rename package

Borda · Borda · commit 8be429a31b6f · 2019-03-04T12:34:11.000+01:00
* refactor circleCI
* update setup.py
diff --git a/.shippable.yml b/.shippable.yml
@@ -38,7 +38,7 @@ install:
 script:
   - mkdir results
   # - nosetests --with-xunit --xunit-file=shippable/testresults/nosetests.xml
-  - nosetests -v --exe --with-doctest --with-coverage --with-xunit --cover-package=benchmark --xunit-file=shippable/testresults/nosetests.xml
+  - nosetests -v --exe --with-doctest --with-coverage --with-xunit --cover-package=birl --xunit-file=shippable/testresults/nosetests.xml
 
 after_success:
   - codecov
diff --git a/.travis.yml b/.travis.yml
@@ -37,8 +37,8 @@ script:
   - tox
   - mkdir results
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1
-  - python benchmark/bm_template.py -c ./data_images/pairs-imgs-lnds_mix.csv -o ./results --visual --unique --an_executable none
-  - python benchmark/bm_template.py -c ./data_images/pairs-imgs-lnds_anhir.csv -d ./data_images -o ./results --an_executable none
+  - python birl/bm_template.py -c ./data_images/pairs-imgs-lnds_mix.csv -o ./results --visual --unique --an_executable none
+  - python birl/bm_template.py -c ./data_images/pairs-imgs-lnds_anhir.csv -d ./data_images -o ./results --an_executable none
   - python bm_experiments/evaluate_experiment.py -d ./data_images -e ./results/BmTemplate --visual
 
 after_success:
diff --git a/README.md b/README.md
@@ -140,15 +140,15 @@ For each registration method, different experiments can be performed independent
 Sample execution of the "empty" benchmark template:
 ```bash
 mkdir results
-python benchmark/bm_template.py \
+python birl/bm_template.py \
     -c ./data_images/pairs-imgs-lnds_mix.csv \
     -o ./results \
     --an_executable none \
     --unique --visual
 ```
 or with relative paths:
 ```bash
-python benchmark/bm_template.py \
+python birl/bm_template.py \
     -c ./data_images/pairs-imgs-lnds_anhir.csv \
     -d ./data_images \
     -o ./results \
@@ -165,7 +165,7 @@ This script generate simple report exported in JSON file on given output path.
 
 ### Add custom registration method
 
-The only limitation of adding costume image registration methods that it has to be launched from python script or command line. The new registration benchmark should be inherited from [ImRegBenchmark](benchmark/cls_benchmark.py) as for example [BmTemplate](benchmark/bm_template.py).
+The only limitation of adding costume image registration methods that it has to be launched from python script or command line. The new registration benchmark should be inherited from [ImRegBenchmark](birl/cls_benchmark.py) as for example [BmTemplate](birl/bm_template.py).
 
 The benchmark workflow is the following:
 1. `self._prepare()` prepare the experiment, e.g. create experiment folder, copy configurations, etc.
diff --git a/appveyor.yml b/appveyor.yml
@@ -65,7 +65,7 @@ test_script:
   - tox
   - mkdir results
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1
-  - python benchmark/bm_template.py -c ./data_images/pairs-imgs-lnds_mix.csv -o ./results --unique --visual --an_executable none
+  - python birl/bm_template.py -c ./data_images/pairs-imgs-lnds_mix.csv -o ./results --unique --visual --an_executable none
 
 on_success:
   - coverage report
diff --git a/benchmark/__init__.py b/benchmark/__init__.py
diff --git a/birl/__init__.py b/birl/__init__.py
@@ -0,0 +1,3 @@
+import birl.utilities
+
+birl.utilities
diff --git a/birl/bm_template.py b/birl/bm_template.py
@@ -7,7 +7,7 @@
 
 EXAMPLE (usage):
 >> mkdir ./results
->> python benchmark/bm_template.py \
+>> python birl/bm_template.py \
     -c ./data_images/pairs-imgs-lnds_anhir.csv -d ./data_images \
     -o ./results --visual --unique \
     --an_executable none
@@ -21,9 +21,8 @@
 import logging
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.experiments import create_basic_parse, parse_arg_params
-from benchmark.cls_benchmark import (
-    ImRegBenchmark, COL_REG_DIR, COL_IMAGE_MOVE, COL_POINTS_MOVE)
+from birl.utilities.experiments import create_basic_parse, parse_arg_params
+from birl.cls_benchmark import ImRegBenchmark, COL_REG_DIR, COL_IMAGE_MOVE, COL_POINTS_MOVE
 
 
 def extend_parse(a_parser):
@@ -58,7 +57,7 @@ class BmTemplate(ImRegBenchmark):
     image and landmarks. It means that there was no registration performed.
