diff --git a/.gitignore b/.gitignore
index 262ae6b8cba167fb5298fe31000440c177728bef..9ad21f1b872740002de4ebc6bf7b6e9a2fd3aa3a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,6 +17,6 @@ eggs
html/
parts
sphinx
-src/
submitted.sql3
*.DS_Store
+.gitlab-ci-local*
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 845b719f2378d396a8b75296a68d1e32c840e7c7..9a479703105d5241942420e9cfdf0867cc3183e5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1 +1,4 @@
-include: 'https://gitlab.idiap.ch/bob/bob.devtools/raw/master/bob/devtools/data/gitlab-ci/single-package.yaml'
+include:
+ - project: bob/dev-profile
+ ref: main
+ file: gitlab/python.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b4d1d1ca583eb211cc4b0a5ab9b2243c715bb45e..49337196592599a11942ecd8fc24a4230c5a196d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,20 +2,20 @@
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/timothycrosley/isort
- rev: 5.10.1
+ rev: 5.12.0
hooks:
- id: isort
args: [--settings-path, "pyproject.toml"]
- repo: https://github.com/psf/black
- rev: 22.3.0
+ rev: 23.1.0
hooks:
- id: black
- repo: https://github.com/pycqa/flake8
- rev: 3.9.2
+ rev: 6.0.0
hooks:
- id: flake8
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.2.0
+ rev: v4.4.0
hooks:
- id: check-ast
- id: check-case-conflict
diff --git a/MANIFEST.in b/MANIFEST.in
index 082c42f1bfebeb796d77083d66bdd398664f2070..9d478e091f8ef57d74618c263e475a20010f9744 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
-include README.rst buildout.cfg develop.cfg COPYING version.txt requirements.txt test-requirements.txt
+include README.rst COPYING
recursive-include doc *.py *.rst
recursive-include bob/bio/vein/tests *.png *.txt *.hdf5
diff --git a/README.rst b/README.rst
index 4a86bb06f541c3cb58ba94ae2b292091807f77af..72fcb4e9bb7e73ecb478d9b19750c90cd3b605c7 100644
--- a/README.rst
+++ b/README.rst
@@ -2,11 +2,11 @@
.. Fri 19 Aug 2016 13:32:51 CEST
.. image:: https://img.shields.io/badge/docs-latest-orange.svg
- :target: https://www.idiap.ch/software/bob/docs/bob/bob.bio.vein/master/index.html
+ :target: https://www.idiap.ch/software/bob/docs/bob/bob.bio.vein/master/sphinx/index.html
.. image:: https://gitlab.idiap.ch/bob/bob.bio.vein/badges/master/pipeline.svg
:target: https://gitlab.idiap.ch/bob/bob.bio.vein/commits/master
.. image:: https://gitlab.idiap.ch/bob/bob.bio.vein/badges/master/coverage.svg
- :target: https://gitlab.idiap.ch/bob/bob.bio.vein/commits/master
+ :target: https://www.idiap.ch/software/bob/docs/bob/bob.bio.vein/master/coverage/
.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
:target: https://gitlab.idiap.ch/bob/bob.bio.vein
diff --git a/buildout.cfg b/buildout.cfg
deleted file mode 100644
index e521a2b53e80dad5b472b68ab67a481d73c6cbac..0000000000000000000000000000000000000000
--- a/buildout.cfg
+++ /dev/null
@@ -1,16 +0,0 @@
-; vim: set fileencoding=utf-8 :
-; Fri 19 Aug 2016 13:22:13 CEST
-
-[buildout]
-parts = scripts
-eggs = bob.bio.vein
-
-extensions = bob.buildout
-develop = .
-
-newest = false
-verbose = true
-
-[scripts]
-recipe = bob.buildout:scripts
-dependent-scripts = true
diff --git a/conda/meta.yaml b/conda/meta.yaml
index f5d44b2f7d8a933d955091b658b891923441b331..5dd6d09de2c989ff4485c83f80fa4215128f3a40 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,24 +1,20 @@
-{% set name = 'bob.bio.vein' %}
-{% set project_dir = environ.get('RECIPE_DIR') + '/..' %}
+{% set data = load_file_data(RECIPE_DIR + '/../pyproject.toml') %}
+{% set name = data['project']['name'] %}
package:
name: {{ name }}
- version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
+ version: {{ data['project']['version'] }}
+
+source:
+ path: ..
build:
- entry_points:
- - compare_rois.py = bob.bio.vein.script.compare_rois:main
- - view_sample.py = bob.bio.vein.script.view_sample:main
- - blame.py = bob.bio.vein.script.blame:main
+ noarch: python
number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
run_exports:
- {{ pin_subpackage(name) }}
script:
- - cd {{ project_dir }}
- {% if environ.get('BUILD_EGG') %}
- - "{{ PYTHON }} setup.py sdist --formats=zip"
- {% endif %}
- - "{{ PYTHON }} -m pip install . -vv"
+ - "{{ PYTHON }} -m pip install {{ SRC_DIR }} -vv"
requirements:
host:
@@ -32,6 +28,7 @@ requirements:
- docopt {{ docopt }}
- scikit-image {{ scikit_image }}
- matplotlib {{ matplotlib }}
+ - clapp
- bob.extension
- bob.io.base
- bob.bio.base
@@ -39,6 +36,10 @@ requirements:
run:
- python
- setuptools
+ - clapp
+ - bob.extension
+ - bob.io.base
+ - bob.bio.base
- {{ pin_compatible('numpy') }}
- {{ pin_compatible('scipy') }}
- {{ pin_compatible('pillow') }}
@@ -49,14 +50,8 @@ requirements:
test:
imports:
- - {{ name }}
+ - {{ name.replace('-','_') }}
commands:
- - compare_rois.py --help
- - view_sample.py --help
- - blame.py --help
- - pytest --verbose --cov {{ name }} --cov-report term-missing --cov-report html:{{ project_dir }}/sphinx/coverage --cov-report xml:{{ project_dir }}/coverage.xml --pyargs {{ name }}
- - sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
- - sphinx-build -aEb doctest {{ project_dir }}/doc sphinx
- conda inspect linkages -p $PREFIX {{ name }} # [not win]
- conda inspect objects -p $PREFIX {{ name }} # [osx]
requires:
@@ -67,7 +62,7 @@ test:
- sphinx_rtd_theme {{ sphinx_rtd_theme }}
about:
- home: https://www.idiap.ch/software/bob/
- license: GNU General Public License v3 (GPLv3)
- summary: Vein Recognition Library
+ home: {{ data['project']['urls']['homepage'] }}
+ summary: {{ data['project']['description'] }}
+ license: {{ data['project']['license']['text'] }}
license_family: GPL
diff --git a/doc/conf.py b/doc/conf.py
index 755aff1c6ef86a0ec4c156634d6014630547b395..1faa7b5c308abbb9e27bdc4c08bbac7c084024b1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -24,6 +24,7 @@ extensions = [
"sphinx.ext.napoleon",
"sphinx.ext.viewcode",
"sphinx.ext.mathjax",
+ "auto_intersphinx",
]
# Be picky about warnings
@@ -231,23 +232,8 @@ autodoc_default_options = {
"show-inheritance": True,
}
-# For inter-documentation mapping:
-from bob.extension.utils import link_documentation, load_requirements
-
-sphinx_requirements = "extra-intersphinx.txt"
-if os.path.exists(sphinx_requirements):
- intersphinx_mapping = link_documentation(
- additional_packages=load_requirements(sphinx_requirements)
- )
-else:
- intersphinx_mapping = link_documentation()
-
-# Add scikit-image link
-skimage_version = pkg_resources.require("scikit-image")[0].version
-skimage_version = ".".join(skimage_version.split(".")[:2])
-intersphinx_mapping[
- "http://scikit-image.org/docs/%s.x" % skimage_version
-] = None
-
-# Add PIL link
