add GH action & min req.

* add CI testing
* add CI experiments
* fix min requirements
* version++

.github/workflows/ci-experiment.yml

@@ -0,0 +1,111 @@
+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]
+
+jobs:
+  pytest:
+
+    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 requirements-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

.github/workflows/ci-testing.yml

@@ -0,0 +1,124 @@
+name: CI testing
+
+# 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]
+
+jobs:
+  pytest:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04, windows-2019, macOS-10.15]
+        python-version: [2.7, 3.6, 3.8]
+        requires: ['minimal', 'latest']
+        exclude:
+          - python-version: 2.7
+            requires: 'minimal'
+          - python-version: 3.8
+            requires: 'minimal'
+
+    # 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 requirements-py27.txt requirements.txt
+
+    - name: Set min. dependencies
+      if: matrix.requires == 'minimal'
+      run: |
+        python -c "fname = 'requirements.txt' ; req = open(fname).read().replace('>=', '==') ; open(fname, 'w').write(req)"
+        python -c "fname = 'tests/requirements.txt' ; req = open(fname).read().replace('>=', '==') ; open(fname, 'w').write(req)"
+
+    # 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: Get pip cache
+      id: pip-cache
+      run: |
+        python -c "from pip._internal.locations import USER_CACHE_DIR; print('::set-output name=dir::' + USER_CACHE_DIR)"
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ matrix.requires }}-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ matrix.requires }}-
+
+    - name: Install dependencies
+      run: |
+        pip install $(grep "numpy" requirements.txt)
+        # required for matplotlib @py2
+        pip install -U backports.functools_lru_cache
+        # v46 crashes openslide-python install
+        pip install "setuptools<46" -U
+        pip install --requirement requirements.txt --quiet --upgrade
+        pip install --requirement tests/requirements.txt --quiet --upgrade
+        python --version
+        pip --version
+        pip list
+      shell: bash
+
+    - name: Tests
+      env:
+        DISPLAY: ""
+      run: |
+        check-manifest --ignore tox.ini
+        python setup.py check --metadata --strict
+        python setup.py install --dry-run --user
+        coverage run --source birl -m py.test birl tests bm_dataset bm_experiments bm_ANHIR -v --doctest-modules --durations=25 --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
+        flake8 .
+
+    - name: Upload pytest test results
+      uses: actions/upload-artifact@master
+      with:
+        name: pytest-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}
+        path: junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
+      # Use always() to always run this step to publish test results when there are test failures
+      if: always()
+
+    - name: Statistics
+      if: success()
+      run: |
+        coverage report
+        coverage xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      if: success()
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.xml
+        flags: cpu,pytest
+        name: CPU-coverage
+        fail_ci_if_error: false
+
+    - name: Run sample experiment
+      run: |
+        mkdir results
+        touch configs/sample_config.yaml
+        python bm_experiments/bm_comp_perform.py -o ./results -n 1
+        python birl/bm_template.py -t ./data-images/pairs-imgs-lnds_mix.csv -o ./results --visual --unique -cfg configs/sample_config.yaml
+        # remove target landmarks from histol. tissue
+        rm ./data-images/*_/*/*_HE.csv
+        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
+      shell: bash

birl/__init__.py

@@ -13,7 +13,7 @@
     traceback.print_exc()
 
 
-__version__ = "0.2.4"
+__version__ = "0.2.5"
 __author__ = "Jiri Borovec"
 __author_email__ = "[email protected]"
 __license__ = "BSD 3-clause"

birl/utilities/registration.py

@@ -34,7 +34,7 @@ def estimate_affine_transform(points_0, points_1):
     >>> pts0 = np.array([[4., 116.], [4., 4.], [26., 4.], [26., 116.]], dtype=int)
     >>> pts1 = np.array([[61., 56.], [61., -56.], [39., -56.], [39., 56.]])
     >>> mx, mx_inv, pts0_w, pts1_w = estimate_affine_transform(pts0, pts1)
-    >>> np.round(mx, 2)
+    >>> np.round(mx, 2) + 0.  # eliminate negative zeros
     array([[ -1.,   0.,  65.],
            [  0.,   1., -60.],
            [  0.,   0.,   1.]])

bm_experiments/__init__.py

@@ -1,3 +1,3 @@
 import birl
 
-birl
+birl.utilities

bm_experiments/bm_comp_perform.py

@@ -35,6 +35,8 @@
 from functools import partial
 
 import tqdm
+import matplotlib
+matplotlib.use('Agg')
 import numpy as np
 from skimage import data, io, __version__ as skimage__version
 from skimage.transform import resize, warp, AffineTransform

circle.yml

@@ -190,6 +190,6 @@ workflows:
       - Formatting
       - Py2-Tests
       - Py3-Tests
-      - Py2-Experiments
-      - Py3-Experiments
+      #- Py2-Experiments
+      #- Py3-Experiments
       - Build-Docs

requirements.txt

@@ -1,15 +1,15 @@
-numpy>=1.8.2
-scipy>=0.10.0
-pandas>=0.17.1
-six>=1.7.3
-pillow>=2.1.0, !=7.1 # 7.x fails to load PNG via skimage
+numpy>=1.13.3
+scipy>=1.0
+pandas>=0.21
+six>=1.10
+pillow>=4.0, !=7.1 # 7.x fails to load PNG via skimage
 matplotlib>=2.0.2
 tqdm>=4.7.4
-pyyaml
-scikit-image
-opencv-python-headless
-openslide-python
-nibabel
+pyyaml>=3.12
+scikit-image>=0.13
+opencv-python-headless>=3.4.0.14
+openslide-python>=1.0
+nibabel>=2.1
 SimpleITK
 psutil
 pathos

tests/requirements.txt

@@ -1,7 +1,7 @@
-nose>=1.3.7
+nose>=1.0
 coverage
 codecov
-pytest>=3.0.5
+pytest>4.0
 pytest-cov
 flake8
 check-manifest