Counting objects: 100% (179/179), done.\u001b[K\n",
"remote: Compressing objects: 100% (125/125), done.\u001b[K\n",
"remote: Total 179 (delta 91), reused 109 (delta 47), pack-reused 0\u001b[K\n",
"Receiving objects: 100% (179/179), 37.21 KiB | 3.72 MiB/s, done.\n",
"Resolving deltas: 100% (91/91), done.\n",
"created virtual environment CPython3.7.17.final.0-64 in 1334ms\n",
" creator CPython3Posix(dest=/content/venv, clear=True, no_vcs_ignore=False, global=False)\n",
" seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/root/.local/share/virtualenv)\n",
" added seed packages: pip==23.1.2, setuptools==67.8.0, wheel==0.40.0\n",
" activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator\n",
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Collecting raidionicsrads@ git+https://github.com/andreped/raidionics_rads_lib\n",
" Cloning https://github.com/andreped/raidionics_rads_lib to /tmp/pip-install-ygos5ket/raidionicsrads\n",
" Running command git clone -q https://github.com/andreped/raidionics_rads_lib /tmp/pip-install-ygos5ket/raidionicsrads\n",
" Running command git submodule update --init --recursive -q\n",
"Collecting gradio==3.32.0\n",
" Downloading gradio-3.32.0-py3-none-any.whl (19.9 MB)\n",
"\u001b[K |████████████████████████████████| 19.9 MB 1.4 MB/s \n",
"\u001b[?25hCollecting MedPy==0.4.0\n",
" Downloading MedPy-0.4.0.tar.gz (151 kB)\n",
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"\u001b[?25hCollecting antspyx\n",
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"\u001b[K |████████████████████████████████| 326.4 MB 30 kB/s \n",
"\u001b[?25hCollecting raidionicsseg@ git+https://github.com/dbouget/raidionics_seg_lib.git@master#egg=raidionicsseg\n",
" Cloning https://github.com/dbouget/raidionics_seg_lib.git (to revision master) to /tmp/pip-install-ygos5ket/raidionicsseg\n",
" Running command git clone -q https://github.com/dbouget/raidionics_seg_lib.git /tmp/pip-install-ygos5ket/raidionicsseg\n",
"Collecting orjson\n",
" Downloading orjson-3.9.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (136 kB)\n",
"\u001b[K |████████████████████████████████| 136 kB 34.7 MB/s \n",
"\u001b[?25hCollecting semantic-version\n",
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"\u001b[K |████████████████████████████████| 45 kB 2.7 MB/s \n",
"\u001b[?25hCollecting markupsafe\n",
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"Collecting pandas\n",
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"\u001b[K |████████████████████████████████| 15.7 MB 74.7 MB/s \n",
"\u001b[?25hRequirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from gradio==3.32.0->-r neukit/requirements.txt (line 4)) (4.6.3)\n",
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"\u001b[K |████████████████████████████████| 948 kB 74.3 MB/s \n",
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"\u001b[K |████████████████████████████████| 471 kB 69.7 MB/s \n",
"\u001b[?25hCollecting markdown-it-py[linkify]>=2.0.0\n",
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"\u001b[?25hCollecting pydantic\n",
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"\u001b[?25hCollecting SimpleITK>=1.1.0\n",
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"\u001b[?25hCollecting debugpy>=1.0\n",
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"Installing collected packages: pyzmq, nest-asyncio, tornado, traitlets, matplotlib-inline, psutil, debugpy, parso, jedi, wcwidth, prompt-toolkit, ptyprocess, pexpect, pickleshare, decorator, backcall, ipython, entrypoints, jupyter-core, jupyter-client, ipykernel\n",
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]
}
],
"source": [
"# Setup virtual environment and app\n",
"!git clone https://github.com/andreped/neukit.git\n",
"!cd neukit/\n",
"\n",
"!python3.7 -m virtualenv -ppython3 venv/ --clear\n",
"!source venv/bin/activate\n",
"!python3.7 -m pip install -r neukit/requirements.txt\n",
"!python3.7 -m pip install ipykernel"
]
},
{
"cell_type": "code",
"source": [
"# Download pretrained models\n",
"!wget \"https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Meningioma-ONNX-v12.zip\" && \\\n",
" unzip \"Raidionics-MRI_Meningioma-ONNX-v12.zip\" && mkdir -p resources/models/ && mv MRI_Meningioma/ resources/models/MRI_Meningioma/\n",
"!wget \"https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_LGGlioma-ONNX-v12.zip\" && \\\n",
" unzip \"Raidionics-MRI_LGGlioma-ONNX-v12.zip\" && mv MRI_LGGlioma/ resources/models/MRI_LGGlioma/\n",
"!wget \"https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Metastasis-ONNX-v12.zip\" && \\\n",
" unzip \"Raidionics-MRI_Metastasis-ONNX-v12.zip\" && mv MRI_Metastasis/ resources/models/MRI_Metastasis/\n",
"!wget \"https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_GBM-ONNX-v12.zip\" && \\\n",
