diff --git a/README.rst b/README.rst
index a413a5c2350cc07affec4b5dd3ef9473b2dd5110..a0e3eafb903fa54eae99e82a9d28c442218be4bc 100644
--- a/README.rst
+++ b/README.rst
@@ -18,7 +18,8 @@
Binary Segmentation Benchmark Package for Bob
===============================================
-This package is part of the signal-processing and machine learning toolbox Bob_.
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It implements training and inference for binary segmentation tasks.
Installation
@@ -40,4 +41,4 @@ development `mailing list`_.
.. Place your references here:
.. _bob: https://www.idiap.ch/software/bob
.. _installation: https://www.idiap.ch/software/bob/install
-.. _mailing list: https://www.idiap.ch/software/bob/discuss
\ No newline at end of file
+.. _mailing list: https://www.idiap.ch/software/bob/discuss
diff --git a/buildout.cfg b/buildout.cfg
index c099fad3ed9450e71eb60767c56dbec3e8ab9d6b..d81157019c5d7bac9d3f513f08e38a9703f24e69 100644
--- a/buildout.cfg
+++ b/buildout.cfg
@@ -11,4 +11,4 @@ verbose = true
[scripts]
recipe = bob.buildout:scripts
-dependent-scripts = true
\ No newline at end of file
+dependent-scripts = true
diff --git a/conda/meta.yaml b/conda/meta.yaml
index df7c9fa7738805f846d7ba135000669b5df5d467..5d72a8f05e20b5a2d9acb41b3bfd68d7ea9f928c 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -75,4 +75,4 @@ about:
home: https://www.idiap.ch/software/bob/
license: GNU General Public License v3 (GPLv3)
license_family: GPL
- license_file: ../COPYING
\ No newline at end of file
+ license_file: ../COPYING
diff --git a/develop.cfg b/develop.cfg
index ed525115723cba4023ba4de2434ed169a3292574..9229bdf942a37e259b48ae2e724027d8b228f214 100644
--- a/develop.cfg
+++ b/develop.cfg
@@ -3,17 +3,46 @@
[buildout]
parts = scripts
-develop = .
eggs = bob.ip.binseg
+ bob.db.drive
+ bob.db.stare
+ bob.db.chasedb1
+ bob.db.hrf
+ bob.db.drionsdb
+ bob.db.rimoner3
+ bob.db.drishtigs1
+ bob.db.refuge
+ bob.db.iostar
extensions = bob.buildout
- bob.blitz
- bob.core
+ mr.developer
+auto-checkout = *
+develop = src/bob.db.drive
+ src/bob.db.stare
+ src/bob.db.chasedb1
+ src/bob.db.hrf
+ src/bob.db.drionsdb
+ src/bob.db.rimoner3
+ src/bob.db.drishtigs1
+ src/bob.db.refuge
+ src/bob.db.iostar
+ .
; options for bob.buildout extension
debug = true
verbose = true
newest = false
+[sources]
+bob.db.drive = git git@gitlab.idiap.ch:bob/bob.db.drive
+bob.db.stare = git git@gitlab.idiap.ch:bob/bob.db.stare
+bob.db.chasedb1 = git git@gitlab.idiap.ch:bob/bob.db.chasedb1
+bob.db.hrf = git git@gitlab.idiap.ch:bob/bob.db.hrf
+bob.db.drionsdb = git git@gitlab.idiap.ch:bob/bob.db.drionsdb
+bob.db.rimoner3 = git git@gitlab.idiap.ch:bob/bob.db.rimoner3
+bob.db.drishtigs1 = git git@gitlab.idiap.ch:bob/bob.db.drishtigs1
+bob.db.refuge = git git@gitlab.idiap.ch:bob/bob.db.refuge
+bob.db.iostar = git git@gitlab.idiap.ch:bob/bob.db.iostar
+
[scripts]
recipe = bob.buildout:scripts
dependent-scripts=true
diff --git a/requirements.txt b/requirements.txt
index 262a99b9420fe095e958bb0b9ec8aa2bb8ab2ace..719383e1b5ee6b907c96f6edf6e7da9de184b5a9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,4 @@ torchvision
pandas
matplotlib
tqdm
-tabulate
\ No newline at end of file
+tabulate
diff --git a/setup.py b/setup.py
index 2cc4f344b0380941d52b36d37f2f638c2cec4b63..8a7dd13d8cb3f4ce5e7730167eccbc9db5f49405 100644
--- a/setup.py
+++ b/setup.py
@@ -2,124 +2,108 @@
# -*- coding: utf-8 -*-
from setuptools import setup, dist
-dist.Distribution(dict(setup_requires=['bob.extension']))
+
+dist.Distribution(dict(setup_requires=["bob.extension"]))
from bob.extension.utils import load_requirements, find_packages
+
install_requires = load_requirements()
setup(
-
- name='bob.ip.binseg',
+ name="bob.ip.binseg",
version=open("version.txt").read().rstrip(),
- description='Binary Segmentation Benchmark Package for Bob',
-
- url='https://gitlab.idiap.ch/bob/bob.ip.binseg',
- license='GPLv3',
-
+ description="Binary Segmentation Benchmark Package for Bob",
+ url="https://gitlab.idiap.ch/bob/bob.ip.binseg",
+ license="GPLv3",
# there may be multiple authors (separate entries by comma)
- author='Tim Laibacher',
- author_email='tim.laibacher@idiap.ch',
-
+ author="Tim Laibacher",
+ author_email="tim.laibacher@idiap.ch",
# there may be a maintainer apart from the author - you decide
- #maintainer='?'
