Initial commit

.circleci/config.yml

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+version: 2.1
+
+orbs:
+  # https://circleci.com/orbs/registry/orb/circleci/docker-publish
+  docker-publish: circleci/[email protected]
+
+jobs:
+
+  build:
+    environment:
+      - TZ: "/usr/share/zoneinfo/Canada/Toronto"
+      - CONTAINER_NAME: "mgoubran/hippmapper"
+    docker:
+      - image: docker:18.06.3-ce-git
+    working_directory: /tmp/src/HippMapp3r
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          name: Build Docker images
+          no_output_timeout: 60m
+          command: |
+            # Build docker image
+            hippmapper_VERSION=$(cat /tmp/src/HippMapp3r/hippmapper/__init__.py | tr -dc '0-9' | sed 's/./&./g')
+            echo "hippmapper version is ${hippmapper_VERSION}"
+            e=1 && for i in {1..5}; do
+              docker build \
+                --rm=false \
+                -t ${CONTAINER_NAME} \
+                -f /tmp/src/HippMapp3r/Dockerfile \
+                --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+                --build-arg VCS_REF=`git rev-parse --short HEAD` \
+                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
+              && e=0 && break || sleep 15
+            done && [ "$e" -eq "0" ]
+      - run:
+          name: Run Tests
+          no_output_timeout: 2h
+          command: |
+
+             echo "Runing tests:"
+             docker run --entrypoint bash -it mgoubran/hippmapper -c "hippmapper seg_hipp -t1 /HippMapp3r/data/test_case/mprage.nii.gz"
+
+      - store_test_results:
+          path: /home/circleci/out/tests
+
+
+workflows:
+  build_and_test:
+    jobs:
+      - build:
+          filters:
+            tags:
+              only: /.*/
+
+  # This workflow will deploy images on merge to master only
+  docker_with_lifecycle:
+    jobs:
+      - docker-publish/publish:
+          image: mgoubran/hippmapper
+          tag: latest
+          filters:
+            branches:
+             only: master
+          after_build:
+            - run:
+                name: Publish Docker Tag with hippmapper Version
+                command: |
+                   docker tag mgoubran/hippmapper:latest mgoubran/hippmapper:0.1.0

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# models directory
+models/
+
+# .idea directory
+.idea/

Dockerfile

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+# Use a Linux Distro as a parent image
+FROM ubuntu:16.04
+
+# Set up
+RUN apt-get update && apt-get install -y git wget build-essential g++ gcc cmake curl clang && \
+    apt-get install -y libfreetype6-dev apt-utils pkg-config vim gfortran && \
+    apt-get install -y binutils make linux-source unzip && \
+    apt install -y libsm6 libxext6 libfontconfig1 libxrender1 libgl1-mesa-glx
+
+# Install c3d
+RUN wget https://downloads.sourceforge.net/project/c3d/c3d/Nightly/c3d-nightly-Linux-x86_64.tar.gz && \
+    tar -xzvf c3d-nightly-Linux-x86_64.tar.gz && mv c3d-1.1.0-Linux-x86_64 /opt/c3d && \
+    rm c3d-nightly-Linux-x86_64.tar.gz
+ENV PATH /opt/c3d/bin:${PATH}
+
+# FSL
+# Installing Neurodebian packages FSL
+RUN wget -O- http://neuro.debian.net/lists/xenial.us-tn.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
+RUN apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
+
+# Install FSL
+RUN apt-get update && apt-get install -y fsl
+
+ENV FSLDIR="/usr/share/fsl/5.0" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    POSSUMDIR="/usr/share/fsl/5.0" \
+    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
+    FSLTCLSH="/usr/bin/tclsh" \
+    FSLWISH="/usr/bin/wish" \
+    POSSUMDIR="/usr/share/fsl/5.0"
+
+ENV PATH="/usr/lib/fsl/5.0":${PATH}
+
+# Install ANTs
+ENV ANTSPATH /opt/ANTs
+RUN mkdir -p /opt/ANTs && \
+    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=${ANTSPATH}:${PATH}
+
+# Install miniconda
+RUN curl -LO https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda -b && \
+    rm Miniconda3-latest-Linux-x86_64.sh
+ENV PATH=/opt/miniconda/bin:${PATH}
+
+# Install all needed packages based on pip installation
+RUN git clone https://github.com/mgoubran/HippMapp3r.git && \
+    cd HippMapp3r && \
+    pip install git+https://www.github.com/keras-team/keras-contrib.git && \
+    pip install -e .[hippmapper]
+
+# Download models, store in directory
+RUN mkdir /HippMapp3r/models && \
+    wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1ftE79HF-sWXGa_X2bOUc-ldyWQEB5-Dz' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1ftE79HF-sWXGa_X2bOUc-ldyWQEB5-Dz" -O /HippMapp3r/models/hipp_model.json && \
+    rm -rf /tmp/cookies.txt && \
+    wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=19zEi7552X93_5JbEokfry2Y28gFeVGt2' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=19zEi7552X93_5JbEokfry2Y28gFeVGt2" -O /HippMapp3r/models/hipp_model_weights.h5 && \
+    rm -rf /tmp/cookies.txt && \
+    wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1NmyniIkAk_wY2OW4YqEp9vF7IlVsRfrA' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1NmyniIkAk_wY2OW4YqEp9vF7IlVsRfrA" -O /HippMapp3r/models/hipp_zoom_model.json && \
+    rm -rf /tmp/cookies.txt && \
+    wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=10uPh9byC-7Qj7Duwgh9gyQcSXH-CwWz1' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=10uPh9byC-7Qj7Duwgh9gyQcSXH-CwWz1" -O /HippMapp3r/models/hipp_zoom_model_weights.h5 && \
+    rm -rf /tmp/cookies.txt
+
+# Run hippmapper when the container launches
+ENTRYPOINT /bin/bash