-intersphinx_mapping["http://pillow.readthedocs.io/en/stable"] = None
+auto_intersphinx_packages = [
+ ("python", "3"),
+ "numpy",
+ "bob.bio.base",
+]
diff --git a/pyproject.toml b/pyproject.toml
index b738dc847ff9705c5769673db7415f2eb9a75f4d..49d3a4113c0de450df785f0f2143449ed525e9b6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,105 @@
[build-system]
- requires = ["setuptools", "wheel", "bob.extension"]
+ requires = ["setuptools>=61.0.0", "wheel"]
build-backend = "setuptools.build_meta"
+[project]
+ name = "bob.bio.vein"
+ version = "4.0.4b0"
+ requires-python = ">=3.9"
+ description = "Vein Recognition Library"
+ dynamic = ["readme"]
+ license = {text = "GPLv3 License"}
+ authors = [
+ {name = "Andre Anjos", email = "andre.anjos@idiap.ch"},
+ {name = "Pedro Tome", email = "pedro.tome@idiap.ch"},
+ ]
+ keywords = ["bob", "biometric recognition", "evaluation", "vein"]
+
+ 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",
+ ]
+ dependencies = [
+ "setuptools",
+ "numpy",
+ "scipy",
+ "pillow",
+ "schema",
+ "docopt",
+ "scikit-image",
+ "matplotlib",
+ "clapp",
+ "bob.extension",
+ "bob.io.base",
+ "bob.bio.base",
+ ]
+
+[project.urls]
+ documentation = "https://www.idiap.ch/software/bob/docs/bob/bob.bio.vein/stable/"
+ homepage = "https://pypi.org/project/bob.bio.vein/"
+ repository = "https://gitlab.idiap.ch/bob/bob.bio.vein"
+ changelog = "https://gitlab.idiap.ch/bob/bob.bio.vein/-/releases"
+
+[project.optional-dependencies]
+ qa = ["pre-commit"]
+ doc = [
+ "sphinx",
+ "sphinx_rtd_theme",
+ "sphinx-autodoc-typehints",
+ "auto-intersphinx",
+ "sphinxcontrib-programoutput",
+ ]
+ test = [
+ "pytest",
+ "pytest-cov",
+ "coverage",
+ ]
+
+[tool.setuptools]
+ zip-safe = false
+ package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+ readme = {file = "README.rst"}
+
+[project.entry-points."bob.bio.config"]
+ # protocols (must be specified before the database in the cmd)
+ # utfvp
+ nom = "bob.bio.vein.config.database.utfvp_nom"
+ full = "bob.bio.vein.config.database.utfvp_full"
+ 1vsall = "bob.bio.vein.config.database.utfvp_1vsall"
+ # legacy baselines
+ mc = "bob.bio.vein.config.maximum_curvature"
+ rlt = "bob.bio.vein.config.repeated_line_tracking"
+ wld = "bob.bio.vein.config.wide_line_detector"
+ # verafinger contactless
+ vera_nom = "bob.bio.vein.config.database.verafinger_contactless_nom"
+
+[project.entry-points."bob.bio.database"]
+ utfvp = "bob.bio.vein.config.database.utfvp_nom:database"
+ verafinger_contactless = "bob.bio.vein.config.database.verafinger_contactless_nom:database"
+
+[project.entry-points."bob.bio.pipeline"]
+ wld = "bob.bio.vein.config.wide_line_detector:pipeline"
+ mc = "bob.bio.vein.config.maximum_curvature:pipeline"
+ rlt = "bob.bio.vein.config.repeated_line_tracking:pipeline"
+
+[project.scripts]
+ bob_bio_vein_compare_rois = "bob.bio.vein.script.compare_rois:main"
+ bob_bio_vein_view_sample = "bob.bio.vein.script.view_sample:main"
+ bob_bio_vein_blame = "bob.bio.vein.script.blame:main"
+
+
+[tool.distutils.bdist_wheel]
+ universal = true
+
[tool.isort]
profile = "black"
line_length = 80
@@ -10,3 +108,15 @@
[tool.black]
line-length = 80
+
+[tool.coverage.run]
+ relative_files = true
+
+[tool.pytest.ini_options]
+ addopts = [
+ "--import-mode=append",
+ "--cov-report=term-missing",
+ "--cov=bob.bio.vein",
+ ]
+ junit_logging = "all"
+ junit_log_passing_tests = false
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index adbae3723a882edfb08d541019618ea16484920b..0000000000000000000000000000000000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-setuptools
-numpy
-scipy
-pillow
-schema
-docopt
-scikit-image
-matplotlib
-bob.extension
-bob.io.base
-bob.bio.base
diff --git a/setup.py b/setup.py
index e2a0e0da8465ea11bab98be6f7c8974ba7329259..3a3aaadbd1b7a7371f5208fe978855323b3c5291 100644
--- a/setup.py
+++ b/setup.py
@@ -1,66 +1,6 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-from setuptools import dist, setup
+from setuptools import setup
-dist.Distribution(dict(setup_requires=["bob.extension"]))
-
-from bob.extension.utils import find_packages, load_requirements
-
-install_requires = load_requirements()
-
-setup(
- name="bob.bio.vein",
- version=open("version.txt").read().rstrip(),
- description="Vein Recognition Library",
- url="https://gitlab.idiap.ch/bob/bob.bio.vein",
- license="GPLv3",
- author="Andre Anjos,Pedro Tome",
- author_email="andre.anjos@idiap.ch,pedro.tome@idiap.ch",
- keywords="bob, biometric recognition, evaluation, vein",
- long_description=open("README.rst").read(),
- packages=find_packages(),
- include_package_data=True,
- zip_safe=False,
- install_requires=install_requires,
- entry_points={
- "bob.bio.config": [
- # protocols (must be specified before the database in the cmd)
- # utfvp
- "nom = bob.bio.vein.config.database.utfvp_nom",
- "full = bob.bio.vein.config.database.utfvp_full",
- "1vsall = bob.bio.vein.config.database.utfvp_1vsall",
- # legacy baselines
- "mc = bob.bio.vein.config.maximum_curvature",
- "rlt = bob.bio.vein.config.repeated_line_tracking",
- "wld = bob.bio.vein.config.wide_line_detector",
- # verafinger contactless
- "vera_nom = bob.bio.vein.config.database.verafinger_contactless_nom",
- ],
- "bob.bio.database": [
- "utfvp = bob.bio.vein.config.database.utfvp_nom:database",
- "verafinger_contactless = bob.bio.vein.config.database.verafinger_contactless_nom:database",
- ],
- "bob.bio.pipeline": [
- "wld = bob.bio.vein.config.wide_line_detector:pipeline",
- "mc = bob.bio.vein.config.maximum_curvature:pipeline",
- "rlt = bob.bio.vein.config.repeated_line_tracking:pipeline",
- ],
- "console_scripts": [
- "bob_bio_vein_compare_rois.py = bob.bio.vein.script.compare_rois:main",
- "bob_bio_vein_view_sample.py = bob.bio.vein.script.view_sample:main",
- "bob_bio_vein_blame.py = bob.bio.vein.script.blame:main",
- ],
- },
- 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",
- ],
-)
+setup()
diff --git a/bob/__init__.py b/src/bob/__init__.py
similarity index 100%
rename from bob/__init__.py
rename to src/bob/__init__.py
diff --git a/bob/bio/__init__.py b/src/bob/bio/__init__.py
similarity index 100%
rename from bob/bio/__init__.py
rename to src/bob/bio/__init__.py
diff --git a/bob/bio/vein/__init__.py b/src/bob/bio/vein/__init__.py
similarity index 52%
rename from bob/bio/vein/__init__.py
rename to src/bob/bio/vein/__init__.py
index 4163a15ccd4b2c984a8a05a9fa760b9826d6c7c3..010965abd1aaf385776f4d48d87a73a3c8f79b64 100644
--- a/bob/bio/vein/__init__.py
+++ b/src/bob/bio/vein/__init__.py
@@ -1,15 +1,5 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# isort: skip_file
-
-
-def get_config():
- """Returns a string containing the configuration information."""