" unzip \"Raidionics-MRI_GBM-ONNX-v12.zip\" && mv MRI_GBM/ resources/models/MRI_GBM/\n",
"!wget \"https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Brain-ONNX-v12.zip\" && \\\n",
" unzip \"Raidionics-MRI_Brain-ONNX-v12.zip\" && mv MRI_Brain/ resources/models/MRI_Brain/\n",
"!rm -r *.zip\n",
"\n",
"# Download test sample\n",
"!wget \"https://github.com/andreped/neukit/releases/download/test-data/RegLib_C01_1.nii\" && \\\n",
" wget \"https://github.com/andreped/neukit/releases/download/test-data/RegLib_C01_2.nii\" && \\\n",
" mv RegLib_C01_* neukit/"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "rAUQA1OVfLjG",
"outputId": "067f299d-e833-4e7d-9e76-77376fc33715"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"--2023-06-18 12:45:17-- https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Meningioma-ONNX-v12.zip\n",
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"\n",
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"\n",
"Archive: Raidionics-MRI_Meningioma-ONNX-v12.zip\n",
" creating: MRI_Meningioma/\n",
" inflating: MRI_Meningioma/model.onnx \n",
" inflating: MRI_Meningioma/model_config.txt \n",
" inflating: MRI_Meningioma/pre_processing.ini \n",
" inflating: MRI_Meningioma/pipeline.json \n",
"--2023-06-18 12:45:19-- https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_LGGlioma-ONNX-v12.zip\n",
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"Saving to: ‘Raidionics-MRI_LGGlioma-ONNX-v12.zip’\n",
"\n",
"Raidionics-MRI_LGGl 100%[===================>] 65.84M 146MB/s in 0.5s \n",
"\n",
"2023-06-18 12:45:20 (146 MB/s) - ‘Raidionics-MRI_LGGlioma-ONNX-v12.zip’ saved [69041134/69041134]\n",
"\n",
"Archive: Raidionics-MRI_LGGlioma-ONNX-v12.zip\n",
" creating: MRI_LGGlioma/\n",
" inflating: MRI_LGGlioma/model.onnx \n",
" inflating: MRI_LGGlioma/model_config.txt \n",
" inflating: MRI_LGGlioma/pre_processing.ini \n",
" inflating: MRI_LGGlioma/pipeline.json \n",
"--2023-06-18 12:45:21-- https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Metastasis-ONNX-v12.zip\n",
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"\n",
"Raidionics-MRI_Meta 100%[===================>] 65.62M 151MB/s in 0.4s \n",
"\n",
"2023-06-18 12:45:22 (151 MB/s) - ‘Raidionics-MRI_Metastasis-ONNX-v12.zip’ saved [68802585/68802585]\n",
"\n",
"Archive: Raidionics-MRI_Metastasis-ONNX-v12.zip\n",
" creating: MRI_Metastasis/\n",
" inflating: MRI_Metastasis/model.onnx \n",
" inflating: MRI_Metastasis/model_config.txt \n",
" inflating: MRI_Metastasis/pre_processing.ini \n",
" inflating: MRI_Metastasis/pipeline.json \n",
"--2023-06-18 12:45:23-- https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_GBM-ONNX-v12.zip\n",
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"\n",
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"\n",
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"\n",
"Archive: Raidionics-MRI_GBM-ONNX-v12.zip\n",
" creating: MRI_GBM/\n",
" inflating: MRI_GBM/model.onnx \n",
" inflating: MRI_GBM/model_config.txt \n",
" inflating: MRI_GBM/pre_processing.ini \n",
" inflating: MRI_GBM/pipeline.json \n",
"--2023-06-18 12:45:26-- https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Brain-ONNX-v12.zip\n",
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"Raidionics-MRI_Brai 100%[===================>] 65.93M 113MB/s in 0.6s \n",
"\n",
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"\n",
"Archive: Raidionics-MRI_Brain-ONNX-v12.zip\n",
" creating: MRI_Brain/\n",
" inflating: MRI_Brain/model.onnx \n",
" inflating: MRI_Brain/model_config.txt \n",
" inflating: MRI_Brain/pre_processing.ini \n",
" inflating: MRI_Brain/pipeline.json \n",
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"\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"# Run app\n",
"!python3.7 ./neukit/app.py --cwd ./neukit/ --share 1\n",
"\n",
"# To view the app, click on the \"public URL\" link."
],
"metadata": {
"id": "MT-WcUFAKlsF",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "c2bfda1c-8b43-409f-d9c4-f8f6f24944a7"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Current working directory: ./neukit/\n",
"Launching demo...\n",
"/usr/local/lib/python3.7/dist-packages/gradio/components.py:164: UserWarning: Unknown style parameter: height\n",
" warnings.warn(f\"Unknown style parameter: {key}\")\n",
"/content/neukit/neukit/gui.py:118: UserWarning: You have unused kwarg parameters in Dropdown, please remove them: {'size': 'sm'}\n",
" size=\"sm\",\n",
"Caching examples at: '/content/gradio_cached_examples/8'\n",
"Running on local URL: http://0.0.0.0:7860\n",
"Running on public URL: https://d6a081c800abb552ed.gradio.live\n",
"\n",
"This share link expires in 72 hours. For free permanent hosting and GPU upgrades (NEW!), check out Spaces: https://huggingface.co/spaces\n"
]
}
]
}
]
}
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