- #maintainer_email='email@example.com'
-
+ maintainer="Andre Anjos",
+ maintainer_email="andre.anjos@idiap.ch",
# you may add more keywords separating those by commas (a, b, c, ...)
- keywords = "bob",
-
- long_description=open('README.rst').read(),
-
+ keywords="bob",
+ long_description=open("README.rst").read(),
# leave this here, it is pretty standard
packages=find_packages(),
include_package_data=True,
- zip_safe = False,
-
+ zip_safe=False,
install_requires=install_requires,
-
- entry_points={
-
- # main entry for bob hed cli
- 'bob.cli': [
- 'binseg = bob.ip.binseg.script.binseg:binseg',
+ entry_points={
+ # main entry for bob binseg cli
+ "bob.cli": ["binseg = bob.ip.binseg.script.binseg:binseg"],
+ # bob hed sub-commands
+ "bob.ip.binseg.cli": [
+ "train = bob.ip.binseg.script.binseg:train",
+ "test = bob.ip.binseg.script.binseg:test",
+ "compare = bob.bin.binseg.script.binseg:compare",
+ "gridtable = bob.ip.binseg.script.binseg:testcheckpoints",
+ "visualize = bob.ip.binseg.script.binseg:visualize",
],
-
- #bob hed sub-commands
- 'bob.ip.binseg.cli': [
- 'train = bob.ip.binseg.script.binseg:train',
- 'test = bob.ip.binseg.script.binseg:test',
- 'compare = bob.bin.binseg.script.binseg:compare',
- 'gridtable = bob.ip.binseg.script.binseg:testcheckpoints',
- 'visualize = bob.ip.binseg.script.binseg:visualize',
+ # bob train configurations
+ "bob.ip.binseg.config": [
+ "DRIU = bob.ip.binseg.configs.models.driu",
+ "DRIUBN = bob.ip.binseg.configs.models.driubn",
+ "DRIUSSL = bob.ip.binseg.configs.models.driussl",
+ "DRIUBNSSL = bob.ip.binseg.configs.models.driubnssl",
+ "DRIUOD = bob.ip.binseg.configs.models.driuod",
+ "HED = bob.ip.binseg.configs.models.hed",
+ "M2UNet = bob.ip.binseg.configs.models.m2unet",
+ "M2UNetSSL = bob.ip.binseg.configs.models.m2unetssl",
+ "UNet = bob.ip.binseg.configs.models.unet",
+ "ResUNet = bob.ip.binseg.configs.models.resunet",
+ "IMAGEFOLDER = bob.ip.binseg.configs.datasets.imagefolder",
+ "CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1",
+ "CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test",
+ "COVD-DRIVE = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544",
+ "COVD-DRIVE_SSL = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive",
+ "COVD-STARE = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608",
+ "COVD-STARE_SSL = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare",
+ "COVD-IOSTARVESSEL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024",
+ "COVD-IOSTARVESSEL_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar",
+ "COVD-HRF = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168",
+ "COVD-HRF_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf",
+ "COVD-CHASEDB1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960",
+ "COVD-CHASEDB1_SSL = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase",
+ "DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb",
+ "DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest",
+ "DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od",
+ "DRISHTIGS1ODTEST = bob.ip.binseg.configs.datasets.dristhigs1odtest",
+ "DRISHTIGS1CUP = bob.ip.binseg.configs.datasets.dristhigs1cup",
+ "DRISHTIGS1CUPTEST = bob.ip.binseg.configs.datasets.dristhigs1cuptest",
+ "DRIVE = bob.ip.binseg.configs.datasets.drive",
+ "DRIVETEST = bob.ip.binseg.configs.datasets.drivetest",
+ "HRF = bob.ip.binseg.configs.datasets.hrf1168",
+ "HRFTEST = bob.ip.binseg.configs.datasets.hrftest",
+ "IOSTAROD = bob.ip.binseg.configs.datasets.iostarod",
+ "IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest",
+ "IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel",
+ "IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest",
+ "REFUGECUP = bob.ip.binseg.configs.datasets.refugecup",
+ "REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest",
+ "REFUGEOD = bob.ip.binseg.configs.datasets.refugeod",
+ "REFUGEODTEST = bob.ip.binseg.configs.datasets.refugeodtest",
+ "RIMONER3CUP = bob.ip.binseg.configs.datasets.rimoner3cup",
+ "RIMONER3CUPTEST = bob.ip.binseg.configs.datasets.rimoner3cuptest",
+ "RIMONER3OD = bob.ip.binseg.configs.datasets.rimoner3od",