-
- import bob.extension
-
- return bob.extension.get_config(__name__)
-
-
# gets sphinx autodoc done right - don't remove it
__all__ = [_ for _ in dir() if not _.startswith("_")]
diff --git a/bob/bio/vein/algorithm/Correlate.py b/src/bob/bio/vein/algorithm/Correlate.py
similarity index 100%
rename from bob/bio/vein/algorithm/Correlate.py
rename to src/bob/bio/vein/algorithm/Correlate.py
diff --git a/bob/bio/vein/algorithm/HammingDistance.py b/src/bob/bio/vein/algorithm/HammingDistance.py
similarity index 100%
rename from bob/bio/vein/algorithm/HammingDistance.py
rename to src/bob/bio/vein/algorithm/HammingDistance.py
diff --git a/bob/bio/vein/algorithm/MiuraMatch.py b/src/bob/bio/vein/algorithm/MiuraMatch.py
similarity index 100%
rename from bob/bio/vein/algorithm/MiuraMatch.py
rename to src/bob/bio/vein/algorithm/MiuraMatch.py
diff --git a/bob/bio/vein/algorithm/__init__.py b/src/bob/bio/vein/algorithm/__init__.py
similarity index 99%
rename from bob/bio/vein/algorithm/__init__.py
rename to src/bob/bio/vein/algorithm/__init__.py
index 07c12d726e46f970662aa5ccd8976611d2315b55..603b850a9ecc49d01083715739e7aae73950de31 100644
--- a/bob/bio/vein/algorithm/__init__.py
+++ b/src/bob/bio/vein/algorithm/__init__.py
@@ -3,6 +3,7 @@ from .MiuraMatch import MiuraMatch
from .Correlate import Correlate
from .HammingDistance import HammingDistance
+
# gets sphinx autodoc done right - don't remove it
def __appropriate__(*args):
"""Says object was actually declared here, an not on the import module.
diff --git a/bob/bio/vein/config/__init__.py b/src/bob/bio/vein/config/__init__.py
similarity index 100%
rename from bob/bio/vein/config/__init__.py
rename to src/bob/bio/vein/config/__init__.py
diff --git a/bob/bio/vein/config/database/__init__.py b/src/bob/bio/vein/config/database/__init__.py
similarity index 100%
rename from bob/bio/vein/config/database/__init__.py
rename to src/bob/bio/vein/config/database/__init__.py
diff --git a/bob/bio/vein/config/database/utfvp_1vsall.py b/src/bob/bio/vein/config/database/utfvp_1vsall.py
similarity index 100%
rename from bob/bio/vein/config/database/utfvp_1vsall.py
rename to src/bob/bio/vein/config/database/utfvp_1vsall.py
diff --git a/bob/bio/vein/config/database/utfvp_full.py b/src/bob/bio/vein/config/database/utfvp_full.py
similarity index 100%
rename from bob/bio/vein/config/database/utfvp_full.py
rename to src/bob/bio/vein/config/database/utfvp_full.py
diff --git a/bob/bio/vein/config/database/utfvp_nom.py b/src/bob/bio/vein/config/database/utfvp_nom.py
similarity index 100%
rename from bob/bio/vein/config/database/utfvp_nom.py
rename to src/bob/bio/vein/config/database/utfvp_nom.py
diff --git a/bob/bio/vein/config/database/verafinger_contactless_nom.py b/src/bob/bio/vein/config/database/verafinger_contactless_nom.py
similarity index 100%
rename from bob/bio/vein/config/database/verafinger_contactless_nom.py
rename to src/bob/bio/vein/config/database/verafinger_contactless_nom.py
diff --git a/bob/bio/vein/config/maximum_curvature.py b/src/bob/bio/vein/config/maximum_curvature.py
similarity index 100%
rename from bob/bio/vein/config/maximum_curvature.py
rename to src/bob/bio/vein/config/maximum_curvature.py
diff --git a/bob/bio/vein/config/principal_curvature.py b/src/bob/bio/vein/config/principal_curvature.py
similarity index 100%
rename from bob/bio/vein/config/principal_curvature.py
rename to src/bob/bio/vein/config/principal_curvature.py
diff --git a/bob/bio/vein/config/repeated_line_tracking.py b/src/bob/bio/vein/config/repeated_line_tracking.py
similarity index 100%
rename from bob/bio/vein/config/repeated_line_tracking.py
rename to src/bob/bio/vein/config/repeated_line_tracking.py
diff --git a/bob/bio/vein/config/wide_line_detector.py b/src/bob/bio/vein/config/wide_line_detector.py
similarity index 100%
rename from bob/bio/vein/config/wide_line_detector.py
rename to src/bob/bio/vein/config/wide_line_detector.py
diff --git a/bob/bio/vein/database/__init__.py b/src/bob/bio/vein/database/__init__.py
similarity index 100%
rename from bob/bio/vein/database/__init__.py
rename to src/bob/bio/vein/database/__init__.py
diff --git a/bob/bio/vein/database/database.py b/src/bob/bio/vein/database/database.py
similarity index 100%
rename from bob/bio/vein/database/database.py
rename to src/bob/bio/vein/database/database.py
diff --git a/bob/bio/vein/database/roi_annotation.py b/src/bob/bio/vein/database/roi_annotation.py
similarity index 100%
rename from bob/bio/vein/database/roi_annotation.py
rename to src/bob/bio/vein/database/roi_annotation.py
diff --git a/bob/bio/vein/database/utfvp.py b/src/bob/bio/vein/database/utfvp.py
similarity index 99%
rename from bob/bio/vein/database/utfvp.py
rename to src/bob/bio/vein/database/utfvp.py
index aab0982ee3be82f56d2f2e04c6957db4b3ac1801..079e4188e11804cdbfd62d63982153ae89d21238 100644
--- a/bob/bio/vein/database/utfvp.py
+++ b/src/bob/bio/vein/database/utfvp.py
@@ -6,13 +6,15 @@
Utfvp database implementation
"""
+from clapp.rc import UserDefaults
from sklearn.pipeline import make_pipeline
import bob.io.base
from bob.bio.base.database import CSVDatabase, FileSampleLoader
from bob.bio.vein.database.roi_annotation import ROIAnnotation
-from bob.extension import rc
+
+rc = UserDefaults("~/.bobrc")
class UtfvpDatabase(CSVDatabase):
@@ -164,7 +166,6 @@ class UtfvpDatabase(CSVDatabase):
dataset_protocols_hash = "fe51ba85"
def __init__(self, protocol):
-
super().__init__(
name=self.name,
protocol=protocol,
diff --git a/bob/bio/vein/database/verafinger_contactless.py b/src/bob/bio/vein/database/verafinger_contactless.py
similarity index 97%
rename from bob/bio/vein/database/verafinger_contactless.py
rename to src/bob/bio/vein/database/verafinger_contactless.py
index 4c71ff66cda9e05af6738f97c26d411990f64bfc..54af332a20e722b94b8a8186cd27e76561b37d69 100644
--- a/bob/bio/vein/database/verafinger_contactless.py
+++ b/src/bob/bio/vein/database/verafinger_contactless.py
@@ -6,10 +6,13 @@
VERA-Fingervein-Contactless database implementation
"""
+from clapp.rc import UserDefaults
+
import bob.io.base
from bob.bio.base.database import CSVDatabase, FileSampleLoader
-from bob.extension import rc
+
+rc = UserDefaults("~/.bobrc")
class VerafingerContactless(CSVDatabase):
@@ -60,7 +63,6 @@ class VerafingerContactless(CSVDatabase):
dataset_protocols_hash = "656ef935"
def __init__(self, protocol):
-
super().__init__(
name=self.name,
protocol=protocol,
diff --git a/bob/bio/vein/extractor/MaximumCurvature.py b/src/bob/bio/vein/extractor/MaximumCurvature.py
similarity index 99%
rename from bob/bio/vein/extractor/MaximumCurvature.py
rename to src/bob/bio/vein/extractor/MaximumCurvature.py
index 518d5620f6102fc2bea09b79e528d56c72a30b0d..9119f7e0de0a233dd6241d0331d3fedb19e2c30d 100644
--- a/bob/bio/vein/extractor/MaximumCurvature.py
+++ b/src/bob/bio/vein/extractor/MaximumCurvature.py
@@ -472,7 +472,6 @@ class MaximumCurvature(Extractor):
plt.show()
def __call__(self, image):
-
finger_image = image[0].astype("float64")
finger_mask = image[1]
diff --git a/bob/bio/vein/extractor/NormalisedCrossCorrelation.py b/src/bob/bio/vein/extractor/NormalisedCrossCorrelation.py
similarity index 100%
rename from bob/bio/vein/extractor/NormalisedCrossCorrelation.py
rename to src/bob/bio/vein/extractor/NormalisedCrossCorrelation.py
diff --git a/bob/bio/vein/extractor/PrincipalCurvature.py b/src/bob/bio/vein/extractor/PrincipalCurvature.py
similarity index 100%
rename from bob/bio/vein/extractor/PrincipalCurvature.py
rename to src/bob/bio/vein/extractor/PrincipalCurvature.py
diff --git a/bob/bio/vein/extractor/RepeatedLineTracking.py b/src/bob/bio/vein/extractor/RepeatedLineTracking.py
similarity index 99%
rename from bob/bio/vein/extractor/RepeatedLineTracking.py
rename to src/bob/bio/vein/extractor/RepeatedLineTracking.py
index 6a9ec79752c833ba2586528ece614e4c9a841da5..dd62de036d065132124b73a6bcf57bace8a0a8e3 100644
--- a/bob/bio/vein/extractor/RepeatedLineTracking.py
+++ b/src/bob/bio/vein/extractor/RepeatedLineTracking.py
@@ -28,7 +28,6 @@ class RepeatedLineTracking(Extractor):
