diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f26a01e948cdc392cfffaa8447e4eeb8aac6ff48
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,254 @@
+# This build file is defined in two parts: 1) a generic set of instructions you
+# probably **don't** need to change and 2) a part you may have to tune to your
+# project. It heavily uses template features from YAML to help you in only
+# changing a minimal part of it and avoid code duplication to a maximum while
+# still providing a nice pipeline display on your package.
+
+
+# 1) Generic instructions (only change if you know what you're doing)
+# -------------------------------------------------------------------
+
+# Definition of our build pipeline
+stages:
+ - build
+ - test
+ - docs
+ - wheels
+
+
+# Global variables
+variables:
+ CONDA_PREFIX: env
+
+
+# Template for the build stage
+# Needs to run on all supported architectures, platforms and python versions
+.build_template: &build_job
+ stage: build
+ before_script:
+ - git clean -ffdx
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/7/raw | tr -d '\r' > bootstrap-conda.sh
+ - chmod 755 ./bootstrap-conda.sh
+ - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+ variables: &build_variables
+ BOB_DOCUMENTATION_SERVER: "http://www.idiap.ch/software/bob/docs/latest/bob/%s/master/"
+ script:
+ - ./bin/buildout
+ - if [ -x ./bin/bob_dbmanage.py ]; then ./bin/bob_dbmanage.py all download --force; fi
+ - ./bin/sphinx-build doc sphinx
+ - ./bin/python setup.py bdist_wheel --python-tag ${WHEEL_TAG}
+ after_script:
+ - rm -rf ${CONDA_PREFIX}
+ artifacts:
+ expire_in: 1 day
+ paths:
+ - bootstrap-conda.sh
+ - dist/
+ - sphinx/
+
+
+# Template for building on a Linux machine
+.build_linux_template: &linux_build_job
+ <<: *build_job
+ variables: &linux_build_variables
+ <<: *build_variables
+ CONDA_FOLDER: "/local/conda"
+ CFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+ CXXFLAGS: "-D_GLIBCXX_USE_CXX11_ABI=0 -coverage"
+
+
+# Template for building on a Mac OSX machine
+.build_mac_template: &macosx_build_job
+ <<: *build_job
+ variables: &macosx_build_variables
+ <<: *build_variables
+ CONDA_FOLDER: "/opt/conda"
+ MACOSX_DEPLOYMENT_TARGET: "10.9"
+ CFLAGS: "-pthread -coverage"
+ CXXFLAGS: "-pthread -coverage"
+ LDFLAGS: "-lpthread"
+
+
+# Template for the test stage - re-install from uploaded wheels
+# Needs to run on all supported architectures, platforms and python versions
+.test_template: &test_job
+ stage: test
+ before_script:
+ - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
+ - source ${CONDA_FOLDER}/bin/activate ${CONDA_PREFIX}
+ - pip install --use-wheel --no-index --pre dist/*.whl
+ script:
+ - cd ${CONDA_PREFIX}
+ - python -c "from ${CI_PROJECT_NAME} import get_config; print(get_config())"
+ - coverage run --source=${CI_PROJECT_NAME} ./bin/nosetests -sv ${CI_PROJECT_NAME}
+ - coverage report
+ - sphinx-build -b doctest ../doc ../sphinx
+ after_script:
+ - rm -rf ${CONDA_PREFIX}
+
+
+# Template for the wheel uploading stage
+# Needs to run against one combination of python 2.x and 3.x if it is a python
+# only package, otherwise, needs to run in both pythons to all supported
+# architectures (Linux and Mac OSX 64-bit)
+.wheels_template: &wheels_job
+ stage: wheels
+ only:
+ - master
+ - tags
+ before_script:
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/8/raw | tr -d '\r' > upload-wheel.sh
+ - chmod 755 upload-wheel.sh
+ script:
+ - ./upload-wheel.sh
+
+
+# Template for (latest) documentation upload stage
+# Only one real job needs to do this
+.docs_template: &docs_job
+ stage: docs
+ only:
+ - master
+ before_script:
+ - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/9/raw | tr -d '\r' > upload-sphinx.sh
+ - chmod 755 upload-sphinx.sh
+ script:
+ - ./upload-sphinx.sh
+
+
+# 2) Package specific instructions (you may tune this if needed)
+# --------------------------------------------------------------
+
+# Linux + Python 2.7: Builds, tests, uploads wheel
+build_linux_27:
+ <<: *linux_build_job
+ variables: &linux_27_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "2.7"
+ WHEEL_TAG: "py27"
+ tags:
+ - conda-linux
+
+test_linux_27:
+ <<: *test_job
+ variables: *linux_27_build_variables
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+wheels_linux_27:
+ <<: *wheels_job
+ dependencies:
+ - build_linux_27
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.4: Builds and tests
+build_linux_34:
+ <<: *linux_build_job
+ variables: &linux_34_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "3.4"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-linux
+
+test_linux_34:
+ <<: *test_job
+ variables: *linux_34_build_variables
+ dependencies:
+ - build_linux_34
+ tags:
+ - conda-linux
+
+
+# Linux + Python 3.5: Builds, tests, uploads wheel
+build_linux_35:
+ <<: *linux_build_job
+ variables: &linux_35_build_variables
+ <<: *linux_build_variables
+ PYTHON_VER: "3.5"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-linux
+
+test_linux_35:
+ <<: *test_job
+ variables: *linux_35_build_variables
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+wheels_linux_35:
+ <<: *wheels_job
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+docs_linux_35:
+ <<: *docs_job
+ dependencies:
+ - build_linux_35
+ tags:
+ - conda-linux
+
+
+# Mac OSX + Python 2.7: Builds and tests
+build_macosx_27:
+ <<: *macosx_build_job
+ variables: &macosx_27_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "2.7"
+ WHEEL_TAG: "py27"
+ tags:
+ - conda-macosx
+
+test_macosx_27:
+ <<: *test_job
+ variables: *macosx_27_build_variables
+ dependencies:
+ - build_macosx_27
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.4: Builds and tests
+build_macosx_34:
+ <<: *macosx_build_job
+ variables: &macosx_34_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "3.4"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-macosx
+
+test_macosx_34:
+ <<: *test_job
+ variables: *macosx_34_build_variables
+ dependencies:
+ - build_macosx_34
+ tags:
+ - conda-macosx
+
+
+# Mac OSX + Python 3.5: Builds and tests
+build_macosx_35:
+ <<: *macosx_build_job
+ variables: &macosx_35_build_variables
+ <<: *macosx_build_variables
+ PYTHON_VER: "3.5"
+ WHEEL_TAG: "py3"
+ tags:
+ - conda-macosx
+
+test_macosx_35:
+ <<: *test_job
+ variables: *macosx_35_build_variables
+ dependencies:
+ - build_macosx_35
+ tags:
+ - conda-macosx
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 0bdb952d0e577d1660c1426b8fe2ee566d94c8fd..0000000000000000000000000000000000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-language: python
-matrix:
- include:
- - python: 2.7
- env:
- - secure: 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
- - secure: 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
- - BOB_DOCUMENTATION_SERVER=https://www.idiap.ch/software/bob/docs/latest/bioidiap/%s/master
- - BOB_UPLOAD_WHEEL="--universal"
- - python: 3.3
- - python: 3.4
- - python: 3.5
-before_install:
-- sudo add-apt-repository -y ppa:biometrics/bob
-- sudo apt-get update -qq
-- sudo apt-get install -qq --force-yes libjpeg8-dev libnetpbm10-dev libpng12-dev libtiff4-dev libgif-dev libboost-all-dev libblitz1-dev libhdf5-serial-dev libvl-dev dvipng texlive-latex-base texlive-latex-extra texlive-math-extra texlive-latex-recommended texlive-fonts-recommended libatlas-dev libatlas-base-dev liblapack-dev gfortran
-- pip install --upgrade pip
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel sphinx nose numpy scipy matplotlib coverage
-- pip install --find-links https://www.idiap.ch/software/bob/wheels/travis/ --use-wheel --pre -r requirements.txt coveralls
-install:
-- python bootstrap-buildout.py
-- ./bin/buildout buildout:develop=. buildout:extensions=bob.buildout buildout:auto-checkout=
-script:
-- ./bin/python -c 'import pkg_resources; from bob.bio.base import get_config; print(get_config())'
-- ./bin/coverage run --source=bob.bio.base ./bin/nosetests -sv
-- ./bin/sphinx-build -b doctest doc sphinx
-- ./bin/sphinx-build -b html doc sphinx
-after_success:
-- coveralls
-- wget https://raw.githubusercontent.com/bioidiap/bob.extension/master/scripts/upload-{sphinx,wheel}.sh
-- chmod a+x upload-sphinx.sh upload-wheel.sh
-- ./upload-sphinx.sh
-- ./upload-wheel.sh
diff --git a/COPYING b/COPYING
deleted file mode 100644
index 94a9ed024d3859793618152ea559a168bbcbb5e2..0000000000000000000000000000000000000000
--- a/COPYING
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
- To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights. Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
- For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received. You must make sure that they, too, receive
-or can get the source code. And you must show them these terms so they
-know their rights.
-
- Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
-
- For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software. For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
- Some devices are designed to deny users access to install or run
-modified versions of the software inside them, although the manufacturer
-can do so. This is fundamentally incompatible with the aim of
-protecting users' freedom to change the software. The systematic
-pattern of such abuse occurs in the area of products for individuals to
-use, which is precisely where it is most unacceptable. Therefore, we
-have designed this version of the GPL to prohibit the practice for those
-products. If such problems arise substantially in other domains, we
-stand ready to extend this provision to those domains in future versions
-of the GPL, as needed to protect the freedom of users.
-
- Finally, every program is threatened constantly by software patents.
-States should not allow patents to restrict development and use of
-software on general-purpose computers, but in those that do, we wish to
-avoid the special danger that patents applied to a free program could
-make it effectively proprietary. To prevent this, the GPL assures that
-patents cannot be used to render the program non-free.
-
- The precise terms and conditions for copying, distribution and
-modification follow.
-
- TERMS AND CONDITIONS
-
- 0. Definitions.
-
- "This License" refers to version 3 of the GNU General Public License.
-
- "Copyright" also means copyright-like laws that apply to other kinds of
-works, such as semiconductor masks.
-
- "The Program" refers to any copyrightable work licensed under this
-License. Each licensee is addressed as "you". "Licensees" and
-"recipients" may be individuals or organizations.
-
- To "modify" a work means to copy from or adapt all or part of the work
-in a fashion requiring copyright permission, other than the making of an
-exact copy. The resulting work is called a "modified version" of the
-earlier work or a work "based on" the earlier work.
-
- A "covered work" means either the unmodified Program or a work based
-on the Program.
-
- To "propagate" a work means to do anything with it that, without
-permission, would make you directly or secondarily liable for
-infringement under applicable copyright law, except executing it on a
-computer or modifying a private copy. Propagation includes copying,
-distribution (with or without modification), making available to the
-public, and in some countries other activities as well.
-
- To "convey" a work means any kind of propagation that enables other
-parties to make or receive copies. Mere interaction with a user through
-a computer network, with no transfer of a copy, is not conveying.
-
- An interactive user interface displays "Appropriate Legal Notices"
-to the extent that it includes a convenient and prominently visible
-feature that (1) displays an appropriate copyright notice, and (2)
-tells the user that there is no warranty for the work (except to the
-extent that warranties are provided), that licensees may convey the
-work under this License, and how to view a copy of this License. If
-the interface presents a list of user commands or options, such as a
-menu, a prominent item in the list meets this criterion.
-
- 1. Source Code.
-
- The "source code" for a work means the preferred form of the work
-for making modifications to it. "Object code" means any non-source
-form of a work.
-
- A "Standard Interface" means an interface that either is an official
-standard defined by a recognized standards body, or, in the case of
-interfaces specified for a particular programming language, one that
-is widely used among developers working in that language.
-
- The "System Libraries" of an executable work include anything, other
-than the work as a whole, that (a) is included in the normal form of
-packaging a Major Component, but which is not part of that Major
-Component, and (b) serves only to enable use of the work with that
-Major Component, or to implement a Standard Interface for which an
-implementation is available to the public in source code form. A
-"Major Component", in this context, means a major essential component
-(kernel, window system, and so on) of the specific operating system
-(if any) on which the executable work runs, or a compiler used to
-produce the work, or an object code interpreter used to run it.
-
- The "Corresponding Source" for a work in object code form means all
-the source code needed to generate, install, and (for an executable
-work) run the object code and to modify the work, including scripts to
-control those activities. However, it does not include the work's
-System Libraries, or general-purpose tools or generally available free
-programs which are used unmodified in performing those activities but
-which are not part of the work. For example, Corresponding Source
-includes interface definition files associated with source files for
-the work, and the source code for shared libraries and dynamically
-linked subprograms that the work is specifically designed to require,
-such as by intimate data communication or control flow between those
-subprograms and other parts of the work.
-
- The Corresponding Source need not include anything that users
-can regenerate automatically from other parts of the Corresponding
-Source.
-
- The Corresponding Source for a work in source code form is that
-same work.
-
- 2. Basic Permissions.
-
- All rights granted under this License are granted for the term of
-copyright on the Program, and are irrevocable provided the stated
-conditions are met. This License explicitly affirms your unlimited
-permission to run the unmodified Program. The output from running a
-covered work is covered by this License only if the output, given its
-content, constitutes a covered work. This License acknowledges your
-rights of fair use or other equivalent, as provided by copyright law.
-
- You may make, run and propagate covered works that you do not
-convey, without conditions so long as your license otherwise remains
-in force. You may convey covered works to others for the sole purpose
-of having them make modifications exclusively for you, or provide you
-with facilities for running those works, provided that you comply with
-the terms of this License in conveying all material for which you do
-not control copyright. Those thus making or running the covered works
-for you must do so exclusively on your behalf, under your direction
-and control, on terms that prohibit them from making any copies of
-your copyrighted material outside their relationship with you.
-
- Conveying under any other circumstances is permitted solely under
-the conditions stated below. Sublicensing is not allowed; section 10
-makes it unnecessary.
-
- 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
-
- No covered work shall be deemed part of an effective technological
-measure under any applicable law fulfilling obligations under article
-11 of the WIPO copyright treaty adopted on 20 December 1996, or
-similar laws prohibiting or restricting circumvention of such
-measures.
-
- When you convey a covered work, you waive any legal power to forbid
-circumvention of technological measures to the extent such circumvention
-is effected by exercising rights under this License with respect to
-the covered work, and you disclaim any intention to limit operation or
-modification of the work as a means of enforcing, against the work's
-users, your or third parties' legal rights to forbid circumvention of
-technological measures.
