relative pkg imports (#4)

* pkg relative imports
* minor packages fix
* update init info
* update CI configs
* drop Shippable
* rename NB_THREADS -> NB_WORKERS

.shippable.yml

@@ -1,74 +0,0 @@
-# vim ft=yaml
-
-# After changing this file, check it on:
-# http://yaml-online-parser.appspot.com/
-
-build:
- # https://github.com/Shippable/support/issues/3873
- ci:
- - echo $CI_REPORTS && mkdir -p $CI_REPORTS
- - echo $COVERAGE_REPORTS && mkdir -p $COVERAGE_REPORTS
-
-env:
- global:
- - CI_REPORTS=shippable/testresults
- - COVERAGE_REPORTS=shippable/codecoverage
- - DISPLAY=""
-
-language: python
-
-sudo: true
-
-python:
- - 2.7
- - 3.5
-
-cache: pip
-
-before_install:
- - apt-get update --fix-missing
- - apt-get install freetype*
- - apt-get install python-dev python-tk
- - apt-get install python3-dev python3-tk
- - apt-get install pkg-config
- - pip install --upgrade pip
- - gcc --version ; python --version ; pip --version ; pwd ; ls -l
-
-install:
- - pip install -r requirements.txt
- - pip install "nose>=1.3.7" coverage codecov "pytest>=3.0.5" flake8
- - pip list
-
-script:
- - unset DISPLAY
- - mkdir results
- - python setup.py check -m -s
- # - nosetests --with-xunit --xunit-file=shippable/testresults/nosetests.xml
- - nosetests bpdl -v --exe --with-doctest --with-coverage --cover-package=bpdl
- - python experiments/run_dataset_generate.py --nb_samples 25 --nb_patterns 2 --image_size 64 64
- - python experiments/run_dataset_add_noise.py -p ./data_images
- - nosetests experiments -v --exe --with-doctest --with-xunit --xunit-file=shippable/testresults/nosetests.xml
- - flake8 . --ignore=E402,E731 --max-line-length=100
-
-# - rm -rf results && mkdir results
-# # EXPERIMENTS: pre-processing
-# - python experiments/run_cut_minimal_images.py -i "./data_images/imaginal_discs/gene/*.png" -o ./data_images/imaginal_discs/gene_cut
-# - python experiments/run_extract_fuzzy_activation.py -i "./data_images/ovary_stage-2/image/*.png" -o ./data_images/ovary_stage-2/gene
-# - python experiments/run_extract_fuzzy_activation.py -i "./data_images/ovary_stage-3/image/*.png" -o ./data_images/ovary_stage-3/gene
-#
-# # EXPERIMENTS: core
-# - python experiments/run_experiments.py --type synth -i ./data_images/syntheticDataset_vX -o ./results -c ./data_images/sample_config.yml
-# - python experiments/run_experiments.py --type real -i ./data_images/imaginal_discs -o ./results --dataset gene_small --nb_workers 2
-# - python experiments/run_reconstruction.py -e ./results/ExperimentBPDL_real_imaginal_discs_gene_small --visual
-#
-# # EXPERIMENTS: post-processing
-# - python experiments/run_parse_experiments_result.py -i ./results -r results.csv
-# - python experiments/run_recompute_experiments_result.py -i ./results
-# - python experiments/run_parse_experiments_result.py -i ./results -r results_NEW.csv
-
-after_success:
- - python setup.py install
-
- - codecov -t 9507eeee-6a1e-4313-87fa-f73064c539c9
- - coverage xml -o $COVERAGE_REPORTS/coverage.xml
- - coverage report

.travis.yml

@@ -48,7 +48,7 @@ script:
  - flake8 . --ignore=E402,E731 --max-line-length=100
 
 after_success:
- - python setup.py install
+ - python setup.py install --user
  - codecov # public repository on Travis CI
  - coverage xml
  - python-codacy-coverage -r coverage.xml