rescale=True,
seed=0, # Seed for the algorithm's random walk
):
-
# call base class constructor
Extractor.__init__(
self,
diff --git a/bob/bio/vein/extractor/WideLineDetector.py b/src/bob/bio/vein/extractor/WideLineDetector.py
similarity index 99%
rename from bob/bio/vein/extractor/WideLineDetector.py
rename to src/bob/bio/vein/extractor/WideLineDetector.py
index d64899ffcc42a25a9cdc5695d173658a59beeefe..8eace9a6ae0f28e72da5534c5fe6be054ec05beb 100644
--- a/bob/bio/vein/extractor/WideLineDetector.py
+++ b/src/bob/bio/vein/extractor/WideLineDetector.py
@@ -22,7 +22,6 @@ class WideLineDetector(Extractor):
g=41, # Sum of neigbourhood threshold
rescale=True,
):
-
# call base class constructor
Extractor.__init__(
self,
diff --git a/bob/bio/vein/extractor/__init__.py b/src/bob/bio/vein/extractor/__init__.py
similarity index 100%
rename from bob/bio/vein/extractor/__init__.py
rename to src/bob/bio/vein/extractor/__init__.py
diff --git a/bob/bio/vein/img_test/Vt.mat b/src/bob/bio/vein/img_test/Vt.mat
similarity index 100%
rename from bob/bio/vein/img_test/Vt.mat
rename to src/bob/bio/vein/img_test/Vt.mat
diff --git a/bob/bio/vein/img_test/Vt.mat.hdf5 b/src/bob/bio/vein/img_test/Vt.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/Vt.mat.hdf5
rename to src/bob/bio/vein/img_test/Vt.mat.hdf5
diff --git a/bob/bio/vein/img_test/bla.mat b/src/bob/bio/vein/img_test/bla.mat
similarity index 100%
rename from bob/bio/vein/img_test/bla.mat
rename to src/bob/bio/vein/img_test/bla.mat
diff --git a/bob/bio/vein/img_test/bla.mat.hdf5 b/src/bob/bio/vein/img_test/bla.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/bla.mat.hdf5
rename to src/bob/bio/vein/img_test/bla.mat.hdf5
diff --git a/bob/bio/vein/img_test/bla3.mat b/src/bob/bio/vein/img_test/bla3.mat
similarity index 100%
rename from bob/bio/vein/img_test/bla3.mat
rename to src/bob/bio/vein/img_test/bla3.mat
diff --git a/bob/bio/vein/img_test/bla3.mat.hdf5 b/src/bob/bio/vein/img_test/bla3.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/bla3.mat.hdf5
rename to src/bob/bio/vein/img_test/bla3.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr255.mat b/src/bob/bio/vein/img_test/fvr255.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr255.mat
rename to src/bob/bio/vein/img_test/fvr255.mat
diff --git a/bob/bio/vein/img_test/fvr255.mat.hdf5 b/src/bob/bio/vein/img_test/fvr255.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr255.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr255.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr_huang.mat b/src/bob/bio/vein/img_test/fvr_huang.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr_huang.mat
rename to src/bob/bio/vein/img_test/fvr_huang.mat
diff --git a/bob/bio/vein/img_test/fvr_huang.mat.hdf5 b/src/bob/bio/vein/img_test/fvr_huang.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr_huang.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr_huang.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr_mask.mat b/src/bob/bio/vein/img_test/fvr_mask.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr_mask.mat
rename to src/bob/bio/vein/img_test/fvr_mask.mat
diff --git a/bob/bio/vein/img_test/fvr_mask.mat.hdf5 b/src/bob/bio/vein/img_test/fvr_mask.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr_mask.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr_mask.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr_matlab.mat b/src/bob/bio/vein/img_test/fvr_matlab.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab.mat
rename to src/bob/bio/vein/img_test/fvr_matlab.mat
diff --git a/bob/bio/vein/img_test/fvr_matlab.mat.hdf5 b/src/bob/bio/vein/img_test/fvr_matlab.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr_matlab.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr_matlab_double_align.mat b/src/bob/bio/vein/img_test/fvr_matlab_double_align.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab_double_align.mat
rename to src/bob/bio/vein/img_test/fvr_matlab_double_align.mat
diff --git a/bob/bio/vein/img_test/fvr_matlab_double_align.mat.hdf5 b/src/bob/bio/vein/img_test/fvr_matlab_double_align.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab_double_align.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr_matlab_double_align.mat.hdf5
diff --git a/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat b/src/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat
rename to src/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat
diff --git a/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat.hdf5 b/src/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat.hdf5
rename to src/bob/bio/vein/img_test/fvr_matlab_double_align_reduced.mat.hdf5
diff --git a/bob/bio/vein/img_test/image.mat b/src/bob/bio/vein/img_test/image.mat
similarity index 100%
rename from bob/bio/vein/img_test/image.mat
rename to src/bob/bio/vein/img_test/image.mat
diff --git a/bob/bio/vein/img_test/image.mat.hdf5 b/src/bob/bio/vein/img_test/image.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/image.mat.hdf5
rename to src/bob/bio/vein/img_test/image.mat.hdf5
diff --git a/bob/bio/vein/img_test/img.mat b/src/bob/bio/vein/img_test/img.mat
similarity index 100%
rename from bob/bio/vein/img_test/img.mat
rename to src/bob/bio/vein/img_test/img.mat
diff --git a/bob/bio/vein/img_test/img.mat.hdf5 b/src/bob/bio/vein/img_test/img.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img.mat.hdf5
rename to src/bob/bio/vein/img_test/img.mat.hdf5
diff --git a/bob/bio/vein/img_test/imgUTFVP.mat b/src/bob/bio/vein/img_test/imgUTFVP.mat
similarity index 100%
rename from bob/bio/vein/img_test/imgUTFVP.mat
rename to src/bob/bio/vein/img_test/imgUTFVP.mat
diff --git a/bob/bio/vein/img_test/imgUTFVP.mat.hdf5 b/src/bob/bio/vein/img_test/imgUTFVP.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/imgUTFVP.mat.hdf5
rename to src/bob/bio/vein/img_test/imgUTFVP.mat.hdf5
diff --git a/bob/bio/vein/img_test/imgUTFVPdouble.mat b/src/bob/bio/vein/img_test/imgUTFVPdouble.mat
similarity index 100%
rename from bob/bio/vein/img_test/imgUTFVPdouble.mat
rename to src/bob/bio/vein/img_test/imgUTFVPdouble.mat
diff --git a/bob/bio/vein/img_test/imgUTFVPdouble.mat.hdf5 b/src/bob/bio/vein/img_test/imgUTFVPdouble.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/imgUTFVPdouble.mat.hdf5
rename to src/bob/bio/vein/img_test/imgUTFVPdouble.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_001_L_1.mat b/src/bob/bio/vein/img_test/img_001_L_1.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_001_L_1.mat
rename to src/bob/bio/vein/img_test/img_001_L_1.mat
diff --git a/bob/bio/vein/img_test/img_001_L_1.mat.hdf5 b/src/bob/bio/vein/img_test/img_001_L_1.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_001_L_1.mat.hdf5
rename to src/bob/bio/vein/img_test/img_001_L_1.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_001_L_2.mat b/src/bob/bio/vein/img_test/img_001_L_2.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_001_L_2.mat
rename to src/bob/bio/vein/img_test/img_001_L_2.mat
diff --git a/bob/bio/vein/img_test/img_001_L_2.mat.hdf5 b/src/bob/bio/vein/img_test/img_001_L_2.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_001_L_2.mat.hdf5
rename to src/bob/bio/vein/img_test/img_001_L_2.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_huang.mat b/src/bob/bio/vein/img_test/img_huang.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_huang.mat
rename to src/bob/bio/vein/img_test/img_huang.mat
diff --git a/bob/bio/vein/img_test/img_huang.mat.hdf5 b/src/bob/bio/vein/img_test/img_huang.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_huang.mat.hdf5
rename to src/bob/bio/vein/img_test/img_huang.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_matlab.mat b/src/bob/bio/vein/img_test/img_matlab.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab.mat
rename to src/bob/bio/vein/img_test/img_matlab.mat
diff --git a/bob/bio/vein/img_test/img_matlab.mat.hdf5 b/src/bob/bio/vein/img_test/img_matlab.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab.mat.hdf5