 
     Running in single thread:
-    >>> from benchmark.utilities.data_io import create_folder, update_path
+    >>> from birl.utilities.data_io import create_folder, update_path
     >>> path_out = create_folder('temp_results')
     >>> path_csv = os.path.join(update_path('data_images'), 'pairs-imgs-lnds_mix.csv')
     >>> main({'nb_workers': 1, 'unique': False, 'visual': True,
@@ -69,7 +68,7 @@ class BmTemplate(ImRegBenchmark):
     >>> shutil.rmtree(path_out, ignore_errors=True)
 
     Running in multiple parallel threads:
-    >>> from benchmark.utilities.data_io import create_folder, update_path
+    >>> from birl.utilities.data_io import create_folder, update_path
     >>> path_out = create_folder('temp_results')
     >>> path_csv = os.path.join(update_path('data_images'), 'pairs-imgs-lnds_mix.csv')
     >>> params = {'nb_workers': 2, 'unique': False, 'visual': True,
diff --git a/birl/cls_benchmark.py b/birl/cls_benchmark.py
@@ -24,13 +24,13 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.data_io import (
+from birl.utilities.data_io import (
     update_path, create_folder, image_size, load_landmarks, load_image, save_image)
-from benchmark.utilities.experiments import (
+from birl.utilities.experiments import (
     run_command_line, string_dict, compute_points_dist_statistic, wrap_execute_sequence)
-from benchmark.utilities.visualisation import (
+from birl.utilities.visualisation import (
     export_figure, draw_image_points, draw_images_warped_landmarks)
-from benchmark.utilities.cls_experiment import Experiment
+from birl.utilities.cls_experiment import Experiment
 
 #: number of available threads on this computer
 NB_THREADS = int(mproc.cpu_count())
@@ -130,7 +130,7 @@ class ImRegBenchmark(Experiment):
     is alignment (consistent warping) between resulting landmarks and image.
 
     Running in single thread:
-    >>> from benchmark.utilities.data_io import create_folder, update_path
+    >>> from birl.utilities.data_io import create_folder, update_path
     >>> path_out = create_folder('temp_results')
     >>> path_csv = os.path.join(update_path('data_images'), 'pairs-imgs-lnds_mix.csv')
     >>> params = {'nb_workers': 1, 'unique': False, 'visual': True,
@@ -143,7 +143,7 @@ class ImRegBenchmark(Experiment):
     >>> shutil.rmtree(path_out, ignore_errors=True)
 
     Running in multiple parallel threads:
-    >>> from benchmark.utilities.data_io import create_folder, update_path
+    >>> from birl.utilities.data_io import create_folder, update_path
     >>> path_out = create_folder('temp_results')
     >>> path_csv = os.path.join(update_path('data_images'), 'pairs-imgs-lnds_mix.csv')
     >>> params = {'nb_workers': 2, 'unique': False, 'visual': True,
diff --git a/birl/test_benchmark.py b/birl/test_benchmark.py
@@ -22,16 +22,16 @@
 from numpy.testing import assert_raises, assert_array_almost_equal
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.data_io import update_path
-from benchmark.utilities.dataset import args_expand_parse_images
-from benchmark.utilities.experiments import (parse_arg_params, try_decorator)
-from benchmark.cls_benchmark import ImRegBenchmark
-from benchmark.cls_benchmark import (
+from birl.utilities.data_io import update_path
+from birl.utilities.dataset import args_expand_parse_images
+from birl.utilities.experiments import (parse_arg_params, try_decorator)
+from birl.cls_benchmark import ImRegBenchmark
+from birl.cls_benchmark import (
     NAME_CSV_RESULTS, NAME_TXT_RESULTS, NAME_CSV_REGISTRATION_PAIRS, COVER_COLUMNS,
     COL_IMAGE_MOVE_WARP, COL_POINTS_REF_WARP, COL_POINTS_MOVE_WARP,
     _visual_image_move_warp_lnds_move_warp, _visual_image_ref_warp_lnds_move_warp,
     visualise_registration)
-from benchmark.bm_template import BmTemplate
+from birl.bm_template import BmTemplate
 