-
- 4. Conveying Verbatim Copies.
-
- You may convey verbatim copies of the Program's source code as you
-receive it, in any medium, provided that you conspicuously and
-appropriately publish on each copy an appropriate copyright notice;
-keep intact all notices stating that this License and any
-non-permissive terms added in accord with section 7 apply to the code;
-keep intact all notices of the absence of any warranty; and give all
-recipients a copy of this License along with the Program.
-
- You may charge any price or no price for each copy that you convey,
-and you may offer support or warranty protection for a fee.
-
- 5. Conveying Modified Source Versions.
-
- You may convey a work based on the Program, or the modifications to
-produce it from the Program, in the form of source code under the
-terms of section 4, provided that you also meet all of these conditions:
-
- a) The work must carry prominent notices stating that you modified
- it, and giving a relevant date.
-
- b) The work must carry prominent notices stating that it is
- released under this License and any conditions added under section
- 7. This requirement modifies the requirement in section 4 to
- "keep intact all notices".
-
- c) You must license the entire work, as a whole, under this
- License to anyone who comes into possession of a copy. This
- License will therefore apply, along with any applicable section 7
- additional terms, to the whole of the work, and all its parts,
- regardless of how they are packaged. This License gives no
- permission to license the work in any other way, but it does not
- invalidate such permission if you have separately received it.
-
- d) If the work has interactive user interfaces, each must display
- Appropriate Legal Notices; however, if the Program has interactive
- interfaces that do not display Appropriate Legal Notices, your
- work need not make them do so.
-
- A compilation of a covered work with other separate and independent
-works, which are not by their nature extensions of the covered work,
-and which are not combined with it such as to form a larger program,
-in or on a volume of a storage or distribution medium, is called an
-"aggregate" if the compilation and its resulting copyright are not
-used to limit the access or legal rights of the compilation's users
-beyond what the individual works permit. Inclusion of a covered work
-in an aggregate does not cause this License to apply to the other
-parts of the aggregate.
-
- 6. Conveying Non-Source Forms.
-
- You may convey a covered work in object code form under the terms
-of sections 4 and 5, provided that you also convey the
-machine-readable Corresponding Source under the terms of this License,
-in one of these ways:
-
- a) Convey the object code in, or embodied in, a physical product
- (including a physical distribution medium), accompanied by the
- Corresponding Source fixed on a durable physical medium
- customarily used for software interchange.
-
- b) Convey the object code in, or embodied in, a physical product
- (including a physical distribution medium), accompanied by a
- written offer, valid for at least three years and valid for as
- long as you offer spare parts or customer support for that product
- model, to give anyone who possesses the object code either (1) a
- copy of the Corresponding Source for all the software in the
- product that is covered by this License, on a durable physical
- medium customarily used for software interchange, for a price no
- more than your reasonable cost of physically performing this
- conveying of source, or (2) access to copy the
- Corresponding Source from a network server at no charge.
-
- c) Convey individual copies of the object code with a copy of the
- written offer to provide the Corresponding Source. This
- alternative is allowed only occasionally and noncommercially, and
- only if you received the object code with such an offer, in accord
- with subsection 6b.
-
- d) Convey the object code by offering access from a designated
- place (gratis or for a charge), and offer equivalent access to the
- Corresponding Source in the same way through the same place at no
- further charge. You need not require recipients to copy the
- Corresponding Source along with the object code. If the place to
- copy the object code is a network server, the Corresponding Source
- may be on a different server (operated by you or a third party)
- that supports equivalent copying facilities, provided you maintain
- clear directions next to the object code saying where to find the
- Corresponding Source. Regardless of what server hosts the
- Corresponding Source, you remain obligated to ensure that it is
- available for as long as needed to satisfy these requirements.
-
- e) Convey the object code using peer-to-peer transmission, provided
- you inform other peers where the object code and Corresponding
- Source of the work are being offered to the general public at no
- charge under subsection 6d.
-
- A separable portion of the object code, whose source code is excluded
-from the Corresponding Source as a System Library, need not be
-included in conveying the object code work.
-
- A "User Product" is either (1) a "consumer product", which means any
-tangible personal property which is normally used for personal, family,
-or household purposes, or (2) anything designed or sold for incorporation
-into a dwelling. In determining whether a product is a consumer product,
-doubtful cases shall be resolved in favor of coverage. For a particular
-product received by a particular user, "normally used" refers to a
-typical or common use of that class of product, regardless of the status
-of the particular user or of the way in which the particular user
-actually uses, or expects or is expected to use, the product. A product
-is a consumer product regardless of whether the product has substantial
-commercial, industrial or non-consumer uses, unless such uses represent
-the only significant mode of use of the product.
-
- "Installation Information" for a User Product means any methods,
-procedures, authorization keys, or other information required to install
-and execute modified versions of a covered work in that User Product from
-a modified version of its Corresponding Source. The information must
-suffice to ensure that the continued functioning of the modified object
-code is in no case prevented or interfered with solely because
-modification has been made.
-
- If you convey an object code work under this section in, or with, or
-specifically for use in, a User Product, and the conveying occurs as
-part of a transaction in which the right of possession and use of the
-User Product is transferred to the recipient in perpetuity or for a
-fixed term (regardless of how the transaction is characterized), the
-Corresponding Source conveyed under this section must be accompanied
-by the Installation Information. But this requirement does not apply
-if neither you nor any third party retains the ability to install
-modified object code on the User Product (for example, the work has
-been installed in ROM).
-
- The requirement to provide Installation Information does not include a
-requirement to continue to provide support service, warranty, or updates
-for a work that has been modified or installed by the recipient, or for
-the User Product in which it has been modified or installed. Access to a
-network may be denied when the modification itself materially and
-adversely affects the operation of the network or violates the rules and
-protocols for communication across the network.
-
- Corresponding Source conveyed, and Installation Information provided,
-in accord with this section must be in a format that is publicly
-documented (and with an implementation available to the public in
-source code form), and must require no special password or key for
-unpacking, reading or copying.
-
- 7. Additional Terms.
-
- "Additional permissions" are terms that supplement the terms of this
-License by making exceptions from one or more of its conditions.
-Additional permissions that are applicable to the entire Program shall
-be treated as though they were included in this License, to the extent
-that they are valid under applicable law. If additional permissions
-apply only to part of the Program, that part may be used separately
-under those permissions, but the entire Program remains governed by
-this License without regard to the additional permissions.
-
- When you convey a copy of a covered work, you may at your option
-remove any additional permissions from that copy, or from any part of
-it. (Additional permissions may be written to require their own
-removal in certain cases when you modify the work.) You may place
-additional permissions on material, added by you to a covered work,
-for which you have or can give appropriate copyright permission.
-
- Notwithstanding any other provision of this License, for material you
-add to a covered work, you may (if authorized by the copyright holders of
-that material) supplement the terms of this License with terms:
-
- a) Disclaiming warranty or limiting liability differently from the
- terms of sections 15 and 16 of this License; or
-
- b) Requiring preservation of specified reasonable legal notices or
- author attributions in that material or in the Appropriate Legal
- Notices displayed by works containing it; or
-
- c) Prohibiting misrepresentation of the origin of that material, or
- requiring that modified versions of such material be marked in
- reasonable ways as different from the original version; or
-
- d) Limiting the use for publicity purposes of names of licensors or
- authors of the material; or
-
- e) Declining to grant rights under trademark law for use of some
- trade names, trademarks, or service marks; or
-
- f) Requiring indemnification of licensors and authors of that
- material by anyone who conveys the material (or modified versions of
- it) with contractual assumptions of liability to the recipient, for
- any liability that these contractual assumptions directly impose on
- those licensors and authors.
-
- All other non-permissive additional terms are considered "further
-restrictions" within the meaning of section 10. If the Program as you
-received it, or any part of it, contains a notice stating that it is
-governed by this License along with a term that is a further
-restriction, you may remove that term. If a license document contains
-a further restriction but permits relicensing or conveying under this
-License, you may add to a covered work material governed by the terms
-of that license document, provided that the further restriction does
-not survive such relicensing or conveying.
-
- If you add terms to a covered work in accord with this section, you
-must place, in the relevant source files, a statement of the
-additional terms that apply to those files, or a notice indicating
-where to find the applicable terms.
-
- Additional terms, permissive or non-permissive, may be stated in the
-form of a separately written license, or stated as exceptions;
-the above requirements apply either way.
-
- 8. Termination.
-
- You may not propagate or modify a covered work except as expressly
-provided under this License. Any attempt otherwise to propagate or
-modify it is void, and will automatically terminate your rights under
-this License (including any patent licenses granted under the third
-paragraph of section 11).
-
- However, if you cease all violation of this License, then your
-license from a particular copyright holder is reinstated (a)
-provisionally, unless and until the copyright holder explicitly and
-finally terminates your license, and (b) permanently, if the copyright
-holder fails to notify you of the violation by some reasonable means
-prior to 60 days after the cessation.
-
- Moreover, your license from a particular copyright holder is
-reinstated permanently if the copyright holder notifies you of the
-violation by some reasonable means, this is the first time you have
-received notice of violation of this License (for any work) from that
-copyright holder, and you cure the violation prior to 30 days after
-your receipt of the notice.
-
- Termination of your rights under this section does not terminate the
-licenses of parties who have received copies or rights from you under
-this License. If your rights have been terminated and not permanently
-reinstated, you do not qualify to receive new licenses for the same
-material under section 10.
-
- 9. Acceptance Not Required for Having Copies.
-
- You are not required to accept this License in order to receive or
-run a copy of the Program. Ancillary propagation of a covered work
-occurring solely as a consequence of using peer-to-peer transmission
-to receive a copy likewise does not require acceptance. However,
-nothing other than this License grants you permission to propagate or
-modify any covered work. These actions infringe copyright if you do
-not accept this License. Therefore, by modifying or propagating a
-covered work, you indicate your acceptance of this License to do so.
-
- 10. Automatic Licensing of Downstream Recipients.
-
- Each time you convey a covered work, the recipient automatically
-receives a license from the original licensors, to run, modify and
-propagate that work, subject to this License. You are not responsible
-for enforcing compliance by third parties with this License.
-
- An "entity transaction" is a transaction transferring control of an
-organization, or substantially all assets of one, or subdividing an
-organization, or merging organizations. If propagation of a covered
-work results from an entity transaction, each party to that
-transaction who receives a copy of the work also receives whatever
-licenses to the work the party's predecessor in interest had or could
-give under the previous paragraph, plus a right to possession of the
-Corresponding Source of the work from the predecessor in interest, if
-the predecessor has it or can get it with reasonable efforts.
-
- You may not impose any further restrictions on the exercise of the
-rights granted or affirmed under this License. For example, you may
-not impose a license fee, royalty, or other charge for exercise of
-rights granted under this License, and you may not initiate litigation
-(including a cross-claim or counterclaim in a lawsuit) alleging that
-any patent claim is infringed by making, using, selling, offering for
-sale, or importing the Program or any portion of it.
-
- 11. Patents.
-
- A "contributor" is a copyright holder who authorizes use under this
-License of the Program or a work on which the Program is based. The
-work thus licensed is called the contributor's "contributor version".
-
- A contributor's "essential patent claims" are all patent claims
-owned or controlled by the contributor, whether already acquired or
-hereafter acquired, that would be infringed by some manner, permitted
-by this License, of making, using, or selling its contributor version,
-but do not include claims that would be infringed only as a
-consequence of further modification of the contributor version. For
-purposes of this definition, "control" includes the right to grant
-patent sublicenses in a manner consistent with the requirements of
-this License.
-
- Each contributor grants you a non-exclusive, worldwide, royalty-free
-patent license under the contributor's essential patent claims, to
-make, use, sell, offer for sale, import and otherwise run, modify and
-propagate the contents of its contributor version.
-
- In the following three paragraphs, a "patent license" is any express
-agreement or commitment, however denominated, not to enforce a patent
-(such as an express permission to practice a patent or covenant not to
-sue for patent infringement). To "grant" such a patent license to a
-party means to make such an agreement or commitment not to enforce a
-patent against the party.
-
- If you convey a covered work, knowingly relying on a patent license,
-and the Corresponding Source of the work is not available for anyone
-to copy, free of charge and under the terms of this License, through a
-publicly available network server or other readily accessible means,
-then you must either (1) cause the Corresponding Source to be so
-available, or (2) arrange to deprive yourself of the benefit of the
-patent license for this particular work, or (3) arrange, in a manner
-consistent with the requirements of this License, to extend the patent
-license to downstream recipients. "Knowingly relying" means you have
-actual knowledge that, but for the patent license, your conveying the
-covered work in a country, or your recipient's use of the covered work
-in a country, would infringe one or more identifiable patents in that
-country that you have reason to believe are valid.
-
- If, pursuant to or in connection with a single transaction or
-arrangement, you convey, or propagate by procuring conveyance of, a
-covered work, and grant a patent license to some of the parties
-receiving the covered work authorizing them to use, propagate, modify
-or convey a specific copy of the covered work, then the patent license
-you grant is automatically extended to all recipients of the covered
-work and works based on it.
-
- A patent license is "discriminatory" if it does not include within
-the scope of its coverage, prohibits the exercise of, or is
-conditioned on the non-exercise of one or more of the rights that are
-specifically granted under this License. You may not convey a covered
-work if you are a party to an arrangement with a third party that is
-in the business of distributing software, under which you make payment
-to the third party based on the extent of your activity of conveying
-the work, and under which the third party grants, to any of the
-parties who would receive the covered work from you, a discriminatory
-patent license (a) in connection with copies of the covered work
-conveyed by you (or copies made from those copies), or (b) primarily
-for and in connection with specific products or compilations that
-contain the covered work, unless you entered into that arrangement,
-or that patent license was granted, prior to 28 March 2007.
-
- Nothing in this License shall be construed as excluding or limiting
-any implied license or other defenses to infringement that may
-otherwise be available to you under applicable patent law.
-
- 12. No Surrender of Others' Freedom.
-
- If conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License. If you cannot convey a
-covered work so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you may
-not convey it at all. For example, if you agree to terms that obligate you
-to collect a royalty for further conveying from those to whom you convey
-the Program, the only way you could satisfy both those terms and this
-License would be to refrain entirely from conveying the Program.
-
- 13. Use with the GNU Affero General Public License.
