ci_experiment.yml

name: CI experiments

# see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
on:  # Trigger the workflow on push or pull request, but only for the master branch
  push:
    branches: [master]
  pull_request:
    branches: [master]
    types: [opened, reopened, ready_for_review, synchronize]

jobs:

  bash-expt:
    if: github.event.pull_request.draft == false
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-18.04]
        python-version: [2.7, 3.6, 3.8]

    # Timeout: https://stackoverflow.com/a/59076067/4521646
    timeout-minutes: 35

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}

    - name: Update Pip
      run: |
        pip install --quiet "pip>=20.1" --upgrade --user  # needed for get pip cacher folder

    - name: Set py2.7 dependencies
      if: matrix.python-version == 2.7
      run: |
        cp -r require-py27.txt requirements.txt

    # Note: This uses an internal pip API and may not always work
    # https://github.com/actions/cache/blob/master/examples.md#multiple-oss-in-a-workflow
    - name: Cache pip
      uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-py${{ matrix.python-version }}-

    - name: Install dependencies
      run: |
        pip install $(grep "numpy" requirements.txt)
        # required for matplotlib @py2
        pip install -U backports.functools_lru_cache
        # v46 crashes openslide-python install
        pip install "setuptools<46" -U
        pip install --requirement requirements.txt --quiet
        python --version
        pip --version
        pip list
      shell: bash

    - name: update OS
      run: |
        sudo apt-get install -y openslide-tools tree

    - name: Dataset processing
      run: |
        mkdir output
        python bm_dataset/rescale_tissue_images.py -i "./data-images/rat-kidney_/scale-5pc/*.jpg" --scales 5 -ext .png --nb_workers 2
        python bm_dataset/rescale_tissue_landmarks.py -a ./data-images -d ./output --nb_selected 0.5 --nb_total 200
        python bm_dataset/generate_regist_pairs.py -i "./data-images/images/artificial_*.jpg" -l "./data-images/landmarks/artificial_*.csv" -csv ./data-images/cover_artificial.csv --mode each2all

    - name: General experiments
      run: |
        mkdir applications && mkdir results && touch configs/sample_config.yaml
        # python bm_experiments/bm_comp_perform.py  -o ./results -n 1 # reach time-out while running in 36 threads
        python birl/bm_template.py -t ./data-images/pairs-imgs-lnds_mix.csv -o ./results --visual --unique -cfg configs/sample_config.yaml
        rm ./data-images/*_/*/*_HE.csv  # remove target landmarks from histol. tissue
        python birl/bm_template.py -n anhir -t ./data-images/pairs-imgs-lnds_histol.csv -d ./data-images -o ./results --preprocessing matching-rgb gray -cfg configs/sample_config.yaml
        python bm_experiments/evaluate_experiment.py -d ./data-images -e ./results/BmTemplate_anhir --visual
        tree ./results/BmTemplate
      shell: bash

    - name: prepare Fiji
      run: |
        # todo: cache this app and dowload only if needed
        wget https://downloads.imagej.net/fiji/archive/20200708-1553/fiji-linux64.zip -O applications/fiji-linux64.zip --progress=bar:force:noscroll
        unzip -q applications/fiji-linux64.zip -d applications/
        rm applications/fiji-linux64.zip
      shell: bash

    - name: Experiment - bUnwarpJ
      env:
        DISPLAY: ""
      run: |
        rm -rf results && mkdir results
        python bm_experiments/bm_bUnwarpJ.py -n mix -t ./data-images/pairs-imgs-lnds_mix.csv -o ./results -Fiji ./applications/Fiji.app/ImageJ-linux64 -cfg ./configs/ImageJ_bUnwarpJ_histol.yaml --preprocessing matching-rgb --visual
        python bm_experiments/bm_bUnwarpJ.py -n anhir -t ./data-images/pairs-imgs-lnds_histol.csv -d ./data-images -o ./results -Fiji ./applications/Fiji.app/ImageJ-linux64 -cfg ./configs/ImageJ_bUnwarpJ-SIFT_histol.yaml --unique
        tree -L 3 ./results
        rm -rf ./applications/Fiji.app
      shell: bash

    - name: Experiment - RVSS
      env:
        DISPLAY: ""
      run: |
        rm -rf results && mkdir results
        python bm_experiments/bm_RVSS.py -t ./data-images/pairs-imgs-lnds_mix.csv -o ./results -Fiji ./applications/Fiji.app/ImageJ-linux64 -cfg ./configs/ImageJ_RVSS_histol.yaml --visual
        tree -L 3 ./results
        rm -rf ./applications/Fiji.app
      shell: bash