rename to src/bob/bio/vein/img_test/img_matlab.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_matlab_double_align.mat b/src/bob/bio/vein/img_test/img_matlab_double_align.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_double_align.mat
rename to src/bob/bio/vein/img_test/img_matlab_double_align.mat
diff --git a/bob/bio/vein/img_test/img_matlab_double_align.mat.hdf5 b/src/bob/bio/vein/img_test/img_matlab_double_align.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_double_align.mat.hdf5
rename to src/bob/bio/vein/img_test/img_matlab_double_align.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat b/src/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_double_align_reduced.mat
rename to src/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat
diff --git a/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat.hdf5 b/src/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_double_align_reduced.mat.hdf5
rename to src/bob/bio/vein/img_test/img_matlab_double_align_reduced.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_matlab_uint8.mat b/src/bob/bio/vein/img_test/img_matlab_uint8.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_uint8.mat
rename to src/bob/bio/vein/img_test/img_matlab_uint8.mat
diff --git a/bob/bio/vein/img_test/img_matlab_uint8.mat.hdf5 b/src/bob/bio/vein/img_test/img_matlab_uint8.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_matlab_uint8.mat.hdf5
rename to src/bob/bio/vein/img_test/img_matlab_uint8.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_o.mat b/src/bob/bio/vein/img_test/img_o.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_o.mat
rename to src/bob/bio/vein/img_test/img_o.mat
diff --git a/bob/bio/vein/img_test/img_o.mat.hdf5 b/src/bob/bio/vein/img_test/img_o.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_o.mat.hdf5
rename to src/bob/bio/vein/img_test/img_o.mat.hdf5
diff --git a/bob/bio/vein/img_test/img_ouint8.mat b/src/bob/bio/vein/img_test/img_ouint8.mat
similarity index 100%
rename from bob/bio/vein/img_test/img_ouint8.mat
rename to src/bob/bio/vein/img_test/img_ouint8.mat
diff --git a/bob/bio/vein/img_test/img_ouint8.mat.hdf5 b/src/bob/bio/vein/img_test/img_ouint8.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/img_ouint8.mat.hdf5
rename to src/bob/bio/vein/img_test/img_ouint8.mat.hdf5
diff --git a/bob/bio/vein/img_test/k.mat b/src/bob/bio/vein/img_test/k.mat
similarity index 100%
rename from bob/bio/vein/img_test/k.mat
rename to src/bob/bio/vein/img_test/k.mat
diff --git a/bob/bio/vein/img_test/k.mat.hdf5 b/src/bob/bio/vein/img_test/k.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/k.mat.hdf5
rename to src/bob/bio/vein/img_test/k.mat.hdf5
diff --git a/bob/bio/vein/img_test/k1.mat b/src/bob/bio/vein/img_test/k1.mat
similarity index 100%
rename from bob/bio/vein/img_test/k1.mat
rename to src/bob/bio/vein/img_test/k1.mat
diff --git a/bob/bio/vein/img_test/k1.mat.hdf5 b/src/bob/bio/vein/img_test/k1.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/k1.mat.hdf5
rename to src/bob/bio/vein/img_test/k1.mat.hdf5
diff --git a/bob/bio/vein/img_test/k2.mat b/src/bob/bio/vein/img_test/k2.mat
similarity index 100%
rename from bob/bio/vein/img_test/k2.mat
rename to src/bob/bio/vein/img_test/k2.mat
diff --git a/bob/bio/vein/img_test/k2.mat.hdf5 b/src/bob/bio/vein/img_test/k2.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/k2.mat.hdf5
rename to src/bob/bio/vein/img_test/k2.mat.hdf5
diff --git a/bob/bio/vein/img_test/mask_001_L_1.mat b/src/bob/bio/vein/img_test/mask_001_L_1.mat
similarity index 100%
rename from bob/bio/vein/img_test/mask_001_L_1.mat
rename to src/bob/bio/vein/img_test/mask_001_L_1.mat
diff --git a/bob/bio/vein/img_test/mask_001_L_1.mat.hdf5 b/src/bob/bio/vein/img_test/mask_001_L_1.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/mask_001_L_1.mat.hdf5
rename to src/bob/bio/vein/img_test/mask_001_L_1.mat.hdf5
diff --git a/bob/bio/vein/img_test/mask_001_L_2.mat b/src/bob/bio/vein/img_test/mask_001_L_2.mat
similarity index 100%
rename from bob/bio/vein/img_test/mask_001_L_2.mat
rename to src/bob/bio/vein/img_test/mask_001_L_2.mat
diff --git a/bob/bio/vein/img_test/mask_001_L_2.mat.hdf5 b/src/bob/bio/vein/img_test/mask_001_L_2.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/mask_001_L_2.mat.hdf5
rename to src/bob/bio/vein/img_test/mask_001_L_2.mat.hdf5
diff --git a/bob/bio/vein/img_test/template_001_L_1.mat b/src/bob/bio/vein/img_test/template_001_L_1.mat
similarity index 100%
rename from bob/bio/vein/img_test/template_001_L_1.mat
rename to src/bob/bio/vein/img_test/template_001_L_1.mat
diff --git a/bob/bio/vein/img_test/template_001_L_1.mat.hdf5 b/src/bob/bio/vein/img_test/template_001_L_1.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/template_001_L_1.mat.hdf5
rename to src/bob/bio/vein/img_test/template_001_L_1.mat.hdf5
diff --git a/bob/bio/vein/img_test/template_001_L_2.mat b/src/bob/bio/vein/img_test/template_001_L_2.mat
similarity index 100%
rename from bob/bio/vein/img_test/template_001_L_2.mat
rename to src/bob/bio/vein/img_test/template_001_L_2.mat
diff --git a/bob/bio/vein/img_test/template_001_L_2.mat.hdf5 b/src/bob/bio/vein/img_test/template_001_L_2.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/template_001_L_2.mat.hdf5
rename to src/bob/bio/vein/img_test/template_001_L_2.mat.hdf5
diff --git a/bob/bio/vein/img_test/test_fvr.mat b/src/bob/bio/vein/img_test/test_fvr.mat
similarity index 100%
rename from bob/bio/vein/img_test/test_fvr.mat
rename to src/bob/bio/vein/img_test/test_fvr.mat
diff --git a/bob/bio/vein/img_test/test_fvr.mat.hdf5 b/src/bob/bio/vein/img_test/test_fvr.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/test_fvr.mat.hdf5
rename to src/bob/bio/vein/img_test/test_fvr.mat.hdf5
diff --git a/bob/bio/vein/img_test/test_img.mat b/src/bob/bio/vein/img_test/test_img.mat
similarity index 100%
rename from bob/bio/vein/img_test/test_img.mat
rename to src/bob/bio/vein/img_test/test_img.mat
diff --git a/bob/bio/vein/img_test/test_img.mat.hdf5 b/src/bob/bio/vein/img_test/test_img.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/test_img.mat.hdf5
rename to src/bob/bio/vein/img_test/test_img.mat.hdf5
diff --git a/bob/bio/vein/img_test/veins.mat b/src/bob/bio/vein/img_test/veins.mat
similarity index 100%
rename from bob/bio/vein/img_test/veins.mat
rename to src/bob/bio/vein/img_test/veins.mat
diff --git a/bob/bio/vein/img_test/veins.mat.hdf5 b/src/bob/bio/vein/img_test/veins.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/veins.mat.hdf5
rename to src/bob/bio/vein/img_test/veins.mat.hdf5
diff --git a/bob/bio/vein/img_test/xs.mat b/src/bob/bio/vein/img_test/xs.mat
similarity index 100%
rename from bob/bio/vein/img_test/xs.mat
rename to src/bob/bio/vein/img_test/xs.mat
diff --git a/bob/bio/vein/img_test/xs.mat.hdf5 b/src/bob/bio/vein/img_test/xs.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/xs.mat.hdf5
rename to src/bob/bio/vein/img_test/xs.mat.hdf5
diff --git a/bob/bio/vein/img_test/ys.mat b/src/bob/bio/vein/img_test/ys.mat
similarity index 100%
rename from bob/bio/vein/img_test/ys.mat
rename to src/bob/bio/vein/img_test/ys.mat
diff --git a/bob/bio/vein/img_test/ys.mat.hdf5 b/src/bob/bio/vein/img_test/ys.mat.hdf5
similarity index 100%
rename from bob/bio/vein/img_test/ys.mat.hdf5
rename to src/bob/bio/vein/img_test/ys.mat.hdf5
diff --git a/bob/bio/vein/preprocessor/__init__.py b/src/bob/bio/vein/preprocessor/__init__.py
similarity index 99%
rename from bob/bio/vein/preprocessor/__init__.py
rename to src/bob/bio/vein/preprocessor/__init__.py
index 51771f946176a8d461e9b5dde7f04eec846c3a81..c5e182e857c267b341f813302003490955f56321 100644
--- a/bob/bio/vein/preprocessor/__init__.py
+++ b/src/bob/bio/vein/preprocessor/__init__.py
@@ -6,6 +6,7 @@ from .normalize import Normalizer, NoNormalization, HuangNormalization
from .filters import Filter, NoFilter, HistogramEqualization
from .preprocessor import Preprocessor
+
# gets sphinx autodoc done right - don't remove it
def __appropriate__(*args):
"""Says object was actually declared here, an not on the import module.