-
- Notwithstanding any other provision of this License, you have
-permission to link or combine any covered work with a work licensed
-under version 3 of the GNU Affero General Public License into a single
-combined work, and to convey the resulting work. The terms of this
-License will continue to apply to the part which is the covered work,
-but the special requirements of the GNU Affero General Public License,
-section 13, concerning interaction through a network will apply to the
-combination as such.
-
- 14. Revised Versions of this License.
-
- The Free Software Foundation may publish revised and/or new versions of
-the GNU General Public License from time to time. Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
- Each version is given a distinguishing version number. If the
-Program specifies that a certain numbered version of the GNU General
-Public License "or any later version" applies to it, you have the
-option of following the terms and conditions either of that numbered
-version or of any later version published by the Free Software
-Foundation. If the Program does not specify a version number of the
-GNU General Public License, you may choose any version ever published
-by the Free Software Foundation.
-
- If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
- Later license versions may give you additional or different
-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
- 15. Disclaimer of Warranty.
-
- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- <program> Copyright (C) <year> <name of author>
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..bd46ce15068f2d3b5a1b23ac6c68a33ec808d95d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,27 @@
+Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
+Written by Andre Anjos <andre.anjos@idiap.ch>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
index c0106740d21316a15c6f33c05067529ab74b5d85..3f5b45f9c17aab02d59efaf41dc62304455c5323 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
-include README.rst bootstrap-buildout.py buildout.cfg COPYING version.txt requirements.txt
+include README.rst bootstrap-buildout.py buildout.cfg develop.cfg COPYING version.txt requirements.txt test-requirements.txt
recursive-include doc *.py *.rst
-recursive-include bob/bio/base/test/data *.lst *.hdf5 *-dev
+recursive-include bob/bio/base/test/data *.lst *.hdf5 *-dev
diff --git a/README.rst b/README.rst
index c7d4a09fae30317b1260c92bb06616bc30d31469..0558ff22ef2f684d01e975bc834fc60ab691a29e 100644
--- a/README.rst
+++ b/README.rst
@@ -1,63 +1,50 @@
.. vim: set fileencoding=utf-8 :
-.. Andre Anjos <andre.anjos@idiap.ch>
-.. Thu 30 Jan 08:46:53 2014 CET
+.. Tue 16 Aug 15:00:20 CEST 2016
.. image:: http://img.shields.io/badge/docs-stable-yellow.png
:target: http://pythonhosted.org/bob.bio.base/index.html
.. image:: http://img.shields.io/badge/docs-latest-orange.png
:target: https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.base/master/index.html
-.. image:: http://travis-ci.org/bioidiap/bob.bio.base.svg?branch=master
- :target: https://travis-ci.org/bioidiap/bob.bio.base?branch=master
-.. image:: https://coveralls.io/repos/bioidiap/bob.bio.base/badge.svg?branch=master
- :target: https://coveralls.io/r/bioidiap/bob.bio.base?branch=master
-.. image:: https://img.shields.io/badge/github-master-0000c0.png
- :target: https://github.com/bioidiap/bob.bio.base/tree/master
+.. image:: https://gitlab.idiap.ch/bob/bob.bio.base/badges/master/build.svg
+ :target: https://gitlab.idiap.ch/bob/bob.bio.base/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+ :target: https://gitlab.idiap.ch/bob/bob.bio.base
.. image:: http://img.shields.io/pypi/v/bob.bio.base.png
:target: https://pypi.python.org/pypi/bob.bio.base
.. image:: http://img.shields.io/pypi/dm/bob.bio.base.png
:target: https://pypi.python.org/pypi/bob.bio.base
-==================================================
- Scripts to run biometric recognition experiments
-==================================================
-This package is part of the ``bob.bio`` packages, which allow to run comparable and reproducible biometric recognition experiments on publicly available databases.
+================================================
+ Tools to run biometric recognition experiments
+================================================
-This package contains basic functionality to run biometric recognition experiments.
-It provides a generic ``./bin/verify.py`` script that takes several parameters, including:
+This package is part of the signal-processing and machine learning toolbox
+Bob_. It provides tools to run comparable and reproducible biometric
+recognition experiments on publicly available databases.
-* A database and its evaluation protocol
-* A data preprocessing algorithm
-* A feature extraction algorithm
-* A biometric recognition algorithm
+The `User Guide`_ provides installation and usage instructions.
-All these steps of the biometric recognition system are given as configuration files.
-
-In this base class implementation, only a few algorithms (such as PCA, LDA, PLDA, BIC) are implemented, while most algorithms that are more specialized are provided by other packages, which are usually in the ``bob.bio`` namespace, such as:
-
-* `bob.bio.spear <http://pypi.python.org/pypi/bob.bio.spear>`__ for speaker recognition recognition databases, features and algorithms
-* `bob.bio.face <http://pypi.python.org/pypi/bob.bio.face>`__ for face recognition databases, features and algorithms
-* `bob.bio.video <http://pypi.python.org/pypi/bob.bio.video>`__ for video-based databases and algorithms
-* `bob.bio.gmm <http://pypi.python.org/pypi/bob.bio.gmm>`__ for Gaussian-mixture-model-based algorithms
-* `bob.bio.csu <http://pypi.python.org/pypi/bob.bio.csu>`__ for wrapper classes of the `CSU Face Recognition Resources <http://www.cs.colostate.edu/facerec>`__ (see `Installation Instructions <http://pythonhosted.org/bob.bio.csu/installation.html>`__ of ``bob.bio.csu``).
+Installation
+------------
-Moreover, a script for score fusion ``./bin/fusion_llr.py`` is provided to do score-level fusion using Logistic regression to combine outputs from different systems.
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
-Additionally, a generic script ``./bin/evaluate.py`` is provided that can generate several types of plots (such as ROC, DET and CMC curves) and compute several measures (such as HTER, Cllr) to evaluate your experiments.
+ $ python bootstrap-buildout.py
+ $ ./bin/buildout
-Installation
-------------
-To create your own working package using one or more of the ``bob.bio`` packages, please follow the `Installation Instructions <http://pythonhosted.org/bob.bio.base/installation.html>`__ of the ``bob.bio`` packages.
+Contact
+-------
-To install this package -- alone or together with other `Packages of Bob <https://github.com/idiap/bob/wiki/Packages>`_ -- please read the `Installation Instructions <https://github.com/idiap/bob/wiki/Installation>`__.
-For Bob_ to be able to work properly, some dependent packages are required to be installed.
-Please make sure that you have read the `Dependencies <https://github.com/idiap/bob/wiki/Dependencies>`_ for your operating system.
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
-Documentation
--------------
-For further documentation on this package, please read the `Stable Version <http://pythonhosted.org/bob.bio.base/index.html>`_ or the `Latest Version <https://www.idiap.ch/software/bob/docs/latest/bioidiap/bob.bio.base/master/index.html>`_ of the documentation.
-For a list of tutorials on this or the other packages ob Bob_, or information on submitting issues, asking questions and starting discussions, please visit its website.
+.. Place your references here:
.. _bob: https://www.idiap.ch/software/bob
+.. _installation: https://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel
+.. _user guide: http://pythonhosted.org/bob.bio.base
diff --git a/bob/bio/base/__init__.py b/bob/bio/base/__init__.py
index 5b2461a9b9400164f5010f4413fbabf26d2c17b3..48dbde118eeb3b217a39ed298c8f7c45e6065dfc 100644
--- a/bob/bio/base/__init__.py
+++ b/bob/bio/base/__init__.py
@@ -1,5 +1,4 @@
from .utils import *
-from . import database
from . import preprocessor
from . import extractor
from . import algorithm
diff --git a/bob/bio/base/algorithm/Algorithm.py b/bob/bio/base/algorithm/Algorithm.py
index 6023d3df0cf00e6a16e38cbd79930120094ac6b5..8935d4d6ac63c5fcde6ced57f0e32d8c4791b55d 100644
--- a/bob/bio/base/algorithm/Algorithm.py
+++ b/bob/bio/base/algorithm/Algorithm.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Tue Oct 2 12:12:39 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
import numpy
import os
diff --git a/bob/bio/base/database/Database.py b/bob/bio/base/database/Database.py
deleted file mode 100644
index cb9cc675149c819307f025922e467fbd5cd41e04..0000000000000000000000000000000000000000
--- a/bob/bio/base/database/Database.py
+++ /dev/null
@@ -1,490 +0,0 @@
-class Database:
- """This class represents the basic API for database access.
- Please use this class as a base class for your database access classes.
- Do not forget to call the constructor of this base class in your derived class.
-
- **Parameters:**
-
- name : str
- A unique name for the database.
-
- original_directory : str
- The directory where the original data of the database are stored.
-
- original_extension : str
- The file name extension of the original data.
-
- annotation_directory : str
- The directory where the image annotations of the database are stored, if any.
-
- annotation_extension : str
- The file name extension of the annotation files.
-
- annotation_type : str
- The type of the annotation file to read, see :py:func:`bob.db.verification.utils.read_annotation_file` for accepted formats.
-
- protocol : str or ``None``
- The name of the protocol that defines the default experimental setup for this database.
-
- .. todo:: Check if the ``None`` protocol is supported.
-
- training_depends_on_protocol : bool
- Specifies, if the training set used for training the extractor and the projector depend on the protocol.
- This flag is used to avoid re-computation of data when running on the different protocols of the same database.
-
- models_depend_on_protocol : bool
- Specifies, if the models depend on the protocol.
- This flag is used to avoid re-computation of models when running on the different protocols of the same database.
-
- kwargs
- Ignored extra arguments.
- """
-
- def __init__(
- self,
- name,
- original_directory = None,
- original_extension = None,
- annotation_directory = None,
- annotation_extension = '.pos',
- annotation_type = None,
- protocol = 'Default',
- training_depends_on_protocol = False,
- models_depend_on_protocol = False,
- **kwargs
- ):
- assert isinstance(name, str)
-
- self.name = name
- self.original_directory = original_directory
- self.original_extension = original_extension
- self.annotation_directory = annotation_directory
- self.annotation_extension = annotation_extension
- self.annotation_type = annotation_type
- self.protocol = protocol
- self.training_depends_on_protocol = training_depends_on_protocol
- self.models_depend_on_protocol = models_depend_on_protocol
-
-
- def __str__(self):
- """__str__() -> info
-
- This function returns all parameters of this class.
-
- **Returns:**
-
- info : str
- A string containing the full information of all parameters of this class.
- """
- params = "name=%s, protocol=%s, original_directory=%s, original_extension=%s" % (self.name, self.protocol, self.original_directory, self.original_extension)
- if self.annotation_type is not None:
- params += ", annotation_type=%s" % annotation_type
- if self.annotation_directory: params += ", annotation_directory=%s" % self.annotation_directory
- params += ", annotation_extension=%s" % self.annotation_extension
- params += ", training_depends_on_protocol=%s, models_depend_on_protocol=%s" % (self.training_depends_on_protocol, self.models_depend_on_protocol)
- return "%s(%s)" % (str(self.__class__), params)
-
-
- ###########################################################################
- ### Helper functions that you might want to use in derived classes
- ###########################################################################
- def sort(self, files):
- """sort(files) -> sorted
-
- Returns a sorted version of the given list of File's (or other structures that define an 'id' data member).
- The files will be sorted according to their id, and duplicate entries will be removed.
-
- **Parameters:**
-
- files : [:py:class:`File`]
- The list of files to be uniquified and sorted.
-
- **Returns:**
-
- sorted : [:py:class:`File`]
- The sorted list of files, with duplicate :py:attr:`File.id`\s being removed.
- """
- # sort files using their sort function
- sorted_files = sorted(files)
- # remove duplicates
- return [f for i,f in enumerate(sorted_files) if not i or sorted_files[i-1].id != f.id]
-
-
- def arrange_by_client(self, files):
- """arrange_by_client(files) -> files_by_client
-
- Arranges the given list of files by client id.
- This function returns a list of lists of File's.
-
- **Parameters:**
-
- files : :py:class:`File`
- A list of files that should be split up by :py:attr:`File.client_id`.
-
- **Returns:**
-
- files_by_client : [[:py:class:`File`]]
- The list of lists of files, where each sub-list groups the files with the same :py:attr:`File.client_id`
- """
- client_files = {}
- for file in files:
- if file.client_id not in client_files:
- client_files[file.client_id] = []
- client_files[file.client_id].append(file)
-
- files_by_clients = []
- for client in sorted(client_files.keys()):
- files_by_clients.append(client_files[client])
- return files_by_clients
-
-
- def annotations(self, file):
- """annotations(file) -> annots
-
- Returns the annotations for the given File object, if available.
- It uses :py:func:`bob.db.verification.utils.read_annotation_file` to load the annotations.
-
- **Parameters:**
-
- file : :py:class:`File`
- The file for which annotations should be returned.
-
- **Returns:**
-
- annots : dict or None
- The annotations for the file, if available.
- """
- if self.annotation_directory:
- try:
- import bob.db.verification.utils
- annotation_path = os.path.join(self.annotation_directory, file.path + self.annotation_extension)
- return bob.db.verification.utils.read_annotation_file(annotation_path, self.annotation_type)
- except ImportError as e:
- from .. import utils
- utils.error("Cannot import bob.db.verification.utils: '%s'. No annotation is read." % e)
-
- return None
-
-
- def uses_probe_file_sets(self):
- """Defines if, for the current protocol, the database uses several probe files to generate a score.
- By default, ``False`` is returned. Overwrite the default if you need different behavior."""
- return False
-
-
- def file_names(self, files, directory, extension):
- """file_names(files, directory, extension) -> paths
-
- Returns the full path of the given File objects.
-
- **Parameters:**
-
- files : [:py:class:`File`]
- The list of file object to retrieve the file names for.
-
- directory : str
- The base directory, where the files can be found.
-
- extension : str
- The file name extension to add to all files.
-
- **Returns:**
-
- paths : [str] or [[str]]
- The paths extracted for the files, in the same order.
- If this database provides file sets, a list of lists of file names is returned, one sub-list for each file set.
- """
- # return the paths of the files
- if self.uses_probe_file_sets() and files and hasattr(files[0], 'files'):
- # List of Filesets: do not remove duplicates
- return [[f.make_path(directory, extension) for f in file_set.files] for file_set in files]
- else:
- # List of files, do not remove duplicates
- return [f.make_path(directory, extension) for f in files]
-
- def original_file_names(self, files):
- """original_file_names(files) -> paths
-
- Returns the full path of the original data of the given File objects.
-
- **Parameters:**
-
- files : [:py:class:`File`]
- The list of file object to retrieve the original data file names for.