 PATH_DATA = update_path('data_images')
 PATH_CSV_COVER_MIX = os.path.join(PATH_DATA, 'pairs-imgs-lnds_mix.csv')
diff --git a/birl/utilities/__init__.py b/birl/utilities/__init__.py
diff --git a/birl/utilities/cls_experiment.py b/birl/utilities/cls_experiment.py
@@ -10,8 +10,8 @@
 import copy
 import logging
 
-from benchmark.utilities.experiments import (set_experiment_logger, string_dict,
-                                             create_experiment_folder, release_logger_files)
+from birl.utilities.experiments import (
+    set_experiment_logger, string_dict, create_experiment_folder, release_logger_files)
 
 #: default date-time format
 FORMAT_DATE_TIME = '%Y%m%d-%H%M%S'
@@ -30,7 +30,7 @@ class Experiment(object):
     Tha basic template for experiment running with specific initialisation
     None, all required parameters used in future have to come in init phase
 
-    >>> import benchmark.utilities.data_io as tl_io
+    >>> import birl.utilities.data_io as tl_io
     >>> path_out = tl_io.create_folder('output')
     >>> params = {'path_out': path_out, 'name': 'my_Experiment'}
     >>> expt = Experiment(params, False)
diff --git a/birl/utilities/data_io.py b/birl/utilities/data_io.py
@@ -191,7 +191,7 @@ def update_path(path_file, lim_depth=5, absolute=True):
     :param bool absolute: return absolute path
     :return str:
 
-    >>> os.path.exists(update_path('benchmark', absolute=False))
+    >>> os.path.exists(update_path('birl', absolute=False))
     True
     >>> os.path.exists(update_path('/', absolute=False))
     True
diff --git a/birl/utilities/dataset.py b/birl/utilities/dataset.py
@@ -578,7 +578,7 @@ def list_sub_folders(path_folder, name='*'):
     :param str name: name pattern
     :return [str]:
 
-    >>> from benchmark.utilities.data_io import update_path
+    >>> from birl.utilities.data_io import update_path
     >>> paths = list_sub_folders(update_path('data_images'))
     >>> list(map(os.path.basename, paths))
     ['images', 'landmarks', 'lesions_', 'rat-kidney_']
diff --git a/birl/utilities/experiments.py b/birl/utilities/experiments.py
@@ -19,7 +19,7 @@
 import numpy as np
 from scipy.spatial import distance
 
-from benchmark.utilities.data_io import create_folder, update_path
+from birl.utilities.data_io import create_folder, update_path
 
 #: number of available threads on this computer
 NB_THREADS = int(mproc.cpu_count())
diff --git a/birl/utilities/registration.py b/birl/utilities/registration.py
diff --git a/birl/utilities/visualisation.py b/birl/utilities/visualisation.py
@@ -11,8 +11,8 @@
 import matplotlib.pylab as plt
 from PIL import ImageDraw
 
-from benchmark.utilities.data_io import convert_ndarray2image
-from benchmark.utilities.dataset import scale_large_images_landmarks
+from birl.utilities.data_io import convert_ndarray2image
+from birl.utilities.dataset import scale_large_images_landmarks
 #: default figure size for visualisations
 MAX_FIGURE_SIZE = 18  # inches
 
diff --git a/bm_ANHIR/copy_sub-scales.py b/bm_ANHIR/copy_sub-scales.py
@@ -12,8 +12,8 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.cls_benchmark import COL_IMAGE_REF, COL_IMAGE_MOVE, COL_POINTS_MOVE
-from benchmark.utilities.dataset import parse_path_scale
+from birl.cls_benchmark import COL_IMAGE_REF, COL_IMAGE_MOVE, COL_POINTS_MOVE
+from birl.utilities.dataset import parse_path_scale
 
 PATH_CSV = '/datagrid/Medical/dataset_ANHIR/images/dataset_medium.csv'
 PATH_IMAGES = '/datagrid/Medical/dataset_ANHIR/images'
diff --git a/bm_ANHIR/evaluate_submission.py b/bm_ANHIR/evaluate_submission.py
@@ -67,10 +67,10 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.data_io import create_folder, load_landmarks, save_landmarks
-from benchmark.utilities.dataset import common_landmarks, parse_path_scale
-from benchmark.utilities.experiments import wrap_execute_sequence, parse_arg_params
