final TMI paper (#48)

* add stain stats @ipynb
* add references
* update Travis
* simple docs

.travis.yml

@@ -13,6 +13,8 @@ env:
     - DISPLAY=""
 
 matrix:
+  # https://blog.travis-ci.com/2019-08-07-extensive-python-testing-on-travis-ci
+  # https://docs.travis-ci.com/user/languages/python/
   include:
     - os: linux
       language: python
@@ -54,14 +56,16 @@ matrix:
       #before_script:
       #  - git lfs install
       #  - git lfs pull
-      # https://blog.travis-ci.com/2019-08-07-extensive-python-testing-on-travis-ci
-      # https://docs.travis-ci.com/user/languages/python/
     - os: windows           # Windows 10.0.17134 N/A Build 17134
       language: shell       # 'language: python' is an error on Travis CI Windows
+      # https://github.com/skvark/opencv-python/issues/263
       before_install:
-        - choco install python --version 3.7.0
+        - choco install -y python --version 3.7.0
         - python -m pip install --upgrade pip
-      env: PATH=/c/Python37:/c/Python37/Scripts:%OPENCV_DIR%/bin:$PATH
+        - choco install -y opencv
+      env:
+        - TOXENV=py37
+        - PATH=/c/Python37:/c/Python37/Scripts:%OPENCV_DIR%/bin:$PATH
   # https://towardsdatascience.com/extensive-python-testing-on-travis-ci-4c24db9bf961
   allow_failures:
     - os: osx

README.md

@@ -320,7 +320,8 @@ The project is using the standard [BSD license](http://opensource.org/licenses/B
 
 For complete references see [bibtex](docs/references.bib).
 1. Borovec, J., Munoz-Barrutia, A., & Kybic, J. (2018). **[Benchmarking of image registration methods for differently stained histological slides](https://www.researchgate.net/publication/325019076_Benchmarking_of_image_registration_methods_for_differently_stained_histological_slides)**. In IEEE International Conference on Image Processing (ICIP) (pp. 3368–3372), Athens. [DOI: 10.1109/ICIP.2018.8451040](https://doi.org/10.1109/ICIP.2018.8451040)
-2. Borovec, J. (2019). BIRL: **Benchmark on Image Registration methods with Landmark validation**. arXiv preprint [arXiv:1912.13452.](https://arxiv.org/abs/1912.13452)
+2. Borovec, J. (2019). **[BIRL: Benchmark on Image Registration methods with Landmark validation](https://www.researchgate.net/publication/338291737_BIRL_Benchmark_on_Image_Registration_methods_with_Landmark_validation)**. arXiv preprint [arXiv:1912.13452](https://arxiv.org/abs/1912.13452).
+3. Borovec, J., Kybic, J., et al. (2020). **[ANHIR: Automatic Non-rigid Histological Image Registration Challenge](https://ieeexplore.ieee.org/document/9058666)**. In IEEE Transaction on Medical Imaging (TMI). [DOI: 10.1109/TMI.2020.2986331](https://www.doi.org/10.1109/TMI.2020.2986331)
 
 ## Appendix - Useful information
 

birl/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Using the try/except import since the init is called in setup  to get pkg info
 before satisfying install requirements
@@ -17,7 +18,7 @@
 __author_email__ = "[email protected]"
 __license__ = "BSD 3-clause"
 __homepage__ = "https://borda.github.io/BIRL",
-__copyright__ = "Copyright (c) 2014-2019, %s." % __author__
+__copyright__ = "Copyright (c) 2014-2020, %s." % __author__
 __doc__ = 'BIRL: Benchmark on Image Registration methods with Landmark validation'
 __long_doc__ = "# %s" % __doc__ + """
 
@@ -35,8 +36,14 @@
 * rerun evaluation and visualisation for finished experiments
 
 ## References
-Borovec, J., Munoz-Barrutia, A., & Kybic, J. (2018). Benchmarking of image
- registration methods for differently stained histological slides.
- In IEEE International Conference on Image Processing (ICIP) (pp. 3368-3372),
- Athens. DOI: 10.1109/ICIP.2018.8451040
+1. Borovec, J., Munoz-Barrutia, A., & Kybic, J. (2018).
+ Benchmarking of image registration methods for differently stained histological slides.
+ In IEEE International Conference on Image Processing (ICIP) (pp. 3368–3372), Athens.
+ DOI: 10.1109/ICIP.2018.8451040
+2. Borovec, J. (2019). BIRL: Benchmark on Image Registration methods with Landmark validation.
+ arXiv preprint arXiv:1912.13452.
+3. Borovec, J., Kybic, J., et al. (2020).
+ ANHIR: Automatic Non-rigid Histological Image Registration Challenge.
+ In IEEE Transaction on Medical Imaging (TMI).
+ DOI: 10.1109/TMI.2020.2986331
 """

birl/utilities/experiments.py

@@ -508,7 +508,7 @@ def exec_commands(commands, path_logger=None, timeout=None):
 #     Process = NoDaemonProcess
 