-
- **Returns:**
-
- paths : [str] or [[str]]
- The paths extracted for the files, in the same order.
- If this database provides file sets, a list of lists of file names is returned, one sub-list for each file set.
- """
- assert self.original_directory is not None
- assert self.original_extension is not None
- return self.file_names(files, self.original_directory, self.original_extension)
-
-
- ###########################################################################
- ### Interface functions that you need to implement in your class.
- ###########################################################################
-
- def all_files(self, groups = None):
- """all_files(groups=None) -> files
-
- Returns all files of the database.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- groups : some of ``('world', 'dev', 'eval')`` or ``None``
- The groups to get the data for.
- If ``None``, data for all groups is returned.
-
- **Returns:**
-
- files : [:py:class:`File`]
- The sorted and unique list of all files of the database.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def training_files(self, step = None, arrange_by_client = False):
- """training_files(step = None, arrange_by_client = False) -> files
-
- Returns all training File objects for the given step, and arranges them by client, if desired.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- step : one of ``('train_extractor', 'train_projector', 'train_enroller')`` or ``None``
- The step for which the training data should be returned.
- Might be ignored in derived class implementations.
-
- arrange_by_client : bool
- Should the training files be arranged by client?
-
- .. note::
- You can use :py:meth:`arrange_by_client` in derived class implementations to arrange the files.
-
- **Returns:**
-
- files : [:py:class:`File`] or [[:py:class:`File`]]
- The (arranged) list of files used for the training of the given step.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def model_ids(self, group = 'dev'):
- """model_ids(group = 'dev') -> ids
-
- Returns a list of model ids for the given group.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for the given group.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def client_id_from_model_id(self, model_id, group = 'dev'):
- """client_id_from_model_id(model_id, group = 'dev') -> client_id
-
- In some databases, each client can contain several models.
- Hence, client and model ids differ.
- This function converts the given model id into its according the client id.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- model_id : int or str
- A unique ID that identifies the model for the client.
-
- group : one of ``('dev', 'eval')``
- The group to get the client ids for.
-
- **Returns:**
-
- client_id : [int] or [str]
- A unique ID that identifies the client, to which the model belongs.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def enroll_files(self, model_id, group = 'dev'):
- """enroll_files(model_id, group = 'dev') -> files
-
- Returns a list of File objects that should be used to enroll the model with the given model id from the given group.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- model_id : int or str
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`File`]
- The list of files used for to enroll the model with the given model id.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def probe_files(self, model_id = None, group = 'dev'):
- """probe_files(model_id = None, group = 'dev') -> files
-
- Returns a list of probe File objects.
- If a ``model_id`` is specified, only the probe files that should be compared with the given model id are returned (for most databases, these are all probe files of the given group).
- Otherwise, all probe files of the given group are returned.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- model_id : int or str or ``None``
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`File`]
- The list of files used for to probe the model with the given model id.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def probe_file_sets(self, model_id = None, group = 'dev'):
- """probe_file_sets(model_id = None, group = 'dev') -> files
-
- Returns a list of probe FileSet objects.
- If a ``model_id`` is specified, only the probe files that should be compared with the given model id are returned (for most databases, these are all probe files of the given group).
- Otherwise, all probe files of the given group are returned.
- This function needs to be implemented in derived class implementations, if the :py:meth:`uses_probe_file_sets` returns ``True``.
-
- **Parameters:**
-
- model_id : int or str or ``None``
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`FileSet`]
- The list of file sets used to probe the model with the given model id."""
- raise NotImplementedError("Please implement this function in derived classes")
-
-
-
-class DatabaseZT (Database):
- """This class defines additional API functions that are required to compute ZT score normalization.
- This class does not define a constructor.
- During construction of a derived class, please call the constructor of the base class :py:class:`Database` directly."""
-
- def t_model_ids(self, group = 'dev'):
- """t_model_ids(group = 'dev') -> ids
-
- Returns a list of model ids of T-Norm models for the given group.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for T-Norm models of the given group.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
-
- def client_id_from_t_model_id(self, t_model_id, group = 'dev'):
- """client_id_from_t_model_id(t_model_id, group = 'dev') -> client_id
-
- Returns the client id for the given T-Norm model id.
- In this base class implementation, we just use the :py:meth:`client_id_from_model_id` function.
- Overload this function if you need another behavior.
-
- **Parameters:**
-
- t_model_id : int or str
- A unique ID that identifies the T-Norm model.
-
- group : one of ``('dev', 'eval')``
- The group to get the client ids for.
-
- **Returns:**
-
- client_id : [int] or [str]
- A unique ID that identifies the client, to which the T-Norm model belongs.
- """
- return self.client_id_from_model_id(t_model_id, group)
-
- def t_enroll_files(self, t_model_id, group = 'dev'):
- """t_enroll_files(t_model_id, group = 'dev') -> files
-
- Returns a list of File objects that should be used to enroll the T-Norm model with the given model id from the given group.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- t_model_id : int or str
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`File`]
- The list of files used for to enroll the model with the given model id.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
- def z_probe_files(self, group = 'dev'):
- """z_probe_files(group = 'dev') -> files
-
- Returns a list of probe File objects used to compute the Z-Norm.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the Z-norm probe files for.
-
- **Returns:**
-
- files : [:py:class:`File`]
- The unique list of files used to compute the Z-norm.
- """
- raise NotImplementedError("Please implement this function in derived classes")
-
- def z_probe_file_sets(self, group = 'dev'):
- """z_probe_file_sets(group = 'dev') -> files
-
- Returns a list of probe FileSet objects used to compute the Z-Norm.
- This function needs to be implemented in derived class implementations.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the Z-norm probe files for.
-
- **Returns:**
-
- files : [:py:class:`FileSet`]
- The unique list of file sets used to compute the Z-norm.
- """
- raise NotImplementedError("Please implement this function in derived classes")
diff --git a/bob/bio/base/database/DatabaseBob.py b/bob/bio/base/database/DatabaseBob.py
deleted file mode 100644
index 38d7857770324d9d7d9eb7616ef5307b3fb6610a..0000000000000000000000000000000000000000
--- a/bob/bio/base/database/DatabaseBob.py
+++ /dev/null
@@ -1,505 +0,0 @@
-from .Database import Database, DatabaseZT
-import os
-
-import bob.db.verification.utils
-
-class DatabaseBob (Database):
- """This class can be used whenever you have a database that follows the Bob verification database interface, which is defined in :py:class:`bob.db.verification.utils.Database`
-
- **Parameters:**
-
- database : derivative of :py:class:`bob.db.verification.utils.Database`
- The database instance (such as a :py:class:`bob.db.atnt.Database`) that provides the actual interface, see :ref:`verification_databases` for a list.
-
- all_files_options : dict
- Dictionary of options passed to the :py:meth:`bob.db.verification.utils.Database.objects` database query when retrieving all data.
-
- extractor_training_options : dict
- Dictionary of options passed to the :py:meth:`bob.db.verification.utils.Database.objects` database query used to retrieve the files for the extractor training.
-
- projector_training_options : dict
- Dictionary of options passed to the :py:meth:`bob.db.verification.utils.Database.objects` database query used to retrieve the files for the projector training.
-
- enroller_training_options : dict
- Dictionary of options passed to the :py:meth:`bob.db.verification.utils.Database.objects` database query used to retrieve the files for the enroller training.
-
- check_original_files_for_existence : bool
- Enables to test for the original data files when querying the database.
-
- kwargs : ``key=value`` pairs
- The arguments of the :py:class:`Database` base class constructor.
-
- .. note:: Usually, the ``name``, ``protocol``, ``training_depends_on_protocol`` and ``models_depend_on_protocol`` keyword parameters of the base class constructor need to be specified.
- """
-
- def __init__(
- self,
- database, # The bob database that is used
- all_files_options = {}, # additional options for the database query that can be used to extract all files
- extractor_training_options = {}, # additional options for the database query that can be used to extract the training files for the extractor training
- projector_training_options = {}, # additional options for the database query that can be used to extract the training files for the extractor training
- enroller_training_options = {}, # additional options for the database query that can be used to extract the training files for the extractor training
- check_original_files_for_existence = False,
- **kwargs # The default parameters of the base class
- ):
-
- Database.__init__(
- self,
- **kwargs
- )
-
- assert isinstance(database, bob.db.verification.utils.Database), "Only databases derived from bob.db.verification.utils.Database are supported by this interface. Please implement your own bob.bio.base.database.Database interface."
-
- self.database = database
- self.original_directory = database.original_directory
- try:
- self.annotation_directory = database.annotation_directory
- except AttributeError:
- pass
-
- self.all_files_options = all_files_options
- self.extractor_training_options = extractor_training_options
- self.projector_training_options = projector_training_options
- self.enroller_training_options = enroller_training_options
- self.check_existence = check_original_files_for_existence
-
- self._kwargs = kwargs
-
-
- def __str__(self):
- """__str__() -> info
-
- This function returns all parameters of this class (and its derived class).
-
- **Returns:**
-
- info : str
- A string containing the full information of all parameters of this (and the derived) class.
- """
- params = ", ".join(["%s=%s" % (key, value) for key, value in self._kwargs.items()])
- params += ", original_directory=%s, original_extension=%s" % (self.original_directory, self.original_extension)
- if self.all_files_options: params += ", all_files_options=%s"%self.all_files_options
- if self.extractor_training_options: params += ", extractor_training_options=%s"%self.extractor_training_options
- if self.projector_training_options: params += ", projector_training_options=%s"%self.projector_training_options
- if self.enroller_training_options: params += ", enroller_training_options=%s"%self.enroller_training_options
-
- return "%s(%s)" % (str(self.__class__), params)
-
-
- def replace_directories(self, replacements = None):
- """This helper function replaces the ``original_directory`` and the ``annotation_directory`` of the database with the directories read from the given replacement file.
-
- This function is provided for convenience, so that the database configuration files do not need to be modified.
- Instead, this function uses the given dictionary of replacements to change the original directory and the original extension (if given).
-
- The given ``replacements`` can be of type ``dict``, including all replacements, or a file name (as a ``str``), in which case the file is read.
- The structure of the file should be:
-
- .. code-block:: text
-
- # Comments starting with # and empty lines are ignored
-
- [YOUR_..._DATA_DIRECTORY] = /path/to/your/data
- [YOUR_..._ANNOTATION_DIRECTORY] = /path/to/your/annotations
-
- If no annotation files are available (e.g. when they are stored inside the ``database``), the annotation directory can be left out.
-
- **Parameters:**
-
- replacements : dict or str
- A dictionary with replacements, or a name of a file to read the dictionary from.
- If the file name does not exist, no directories are replaced.
- """
- if replacements is None:
- return
- if isinstance(replacements, str):
- if not os.path.exists(replacements):
- return
- # Open the database replacement file and reads its content
- with open(replacements) as f:
- replacements = {}
- for line in f:
- if line.strip() and not line.startswith("#"):
- splits = line.split("=")
- assert len(splits) == 2
- replacements[splits[0].strip()] = splits[1].strip()
-
- assert isinstance(replacements, dict)
-
- if self.original_directory in replacements:
- self.original_directory = replacements[self.original_directory]
- self.database.original_directory = replacements[self.database.original_directory]
-
- try:
- if self.annotation_directory in replacements:
- self.annotation_directory = replacements[self.annotation_directory]
- self.database.annotation_directory = replacements[self.database.annotation_directory]
- except AttributeError:
- pass
-
-
- def uses_probe_file_sets(self):
- """Defines if, for the current protocol, the database uses several probe files to generate a score."""
- return self.database.provides_file_set_for_protocol(self.protocol)
-
-
- def all_files(self, groups = None):
- """all_files(groups=None) -> files
-
- Returns all files of the database, respecting the current protocol.
- The files can be limited using the ``all_files_options`` in the constructor.
-
- **Parameters:**
-
- groups : some of ``('world', 'dev', 'eval')`` or ``None``
- The groups to get the data for.
- If ``None``, data for all groups is returned.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The sorted and unique list of all files of the database.
- """
- return self.sort(self.database.objects(protocol = self.protocol, groups = groups, **self.all_files_options))
-
-
- def training_files(self, step = None, arrange_by_client = False):
- """training_files(step = None, arrange_by_client = False) -> files
-
- Returns all training files for the given step, and arranges them by client, if desired, respecting the current protocol.
- The files for the steps can be limited using the ``..._training_options`` defined in the constructor.
-
- **Parameters:**
-
- step : one of ``('train_extractor', 'train_projector', 'train_enroller')`` or ``None``
- The step for which the training data should be returned.
-
- arrange_by_client : bool
- Should the training files be arranged by client?
- If set to ``True``, training files will be returned in [[:py:class:`bob.db.verification.utils.File`]], where each sub-list contains the files of a single client.
- Otherwise, all files will be stored in a simple [:py:class:`bob.db.verification.utils.File`].
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`] or [[:py:class:`bob.db.verification.utils.File`]]
- The (arranged) list of files used for the training of the given step.
- """
- if step is None:
- training_options = self.all_files_options
- elif step == 'train_extractor':
- training_options = self.extractor_training_options
- elif step == 'train_projector':
- training_options = self.projector_training_options
- elif step == 'train_enroller':
- training_options = self.enroller_training_options
- else:
- raise ValueError("The given step '%s' must be one of ('train_extractor', 'train_projector', 'train_enroller')" % step)
-
- files = self.sort(self.database.objects(protocol = self.protocol, groups = 'world', **training_options))
- if arrange_by_client:
- return self.arrange_by_client(files)
- else:
- return files
-
- def test_files(self, groups = ['dev']):
- """test_files(groups = ['dev']) -> files
-
- Returns all test files (i.e., files used for enrollment and probing) for the given groups, respecting the current protocol.
- The files for the steps can be limited using the ``all_files_options`` defined in the constructor.
-
- **Parameters:**
-
- groups : some of ``('dev', 'eval')``
- The groups to get the data for.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The sorted and unique list of test files of the database.
- """
- return self.sort(self.database.test_files(protocol = self.protocol, groups = groups, **self.all_files_options))
-
- def model_ids(self, group = 'dev'):
- """model_ids(group = 'dev') -> ids
-
- Returns a list of model ids for the given group, respecting the current protocol.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for the given group.
- """
- return sorted(self.database.model_ids(protocol = self.protocol, groups = group))
-
-
- def client_id_from_model_id(self, model_id, group = 'dev'):
- """client_id_from_model_id(model_id, group = 'dev') -> client_id
-
- Uses :py:meth:`bob.db.verification.utils.Database.get_client_id_from_model_id` to retrieve the client id for the given model id.
