imports & docs

* absolute imports
* update docstring
* drop enlighten
* update manifest
* fixing CI: xos

.travis.yml

@@ -12,53 +12,66 @@ env:
   global:
     - DISPLAY=""
 
-language: python
-
 matrix:
   include:
-    - os: osx
-      osx_image: xcode9.4
-      language: generic
-      env: TOXENV=py36
-      addons:
-        homebrew:
-          # update: true
-          packages: python3.6
-      before_install:
-        # - brew update && brew install git-lfs
-        - pip3 install virtualenv
-        - virtualenv -p python3 ~/venv
-        - source ~/venv/bin/activate
-      #before_script:
-      #  - git lfs install
-      #  - git lfs pull
     - os: linux
+      language: python
       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: 3.6
       dist: bionic  # Ubuntu 18.04
       env: TOXENV=py36
     - os: linux
+      language: python
       python: 3.7
       dist: bionic  # Ubuntu 18.04
       env: TOXENV=py37
+    - os: osx
+      osx_image: xcode10.3
+      language: generic
+      env: TOXENV=py37
+      addons:
+        homebrew:
+          # update: true
+          packages: openslide
+      before_install:
+        # - brew update && brew install git-lfs
+        - pip3 install virtualenv
+        - virtualenv -p python3 ~/venv
+        - source ~/venv/bin/activate
+      #before_install:
+      #  # - brew update && brew install git-lfs
+      #  - "pyenv install 3.6.8"
+      #  - "pyenv global 3.6.8"
+      #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
+      before_install:
+        - choco install python --version 3.7.0
+        - python -m pip install --upgrade pip
+      env: PATH=/c/Python37:/c/Python37/Scripts:%OPENCV_DIR%/bin:$PATH
   # https://towardsdatascience.com/extensive-python-testing-on-travis-ci-4c24db9bf961
   allow_failures:
     - os: osx
+    - os: windows
 
 # See http://docs.travis-ci.com/user/caching/#pip-cache
 cache: pip
 
 before_install:
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then
-      brew install openslide ;
-    else
+  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then
       sudo apt-get install openslide-tools ;
     fi
 

MANIFEST.in

@@ -18,10 +18,6 @@ recursive-include bm_dataset *.py
 recursive-include bm_experiments *.py
 recursive-exclude bm_experiments *.sh
 
-# exclude challenge scripts
-recursive-exclude bm_ANHIR *
-exclude bm_ANHIR
-
 # exclude tests from package
 recursive-exclude tests *
 exclude tests
@@ -53,4 +49,6 @@ prune .git
 prune .github
 prune notebook*
 prune temp*
-prune test*
+prune test*
+prune bm_ANHIR
+prune bm_CIMA

birl/benchmark.py

@@ -13,7 +13,6 @@
 
 Copyright (C) 2016-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys
@@ -28,17 +27,17 @@
 
 # this is used while calling this file as a script
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from .utilities.data_io import (
+from birl.utilities.data_io import (
     update_path, create_folder, image_sizes, load_landmarks, load_image, save_image)
-from .utilities.dataset import image_histogram_matching, common_landmarks
-from .utilities.evaluate import (
+from birl.utilities.dataset import image_histogram_matching, common_landmarks
+from birl.utilities.evaluate import (
     compute_target_regist_error_statistic, compute_affine_transf_diff, compute_tre_robustness)
-from .utilities.experiments import (
+from birl.utilities.experiments import (
     nb_workers, exec_commands, string_dict, iterate_mproc_map, create_basic_parser,
     parse_arg_params, Experiment)
-from .utilities.drawing import (
+from birl.utilities.drawing import (
     export_figure, draw_image_points, draw_images_warped_landmarks, overlap_two_images)
-from .utilities.registration import estimate_affine_transform
+from birl.utilities.registration import estimate_affine_transform
 
 #: In case provided dataset and complete (true) dataset differ
 COL_PAIRED_LANDMARKS = 'Ration matched landmarks'

birl/bm_template.py

@@ -19,7 +19,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

birl/utilities/dataset.py

@@ -168,7 +168,7 @@ def project_object_edge(img, dimension):
 def load_large_image(img_path):
     """ loading very large images
 
-    Note, for the loading we have to use matplotlib while ImageMagic nor other
+    .. note:: For the loading we have to use matplotlib while ImageMagic nor other
      lib (opencv, skimage, Pillow) is able to load larger images then 64k or 32k.
 
     :param str img_path: path to the image
@@ -189,7 +189,7 @@ def load_large_image(img_path):
 def save_large_image(img_path, img):
     """ saving large images more then 50k x 50k
 
-    Note, for the saving we have to use openCV while other
+    .. note:: For the saving we have to use openCV while other
     lib (matplotlib, Pillow, ITK) is not able to save larger images then 32k.
 