diff --git a/bob/bio/vein/preprocessor/crop.py b/src/bob/bio/vein/preprocessor/crop.py
similarity index 100%
rename from bob/bio/vein/preprocessor/crop.py
rename to src/bob/bio/vein/preprocessor/crop.py
diff --git a/bob/bio/vein/preprocessor/filters.py b/src/bob/bio/vein/preprocessor/filters.py
similarity index 100%
rename from bob/bio/vein/preprocessor/filters.py
rename to src/bob/bio/vein/preprocessor/filters.py
diff --git a/bob/bio/vein/preprocessor/mask.py b/src/bob/bio/vein/preprocessor/mask.py
similarity index 99%
rename from bob/bio/vein/preprocessor/mask.py
rename to src/bob/bio/vein/preprocessor/mask.py
index 3e146fbd7f1487fc138075f337f152bef4b0e6e3..88e5ecd0b8eacef38d1447e5d9e28bec86c996ad 100644
--- a/bob/bio/vein/preprocessor/mask.py
+++ b/src/bob/bio/vein/preprocessor/mask.py
@@ -32,7 +32,6 @@ class Padder(object):
"""
def __init__(self, padding_width=5, padding_constant=51):
-
self.padding_width = padding_width
self.padding_constant = padding_constant
@@ -211,7 +210,6 @@ class KonoMask(Masker):
"""
def __init__(self, sigma=5, padder=Padder()):
-
self.sigma = sigma
self.padder = padder
diff --git a/bob/bio/vein/preprocessor/normalize.py b/src/bob/bio/vein/preprocessor/normalize.py
similarity index 100%
rename from bob/bio/vein/preprocessor/normalize.py
rename to src/bob/bio/vein/preprocessor/normalize.py
diff --git a/bob/bio/vein/preprocessor/preprocessor.py b/src/bob/bio/vein/preprocessor/preprocessor.py
similarity index 99%
rename from bob/bio/vein/preprocessor/preprocessor.py
rename to src/bob/bio/vein/preprocessor/preprocessor.py
index 724c6432c94b868df9ffe4aa6ff1ca431962b7f7..2b45b3dcd19aaa893b422e83b59402fafe0adb0f 100644
--- a/bob/bio/vein/preprocessor/preprocessor.py
+++ b/src/bob/bio/vein/preprocessor/preprocessor.py
@@ -40,14 +40,13 @@ class Preprocessor(BasePreprocessor):
"""
def __init__(self, crop, mask, normalize, filter, **kwargs):
-
BasePreprocessor.__init__(
self,
crop=crop,
mask=mask,
normalize=normalize,
filter=filter,
- **kwargs
+ **kwargs,
)
self.crop = crop
diff --git a/bob/bio/vein/preprocessor/utils.py b/src/bob/bio/vein/preprocessor/utils.py
similarity index 100%
rename from bob/bio/vein/preprocessor/utils.py
rename to src/bob/bio/vein/preprocessor/utils.py
diff --git a/bob/bio/vein/script/__init__.py b/src/bob/bio/vein/script/__init__.py
similarity index 100%
rename from bob/bio/vein/script/__init__.py
rename to src/bob/bio/vein/script/__init__.py
diff --git a/bob/bio/vein/script/blame.py b/src/bob/bio/vein/script/blame.py
similarity index 96%
rename from bob/bio/vein/script/blame.py
rename to src/bob/bio/vein/script/blame.py
index eb2cfde6dde14843797548538fb5f11e2234ddeb..bda0e923331dce1050ec2ad119374b8a6a0fa9a7 100644
--- a/bob/bio/vein/script/blame.py
+++ b/src/bob/bio/vein/script/blame.py
@@ -37,15 +37,13 @@ Examples:
import os
import sys
+import clapp.logging
import numpy
-import bob.extension.log
-
-logger = bob.extension.log.setup("bob.bio.vein")
+logger = clapp.logging.setup("bob.bio.vein")
def main(user_input=None):
-
if user_input is not None:
argv = user_input
else:
@@ -67,7 +65,7 @@ def main(user_input=None):
# Sets-up logging
verbosity = int(args["--verbose"])
- bob.extension.log.set_verbosity_level(logger, verbosity)
+ clapp.logging.set_verbosity_level(logger, verbosity)
# validates number of cases
cases = int(args["--cases"])
diff --git a/bob/bio/vein/script/compare_rois.py b/src/bob/bio/vein/script/compare_rois.py
similarity index 97%
rename from bob/bio/vein/script/compare_rois.py
rename to src/bob/bio/vein/script/compare_rois.py
index 7eb79816774ba10d9e6774221e5c4f75cb71e4aa..07f63e0bc293a178d81ef1e4610e3727cfdf8d0d 100644
--- a/bob/bio/vein/script/compare_rois.py
+++ b/src/bob/bio/vein/script/compare_rois.py
@@ -48,14 +48,11 @@ import operator
import os
import sys
+import clapp.logging
import h5py
import numpy
-import bob.extension.log
-
-logger = bob.extension.log.setup("bob.bio.vein")
-
-import bob.io.base
+logger = clapp.logging.setup("bob.bio.vein")
def make_catalog(d):
@@ -139,7 +136,6 @@ def mean_std_for_column(table, column):
def main(user_input=None):
-
if user_input is not None:
argv = user_input
else:
@@ -161,7 +157,7 @@ def main(user_input=None):
# Sets-up logging
verbosity = int(args["--verbose"])
- bob.extension.log.set_verbosity_level(logger, verbosity)
+ clapp.logging.set_verbosity_level(logger, verbosity)
# Catalogs
gt = make_catalog(args["<ground-truth>"])
diff --git a/bob/bio/vein/script/validate.py b/src/bob/bio/vein/script/validate.py
similarity index 95%
rename from bob/bio/vein/script/validate.py
rename to src/bob/bio/vein/script/validate.py
index 655f4e98dbd94f59a986c2f2bd52e640813ea4cd..937418e90f9aec47fd48f51de55b1dc10fe9b7ed 100644
--- a/bob/bio/vein/script/validate.py
+++ b/src/bob/bio/vein/script/validate.py
@@ -36,9 +36,9 @@ def setup_logger(name, level):
"""
- import bob.extension.log
+ import clapp.logging
- logger = bob.extension.log.setup(name)
+ logger = clapp.logging.setup(name)
if not (0 <= level < 4):
raise schema.SchemaError(
@@ -46,7 +46,7 @@ def setup_logger(name, level):
)
# Sets-up logging
- bob.extension.log.set_verbosity_level(logger, level)
+ clapp.logging.set_verbosity_level(logger, level)
return logger
diff --git a/bob/bio/vein/script/view_sample.py b/src/bob/bio/vein/script/view_sample.py
similarity index 98%
rename from bob/bio/vein/script/view_sample.py
rename to src/bob/bio/vein/script/view_sample.py
index 24511e3ec1664624d51fa59a73c63b46bc94ef62..9bc5041161ed9d133184d0f0fd175462b14ed9e6 100644
--- a/bob/bio/vein/script/view_sample.py
+++ b/src/bob/bio/vein/script/view_sample.py
@@ -46,14 +46,13 @@ Examples:
import os
import sys
+import clapp.logging
import docopt
import h5py
import numpy
import schema
-import bob.extension.log
-
-logger = bob.extension.log.setup("bob.bio.vein")
+logger = clapp.logging.setup("bob.bio.vein")
import matplotlib.pyplot as mpl
@@ -198,7 +197,6 @@ def validate(args):
def main(user_input=None):
-
if user_input is not None:
argv = user_input
else:
diff --git a/test-requirements.txt b/test-requirements.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/bob/bio/vein/tests/__init__.py b/tests/__init__.py
similarity index 100%
rename from bob/bio/vein/tests/__init__.py
rename to tests/__init__.py
diff --git a/bob/bio/vein/tests/algorithms/0001_2_1_120509-135338.mat b/tests/algorithms/0001_2_1_120509-135338.mat
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0001_2_1_120509-135338.mat
rename to tests/algorithms/0001_2_1_120509-135338.mat
diff --git a/bob/bio/vein/tests/algorithms/0001_2_1_120509-135338.mat.hdf5 b/tests/algorithms/0001_2_1_120509-135338.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0001_2_1_120509-135338.mat.hdf5
rename to tests/algorithms/0001_2_1_120509-135338.mat.hdf5
diff --git a/bob/bio/vein/tests/algorithms/0001_2_2_120509-135558.mat b/tests/algorithms/0001_2_2_120509-135558.mat
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0001_2_2_120509-135558.mat
rename to tests/algorithms/0001_2_2_120509-135558.mat
diff --git a/bob/bio/vein/tests/algorithms/0001_2_2_120509-135558.mat.hdf5 b/tests/algorithms/0001_2_2_120509-135558.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0001_2_2_120509-135558.mat.hdf5
rename to tests/algorithms/0001_2_2_120509-135558.mat.hdf5
diff --git a/bob/bio/vein/tests/algorithms/0003_2_1_120509-141255.mat b/tests/algorithms/0003_2_1_120509-141255.mat
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0003_2_1_120509-141255.mat
rename to tests/algorithms/0003_2_1_120509-141255.mat
