Initial full commit [skip ci]

.dockerignore

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+venv/
+*__pycache__/
+resources/
+*.DS_Store
+*.nii
+*.nii.gz
+*.nrrd
+*.obj
+*.zip
+*log.csv
+*.ini
+gradio_cached_examples/
+.idea/

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Windows]
+ - Version: [e.g. 10]
+ - Python: [e.g. 3.8.10]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/deploy.yml

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+name: Deploy
+on:
+  push:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  sync-to-hub:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          lfs: true
+      - name: Push to hub
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: git push https://dbouget:$HF_TOKEN@huggingface.co/spaces/dbouget/Raidionics-HF main

.github/workflows/filesize.yml

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+name: Check file size
+on:               # or directly `on: [push]` to run the action on every push on any branch
+  pull_request:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  check-filesize:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check large files
+        uses: ActionsDesk/lfs-warning@v2.0
+        with:
+          filesizelimit: 10485760 # this is 10MB so we can sync to HF Spaces

.github/workflows/linting.yml

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+name: Linting
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install lint dependencies
+        run: pip install wheel setuptools black==22.3.0 isort==5.10.1 flake8==4.0.1
+
+      - name: Lint the code
+        run: sh shell/lint.sh

.gitignore

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+venv/
+*__pycache__/
+resources/
+*.DS_Store
+*.nii
+*.nii.gz
+*.nrrd
+*.obj
+*.zip
+*log.csv
+*.ini
+gradio_cached_examples/
+.idea/

Dockerfile

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+# read the doc: https://huggingface.co/docs/hub/spaces-sdks-docker
+# you will also find guides on how best to write your Dockerfile
+FROM python:3.8-slim
+
+# set language, format and stuff
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+WORKDIR /code
+
+RUN apt-get update -y
+#RUN apt-get install -y python3 python3-pip
+RUN apt install git --fix-missing -y
+RUN apt install wget -y
+
+# installing other libraries
+RUN apt-get install python3-pip -y && \
+    apt-get -y install sudo
+RUN apt-get install curl -y
+RUN apt-get install nano -y
+RUN apt-get update && apt-get install -y git
+RUN apt-get install libblas-dev -y && apt-get install liblapack-dev -y
+RUN apt-get install gfortran -y
+RUN apt-get install libpng-dev -y
+RUN apt-get install python3-dev -y
+
+WORKDIR /code
+
+# install dependencies
+COPY ./requirements.txt /code/requirements.txt
+RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
+
+# resolve issue with tf==2.4 and gradio dependency collision issue
+RUN pip install --force-reinstall typing_extensions==4.7.1
+
+# Install wget
+RUN apt install wget -y && \
+    apt install unzip
+
+# Set up a new user named "user" with user ID 1000
+RUN useradd -m -u 1000 user
+
+# Switch to the "user" user
+USER user
+
+# Set home to the user's home directory
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+
+# Set the working directory to the user's home directory
+WORKDIR $HOME
+
+# Copy the current directory contents into the container at $HOME/app setting the owner to the user
+COPY --chown=user . $HOME
+
+# Download pretrained models
+RUN mkdir -p resources/models/
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Brain-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_Brain-ONNX-v12.zip" && mv MRI_Brain/ resources/models/MRI_Brain/
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_GBM-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_GBM-ONNX-v12.zip" && mv MRI_GBM/ resources/models/MRI_GBM/ \
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_LGGlioma-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_LGGlioma-ONNX-v12.zip" && mv MRI_LGGlioma/ resources/models/MRI_LGGlioma/ \
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Meningioma-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_Meningioma-ONNX-v12.zip" && mv MRI_Meningioma/ resources/models/MRI_Meningioma/
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Metastasis-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_Metastasis-ONNX-v12.zip" && mv MRI_Metastasis/ resources/models/MRI_Metastasis/
+
+RUN rm -r *.zip
+
+# Download test sample
+RUN wget "https://github.com/raidionics/Raidionics-HF/releases/download/v1.0.0/t1gd.nii.gz"
+
+# CMD ["/bin/bash"]
+CMD ["python3", "app.py"]

app.py

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+import os
+from argparse import ArgumentParser
+
+from src.gui import WebUI
+
+
+def main():
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--cwd",
+        type=str,
+        default="/home/user/app/",
+        help="Set current working directory (path to app.py).",
+    )
+    parser.add_argument(
+        "--share",
+        type=int,
+        default=1,
+        help="Whether to enable the app to be accessible online"
+        "-> setups a public link which requires internet access.",
+    )
+    args = parser.parse_args()
+
+    print("Current working directory:", args.cwd)
+
+    if not os.path.exists(args.cwd):
+        raise ValueError("Chosen 'cwd' is not a valid path!")
+    if args.share not in [0, 1]:
+        raise ValueError(
+            "The 'share' argument can only be set to 0 or 1, but was:",
+            args.share,
+        )
+
+    # initialize and run app
+    print("Launching demo...")
+    app = WebUI(cwd=args.cwd, share=args.share)
+    app.run()
+
+
+if __name__ == "__main__":
+    main()

requirements.txt

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+raidionicsrads@git+https://github.com/dbouget/raidionics_rads_lib
+gradio==3.44.4

setup.cfg

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+[metadata]
+description-file = README.md
+
+[isort]
+force_single_line=True
+known_first_party=aeropath
+line_length=160
+profile=black
+
+[flake8]
+# imported but unused in __init__.py, that's ok.
+per-file-ignores=*__init__.py:F401
+ignore=E203,W503,W605,F632,E266,E731,E712,E741
+max-line-length=160

shell/format.sh

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+#!/bin/bash
+isort --sl demo/src/ demo/app.py
+black --line-length 80 demo/src/ demo/app.py
+flake8 demo/src/ demo/app.py

shell/lint.sh

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+#!/bin/bash
+isort --check --sl -c demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+  exit 1
+fi
+echo "no issues with isort"
+flake8 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please fix the code style issue."
+  exit 1
+fi
+echo "no issues with flake8"
+black --check --line-length 80 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+    exit 1
+fi
+echo "no issues with black"
+echo "linting success!"

src/__init__.py

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+