-
- **Parameters:**
-
- model_id : int or str
- A unique ID that identifies the model for the client.
-
- group : one of ``('dev', 'eval')``
- The group to get the client ids for.
-
- **Returns:**
-
- client_id : [int] or [str]
- A unique ID that identifies the client, to which the model belongs.
- """
- return self.database.get_client_id_from_model_id(model_id)
-
-
- def enroll_files(self, model_id, group = 'dev'):
- """enroll_files(model_id, group = 'dev') -> files
-
- Returns a list of File objects that should be used to enroll the model with the given model id from the given group, respecting the current protocol.
-
- **Parameters:**
-
- model_id : int or str
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The list of files used for to enroll the model with the given model id.
- """
- return self.sort(self.database.objects(protocol = self.protocol, groups = group, model_ids = (model_id,), purposes = 'enroll', **self.all_files_options))
-
-
- def probe_files(self, model_id = None, group = 'dev'):
- """probe_files(model_id = None, group = 'dev') -> files
-
- Returns a list of probe File objects, respecting the current protocol.
- If a ``model_id`` is specified, only the probe files that should be compared with the given model id are returned (for most databases, these are all probe files of the given group).
- Otherwise, all probe files of the given group are returned.
-
- **Parameters:**
-
- model_id : int or str or ``None``
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The list of files used for to probe the model with the given model id.
- """
- if model_id is not None:
- files = self.database.objects(protocol = self.protocol, groups = group, model_ids = (model_id,), purposes = 'probe', **self.all_files_options)
- else:
- files = self.database.objects(protocol = self.protocol, groups = group, purposes = 'probe', **self.all_files_options)
- return self.sort(files)
-
-
- def probe_file_sets(self, model_id = None, group = 'dev'):
- """probe_file_sets(model_id = None, group = 'dev') -> files
-
- Returns a list of probe FileSet objects, respecting the current protocol.
- If a ``model_id`` is specified, only the probe files that should be compared with the given model id are returned (for most databases, these are all probe files of the given group).
- Otherwise, all probe files of the given group are returned.
-
- **Parameters:**
-
- model_id : int or str or ``None``
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`FileSet`] or something similar
- The list of file sets used to probe the model with the given model id."""
- if model_id is not None:
- file_sets = self.database.object_sets(protocol = self.protocol, groups = group, model_ids = (model_id,), purposes = 'probe', **self.all_files_options)
- else:
- file_sets = self.database.object_sets(protocol = self.protocol, groups = group, purposes = 'probe', **self.all_files_options)
- return self.sort(file_sets)
-
-
- def annotations(self, file):
- """annotations(file) -> annots
-
- Returns the annotations for the given File object, if available.
-
- **Parameters:**
-
- file : :py:class:`bob.db.verification.utils.File`
- The file for which annotations should be returned.
-
- **Returns:**
-
- annots : dict or None
- The annotations for the file, if available.
- """
- return self.database.annotations(file)
-
-
- def original_file_names(self, files):
- """original_file_names(files) -> paths
-
- Returns the full path of the original data of the given File objects, as returned by :py:meth:`bob.db.verification.utils.Database.original_file_names`.
-
- **Parameters:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The list of file object to retrieve the original data file names for.
-
- **Returns:**
-
- paths : [str]
- The paths extracted for the files, in the same order.
- """
- return self.database.original_file_names(files, self.check_existence)
-
-
-
-class DatabaseBobZT (DatabaseBob, DatabaseZT):
- """This class can be used whenever you have a database that follows the Bob ZT-norm verification database interface, which is defined in :py:class:`bob.db.verification.utils.ZTDatabase`.
-
- **Parameters:**
-
- database : derivative of :py:class:`bob.db.verification.utils.ZTDatabase`
- The database instance (such as a :py:class:`bob.db.mobio.Database`) that provides the actual interface, see :ref:`verification_databases` for a list.
-
- z_probe_options : dict
- Dictionary of options passed to the :py:meth:`bob.db.verification.utils.ZTDatabase.z_probe_files` database query when retrieving files for Z-probing.
-
- kwargs : ``key=value`` pairs
- The arguments of the :py:class:`DatabaseBob` base class constructor.
-
- .. note:: Usually, the ``name``, ``protocol``, ``training_depends_on_protocol`` and ``models_depend_on_protocol`` keyword parameters of the :py:class:`Database` base class constructor need to be specified.
- """
-
- def __init__(
- self,
- database,
- z_probe_options = {}, # Limit the z-probes
- **kwargs
- ):
-# assert isinstance(database, bob.db.verification.utils.ZTDatabase) // fails in tests
- # call base class constructor, passing all the parameters to it
- DatabaseBob.__init__(self, database = database, z_probe_options = z_probe_options, **kwargs)
-
- self.z_probe_options = z_probe_options
-
-
- def all_files(self, groups = ['dev']):
- """all_files(groups=None) -> files
-
- Returns all files of the database, including those for ZT norm, respecting the current protocol.
- The files can be limited using the ``all_files_options`` and the the ``z_probe_options`` in the constructor.
-
- **Parameters:**
-
- groups : some of ``('world', 'dev', 'eval')`` or ``None``
- The groups to get the data for.
- If ``None``, data for all groups is returned.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The sorted and unique list of all files of the database.
- """
- files = self.database.objects(protocol = self.protocol, groups = groups, **self.all_files_options)
-
- # add all files that belong to the ZT-norm
- for group in groups:
- if group == 'world': continue
- files += self.database.tobjects(protocol = self.protocol, groups = group, model_ids = None)
- files += self.database.zobjects(protocol = self.protocol, groups = group, **self.z_probe_options)
- return self.sort(files)
-
-
- def t_model_ids(self, group = 'dev'):
- """t_model_ids(group = 'dev') -> ids
-
- Returns a list of model ids of T-Norm models for the given group, respecting the current protocol.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for T-Norm models of the given group.
- """
- return sorted(self.database.t_model_ids(protocol = self.protocol, groups = group))
-
-
- def t_enroll_files(self, t_model_id, group = 'dev'):
- """t_enroll_files(t_model_id, group = 'dev') -> files
-
- Returns a list of File objects that should be used to enroll the T-Norm model with the given model id from the given group, respecting the current protocol.
-
- **Parameters:**
-
- t_model_id : int or str
- A unique ID that identifies the model.
-
- group : one of ``('dev', 'eval')``
- The group to get the enrollment files for.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The sorted list of files used for to enroll the model with the given model id.
- """
- return self.sort(self.database.t_enroll_files(protocol = self.protocol, groups = group, model_id = t_model_id))
-
-
- def z_probe_files(self, group = 'dev'):
- """z_probe_files(group = 'dev') -> files
-
- Returns a list of probe files used to compute the Z-Norm, respecting the current protocol.
- The Z-probe files can be limited using the ``z_probe_options`` in the query to :py:meth:`bob.db.verification.utils.ZTDatabase.z_probe_files`
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the Z-norm probe files for.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.utils.File`]
- The unique list of files used to compute the Z-norm.
- """
- files = self.database.z_probe_files(protocol = self.protocol, groups = group, **self.z_probe_options)
- return self.sort(files)
-
-
- def z_probe_file_sets(self, group = 'dev'):
- """z_probe_file_sets(group = 'dev') -> files
-
- Returns a list of probe FileSet objects used to compute the Z-Norm.
- The Z-probe files can be limited using the ``z_probe_options`` in the query to
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the Z-norm probe files for.
-
- **Returns:**
-
- files : [:py:class:`FileSet`] or similar
- The unique list of file sets used to compute the Z-norm.
- """
- file_sets = self.database.z_probe_file_sets(protocol = self.protocol, groups = group, **self.z_probe_options)
- return self.sort(file_sets)
diff --git a/bob/bio/base/database/DatabaseFileList.py b/bob/bio/base/database/DatabaseFileList.py
deleted file mode 100644
index e78bf9465633f8295cb6f539e4d160b6614ec55c..0000000000000000000000000000000000000000
--- a/bob/bio/base/database/DatabaseFileList.py
+++ /dev/null
@@ -1,168 +0,0 @@
-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
-# @date: Wed Oct 3 10:31:51 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-
-from .DatabaseBob import DatabaseBobZT
-import bob.db.verification.filelist
-
-class DatabaseFileList (DatabaseBobZT):
- """This class can be used whenever you have a database that uses the Bob filelist database interface, which is defined in :py:class:`bob.db.verification.filelist.Database`
-
- **Parameters:**
-
- database : a :py:class:`bob.db.verification.filelist.Database`
- The database instance that provides the actual interface.
-
- kwargs : ``key=value`` pairs
- The arguments of the :py:class:`DatabaseBobZT` or :py:class:`DatabaseBob` base class constructors.
-
- .. note:: Usually, the ``name``, ``protocol``, ``training_depends_on_protocol`` and ``models_depend_on_protocol`` keyword parameters of the base class constructor need to be specified.
- """
-
- def __init__(
- self,
- database, # The bob database that is used
- **kwargs # The default parameters of the base class
- ):
-
- DatabaseBobZT.__init__(
- self,
- database = database,
- **kwargs
- )
-
- assert isinstance(database, bob.db.verification.filelist.Database)
-
-
- def all_files(self, groups = ['dev']):
- """all_files(groups=None) -> files
-
- Returns all files of the database, respecting the current protocol.
- If the current protocol is ``'None'``, ``None`` will be used instead.
- When the underlying file list database provides files for ZT score normalization, these files are returned as well.
- The files can be limited using the ``all_files_options`` in the constructor.
-
- **Parameters:**
-
- groups : some of ``('world', 'dev', 'eval')`` or ``None``
- The groups to get the data for.
- If ``None``, data for all groups is returned.
-
- **Returns:**
-
- files : [:py:class:`bob.db.verification.filelist.File`]
- The sorted and unique list of all files of the database.
- """
- protocol = self.protocol if self.protocol != 'None' else None
- files = self.database.objects(protocol = protocol, groups = groups, **self.all_files_options)
-
- # add all files that belong to the ZT-norm
- for group in groups:
- if group == 'world': continue
- if self.database.implements_zt(protocol = protocol, groups = group):
- files += self.database.tobjects(protocol = protocol, groups = group, model_ids = None)
- files += self.database.zobjects(protocol = protocol, groups = group, **self.z_probe_options)
- return self.sort(files)
-
-
- def uses_probe_file_sets(self):
- """File sets are not (yet) supported in the :py:class:`bob.db.verification.filelist.Database`, so this function returns ``False`` throughout."""
- return False
-
-
- def model_ids(self, group = 'dev'):
- """model_ids(group = 'dev') -> ids
-
- Returns a list of model ids for the given group, respecting the current protocol.
- If the current protocol is ``'None'``, ``None`` will be used instead.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [str]
- The list of (unique) model ids for the given group.
- """
- return sorted(self.database.model_ids(protocol = self.protocol if self.protocol != 'None' else None, groups = group))
-
-
- def client_id_from_model_id(self, model_id, group = 'dev'):
- """client_id_from_model_id(model_id, group = 'dev') -> client_id
-
- Uses :py:meth:`bob.db.verification.filelist.Database.get_client_id_from_model_id` to retrieve the client id for the given model id.
- If the current protocol is ``'None'``, ``None`` will be used instead.
-
- **Parameters:**
-
- model_id : str
- A unique ID that identifies the model for the client.
-
- group : one of ``('dev', 'eval')``
- The group to get the client ids for.
-
- **Returns:**
-
- client_id : str
- A unique ID that identifies the client, to which the model belongs.
- """
- return self.database.get_client_id_from_model_id(model_id, groups = group, protocol = self.protocol if self.protocol != 'None' else None)
-
-
- def client_id_from_t_model_id(self, t_model_id, group = 'dev'):
- """client_id_from_t_model_idt_(model_id, group = 'dev') -> client_id
-
- Uses :py:meth:`bob.db.verification.filelist.Database.get_client_id_from_t_model_id` to retrieve the client id for the T-norm given model id.
- If the current protocol is ``'None'``, ``None`` will be used instead.
-
- **Parameters:**
-
- t_model_id : str
- A unique ID that identifies the T-Norm model.
-
- group : one of ``('dev', 'eval')``
- The group to get the client ids for.
-
- **Returns:**
-
- client_id : str
- A unique ID that identifies the client, to which the T-Norm model belongs.
- """
- return self.database.get_client_id_from_tmodel_id(t_model_id, groups = group, protocol = self.protocol if self.protocol != 'None' else None)
-
-
- def t_model_ids(self, group = 'dev'):
- """t_model_ids(group = 'dev') -> ids
-
- Returns a list of model ids of T-Norm models for the given group, respecting the current protocol.
- If the current protocol is ``'None'``, ``None`` will be used instead.
-
- **Parameters:**
-
- group : one of ``('dev', 'eval')``
- The group to get the model ids for.
-
- **Returns:**
-
- ids : [int] or [str]
- The list of (unique) model ids for T-Norm models of the given group.
- """
- return sorted(self.database.tmodel_ids(protocol = self.protocol if self.protocol != 'None' else None, groups = group))
diff --git a/bob/bio/base/database/__init__.py b/bob/bio/base/database/__init__.py
deleted file mode 100644
index 945cd33ebec6cc299460208f41a20b86ee0eeea6..0000000000000000000000000000000000000000
--- a/bob/bio/base/database/__init__.py
+++ /dev/null
@@ -1,8 +0,0 @@
-from .utils import File, FileSet
-
-from .Database import Database, DatabaseZT
-from .DatabaseBob import DatabaseBob, DatabaseBobZT
-from .DatabaseFileList import DatabaseFileList
-
-# gets sphinx autodoc done right - don't remove it
-__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/base/database/utils.py b/bob/bio/base/database/utils.py
deleted file mode 100644
index 8473d07ef4123a15287e587318b57999da7818de..0000000000000000000000000000000000000000
--- a/bob/bio/base/database/utils.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import os
-
-class File:
- """This class defines the minimum interface of a database file that needs to be exported.
-
- Each file has a path, an id and an associated client (aka. identity, person, user).
- Usually, this file is part of a database, which has a common directory for all files.
- The path of this file is usually *relative* to that common directory, and it is usually stored *without* filename extension.
- The file id can be anything hashable, but needs to be unique all over the database.
- The client id can be anything hashable, but needs to be identical for different files of the same client, and different between clients.
-
- **Parameters:**
-
- file_id : str or int
- A unique ID that identifies the file.
- This ID might be identical to the ``path``, though integral IDs perform faster.
-
- client_id : str or int
- A unique ID that identifies the client (user) to which this file belongs.