diff --git a/bob/bio/vein/tests/algorithms/0003_2_1_120509-141255.mat.hdf5 b/tests/algorithms/0003_2_1_120509-141255.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/algorithms/0003_2_1_120509-141255.mat.hdf5
rename to tests/algorithms/0003_2_1_120509-141255.mat.hdf5
diff --git a/bob/bio/vein/tests/algorithms/001_L_1.mat b/tests/algorithms/001_L_1.mat
similarity index 100%
rename from bob/bio/vein/tests/algorithms/001_L_1.mat
rename to tests/algorithms/001_L_1.mat
diff --git a/bob/bio/vein/tests/algorithms/001_L_1.mat.hdf5 b/tests/algorithms/001_L_1.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/algorithms/001_L_1.mat.hdf5
rename to tests/algorithms/001_L_1.mat.hdf5
diff --git a/bob/bio/vein/tests/algorithms/001_L_1_h4w40.mat b/tests/algorithms/001_L_1_h4w40.mat
similarity index 100%
rename from bob/bio/vein/tests/algorithms/001_L_1_h4w40.mat
rename to tests/algorithms/001_L_1_h4w40.mat
diff --git a/bob/bio/vein/tests/algorithms/001_L_1_h4w40.mat.hdf5 b/tests/algorithms/001_L_1_h4w40.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/algorithms/001_L_1_h4w40.mat.hdf5
rename to tests/algorithms/001_L_1_h4w40.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/huangwl_input_fvr.mat b/tests/extractors/huangwl_input_fvr.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_input_fvr.mat
rename to tests/extractors/huangwl_input_fvr.mat
diff --git a/bob/bio/vein/tests/extractors/huangwl_input_fvr.mat.hdf5 b/tests/extractors/huangwl_input_fvr.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_input_fvr.mat.hdf5
rename to tests/extractors/huangwl_input_fvr.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/huangwl_input_img.mat b/tests/extractors/huangwl_input_img.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_input_img.mat
rename to tests/extractors/huangwl_input_img.mat
diff --git a/bob/bio/vein/tests/extractors/huangwl_input_img.mat.hdf5 b/tests/extractors/huangwl_input_img.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_input_img.mat.hdf5
rename to tests/extractors/huangwl_input_img.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/huangwl_output.mat b/tests/extractors/huangwl_output.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_output.mat
rename to tests/extractors/huangwl_output.mat
diff --git a/bob/bio/vein/tests/extractors/huangwl_output.mat.hdf5 b/tests/extractors/huangwl_output.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/huangwl_output.mat.hdf5
rename to tests/extractors/huangwl_output.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/image.hdf5 b/tests/extractors/image.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/image.hdf5
rename to tests/extractors/image.hdf5
diff --git a/bob/bio/vein/tests/extractors/mask.hdf5 b/tests/extractors/mask.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/mask.hdf5
rename to tests/extractors/mask.hdf5
diff --git a/bob/bio/vein/tests/extractors/mc_bin_matlab.hdf5 b/tests/extractors/mc_bin_matlab.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/mc_bin_matlab.hdf5
rename to tests/extractors/mc_bin_matlab.hdf5
diff --git a/bob/bio/vein/tests/extractors/mc_g_matlab.hdf5 b/tests/extractors/mc_g_matlab.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/mc_g_matlab.hdf5
rename to tests/extractors/mc_g_matlab.hdf5
diff --git a/bob/bio/vein/tests/extractors/mc_vt_matlab.hdf5 b/tests/extractors/mc_vt_matlab.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/mc_vt_matlab.hdf5
rename to tests/extractors/mc_vt_matlab.hdf5
diff --git a/bob/bio/vein/tests/extractors/miurarlt_input_fvr.mat b/tests/extractors/miurarlt_input_fvr.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_input_fvr.mat
rename to tests/extractors/miurarlt_input_fvr.mat
diff --git a/bob/bio/vein/tests/extractors/miurarlt_input_fvr.mat.hdf5 b/tests/extractors/miurarlt_input_fvr.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_input_fvr.mat.hdf5
rename to tests/extractors/miurarlt_input_fvr.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/miurarlt_input_img.mat b/tests/extractors/miurarlt_input_img.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_input_img.mat
rename to tests/extractors/miurarlt_input_img.mat
diff --git a/bob/bio/vein/tests/extractors/miurarlt_input_img.mat.hdf5 b/tests/extractors/miurarlt_input_img.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_input_img.mat.hdf5
rename to tests/extractors/miurarlt_input_img.mat.hdf5
diff --git a/bob/bio/vein/tests/extractors/miurarlt_output.mat b/tests/extractors/miurarlt_output.mat
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_output.mat
rename to tests/extractors/miurarlt_output.mat
diff --git a/bob/bio/vein/tests/extractors/miurarlt_output.mat.hdf5 b/tests/extractors/miurarlt_output.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/extractors/miurarlt_output.mat.hdf5
rename to tests/extractors/miurarlt_output.mat.hdf5
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517.png b/tests/preprocessors/0019_3_1_120509-160517.png
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517.png
rename to tests/preprocessors/0019_3_1_120509-160517.png
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517.txt b/tests/preprocessors/0019_3_1_120509-160517.txt
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517.txt
rename to tests/preprocessors/0019_3_1_120509-160517.txt
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat b/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat
rename to tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat.hdf5 b/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat.hdf5
rename to tests/preprocessors/0019_3_1_120509-160517_fvr_lee_huang.mat.hdf5
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat b/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat
rename to tests/preprocessors/0019_3_1_120509-160517_img_lee.mat
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat.hdf5 b/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee.mat.hdf5
rename to tests/preprocessors/0019_3_1_120509-160517_img_lee.mat.hdf5
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat b/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat
rename to tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat
diff --git a/bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat.hdf5 b/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat.hdf5
similarity index 100%
rename from bob/bio/vein/tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat.hdf5
rename to tests/preprocessors/0019_3_1_120509-160517_img_lee_huang.mat.hdf5
diff --git a/bob/bio/vein/tests/test_databases.py b/tests/test_databases.py
similarity index 100%
rename from bob/bio/vein/tests/test_databases.py
rename to tests/test_databases.py
diff --git a/bob/bio/vein/tests/test_tools.py b/tests/test_tools.py
similarity index 94%
rename from bob/bio/vein/tests/test_tools.py
rename to tests/test_tools.py
index c8e045e3a032314ca809f4281393bebb991c0ffa..9d5be0447ea63599df47ae47cc4c059dd025bc17 100644
--- a/bob/bio/vein/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -20,7 +20,7 @@ import pkg_resources
import bob.io.base
-from ..preprocessor import utils as preprocessor_utils
+from bob.bio.vein.preprocessor import utils as preprocessor_utils
def F(parts):
@@ -30,10 +30,9 @@ def F(parts):
def test_cropping():
-
# tests if the cropping stage at preprocessors works as planned
- from ..preprocessor.crop import FixedCrop, NoCrop
+ from bob.bio.vein.preprocessor.crop import FixedCrop, NoCrop
shape = (20, 17)
test_image = numpy.random.randint(0, 1000, size=shape, dtype=int)
@@ -56,7 +55,7 @@ def test_cropping():
assert (test_image[top:-bottom, left:-right] - cropped).sum() == 0
