add Docker for experiments (#51)

* base image
* docker build
* fix init imports
* docker: add Fiji
* docker: add ANTs
* docker: add ANTsPy
* docker: add elastix
* docker: add DROP
* docker: add RNiftyREg
* update tox / travis

.github/workflows/docker-builds.yml

@@ -0,0 +1,34 @@
+name: Publish Docker Image
+# https://www.docker.com/blog/first-docker-github-action-is-here
+# https://github.com/docker/build-push-action
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build-push:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python_version: [3.6, 3.7]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Build and Publish to Docker Hub
+        # publish master
+        uses: docker/build-push-action@v1.1.0
+        # TODO: push to master
+        # if: github.event_name == 'push'
+        with:
+          repository: borda/birl
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          dockerfile: bm_experiments/Dockerfile
+          build_args: PYTHON_VERSION=${{ matrix.python_version }}
+          tags: "SOTA-py${{ matrix.python_version }}"
+        # timeout-minutes: 50

.travis.yml

@@ -21,11 +21,11 @@ matrix:
       python: 2.7
       dist: xenial  # Ubuntu 16.04
       env: TOXENV=py27
-    - os: linux
-      language: python
-      python: 3.5
-      dist: xenial  # Ubuntu 16.04
-      env: TOXENV=py35
+      #- os: linux
+      #  language: python
+      #  python: 3.5
+      #  dist: xenial  # Ubuntu 16.04
+      #  env: TOXENV=py35
     - os: linux
       language: python
       python: 3.6
@@ -36,6 +36,11 @@ matrix:
       python: 3.7
       dist: bionic  # Ubuntu 18.04
       env: TOXENV=py37
+    - os: linux
+      language: python
+      python: 3.8
+      dist: bionic  # Ubuntu 18.04
+      env: TOXENV=py38
     - os: osx
       osx_image: xcode10.3
       language: generic

MANIFEST.in

@@ -17,6 +17,7 @@ recursive-include assets *.jpg
 recursive-include bm_dataset *.py
 recursive-include bm_experiments *.py
 recursive-exclude bm_experiments *.sh
+exclude bm_experiments/Dockerfile
 
 # exclude tests from package
 recursive-exclude tests *

README.md

@@ -196,6 +196,31 @@ python bm_experiments/bm_comp_perform.py -o ./results
 ```
 This script generate simple report exported in JSON file on given output path.
 
+### Prepared experimental docker image 
+
+Used prepared docker image from [Docker Hub](https://hub.docker.com/repository/docker/borda/birl)
+
+```bash
+docker run --rm -it borda/birl:SOTA-py3.7 bash
+```
+
+You can build it on your own, note it takes lots of time, be prepared.
+
+```bash
+git clone <git-repository>
+docker image build \
+    -t birl:py3.6 \
+    -f bm_experiments/Dockerfile \
+    --build-arg PYTHON_VERSION=3.6 \
+    .
+```
+
+To run your docker use
+
+```bash
+docker image list
+docker run --rm -it birl:py3.6 bash
+```
 
 ### Included registration methods
 

birl/utilities/__init__.py

@@ -1,27 +1,38 @@
 import os
 import subprocess
+from distutils.version import LooseVersion
 
-import matplotlib
-import numpy as np
-import pandas as pd
+try:
+    import matplotlib
+except ImportError:
+    print('Package `matplotlib` which shall be configured are missing...')
+else:
+    CMD_TRY_MATPLOTLIB = 'python -c "from matplotlib import pyplot; pyplot.close(pyplot.figure())"'
+    # in case you are running on machine without display, e.g. server
+    if not os.environ.get('DISPLAY', '') and matplotlib.rcParams['backend'] != 'agg':
+        print('No display found. Using non-interactive Agg backend')
+        matplotlib.use('Agg')
+    # _tkinter.TclError: couldn't connect to display "localhost:10.0"
+    elif subprocess.call(CMD_TRY_MATPLOTLIB, stdout=None, stderr=None, shell=True):
+        print('Problem with display. Using non-interactive Agg backend')
+        matplotlib.use('Agg')
 
 
-CMD_TRY_MATPLOTLIB = 'python -c "from matplotlib import pyplot; pyplot.close(pyplot.figure())"'
-# in case you are running on machine without display, e.g. server
-if not os.environ.get('DISPLAY', '') and matplotlib.rcParams['backend'] != 'agg':
-    print('No display found. Using non-interactive Agg backend')
-    matplotlib.use('Agg')
-# _tkinter.TclError: couldn't connect to display "localhost:10.0"
-elif subprocess.call(CMD_TRY_MATPLOTLIB, stdout=None, stderr=None, shell=True):
-    print('Problem with display. Using non-interactive Agg backend')
-    matplotlib.use('Agg')
+try:
+    import numpy as np
+except ImportError:
+    print('Package `numpy` which shall be configured are missing...')
+else:
+    # comparing strings does not work for version lower 1.10
+    if LooseVersion(np.version.full_version) >= LooseVersion('1.14'):
+        # np.set_printoptions(sign='legacy')
+        np.set_printoptions(legacy='1.13')
 
-# parse the numpy versions
-np_version = [int(i) for i in np.version.full_version.split('.')]
-# comparing strings does not work for version lower 1.10
-if np_version >= [1, 14]:
-    # np.set_printoptions(sign='legacy')
-    np.set_printoptions(legacy='1.13')
 
-# default display size was changed in pandas v0.23
-pd.set_option('display.max_columns', 20)
+try:
+    import pandas as pd
+except ImportError:
+    print('Package `pandas` which shall be configured are missing...')
+else:
+    # default display size was changed in pandas v0.23
+    pd.set_option('display.max_columns', 20)

bm_ANHIR/automatic-evaluation.md

@@ -82,7 +82,7 @@ docker image ls
 **Cleaning**
 In case you fail with some builds, you may need to clean your local storage.
 ```bash
-docker image prune
+docker system prune
 ```
 or [Docker - How to cleanup (unused) resources](https://gist.github.com/bastman/5b57ddb3c11942094f8d0a97d461b430)
 ```bash