- This ID might be the name of the person, though integral IDs perform faster.
-
- path : str
- The file path of the file, which is relative to the common database directory, and without filename extension.
- """
-
- def __init__(self, file_id, client_id, path):
- # The **unique** id of the file
- self.id = file_id
- # The id of the client that is attached to the file
- self.client_id = client_id
- # The **relative** path of the file according to the base directory of the database, without file extension
- self.path = path
-
- def __lt__(self, other):
- """Defines an order between files by using the order of the file ids."""
- # compare two File objects by comparing their IDs
- return self.id < other.id
-
- def make_path(self, directory = None, extension = None):
- """make_path(directory = None, extension = None) -> path
-
- Generates the full path using the given directory and filename extension.
-
- **Parameters:**
-
- directory : str or ``None``
- The directory to prepend.
- If ``None``, no directory will be preprended.
-
- extension : str or ``None``
- The filename extension to append.
- If ``None``, no file name extension will be appended.
-
- **Returns:**
-
- path : str
- The full path including directory and extension.
- """
- if directory is None: directory = '.'
- if extension is None: extension = ''
-
- return os.path.join(directory, self.path + extension)
-
-
-class FileSet:
- """This class defines the minimum interface of a set of database files that needs to be exported.
-
- Use this class, whenever the database provides several files that belong to the same probe.
-
- Each file set has an id, and a list of associated files, which are of type :py:class:`File` of the same client.
- The file set id can be anything hashable, but needs to be unique all over the database.
-
- **Parameters:**
-
- file_set_id : str or int
- A unique ID that identifies the file set.
-
- files : [:py:class:`File`]
- A list of File objects that should be stored inside this file.
- All files of that list need to have the same client ID.
- """
-
- def __init__(self, file_set_id, files, path=None):
- # The **unique** id of the file set
- self.id = file_set_id
- # The id of the client that is attached to the file
- assert len(files)
- self.client_id = files[0].client_id
- assert all(f.client_id == self.client_id for f in files)
- # The list of files contained in this set
- self.files = files
- self.path = "+".join(f.path for f in files)
-
- def __lt__(self, other):
- """Defines an order between file sets by using the order of the file set ids."""
- # compare two File set objects by comparing their IDs
- return self.id < other.id
diff --git a/bob/bio/base/extractor/Extractor.py b/bob/bio/base/extractor/Extractor.py
index 6dd59a5536d7ecd604235bb7202f4bcd096cf4ff..4a0dbcd8f0c3aded41d11eecbbfafd44a8da4a67 100644
--- a/bob/bio/base/extractor/Extractor.py
+++ b/bob/bio/base/extractor/Extractor.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Tue Oct 2 12:12:39 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os
diff --git a/bob/bio/base/extractor/Linearize.py b/bob/bio/base/extractor/Linearize.py
index d686bd709421276b1eae6a4839b14de261d490b8..be71e0fe1ad621ffbb1c70029e297d2baff22325 100644
--- a/bob/bio/base/extractor/Linearize.py
+++ b/bob/bio/base/extractor/Linearize.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Fri Oct 26 17:05:40 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
from .Extractor import Extractor
import numpy
diff --git a/bob/bio/base/grid.py b/bob/bio/base/grid.py
index a710bada92feca1c2ed099ba73a4a1bd56244252..def7125b0920f830f3de2dc743499d41da71efc9 100644
--- a/bob/bio/base/grid.py
+++ b/bob/bio/base/grid.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Tue Oct 2 12:12:39 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
PREDEFINED_QUEUES = {
diff --git a/bob/bio/base/preprocessor/Filename.py b/bob/bio/base/preprocessor/Filename.py
index a1ab0f6448d125865bfcf5253ed2ef6a790472cf..06db452fe7b5d051d3f949a86fad7eff88a07c56 100644
--- a/bob/bio/base/preprocessor/Filename.py
+++ b/bob/bio/base/preprocessor/Filename.py
@@ -1,18 +1,5 @@
# @date Wed May 11 12:39:37 MDT 2016
# @author Manuel Gunther <siebenkopf@googlemail.com>
-#
-# Copyright (c) 2016, Regents of the University of Colorado on behalf of the University of Colorado Colorado Springs.
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-#
-# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-#
-# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-#
-# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import bob.io.base
@@ -23,7 +10,7 @@ from .Preprocessor import Preprocessor
class Filename (Preprocessor):
"""This preprocessor is simply passing over the file name, in order to be used in an extractor that loads the data from file.
- The file name that will be returned by the :py:meth:`read_data` function will contain the path of the :py:class:`bob.db.verification.utils.File`, but it might contain more paths (such as the ``--preprocessed-directory`` passed on command line).
+ The file name that will be returned by the :py:meth:`read_data` function will contain the path of the :py:class:`bob.bio.db.BioFile`, but it might contain more paths (such as the ``--preprocessed-directory`` passed on command line).
"""
def __init__(self):
diff --git a/bob/bio/base/preprocessor/Preprocessor.py b/bob/bio/base/preprocessor/Preprocessor.py
index 4203b518afd145fc47dacbff4ae8b57135deca69..268a7b7a16f2fb67864a98f526eca7e64f78f4ca 100644
--- a/bob/bio/base/preprocessor/Preprocessor.py
+++ b/bob/bio/base/preprocessor/Preprocessor.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Tue Oct 2 12:12:39 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
import bob.io.base
diff --git a/bob/bio/base/script/collect_results.py b/bob/bio/base/script/collect_results.py
index b9438c0e2863ebfeade6d857cf0ec59de8fcc429..1aacf2578c99cb5e9119da24de9ac4acadd8d8ca 100644
--- a/bob/bio/base/script/collect_results.py
+++ b/bob/bio/base/script/collect_results.py
@@ -2,20 +2,7 @@
# vim: set fileencoding=utf-8 :
# Manuel Guenther <manuel.guenther@idiap.ch>
# Tue Jul 2 14:52:49 CEST 2013
-#
-# Copyright (C) 2011-2013 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
from __future__ import print_function
"""
diff --git a/bob/bio/base/script/evaluate.py b/bob/bio/base/script/evaluate.py
index 80f47778f3bf7d3e3668ef5284f050362860a0ec..a48eebf0d915aa43d2b01a39311ea0e7a1f29fbd 100644
--- a/bob/bio/base/script/evaluate.py
+++ b/bob/bio/base/script/evaluate.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# Manuel Guenther <manuel.guenther@idiap.ch>
# Tue Jul 2 14:52:49 CEST 2013
-#
-# Copyright (C) 2011-2013 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the ipyplotied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
@@ -70,7 +56,7 @@ def command_line_arguments(command_line_parameters):
parser.add_argument('-R', '--roc', help = "If given, ROC curves will be plotted into the given pdf file.")
parser.add_argument('-D', '--det', help = "If given, DET curves will be plotted into the given pdf file.")
parser.add_argument('-C', '--cmc', help = "If given, CMC curves will be plotted into the given pdf file.")
- parser.add_argument('-E', '--epc', help = "If given, EPC curves will be plotted into the given pdf file. For this plot --eval-files is mandatory.")
+ parser.add_argument('-E', '--epc', help = "If given, EPC curves will be plotted into the given pdf file. For this plot --eval-files is mandatory.")
parser.add_argument('--parser', default = '4column', choices = ('4column', '5column'), help="The style of the resulting score files. The default fits to the usual output of score files.")
# add verbose option
@@ -178,9 +164,9 @@ def _plot_cmc(cmcs, colors, labels, title, fontsize=18, position=None):
pyplot.title(title)
return figure
-
-
-
+
+
+
def _plot_epc(scores_dev, scores_eval, colors, labels, title, fontsize=18, position=None):
if position is None: position = 4
# open new page for current plot
@@ -198,7 +184,7 @@ def _plot_epc(scores_dev, scores_eval, colors, labels, title, fontsize=18, posit
pyplot.legend(loc=position, prop = {'size':fontsize})
pyplot.title(title)
- return figure
+ return figure
@@ -234,15 +220,15 @@ def main(command_line_parameters=None):
# apply threshold to development set
far, frr = bob.measure.farfrr(scores_dev[i][0], scores_dev[i][1], threshold)
if args.criterion == 'FAR':
- print("The FRR at FAR=%2.3f%% of the development set of '%s' is %2.3f%% (CAR: %2.3f%%)" % (args.far_value, args.legends[i], frr * 100., 100.*(1-frr)))
- else:
+ print("The FRR at FAR=%2.3f%% of the development set of '%s' is %2.3f%% (CAR: %2.3f%%)" % (args.far_value, args.legends[i], frr * 100., 100.*(1-frr)))
+ else:
print("The %s of the development set of '%s' is %2.3f%%" % (args.criterion, args.legends[i], (far + frr) * 50.)) # / 2 * 100%
if args.eval_files:
# apply threshold to evaluation set
far, frr = bob.measure.farfrr(scores_eval[i][0], scores_eval[i][1], threshold)
if args.criterion == 'FAR':
print("The FRR of the evaluation set of '%s' is %2.3f%% (CAR: %2.3f%%)" % (args.legends[i], frr * 100., 100.*(1-frr))) # / 2 * 100%
- else:
+ else:
print("The HTER of the evaluation set of '%s' is %2.3f%%" % (args.legends[i], (far + frr) * 50.)) # / 2 * 100%
@@ -318,10 +304,10 @@ def main(command_line_parameters=None):
if args.epc:
logger.info("Plotting EPC curves to file '%s'", args.epc)
-
+
if not args.eval_files:
raise ValueError("To plot the EPC curve the evaluation scores are necessary. Please, set it with the --eval-files option.")
-
+
try:
# create a multi-page PDF for the ROC curve
pdf = PdfPages(args.epc)
diff --git a/bob/bio/base/script/fuse_scores.py b/bob/bio/base/script/fuse_scores.py
index f8b94d0a748d02a22b606f4d915e8089e57c91d9..693e6ec651842210ed42fb2df0213319386386d2 100755
--- a/bob/bio/base/script/fuse_scores.py
+++ b/bob/bio/base/script/fuse_scores.py
@@ -4,20 +4,6 @@
# Elie El Khoury <elie.khoury@idiap.ch>
# Manuel Guenther <siebenkopf@googlemail.com>
# Mon 13 Jul 11:55:34 CEST 2015
-#
-# Copyright (C) 2011-2013 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""This script fuses scores from various systems, from a score file in four or five column format.
diff --git a/bob/bio/base/script/grid_search.py b/bob/bio/base/script/grid_search.py
index 73287b174303e8cf55e584b8af0b2f838f7b3e15..ea2dc5e8594291b8008a9bc06322b78ff4b84a75 100755
--- a/bob/bio/base/script/grid_search.py
+++ b/bob/bio/base/script/grid_search.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Manuel Guenther <Manuel.Guenther@idiap.ch>
+
from __future__ import print_function
from . import verify
diff --git a/bob/bio/base/script/preprocess.py b/bob/bio/base/script/preprocess.py
index ddc175402497ef13e8c673174c42d1fb31035097..1014196ac414a4cb7307fdbc1db5e1171cc95de9 100644
--- a/bob/bio/base/script/preprocess.py
+++ b/bob/bio/base/script/preprocess.py
@@ -6,7 +6,7 @@ import bob.core
logger = bob.core.log.setup("bob.bio.base")
import bob.bio.base
-import bob.db.verification.utils
+import bob.db.base
import numpy
import bob.core
@@ -47,7 +47,7 @@ def main(command_line_parameters=None):
logger.debug("Loading input data from file '%s'%s", args.input_file, " and '%s'" % args.annotation_file if args.annotation_file is not None else "")
data = preprocessor.read_original_data(args.input_file)
- annotations = bob.db.verification.utils.read_annotation_file(args.annotation_file, 'named') if args.annotation_file is not None else None
+ annotations = bob.db.base.annotations.read_annotation_file(args.annotation_file, 'named') if args.annotation_file is not None else None
logger.info("Preprocessing data")
preprocessed = preprocessor(data, annotations)
diff --git a/bob/bio/base/test/dummy/database.py b/bob/bio/base/test/dummy/database.py
index 90c440ea290a024c93fe3fbc5648556fca6f7d0b..d80dc5e4a68bfe605044558609be6e2c4f37ea28 100644
--- a/bob/bio/base/test/dummy/database.py
+++ b/bob/bio/base/test/dummy/database.py
@@ -1,34 +1,40 @@
-import bob.db.atnt
-import os
-
-from bob.bio.base.database import DatabaseBob, DatabaseBobZT
+from bob.bio.db import ZTBioDatabase, AtntBioDatabase
from bob.bio.base.test.utils import atnt_database_directory
-class DummyDatabase (DatabaseBobZT):
- def __init__(self):
- # call base class constructor with useful parameters
- DatabaseBobZT.__init__(
- self,
- database = bob.db.atnt.Database(
- original_directory = atnt_database_directory()
- ),
- name = 'test',
- check_original_files_for_existence = True,
- training_depends_on_protocol = False,
- models_depend_on_protocol = False
- )
+class DummyDatabase(ZTBioDatabase):
+
+ def __init__(self):
+ # call base class constructor with useful parameters
+ super(DummyDatabase, self).__init__(
+ name='test',
+ original_directory=atnt_database_directory(),
+ original_extension='.pgm',
+ check_original_files_for_existence=True,
+ training_depends_on_protocol=False,
+ models_depend_on_protocol=False
+ )
+ self.__db = AtntBioDatabase()
+
+ def model_ids(self, groups=None, protocol=None, gender=None):
+ return self.__db.model_ids(groups, protocol, gender)
+
+ def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
+ return self.__db.objects(groups, protocol, purposes, model_ids, **kwargs)
+
+ def tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs):
+ return []
- def all_files(self, groups = ['dev']):
- return DatabaseBob.all_files(self, groups)
+ def zobjects(self, groups=None, protocol=None, **kwargs):
+ return []
- def t_model_ids(self, group = 'dev'):
- return self.model_ids(group)
+ def tmodel_ids(self, protocol=None, groups=None, **kwargs):
+ return self.__db.model_ids(groups)
- def t_enroll_files(self, t_model_id, group = 'dev'):
- return self.enroll_files(t_model_id, group)
+ def t_enroll_files(self, t_model_id, group='dev'):
+ return self.__db.enroll_files(t_model_id, group)
- def z_probe_files(self, group = 'dev'):
- return self.probe_files(None, group)
+ def z_probe_files(self, group='dev'):
+ return self.__db.probe_files(None, group)
database = DummyDatabase()
diff --git a/bob/bio/base/test/dummy/filelist.py b/bob/bio/base/test/dummy/filelist.py
deleted file mode 100644
index dc59e4a170147bf32fe1e3f274668127df248f32..0000000000000000000000000000000000000000
--- a/bob/bio/base/test/dummy/filelist.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import bob.db.verification.filelist
-from bob.bio.base.database import DatabaseFileList
-from bob.bio.base.test.utils import atnt_database_directory
-import pkg_resources
-
-database = DatabaseFileList(
- database = bob.db.verification.filelist.Database(
- base_dir = pkg_resources.resource_filename('bob.bio.base.test', 'data/atnt'),
- original_directory = atnt_database_directory(),
- original_extension = ".pgm",
- dev_subdir = '.',
- eval_subdir = '.',
- world_filename = 'world.lst',
- models_filename = 'models.lst',
- probes_filename = 'probes.lst',
- tnorm_filename = 'models.lst',
- znorm_filename = 'probes.lst',
- keep_read_lists_in_memory = True
- ),
- name = 'test_filelist',
- protocol = None,
- check_original_files_for_existence = True,
- training_depends_on_protocol = False,
- models_depend_on_protocol = False
-)
diff --git a/bob/bio/base/test/dummy/fileset.py b/bob/bio/base/test/dummy/fileset.py
index 17fb51b7f171001d5d8ade8b2f958ebd5e153e14..9c829bd23faac5fa4cc5bd8b28c39a026e78ad77 100644
--- a/bob/bio/base/test/dummy/fileset.py
+++ b/bob/bio/base/test/dummy/fileset.py
@@ -1,53 +1,60 @@
-import bob.db.atnt
-import os
-
-from bob.bio.base.database import DatabaseBob, DatabaseBobZT, File, FileSet
+from bob.bio.db import ZTBioDatabase, BioFileSet, BioFile, AtntBioDatabase
from bob.bio.base.test.utils import atnt_database_directory
-class FileSetDatabase (DatabaseBobZT):
-
- def __init__(self):
- # call base class constructor with useful parameters
- DatabaseBobZT.__init__(
- self,
- database = bob.db.atnt.Database(
- original_directory = atnt_database_directory(),
- ),
- name = 'test_fileset',
- check_original_files_for_existence = True,
- training_depends_on_protocol = False,
- models_depend_on_protocol = False
- )
-
- def uses_probe_file_sets(self):
- return True
-
- def probe_file_sets(self, model_id = None, group = 'dev'):
- """Returns the list of probe File objects (for the given model id, if given)."""