# tests metadata survives after cropping (and it is corrected)
- from ..database import AnnotatedArray
+ from bob.bio.vein.database import AnnotatedArray
annotations = [
(top - 2, left + 2), # slightly above and to the right
@@ -80,11 +79,14 @@ def test_cropping():
def test_masking():
-
# tests if the masking stage at preprocessors work as planned
- from ..database import AnnotatedArray
- from ..preprocessor.mask import AnnotatedRoIMask, FixedMask, NoMask
+ from bob.bio.vein.database import AnnotatedArray
+ from bob.bio.vein.preprocessor.mask import (
+ AnnotatedRoIMask,
+ FixedMask,
+ NoMask,
+ )
shape = (17, 20)
test_image = numpy.random.randint(0, 1000, size=shape, dtype=int)
@@ -128,7 +130,6 @@ def test_masking():
def test_preprocessor():
-
# tests the whole preprocessing mechanism, compares to matlab source
input_filename = F(("preprocessors", "0019_3_1_120509-160517.png"))
@@ -141,7 +142,7 @@ def test_preprocessor():
img = bob.io.base.load(input_filename)
- from ..preprocessor import (
+ from bob.bio.vein.preprocessor import (
HuangNormalization,
LeeMask,
NoCrop,
@@ -171,7 +172,6 @@ def test_preprocessor():
def test_max_curvature():
-
# Maximum Curvature method against Matlab reference
image = bob.io.base.load(F(("extractors", "image.hdf5")))
@@ -194,7 +194,7 @@ def test_max_curvature():
bin_ref = bin_ref.T
# Apply Python implementation
- from ..extractor.MaximumCurvature import MaximumCurvature
+ from bob.bio.vein.extractor.MaximumCurvature import MaximumCurvature
MC = MaximumCurvature(3) # value used to create references
@@ -228,7 +228,7 @@ def test_max_curvature_HE():
input_img = bob.io.base.load(input_img_filename)
# Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in maximum_curvature.py configuration file + postprocessing)
- from ..preprocessor import (
+ from bob.bio.vein.preprocessor import (
HistogramEqualization,
HuangNormalization,
LeeMask,
@@ -245,7 +245,7 @@ def test_max_curvature_HE():
preproc_data = processor(input_img)
# Extract features from preprocessed and histogram equalized data using MC extractor (same parameters as in maximum_curvature.py configuration file)
- from ..extractor.MaximumCurvature import MaximumCurvature
+ from bob.bio.vein.extractor.MaximumCurvature import MaximumCurvature
MC = MaximumCurvature(sigma=5)
MC(preproc_data)
@@ -253,7 +253,6 @@ def test_max_curvature_HE():
def test_repeated_line_tracking():
-
# Repeated Line Tracking method against Matlab reference
input_img_filename = F(("extractors", "miurarlt_input_img.mat.hdf5"))
@@ -265,7 +264,7 @@ def test_repeated_line_tracking():
input_fvr = bob.io.base.load(input_fvr_filename)
# Apply Python implementation
- from ..extractor.RepeatedLineTracking import RepeatedLineTracking
+ from bob.bio.vein.extractor.RepeatedLineTracking import RepeatedLineTracking
RLT = RepeatedLineTracking(3000, 1, 21, False)
output_img = RLT((input_img, input_fvr))
@@ -286,7 +285,7 @@ def test_repeated_line_tracking_HE():
input_img = bob.io.base.load(input_img_filename)
# Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in repeated_line_tracking.py configuration file + postprocessing)
- from ..preprocessor import (
+ from bob.bio.vein.preprocessor import (
HistogramEqualization,
HuangNormalization,
LeeMask,
@@ -303,7 +302,7 @@ def test_repeated_line_tracking_HE():
preproc_data = processor(input_img)
# Extract features from preprocessed and histogram equalized data using RLT extractor (same parameters as in repeated_line_tracking.py configuration file)
- from ..extractor.RepeatedLineTracking import RepeatedLineTracking
+ from bob.bio.vein.extractor.RepeatedLineTracking import RepeatedLineTracking
# Maximum number of iterations
NUMBER_ITERATIONS = 3000
@@ -321,7 +320,6 @@ def test_repeated_line_tracking_HE():
def test_wide_line_detector():
-
# Wide Line Detector method against Matlab reference
input_img_filename = F(("extractors", "huangwl_input_img.mat.hdf5"))
@@ -333,7 +331,7 @@ def test_wide_line_detector():
input_fvr = bob.io.base.load(input_fvr_filename)
# Apply Python implementation
- from ..extractor.WideLineDetector import WideLineDetector
+ from bob.bio.vein.extractor.WideLineDetector import WideLineDetector
WL = WideLineDetector(5, 1, 41, False)
output_img = WL((input_img, input_fvr))
@@ -353,7 +351,7 @@ def test_wide_line_detector_HE():
input_img = bob.io.base.load(input_img_filename)
# Preprocess the data and apply Histogram Equalization postprocessing (same parameters as in wide_line_detector.py configuration file + postprocessing)
- from ..preprocessor import (
+ from bob.bio.vein.preprocessor import (
HistogramEqualization,
HuangNormalization,
LeeMask,
@@ -370,7 +368,7 @@ def test_wide_line_detector_HE():
preproc_data = processor(input_img)
# Extract features from preprocessed and histogram equalized data using WLD extractor (same parameters as in wide_line_detector.py configuration file)
- from ..extractor.WideLineDetector import WideLineDetector
+ from bob.bio.vein.extractor.WideLineDetector import WideLineDetector
# Radius of the circular neighbourhood region
RADIUS_NEIGHBOURHOOD_REGION = 5
@@ -388,7 +386,6 @@ def test_wide_line_detector_HE():
def test_miura_match():
-
# Match Ratio method against Matlab reference
template_filename = F(("algorithms", "0001_2_1_120509-135338.mat.hdf5"))
@@ -399,7 +396,7 @@ def test_miura_match():
probe_gen_vein = bob.io.base.load(probe_gen_filename)
probe_imp_vein = bob.io.base.load(probe_imp_filename)
- from ..algorithm.MiuraMatch import MiuraMatch
+ from bob.bio.vein.algorithm.MiuraMatch import MiuraMatch
MM = MiuraMatch(ch=18, cw=28)
score_gen = MM.score(template_vein, probe_gen_vein)
@@ -411,7 +408,6 @@ def test_miura_match():
def test_correlate():
-
# Match Ratio method against Matlab reference
template_filename = F(("algorithms", "0001_2_1_120509-135338.mat.hdf5"))
@@ -422,7 +418,7 @@ def test_correlate():
probe_gen_vein = bob.io.base.load(probe_gen_filename)
# probe_imp_vein = bob.io.base.load(probe_imp_filename)
- from ..algorithm.Correlate import Correlate
+ from bob.bio.vein.algorithm.Correlate import Correlate
C = Correlate()
C.score(template_vein, probe_gen_vein)
@@ -431,7 +427,6 @@ def test_correlate():
def test_assert_points():
-
# Tests that point assertion works as expected
area = (10, 5)
inside = [(0, 0), (3, 2), (9, 4)]
@@ -454,7 +449,6 @@ def test_assert_points():
def test_fix_points():
-
# Tests that point clipping works as expected
area = (10, 5)
inside = [(0, 0), (3, 2), (9, 4)]
@@ -478,7 +472,6 @@ def test_fix_points():
def test_poly_to_mask():
-
# Tests we can generate a mask out of a polygon correctly
area = (10, 9) # 10 rows, 9 columns
polygon = [(2, 2), (2, 7), (7, 7), (7, 2)] # square shape, (y, x) format
@@ -525,7 +518,6 @@ def test_poly_to_mask():
def test_mask_to_image():
-
# Tests we can correctly convert a boolean array into an image
# that makes sense according to the data types
sample = numpy.array([False, True])
@@ -560,7 +552,6 @@ def test_mask_to_image():
def test_jaccard_index():
-
# Tests to verify the Jaccard index calculation is accurate
a = numpy.array(
[
@@ -598,7 +589,6 @@ def test_jaccard_index():
def test_intersection_ratio():
-
# Tests to verify the intersection ratio calculation is accurate
a = numpy.array(
[
@@ -664,8 +654,7 @@ def test_intersection_ratio():
def test_hamming_distance():
-
- from ..algorithm.HammingDistance import HammingDistance
+ from bob.bio.vein.algorithm.HammingDistance import HammingDistance
HD = HammingDistance()
diff --git a/version.txt b/version.txt
deleted file mode 100644
index 8f342b8f8fe0ef389fad758f475989b716c252f4..0000000000000000000000000000000000000000
--- a/version.txt
+++ /dev/null
@@ -1 +0,0 @@
-4.0.4b0