     :param str img_path: path to the new image
@@ -330,7 +330,7 @@ def norm_angle(angle, deg=True):
 def is_point_inside_perpendicular(point_begin, point_end, point_test):
     """ If point is left from line and perpendicularly in between line segment
 
-    Note that negative response does not mean that that the point is on tight side
+    .. note:: negative response does not mean that that the point is on tight side
 
     :param list(float) point_begin: starting line point
     :param list(float) point_end: ending line point
@@ -361,7 +361,7 @@ def is_point_inside_perpendicular(point_begin, point_end, point_test):
 def is_point_in_quadrant_left(point_begin, point_end, point_test):
     """ If point is left quadrant from line end point
 
-    Note that negative response does not mean that that the point is on tight side
+    .. note:: negative response does not mean that that the point is on tight side
 
     :param list(float) point_begin: starting line point
     :param list(float) point_end: ending line point

birl/utilities/drawing.py

@@ -3,7 +3,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-# from __future__ import absolute_import
 
 import os
 import logging
@@ -14,9 +13,9 @@
 from PIL import ImageDraw
 from matplotlib import colors as plt_colors, ticker as plt_ticker
 
-from .data_io import convert_ndarray2image
-from .dataset import scale_large_images_landmarks
-from .evaluate import compute_matrix_user_ranking
+from birl.utilities.data_io import convert_ndarray2image
+from birl.utilities.dataset import scale_large_images_landmarks
+from birl.utilities.evaluate import compute_matrix_user_ranking
 
 #: default figure size for visualisations
 MAX_FIGURE_SIZE = 18  # inches

birl/utilities/evaluate.py

@@ -3,7 +3,6 @@
 
 Copyright (C) 2016-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 from itertools import chain
 from collections import Counter
@@ -12,7 +11,7 @@
 import pandas as pd
 from scipy.spatial import distance
 
-from .registration import estimate_affine_transform, get_affine_components, norm_angle
+from birl.utilities.registration import estimate_affine_transform, get_affine_components, norm_angle
 
 
 def compute_tre(points_1, points_2):

birl/utilities/experiments.py

@@ -3,7 +3,6 @@
 
 Copyright (C) 2016-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys
@@ -19,12 +18,12 @@
 import multiprocessing as mproc
 from functools import wraps
 
-import enlighten
+import tqdm
 import numpy as np
 from pathos.multiprocessing import ProcessPool
 
-from .data_io import create_folder, save_config_yaml, update_path
-from .dataset import CONVERT_RGB
+from birl.utilities.data_io import create_folder, save_config_yaml, update_path
+from birl.utilities.dataset import CONVERT_RGB
 
 #: number of available CPUs on this computer
 CPU_COUNT = int(mproc.cpu_count())
@@ -544,9 +543,8 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
     nb_workers = CPU_COUNT if nb_workers < 0 else nb_workers
 
     if desc is not None:
-        pbar = enlighten.Counter(total=len(iterate_vals),
-                                 desc=str('%r @%i-threads' % (desc, nb_workers)),
-                                 stream=sys.stderr)
+        pbar = tqdm.tqdm(total=len(iterate_vals),
+                         desc=str('%r @%i-threads' % (desc, nb_workers)))
     else:
         pbar = None
 

bm_ANHIR/copy_sub-scales.py

@@ -1,7 +1,7 @@
 """
 Copy files as all sub-scales
 
-Note that all paths are hard-coded to be used in CMP grid
+.. note:: all paths are hard-coded to be used in CMP grid
 
 """
 

bm_dataset/crop_tissue_images.py

@@ -1,7 +1,7 @@
 """
 Crop images around major object with set padding
 
-Note, that using these scripts for 1+GB images take several tens of GB RAM
+.. note:: Using these scripts for 1+GB images take several tens of GB RAM
 
 Sample usage::
 

bm_dataset/rescale_tissue_images.py

@@ -3,7 +3,7 @@
 
 With given path pattern to images crete particular scales within the same set
 
-Note, that using these scripts for 1+GB images take several tens of GB RAM
+.. note:: Using these scripts for 1+GB images take several tens of GB RAM
 
 Sample usage::
 

bm_dataset/split_images_two_tissues.py

@@ -1,7 +1,7 @@
 """
 Splitting image containing two samples
 
-Note, that using these scripts for 1+GB images take several tens of GB RAM
+.. note:: Using these scripts for 1+GB images take several tens of GB RAM
 
 Sample usage::
 

bm_experiments/bm_ANTs.py

@@ -72,7 +72,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_ANTsPy.py

@@ -31,7 +31,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_DROP.py

@@ -56,7 +56,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_DROP2.py

@@ -46,7 +46,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_RVSS.py

@@ -37,7 +37,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_bUnwarpJ.py

@@ -48,7 +48,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_elastix.py

@@ -62,7 +62,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

bm_experiments/bm_rNiftyReg.py

@@ -39,7 +39,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

requirements.txt

@@ -7,11 +7,10 @@ matplotlib>=2.0.2,<3.0.0  # new version does not support py2
 tqdm>=4.7.4,<=4.30  # higher fails ascii for py2
 pyyaml
 scikit-image
-opencv-python
+opencv-python-headless
 openslide-python
 nibabel
 SimpleITK
 mock
 psutil
-pathos
-enlighten>=1.3.3  # fix for Windows
+pathos

tests/test_benchmark.py

@@ -4,7 +4,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys

tests/test_data-utils.py

@@ -4,7 +4,6 @@
 
 Copyright (C) 2017-2019 Jiri Borovec <[email protected]>
 """
-from __future__ import absolute_import
 
 import os
 import sys