- files = self.arrange_by_client(self.sort(self.database.objects(protocol = None, groups = group, purposes = 'probe')))
- # arrange files by clients
- file_sets = []
- for client_files in files:
- # convert into our File objects (so that they are tested as well)
- our_files = [File(f.id, f.client_id, f.path) for f in client_files]
- # generate file set for each client
- file_set = FileSet(our_files[0].client_id, our_files)
- file_sets.append(file_set)
- return file_sets
-
- def all_files(self, groups = ['dev']):
- return DatabaseBob.all_files(self, groups)
-
- def t_model_ids(self, group = 'dev'):
- return self.model_ids(group)
-
- def t_enroll_files(self, t_model_id, group = 'dev'):
- return self.enroll_files(t_model_id, group)
-
- def z_probe_files(self, group = 'dev'):
- return self.probe_files(None, group)
-
- def z_probe_file_sets(self, group = 'dev'):
- return self.probe_file_sets(None, group)
-
-database = FileSetDatabase()
+
+class DummyDatabase(ZTBioDatabase):
+
+ def __init__(self):
+ # call base class constructor with useful parameters
+ super(DummyDatabase, self).__init__(
+ name='test_fileset',
+ original_directory=atnt_database_directory(),
+ original_extension='.pgm',
+ check_original_files_for_existence=True,
+ training_depends_on_protocol=False,
+ models_depend_on_protocol=False
+ )
+ self.__db = AtntBioDatabase()
+
+ def uses_probe_file_sets(self):
+ return True
+
+ def probe_file_sets(self, model_id=None, group='dev'):
+ """Returns the list of probe File objects (for the given model id, if given)."""
+ # import ipdb; ipdb.set_trace()
+ files = self.arrange_by_client(self.sort(self.objects(protocol=None, groups=group, purposes='probe')))
+ # arrange files by clients
+ file_sets = []
+ for client_files in files:
+ # convert into our File objects (so that they are tested as well)
+ our_files = [BioFile(f.client_id, f.path, f.id) for f in client_files]
+ # generate file set for each client
+ file_set = BioFileSet(our_files[0].client_id, our_files)
+ file_sets.append(file_set)
+ return file_sets
+
+ def model_ids(self, groups=None, protocol=None, gender=None):
+ return self.__db.model_ids(groups, protocol, gender)
+
+ def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
+ return self.__db.objects(groups, protocol, purposes, model_ids, **kwargs)
+
+ def tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs):
+ return []
+
+ def zobjects(self, groups=None, protocol=None, **kwargs):
+ return []
+
+ def tmodel_ids(self, protocol=None, groups=None, **kwargs):
+ return self.__db.model_ids(groups)
+
+ def t_enroll_files(self, t_model_id, group='dev'):
+ return self.__db.enroll_files(t_model_id, group)
+
+ def z_probe_files(self, group='dev'):
+ return self.__db.probe_files(None, group)
+
+ def z_probe_file_sets(self, group='dev'):
+ return self.probe_file_sets(None, group)
+
+database = DummyDatabase()
diff --git a/bob/bio/base/test/test_algorithms.py b/bob/bio/base/test/test_algorithms.py
index f479f737d799bd56c2b9131003abd24d2acfa671..1afbc7f9c4116127d1f042b5f937646bef8f70f6 100644
--- a/bob/bio/base/test/test_algorithms.py
+++ b/bob/bio/base/test/test_algorithms.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Thu May 24 10:41:42 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os
import shutil
@@ -220,7 +206,7 @@ def test_lda():
def test_distance():
import scipy.spatial
-
+
# assure that the configurations are loadable
distance = bob.bio.base.load_resource("distance-cosine", "algorithm", preferred_package = 'bob.bio.base')
assert isinstance(distance, bob.bio.base.algorithm.Distance)
@@ -231,17 +217,17 @@ def test_distance():
assert distance.use_projected_features_for_enrollment == False
assert distance.split_training_features_by_client == False
assert distance.requires_enroller_training == False
-
+
distance = bob.bio.base.algorithm.Distance(
distance_function = scipy.spatial.distance.cosine,
is_distance_function = True
- )
+ )
# compare model with probe
enroll = utils.random_training_set(5, 5, 0., 255., seed=21);
model = numpy.mean(distance.enroll(enroll),axis=0)
probe = distance.read_probe(pkg_resources.resource_filename('bob.bio.base.test', 'data/lda_projected.hdf5'))
-
+
reference_score = -0.1873371
assert abs(distance.score(model, probe) - reference_score) < 1e-5, "The scores differ: %3.8f, %3.8f" % (distance.score(model, probe), reference_score)
diff --git a/bob/bio/base/test/test_databases.py b/bob/bio/base/test/test_databases.py
deleted file mode 100644
index 8691421ba4464073da3992b99a8f2939d43e91af..0000000000000000000000000000000000000000
--- a/bob/bio/base/test/test_databases.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-# vim: set fileencoding=utf-8 :
-# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
-# @date: Thu May 24 10:41:42 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-
-import os
-from nose.plugins.skip import SkipTest
-
-import bob.bio.base
-
-import pkg_resources
-dummy_dir = pkg_resources.resource_filename('bob.bio.base', 'test/dummy')
-
-def test_verification_filelist():
- try:
- db1 = bob.bio.base.load_resource(os.path.join(dummy_dir, 'database.py'), 'database')
- except Exception as e:
- raise SkipTest("This test is skipped since the atnt database is not available.")
- try:
- db2 = bob.bio.base.load_resource(os.path.join(dummy_dir, 'filelist.py'), 'database')
- except Exception as e:
- raise SkipTest("This test is skipped since the verification.filelist database is not available.")
- # The test of the verification.filelist database is a bit different.
- # here, we test the output of two different ways of querying the AT&T database
- # where actually both ways are uncommon...
-
- # assure that different kind of queries result in the same file lists
- assert set([str(id) for id in db1.model_ids()]) == set(db2.model_ids())
- assert set([str(id) for id in db1.t_model_ids()]) == set(db2.t_model_ids())
-
- def _check_files(f1, f2):
- assert set([file.path for file in f1]) == set([file.path for file in f2])
-
- _check_files(db1.all_files(), db2.all_files())
- _check_files(db1.training_files('train_extractor'), db2.training_files('train_extractor'))
- _check_files(db1.enroll_files(model_id=22), db2.enroll_files(model_id='22'))
- _check_files(db1.probe_files(model_id=22), db2.probe_files(model_id='22'))
-
- _check_files(db1.t_enroll_files(t_model_id=22), db2.t_enroll_files(t_model_id='22'))
- _check_files(db1.z_probe_files(), db2.z_probe_files())
-
- f1 = db1.all_files()[0]
- f2 = [f for f in db2.all_files() if f.path == f1.path][0]
-
- assert f1.make_path(directory='xx', extension='.yy') == f2.make_path(directory='xx', extension='.yy')
-
- m1 = sorted([str(id) for id in db1.model_ids()])[0]
- m2 = sorted([str(id) for id in db2.model_ids()])[0]
- assert str(db1.client_id_from_model_id(m1)) == db2.client_id_from_model_id(m2)
diff --git a/bob/bio/base/test/test_scripts.py b/bob/bio/base/test/test_scripts.py
index 57e10b908c820eca96b008dc9a41fd48eb96dcb2..20cb89a943c4fc1a1b5bfeae42bb5bc9d7f44eba 100644
--- a/bob/bio/base/test/test_scripts.py
+++ b/bob/bio/base/test/test_scripts.py
@@ -214,57 +214,6 @@ def test_verify_fileset():
_verify(parameters, test_dir, 'test_fileset', ref_modifier="-fileset")
-
-def test_verify_filelist():
- try:
- import bob.db.verification.filelist
- except ImportError:
- raise SkipTest("Skipping test since bob.db.verification.filelist is not available")
- test_dir = tempfile.mkdtemp(prefix='bobtest_')
- # define dummy parameters
- parameters = [
- '-d', os.path.join(dummy_dir, 'filelist.py'),
- '-p', 'dummy',
- '-e', 'dummy',
- '-a', 'dummy',
- '--zt-norm',
- '-vs', 'test_filelist',
- '--temp-directory', test_dir,
- '--result-directory', test_dir,
- '--preferred-package', 'bob.bio.base'
- ]
-
- print (bob.bio.base.tools.command_line(parameters))
-
- try:
- from bob.bio.base.script.verify import main
- main(parameters)
-
- # assert that the score file exists
- score_files = [os.path.join(test_dir, 'test_filelist', 'None', norm, 'scores-dev') for norm in ('nonorm', 'ztnorm')]
- assert os.path.exists(score_files[0]), "Score file %s does not exist" % score_files[0]
- assert os.path.exists(score_files[1]), "Score file %s does not exist" % score_files[1]
-
- # assert that the scores are are identical (might be in a different order, though
- reference_files = [os.path.join(data_dir, 'scores-%s-dev' % norm) for norm in ('nonorm', 'ztnorm')]
-
- for i in (0,1):
- # load scores
- a1, b1 = bob.measure.load.split_four_column(score_files[i])
- a2, b2 = bob.measure.load.split_four_column(reference_files[i])
- # sort scores
- a1 = sorted(a1); a2 = sorted(a2); b1 = sorted(b1); b2 = sorted(b2)
-
- # assert that scores are almost equal
- for i in range(len(a1)):
- abs(a1[i] - a2[i]) < 1e-6
- for i in range(len(b1)):
- abs(b1[i] - b2[i]) < 1e-6
-
- finally:
- shutil.rmtree(test_dir)
-
-
def test_verify_missing():
test_dir = tempfile.mkdtemp(prefix='bobtest_')
# define dummy parameters
diff --git a/bob/bio/base/test/utils.py b/bob/bio/base/test/utils.py
index bd1a9ff13957d0d4c08e49733e63cfd854686feb..7d757b036e28af9bf66ecab2d09f38e2ddc0c29d 100644
--- a/bob/bio/base/test/utils.py
+++ b/bob/bio/base/test/utils.py
@@ -2,20 +2,6 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Thu Jul 19 17:09:55 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
import numpy
import os
diff --git a/bob/bio/base/tools/FileSelector.py b/bob/bio/base/tools/FileSelector.py
index 2a3e56df2983f7390a8faa7dc1ad28d835b04b96..16592e26b1fd04593eb3d84e442daf3260ff93ba 100644
--- a/bob/bio/base/tools/FileSelector.py
+++ b/bob/bio/base/tools/FileSelector.py
@@ -110,6 +110,10 @@ class FileSelector:
"""Returns the list of original data that can be used for preprocessing."""
return self.database.original_file_names(self.database.all_files(groups=groups))
+ def original_data_list_files(self, groups = None):
+ """Returns the list of original data that can be used for preprocessing."""
+ return (self.database.all_files(groups=groups), self.database.original_directory, self.database.original_extension)
+
def annotation_list(self, groups = None):
"""Returns the list of annotations objects."""
return self.database.all_files(groups=groups)
@@ -154,7 +158,7 @@ class FileSelector:
def model_ids(self, group):
"""Returns the sorted list of model ids from the given group."""
- return sorted(self.database.model_ids(group = group))
+ return sorted(self.database.model_ids(groups=group))
def enroll_files(self, model_id, group, directory_type):
"""Returns the list of model feature files used for enrollment of the model with the given model_id from the given group.
@@ -186,7 +190,7 @@ class FileSelector:
def t_model_ids(self, group):
"""Returns the sorted list of T-Norm-model ids from the given group."""
- return sorted(self.database.t_model_ids(group = group))
+ return sorted(self.database.t_model_ids(groups = group))
def t_enroll_files(self, t_model_id, group, directory_type):
"""Returns the list of T-norm model files used for enrollment of the given model_id from the given group."""
diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index 765eb0bfc284548b9661cfe0d88ef238d372b25f..23211bb67f5cc09ba062fd27fb528fc5c0101f11 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -8,7 +8,7 @@ logger = bob.core.log.setup("bob.bio.base")
from .. import utils
from . import FileSelector
-from .. import database
+from bob.bio.db import BioDatabase
"""Execute biometric recognition algorithms on a certain biometric database.