-from benchmark.cls_benchmark import (
+from birl.utilities.data_io import create_folder, load_landmarks, save_landmarks
+from birl.utilities.dataset import common_landmarks, parse_path_scale
+from birl.utilities.experiments import wrap_execute_sequence, parse_arg_params
+from birl.cls_benchmark import (
     NAME_CSV_REGISTRATION_PAIRS, COVER_COLUMNS, COVER_COLUMNS_WRAP,
     COL_IMAGE_REF_WARP, COL_POINTS_REF_WARP, COL_POINTS_REF, COL_POINTS_MOVE,
     COL_TIME, COL_ROBUSTNESS, compute_landmarks_statistic, update_path_)
diff --git a/bm_ANHIR/generate_regist_pairs.py b/bm_ANHIR/generate_regist_pairs.py
@@ -15,13 +15,12 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.data_io import image_size
-from benchmark.utilities.dataset import IMAGE_EXTENSIONS, generate_pairing
-from benchmark.cls_benchmark import (COL_IMAGE_REF, COL_IMAGE_MOVE, COL_TIME,
-                                     COL_POINTS_REF, COL_POINTS_MOVE,
-                                     COL_POINTS_REF_WARP, COL_POINTS_MOVE_WARP,
-                                     COL_IMAGE_SIZE, COL_IMAGE_DIAGONAL,
-                                     update_path_)
+from birl.utilities.data_io import image_size
+from birl.utilities.dataset import IMAGE_EXTENSIONS, generate_pairing
+from birl.cls_benchmark import (
+    COL_IMAGE_REF, COL_IMAGE_MOVE, COL_TIME, COL_POINTS_REF, COL_POINTS_MOVE,
+    COL_POINTS_REF_WARP, COL_POINTS_MOVE_WARP, COL_IMAGE_SIZE, COL_IMAGE_DIAGONAL,
+    update_path_)
 
 DATASET_IMAGES = '/datagrid/Medical/dataset_ANHIR/images_private'
 DATASET_LANDMARKS = '/datagrid/Medical/dataset_ANHIR/landmarks_all'
diff --git a/bm_ANHIR/zip_dataset_by_cover.py b/bm_ANHIR/zip_dataset_by_cover.py
@@ -21,7 +21,7 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.cls_benchmark import COL_IMAGE_REF, COL_IMAGE_MOVE, COL_POINTS_MOVE
+from birl.cls_benchmark import COL_IMAGE_REF, COL_IMAGE_MOVE, COL_POINTS_MOVE
 
 ZIP_COMMAND = 'cd %s && zip --split-size 2g %s.zip -r %s'
 
diff --git a/bm_dataset/__init__.py b/bm_dataset/__init__.py
@@ -1,3 +1,3 @@
-import benchmark
+import birl
 
-benchmark
+birl
diff --git a/bm_dataset/convert_tiff2png.py b/bm_dataset/convert_tiff2png.py
@@ -39,8 +39,8 @@
           ' To do so, please follow instructions - https://openslides.org')
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.experiments import wrap_execute_sequence
-from benchmark.utilities.dataset import args_expand_parse_images
+from birl.utilities.experiments import wrap_execute_sequence
+from birl.utilities.dataset import args_expand_parse_images
 
 DEFAULT_LEVEL = 1
 MAX_LOAD_IMAGE_SIZE = 16000
diff --git a/bm_dataset/create_real_synth_dataset.py b/bm_dataset/create_real_synth_dataset.py
@@ -33,8 +33,8 @@
 import matplotlib.pyplot as plt
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.experiments import parse_arg_params
-from benchmark.utilities.data_io import LANDMARK_COORDS
+from birl.utilities.experiments import parse_arg_params
+from birl.utilities.data_io import LANDMARK_COORDS
 
 COLUMNS_COORD = LANDMARK_COORDS
 NB_THREADS = max(1, int(mproc.cpu_count() * .8))
diff --git a/bm_dataset/crop_tissue_images.py b/bm_dataset/crop_tissue_images.py
@@ -26,10 +26,10 @@
 import numpy as np
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.dataset import (
+from birl.utilities.dataset import (
     find_largest_object, project_object_edge, load_large_image, save_large_image,
     args_expand_parse_images)
-from benchmark.utilities.experiments import wrap_execute_sequence, try_decorator
+from birl.utilities.experiments import wrap_execute_sequence, try_decorator
 
 NB_THREADS = max(1, int(mproc.cpu_count() * .5))
 SCALE_SIZE = 512
diff --git a/bm_dataset/generate_regist_pairs.py b/bm_dataset/generate_regist_pairs.py