README.md

@@ -4,11 +4,11 @@
 [![codecov](https://codecov.io/gh/Borda/pyBPDL/branch/master/graph/badge.svg?token=Bgklw7uaB0)](https://codecov.io/gh/Borda/pyBPDL)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/5f4c0dfac2b4444a935d587f663ac9c1)](https://www.codacy.com/app/Borda/pyBPDL?utm_source=github.com&utm_medium=referral&utm_content=Borda/pyBPDL&utm_campaign=Badge_Grade)
 [![CircleCI](https://circleci.com/gh/Borda/pyBPDL.svg?style=svg&circle-token=0b3f34bedf54747d32becd2f13cd0da71fef7548)](https://circleci.com/gh/Borda/pyBPDL)
-[![Run Status](https://api.shippable.com/projects/5937c15c3e246207003bc61b/badge?branch=master)](https://app.shippable.com/github/Borda/pyBPDL)
 [![CodeFactor](https://www.codefactor.io/repository/github/borda/pybpdl/badge)](https://www.codefactor.io/repository/github/borda/pybpdl)
 [![Documentation Status](https://readthedocs.org/projects/pybpdl/badge/?version=latest)](https://pybpdl.readthedocs.io/en/latest/?badge=latest)
 [![Gitter](https://badges.gitter.im/pyBPDL/community.svg)](https://gitter.im/pyBPDL/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 <!--
+[![Run Status](https://api.shippable.com/projects/5937c15c3e246207003bc61b/badge?branch=master)](https://app.shippable.com/github/Borda/pyBPDL)
 [![Coverage Badge](https://api.shippable.com/projects/5937c15c3e246207003bc61b/coverageBadge?branch=master)](https://app.shippable.com/github/Borda/pyBPDL)
 -->
 

bpdl/__init__.py

@@ -24,8 +24,8 @@
  np.set_printoptions(legacy='1.13')
 
  # default display size was changed in pandas v0.23
- if 'display.max_columns' in pd.core.config._registered_options:
- pd.set_option('display.max_columns', 20)
+ pd.set_option('display.max_columns', 20)
+
 except ImportError:
  import traceback
  traceback.print_exc()
@@ -35,8 +35,9 @@
 __author_email__ = 'jiri.borovec@fel.cvut.cz'
 __license__ = 'BSD 3-clause'
 __homepage__ = 'https://borda.github.io/pyBPDL'
-__copyright__ = 'Copyright (c) 2014-2019, Jiri Borovec.'
-__doc__ = """# BPDL - Binary pattern Dictionary Learning
+__copyright__ = 'Copyright (c) 2014-2019, %s.' % __author__
+__doc__ = 'BPDL - Binary pattern Dictionary Learning'
+__long_doc__ = "# %s" % __doc__ + """
 
 The package contain Binary pattern Dictionary Learning (BPDL) which is image processing tool
  for unsupervised pattern extraction and atlas estimation. Moreover the project/repository

bpdl/data_utils.py

@@ -3,8 +3,8 @@
 
 Copyright (C) 2015-2018 Jiri Borovec <jiri.borovec@fel.cvut.cz>
 """
+from __future__ import absolute_import
 
-# from __future__ import absolute_import
 import os
 import glob
 import logging
@@ -31,9 +31,9 @@
 from imsegm.utilities.experiments import WrapExecuteSequence
 from imsegm.utilities.data_io import io_imread, io_imsave
 
-from bpdl.utilities import create_clean_folder
+from .utilities import create_clean_folder
 
-NB_THREADS = mproc.cpu_count()
+NB_WORKERS = mproc.cpu_count()
 IMAGE_SIZE_2D = (128, 128)
 IMAGE_SIZE_3D = (16, 128, 128)
 NB_BIN_PATTERNS = 9
@@ -597,7 +597,7 @@ def generate_rand_patterns_occlusion(idx, im_ptns, out_dir=None,
 
 def dataset_binary_combine_patterns(im_ptns, out_dir=None, nb_samples=NB_SAMPLES,
  ptn_ration=RND_PATTERN_OCCLUSION,
- nb_workers=NB_THREADS, rand_seed=None):
+ nb_workers=NB_WORKERS, rand_seed=None):
  """ generate a Binary dataset composed from N samples and given ration
  of pattern occlusion
 
@@ -815,7 +815,7 @@ def wrapper_image_function(i_img, func, coef, out_dir):
  return i, img_def
 
 
-def dataset_apply_image_function(imgs, out_dir, func, coef=0.5, nb_workers=NB_THREADS):
+def dataset_apply_image_function(imgs, out_dir, func, coef=0.5, nb_workers=NB_WORKERS):
  """ having list if input images create an dataset with randomly deform set
  of these images and export them to the results folder
 

bpdl/dictionary_learning.py

@@ -4,8 +4,8 @@
 
 Copyright (C) 2015-2018 Jiri Borovec <jiri.borovec@fel.cvut.cz>
 """
+from __future__ import absolute_import
 
-# from __future__ import absolute_import
 import os
 import time
 import logging
@@ -25,14 +25,14 @@
 # using https://github.com/Borda/pyGCO
 from gco import cut_general_graph, cut_grid_graph_simple
 