 
-def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
+def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc='', ordered=True):
     """ create a multi-porocessing pool and execute a wrapped function in separate process
 
     :param func wrap_func: function which will be excited in the iterations
@@ -517,6 +517,7 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
     :param int nb_workers: number og jobs running in parallel
     :param str|None desc: description for the bar,
         if it is set None, bar is suppressed
+    :param bool ordered: whether enforce ordering in the parallelism
 
     Waiting reply on:
 
@@ -531,9 +532,9 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
     * http://mindcache.me/2015/08/09/python-multiprocessing-module-daemonic-processes-are-not-allowed-to-have-children.html
     * https://medium.com/@bfortuner/python-multithreading-vs-multiprocessing-73072ce5600b
 
-    >>> list(iterate_mproc_map(np.sqrt, range(5), nb_workers=1))  # doctest: +ELLIPSIS
+    >>> list(iterate_mproc_map(np.sqrt, range(5), nb_workers=1, desc=None))  # doctest: +ELLIPSIS
     [0.0, 1.0, 1.41..., 1.73..., 2.0]
-    >>> list(iterate_mproc_map(sum, [[0, 1]] * 5, nb_workers=2, desc=None))
+    >>> list(iterate_mproc_map(sum, [[0, 1]] * 5, nb_workers=2, ordered=False))
     [1, 1, 1, 1, 1]
     >>> list(iterate_mproc_map(max, [(2, 1)] * 5, nb_workers=2, desc=''))
     [2, 2, 2, 2, 2]
@@ -558,7 +559,7 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
         # pool = NonDaemonPool(nb_workers)
         pool = ProcessPool(nb_workers)
         # pool = Pool(nb_workers)
-        mapping = pool.imap
+        mapping = pool.imap if ordered else pool.uimap
     else:
         logging.debug('perform sequential')
         pool = None

circle.yml

@@ -42,7 +42,7 @@ references:
        # sphinx-apidoc -o ./docs/source ./imsegm **/test_* --force --follow-links
        cd docs
        make html
-       make latexpdf
+       # make latexpdf
 
   run_dataset: &run_dataset
     run:

docs/references.bib

@@ -14,11 +14,12 @@ @inproceedings{Benchmark2018
     url = {ftp://cmp.felk.cvut.cz/pub/cmp/articles/borovec/Borovec-ICIP2018.pdf https://ieeexplore.ieee.org/document/8451040/},
     year = {2018}
 }
-@misc{BIRL2019,
+@report{BIRL2019,
     title={BIRL: Benchmark on Image Registration methods with Landmark validation},
     author={Jiri Borovec},
     year={2019},
     eprint={1912.13452},
     archivePrefix={arXiv},
-    primaryClass={cs.CV}
+    primaryClass={cs.CV},
+    ee={https://arxiv.org/abs/1912.13452},
 }

docs/source/conf.py

@@ -305,7 +305,7 @@ def find_source():
             obj = getattr(obj, part)
         fname = inspect.getsourcefile(obj)
         # https://github.com/rtfd/readthedocs.org/issues/5735
-        if any([s in fname for s in ('readthedocs', 'checkouts')]):
+        if any([s in fname for s in ('readthedocs', 'rtfd', 'checkouts')]):
             # /home/docs/checkouts/readthedocs.org/user_builds/birl/checkouts/
             #  devel/birl/utilities/cls_experiment.py#L26-L176
             path_top = os.path.abspath(os.path.join('..', '..', '..'))
@@ -325,6 +325,10 @@ def find_source():
     # import subprocess
     # tag = subprocess.Popen(['git', 'rev-parse', 'HEAD'], stdout=subprocess.PIPE,
     #                        universal_newlines=True).communicate()[0][:-1]
+    branch = filename.split('/')[0]
+    # do mapping from latest tags to master
+    branch = {'latest': 'master', 'stable': 'master'}.get(branch, branch)
+    filename = '/'.join([branch] + filename.split('/')[1:])
     return "https://github.com/%s/%s/blob/%s" \
            % (github_user, github_repo, filename)