+ "RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest",
+ "STARE = bob.ip.binseg.configs.datasets.stare",
+ "STARETEST = bob.ip.binseg.configs.datasets.staretest",
],
-
- #bob train configurations
- 'bob.ip.binseg.config': [
- 'DRIU = bob.ip.binseg.configs.models.driu',
- 'DRIUBN = bob.ip.binseg.configs.models.driubn',
- 'DRIUSSL = bob.ip.binseg.configs.models.driussl',
- 'DRIUBNSSL = bob.ip.binseg.configs.models.driubnssl',
- 'DRIUOD = bob.ip.binseg.configs.models.driuod',
- 'HED = bob.ip.binseg.configs.models.hed',
- 'M2UNet = bob.ip.binseg.configs.models.m2unet',
- 'M2UNetSSL = bob.ip.binseg.configs.models.m2unetssl',
- 'UNet = bob.ip.binseg.configs.models.unet',
- 'ResUNet = bob.ip.binseg.configs.models.resunet',
- 'IMAGEFOLDER = bob.ip.binseg.configs.datasets.imagefolder',
- 'CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1',
- 'CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test',
- 'COVD-DRIVE = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544',
- 'COVD-DRIVE_SSL = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive',
- 'COVD-STARE = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608',
- 'COVD-STARE_SSL = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare',
- 'COVD-IOSTARVESSEL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024',
- 'COVD-IOSTARVESSEL_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar',
- 'COVD-HRF = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168',
- 'COVD-HRF_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf',
- 'COVD-CHASEDB1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960',
- 'COVD-CHASEDB1_SSL = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase',
- 'DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb',
- 'DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest',
- 'DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od',
- 'DRISHTIGS1ODTEST = bob.ip.binseg.configs.datasets.dristhigs1odtest',
- 'DRISHTIGS1CUP = bob.ip.binseg.configs.datasets.dristhigs1cup',
- 'DRISHTIGS1CUPTEST = bob.ip.binseg.configs.datasets.dristhigs1cuptest',
- 'DRIVE = bob.ip.binseg.configs.datasets.drive',
- 'DRIVETEST = bob.ip.binseg.configs.datasets.drivetest',
- 'HRF = bob.ip.binseg.configs.datasets.hrf1168',
- 'HRFTEST = bob.ip.binseg.configs.datasets.hrftest',
- 'IOSTAROD = bob.ip.binseg.configs.datasets.iostarod',
- 'IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest',
- 'IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel',
- 'IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest',
- 'REFUGECUP = bob.ip.binseg.configs.datasets.refugecup',
- 'REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest',
- 'REFUGEOD = bob.ip.binseg.configs.datasets.refugeod',
- 'REFUGEODTEST = bob.ip.binseg.configs.datasets.refugeodtest',
- 'RIMONER3CUP = bob.ip.binseg.configs.datasets.rimoner3cup',
- 'RIMONER3CUPTEST = bob.ip.binseg.configs.datasets.rimoner3cuptest',
- 'RIMONER3OD = bob.ip.binseg.configs.datasets.rimoner3od',
- 'RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest',
- 'STARE = bob.ip.binseg.configs.datasets.stare',
- 'STARETEST = bob.ip.binseg.configs.datasets.staretest',
- ]
},
-
-
-
# check classifiers, add and remove as you see fit
# full list here: https://pypi.org/classifiers/
# don't remove the Bob framework unless it's not a bob package
- classifiers = [
- 'Framework :: Bob',
- 'Development Status :: 4 - Beta',
- 'Intended Audience :: Science/Research',
- 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
- 'Natural Language :: English',
- 'Programming Language :: Python',
- 'Programming Language :: Python :: 3',
- 'Topic :: Scientific/Engineering :: Artificial Intelligence',
- 'Topic :: Software Development :: Libraries :: Python Modules',
- ],
-
-)
\ No newline at end of file
+ classifiers=[
+ "Framework :: Bob",
+ "Development Status :: 4 - Beta",
+ "Intended Audience :: Science/Research",
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Natural Language :: English",
+ "Programming Language :: Python",
+ "Programming Language :: Python :: 3",
+ "Topic :: Scientific/Engineering :: Artificial Intelligence",
+ "Topic :: Software Development :: Libraries :: Python Modules",
+ ],
+)