@@ -19,10 +19,10 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.data_io import image_size
-from benchmark.utilities.experiments import parse_arg_params
-from benchmark.cls_benchmark import (COVER_COLUMNS, COVER_COLUMNS_EXT, COL_IMAGE_REF,
-                                     COL_IMAGE_SIZE, COL_IMAGE_DIAGONAL)
+from birl.utilities.data_io import image_size
+from birl.utilities.experiments import parse_arg_params
+from birl.cls_benchmark import (
+    COVER_COLUMNS, COVER_COLUMNS_EXT, COL_IMAGE_REF, COL_IMAGE_SIZE, COL_IMAGE_DIAGONAL)
 
 # list of combination options
 OPTIONS_COMBINE = ('first2all', 'each2all')
diff --git a/bm_dataset/rescale_tissue_images.py b/bm_dataset/rescale_tissue_images.py
@@ -27,10 +27,10 @@
 import cv2 as cv
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.experiments import wrap_execute_sequence, is_iterable
-from benchmark.utilities.dataset import (load_large_image, save_large_image,
-                                         parse_path_scale, args_expand_parse_images)
-from benchmark.utilities.data_io import create_folder
+from birl.utilities.experiments import wrap_execute_sequence, is_iterable
+from birl.utilities.dataset import (load_large_image, save_large_image,
+                                    parse_path_scale, args_expand_parse_images)
+from birl.utilities.data_io import create_folder
 
 NB_THREADS = max(1, int(mproc.cpu_count() * .5))
 DEFAULT_SCALES = (5, 10, 15, 20, 25, 50)
diff --git a/bm_dataset/rescale_tissue_landmarks.py b/bm_dataset/rescale_tissue_landmarks.py
@@ -38,12 +38,11 @@
 import pandas as pd
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.experiments import (wrap_execute_sequence,
-                                             parse_arg_params, is_iterable)
-from benchmark.utilities.data_io import create_folder, load_landmarks_csv, save_landmarks_csv
-from benchmark.utilities.dataset import (list_sub_folders, parse_path_scale,
-                                         compute_bounding_polygon, inside_polygon)
-from benchmark.utilities.registration import estimate_affine_transform, transform_points
+from birl.utilities.experiments import wrap_execute_sequence, parse_arg_params, is_iterable
+from birl.utilities.data_io import create_folder, load_landmarks_csv, save_landmarks_csv
+from birl.utilities.dataset import (list_sub_folders, parse_path_scale,
+                                    compute_bounding_polygon, inside_polygon)
+from birl.utilities.registration import estimate_affine_transform, transform_points
 from bm_dataset.rescale_tissue_images import NB_THREADS, DEFAULT_SCALES, FOLDER_TEMPLATE
 
 
diff --git a/bm_dataset/split_images_two_tissues.py b/bm_dataset/split_images_two_tissues.py
@@ -25,10 +25,9 @@
 import cv2 as cv
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
-from benchmark.utilities.dataset import (
-    find_split_objects, project_object_edge, load_large_image, save_large_image,
-    args_expand_parse_images)
-from benchmark.utilities.experiments import wrap_execute_sequence
+from birl.utilities.dataset import (find_split_objects, project_object_edge, load_large_image,
+                                    save_large_image, args_expand_parse_images)
+from birl.utilities.experiments import wrap_execute_sequence
 
 NB_THREADS = max(1, int(mproc.cpu_count() * .5))
 SCALE_SIZE = 512
diff --git a/bm_experiments/__init__.py b/bm_experiments/__init__.py
@@ -1,3 +1,3 @@
-import benchmark
+import birl
 
-benchmark
+birl
diff --git a/bm_experiments/bm_bunwarpj.py b/bm_experiments/bm_bunwarpj.py
diff --git a/bm_experiments/evaluate_experiment.py b/bm_experiments/evaluate_experiment.py
diff --git a/circle.yml b/circle.yml
diff --git a/setup.py b/setup.py
diff --git a/tox.ini b/tox.ini

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+import birl.utilities`
	`2`	`+`
	`3`	`+birl.utilities`