-from bpdl.pattern_atlas import (
+from .pattern_atlas import (
  compute_positive_cost_images_weights, edges_in_image2d_plane, init_atlas_mosaic,
  atlas_split_indep_ptn, reinit_atlas_likely_patterns, compute_relative_penalty_images_weights)
-from bpdl.pattern_weights import (weights_image_atlas_overlap_major,
-   weights_image_atlas_overlap_partial)
-from bpdl.metric_similarity import compare_atlas_adjusted_rand
-from bpdl.data_utils import export_image
-from bpdl.registration import register_images_to_atlas_demons
+from .pattern_weights import (
+ weights_image_atlas_overlap_major, weights_image_atlas_overlap_partial)
+from .metric_similarity import compare_atlas_adjusted_rand
+from .data_utils import export_image
+from .registration import register_images_to_atlas_demons
 
 NB_GRAPH_CUT_ITER = 5
 TEMPLATE_NAME_ATLAS = 'BPDL_{}_{}_iter_{:04d}'

bpdl/pattern_atlas.py

@@ -12,9 +12,9 @@
 from skimage import morphology, measure, segmentation, filters
 from scipy import ndimage as ndi
 
-from bpdl.data_utils import image_deform_elastic, extract_image_largest_element
-from bpdl.pattern_weights import (weights_label_atlas_overlap_threshold,
-   convert_weights_binary2indexes)
+from .data_utils import image_deform_elastic, extract_image_largest_element
+from .pattern_weights import (
+ weights_label_atlas_overlap_threshold, convert_weights_binary2indexes)
 
 REINIT_PATTERN_COMPACT = True
 UNARY_BACKGROUND = 1

bpdl/registration.py

@@ -10,7 +10,7 @@
 
 import time
 import logging
-import multiprocessing as mproc
+# import multiprocessing as mproc
 from functools import partial
 
 import numpy as np
@@ -19,9 +19,9 @@
 from dipy.align import VerbosityLevels
 from dipy.align.imwarp import SymmetricDiffeomorphicRegistration, DiffeomorphicMap
 from dipy.align.metrics import SSDMetric
-from imsegm.utilities.experiments import WrapExecuteSequence
+from imsegm.utilities.experiments import WrapExecuteSequence, nb_workers
 
-NB_THREADS = int(mproc.cpu_count() * .8)
+NB_WORKERS = nb_workers(0.8)
 
 LIST_SDR_PARAMS = ('metric', 'level_iters', 'step_length', 'ss_sigma_factor',
  'opt_tol', 'inv_iter', 'inv_tol', 'callback')
@@ -267,7 +267,7 @@ def wrapper_warp2d_transform_image(idx_img_deform, method='linear', inverse=Fals
 
 
 def warp2d_images_deformations(list_images, list_deforms, method='linear',
- inverse=False, nb_workers=NB_THREADS):
+ inverse=False, nb_workers=NB_WORKERS):
  """ deform whole set of images to expected image domain
 
  :param list(ndarray) list_images:
@@ -335,7 +335,7 @@ def wrapper_register_demons_image_weights(idx_img_weights, atlas, smooth_coef,
 def register_images_to_atlas_demons(list_images, atlas, list_weights,
  smooth_coef=1., params=None,
  interp_method='linear', inverse=False,
- rm_mean=True, nb_workers=NB_THREADS):
+ rm_mean=True, nb_workers=NB_WORKERS):
  """ register whole set of images to estimated atlas and weights
  IDEA: think about parallel registration per sets as for loading images
 

bpdl/utilities.py

@@ -11,15 +11,13 @@
 import logging
 import shutil
 # import multiprocessing.pool
-import multiprocessing as mproc
+# import multiprocessing as mproc
 # from functools import wraps
 
 import numpy as np
 from scipy import stats
 from scipy.spatial import distance
 
-NB_THREADS = mproc.cpu_count()
-
 
 # def update_path(path_file, lim_depth=5, absolute=True):
 # """ bubble in the folder tree up intil it found desired file
@@ -168,7 +166,7 @@ def generate_gauss_2d(mean, std, im_size=None, norm=None):
 # return proc
 
 
-# def wrap_execute_sequence(wrap_func, iterate_vals, nb_workers=NB_THREADS,
+# def wrap_execute_sequence(wrap_func, iterate_vals, nb_workers=NB_WORKERS,
 # desc='', ordered=False):
 # """ wrapper for execution parallel of single thread as for...
 #