"""
@@ -268,7 +268,7 @@ def initialize(parsers, command_line_parameters = None, skips = []):
model_sub_dir = protocol if args.database.models_depend_on_protocol else enroller_sub_dir
# Database directories, which should be automatically replaced
- if isinstance(args.database, database.DatabaseBob):
+ if isinstance(args.database, BioDatabase):
args.database.replace_directories(args.database_directories_file)
# initialize the file selector
diff --git a/bob/bio/base/tools/preprocessor.py b/bob/bio/base/tools/preprocessor.py
index 01dea478a7976255216d159ba4d1653d9c1e05b5..95a3772a758462f3221ecd31cf58c98344c528be 100644
--- a/bob/bio/base/tools/preprocessor.py
+++ b/bob/bio/base/tools/preprocessor.py
@@ -42,7 +42,7 @@ def preprocess(preprocessor, groups = None, indices = None, allow_missing_files
fs = FileSelector.instance()
# get the file lists
- data_files = fs.original_data_list(groups=groups)
+ data_files, original_directory, original_extension = fs.original_data_list_files(groups=groups)
preprocessed_data_files = fs.preprocessed_data_list(groups=groups)
# select a subset of keys to iterate
@@ -60,12 +60,19 @@ def preprocess(preprocessor, groups = None, indices = None, allow_missing_files
# iterate over the selected files
for i in index_range:
preprocessed_data_file = preprocessed_data_files[i]
- file_name = data_files[i]
+ file_object = data_files[i]
+ if isinstance(file_object, list):
+ file_name = [f.make_path(original_directory, original_extension) for f in file_object]
+ else:
+ file_name = file_object.make_path(original_directory, original_extension)
# check for existence
if not utils.check_file(preprocessed_data_file, force, 1000):
logger.debug("... Processing original data file '%s'", file_name)
- data = preprocessor.read_original_data(file_name)
+ if hasattr(file_object, 'load'):
+ data = file_object.load(original_directory, original_extension)
+ else:
+ data = preprocessor.read_original_data(file_name)
# create output directory before reading the data file (is sometimes required, when relative directories are specified, especially, including a .. somewhere)
bob.io.base.create_directories_safe(os.path.dirname(preprocessed_data_file))
diff --git a/bob/bio/base/utils/resources.py b/bob/bio/base/utils/resources.py
index 7a2b72926b4158066aa8bcf3a3af275c382bf5c9..8be8e0304d5dc243ef17b8919dc73557c19a3a4b 100644
--- a/bob/bio/base/utils/resources.py
+++ b/bob/bio/base/utils/resources.py
@@ -2,20 +2,7 @@
# vim: set fileencoding=utf-8 :
# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
# @date: Thu Oct 25 10:05:55 CEST 2012
-#
-# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
from __future__ import print_function
import imp
@@ -72,7 +59,7 @@ def read_config_file(filename, keyword = None):
if not hasattr(config, keyword):
raise ImportError("The desired keyword '%s' does not exist in your configuration file '%s'." %(keyword, filename))
- return eval('config.' + keyword)
+ return getattr(config, keyword)
def _get_entry_points(keyword, strip = [], package_prefix='bob.bio.'):
diff --git a/bootstrap-buildout.py b/bootstrap-buildout.py
index a629566735c1c84fbec7173f0f30015b2b432512..a4599211f741c468cd37a29861d1c7f2c3a641d1 100644
--- a/bootstrap-buildout.py
+++ b/bootstrap-buildout.py
@@ -25,7 +25,10 @@ import tempfile
from optparse import OptionParser
-tmpeggs = tempfile.mkdtemp()
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
usage = '''\
[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
@@ -40,8 +43,9 @@ this script from going over the network.
'''
parser = OptionParser(usage=usage)
-parser.add_option("-v", "--version", help="use a specific zc.buildout version")
-
+parser.add_option("--version",
+ action="store_true", default=False,
+ help=("Return bootstrap.py version."))
parser.add_option("-t", "--accept-buildout-test-releases",
dest='accept_buildout_test_releases',
action="store_true", default=False,
@@ -59,25 +63,33 @@ parser.add_option("-f", "--find-links",
parser.add_option("--allow-site-packages",
action="store_true", default=False,
help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--buildout-version",
+ help="Use a specific zc.buildout version")
parser.add_option("--setuptools-version",
- help="use a specific setuptools version")
-
+ help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+ help=("Allow for re-use of existing directory of "
+ "setuptools versions"))
options, args = parser.parse_args()
+if options.version:
+ print("bootstrap.py version %s" % __version__)
+ sys.exit(0)
+
######################################################################
# load/install setuptools
try:
- if options.allow_site_packages:
- import setuptools
- import pkg_resources
from urllib.request import urlopen
except ImportError:
from urllib2 import urlopen
ez = {}
-exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+if os.path.exists('ez_setup.py'):
+ exec(open('ez_setup.py').read(), ez)
+else:
+ exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
if not options.allow_site_packages:
# ez_setup imports site, which adds site packages
@@ -88,12 +100,19 @@ if not options.allow_site_packages:
# We can't remove these reliably
if hasattr(site, 'getsitepackages'):
for sitepackage_path in site.getsitepackages():
- sys.path[:] = [x for x in sys.path if sitepackage_path not in x]
+ # Strip all site-packages directories from sys.path that
+ # are not sys.prefix; this is because on Windows
+ # sys.prefix is a site-package directory.
+ if sitepackage_path != sys.prefix:
+ sys.path[:] = [x for x in sys.path
+ if sitepackage_path not in x]
setup_args = dict(to_dir=tmpeggs, download_delay=0)
if options.setuptools_version is not None:
setup_args['version'] = options.setuptools_version
+if options.setuptools_to_dir is not None:
+ setup_args['to_dir'] = options.setuptools_to_dir
ez['use_setuptools'](**setup_args)
import setuptools
@@ -110,7 +129,12 @@ for path in sys.path:
ws = pkg_resources.working_set
+setuptools_path = ws.find(
+ pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
cmd = [sys.executable, '-c',
+ 'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
'from setuptools.command.easy_install import main; main()',
'-mZqNxd', tmpeggs]
@@ -123,11 +147,8 @@ find_links = os.environ.get(
if find_links:
cmd.extend(['-f', find_links])
-setuptools_path = ws.find(
- pkg_resources.Requirement.parse('setuptools')).location
-
requirement = 'zc.buildout'
-version = options.version
+version = options.buildout_version
if version is None and not options.accept_buildout_test_releases:
# Figure out the most recent final version of zc.buildout.
import setuptools.package_index
@@ -167,7 +188,7 @@ if version:
cmd.append(requirement)
import subprocess
-if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+if subprocess.call(cmd) != 0:
raise Exception(
"Failed to execute command:\n%s" % repr(cmd)[1:-1])
diff --git a/buildout.cfg b/buildout.cfg
index 026c9c5b43130b84cad35f1baf92784666c3bd78..3a6d45fd0229c89762cb2b7370ac7db21fa05e0b 100644
--- a/buildout.cfg
+++ b/buildout.cfg
@@ -1,53 +1,13 @@
; vim: set fileencoding=utf-8 :
-; Manuel Guenther <manuel.guenther@idiap.ch>
-; Thu Oct 9 16:51:06 CEST 2014
+; Tue 16 Aug 15:00:20 CEST 2016
[buildout]
parts = scripts
+develop = .
eggs = bob.bio.base
- gridtk
-
extensions = bob.buildout
- mr.developer
-auto-checkout = *
-develop = src/bob.extension
- src/bob.blitz
- src/bob.core
- src/bob.io.base
- src/bob.learn.activation
- src/bob.math
- src/bob.learn.linear
- src/bob.sp
- src/bob.learn.em
- src/bob.measure
- src/bob.db.base
- src/bob.db.verification.utils
- src/bob.db.verification.filelist
- src/bob.db.atnt
- src/bob.io.image
- .
-
-; options for bob.buildout
-debug = true
-verbose = true
newest = false
-
-[sources]
-bob.extension = git https://github.com/bioidiap/bob.extension
-bob.blitz = git https://github.com/bioidiap/bob.blitz
-bob.core = git https://github.com/bioidiap/bob.core
-bob.io.base = git https://github.com/bioidiap/bob.io.base
-bob.learn.activation = git https://github.com/bioidiap/bob.learn.activation
-bob.math = git https://github.com/bioidiap/bob.math
-bob.sp = git https://github.com/bioidiap/bob.sp
-bob.learn.linear = git https://github.com/bioidiap/bob.learn.linear
-bob.learn.em = git https://github.com/bioidiap/bob.learn.em
-bob.measure = git https://github.com/bioidiap/bob.measure
-bob.db.base = git https://github.com/bioidiap/bob.db.base
-bob.db.verification.utils = git https://github.com/bioidiap/bob.db.verification.utils
-bob.db.verification.filelist = git https://github.com/bioidiap/bob.db.verification.filelist
-bob.db.atnt = git https://github.com/bioidiap/bob.db.atnt
-bob.io.image = git https://github.com/bioidiap/bob.io.image
+verbose = true
[scripts]
recipe = bob.buildout:scripts
diff --git a/develop.cfg b/develop.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..93d727bbf55adf056552f0fe14884902640cb054
--- /dev/null
+++ b/develop.cfg
@@ -0,0 +1,52 @@
+; vim: set fileencoding=utf-8 :
+; Manuel Guenther <manuel.guenther@idiap.ch>
+; Thu Oct 9 16:51:06 CEST 2014
+
+[buildout]
+parts = scripts
+eggs = bob.bio.base
+ gridtk
+
+extensions = bob.buildout
+ mr.developer
+auto-checkout = *
+develop = src/bob.extension
+ src/bob.blitz
+ src/bob.core
+ src/bob.io.base
+ src/bob.learn.activation
+ src/bob.math
+ src/bob.learn.linear
+ src/bob.sp
+ src/bob.learn.em
+ src/bob.measure
+ src/bob.db.base
+ src/bob.bio.db
+ src/bob.db.atnt
+ src/bob.io.image
+ .
+
+; options for bob.buildout
+debug = true
+verbose = true
+newest = false
+
+[sources]
+bob.extension = git https://gitlab.idiap.ch/bob/bob.extension
+bob.blitz = git https://gitlab.idiap.ch/bob/bob.blitz
+bob.core = git https://gitlab.idiap.ch/bob/bob.core
+bob.io.base = git https://gitlab.idiap.ch/bob/bob.io.base
+bob.learn.activation = git https://gitlab.idiap.ch/bob/bob.learn.activation
+bob.math = git https://gitlab.idiap.ch/bob/bob.math
+bob.sp = git https://gitlab.idiap.ch/bob/bob.sp
+bob.learn.linear = git https://gitlab.idiap.ch/bob/bob.learn.linear
+bob.learn.em = git https://gitlab.idiap.ch/bob/bob.learn.em
+bob.measure = git https://gitlab.idiap.ch/bob/bob.measure
+bob.db.base = git https://gitlab.idiap.ch/bob/bob.db.base
+bob.bio.db = git https://gitlab.idiap.ch/biometric/bob.bio.db
+bob.db.atnt = git https://gitlab.idiap.ch/bob/bob.db.atnt
+bob.io.image = git https://gitlab.idiap.ch/bob/bob.io.image
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true
diff --git a/doc/conf.py b/doc/conf.py
index 22958db4da9789a3eab05df5c2ec4a13255083fc..c4202fa542699899cfda121e7d4b36abe24e0db2 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,46 +1,47 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
-# Mon 13 Aug 2012 12:38:15 CEST
-#
-# Copyright (C) 2011-2014 Idiap Research Institute, Martigny, Switzerland
import os
import sys
import glob
import pkg_resources
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
# -- General configuration -----------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+needs_sphinx = '1.3'
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = [
- 'sphinx.ext.todo',
- 'sphinx.ext.coverage',
- 'sphinx.ext.pngmath',
- 'sphinx.ext.ifconfig',
- 'sphinx.ext.autodoc',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.doctest',
- 'sphinx.ext.intersphinx',
- ]
+ 'sphinx.ext.todo',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.ifconfig',
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.autosummary',
+ 'sphinx.ext.doctest',
+ 'sphinx.ext.graphviz',
+ 'sphinx.ext.intersphinx',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.viewcode',
+ ]
-# The viewcode extension appeared only on Sphinx >= 1.0.0
import sphinx
-if sphinx.__version__ >= "1.0":
- extensions.append('sphinx.ext.viewcode')
+if sphinx.__version__ >= "1.4.1":
+ extensions.append('sphinx.ext.imgmath')
+else:
+ extensions.append('sphinx.ext.pngmath')
# Always includes todos
todo_include_todos = True
+# Generates auto-summary automatically
+autosummary_generate = True
+
+# Create numbers on figures with captions
+numfig = True
+
# If we are on OSX, the 'dvipng' path maybe different
dvipng_osx = '/opt/local/libexec/texlive/binaries/dvipng'
if os.path.exists(dvipng_osx): pngmath_dvipng = dvipng_osx
@@ -58,12 +59,12 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
-project = u'Bobs interface for running biometric recognition experiments'
+project = u'bob.bio.base'
import time
copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
# Grab the setup entry
-distribution = pkg_resources.require('bob.bio.base')[0]
+distribution = pkg_resources.require(project)[0]
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -108,13 +109,18 @@ pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
+# Some variables which are useful for generated material
+project_variable = project.replace('.', '_')
+short_description = u'Tools for running biometric recognition experiments'
+owner = [u'Idiap Research Institute']
+
# -- Options for HTML output ---------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-if sphinx.__version__ >= "1.0":
- html_theme = 'nature'
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
@@ -122,14 +128,14 @@ if sphinx.__version__ >= "1.0":
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = 'bob'
+#html_short_title = project_variable
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
@@ -187,105 +193,48 @@ html_favicon = 'img/favicon.ico'
#html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'bob_bio_base_doc'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-# The paper size ('letter' or 'a4').
-latex_paper_size = 'a4'
-
-# The font size ('10pt', '11pt' or '12pt').
-latex_font_size = '10pt'
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', 'bob_bio_base.tex', u'Bob',
- u'Biometrics Group, Idiap Research Institute', 'manual'),
-]
+htmlhelp_basename = project_variable + u'_doc'
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = ''
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
+# -- Post configuration --------------------------------------------------------
# Included after all input documents
-rst_epilog = ''
-
-# -- Options for manual page output --------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- ('index', 'bob.bio.base', u'Base tools to run biometric recognition experiments', [u'Idiap Research Institute'], 1)
-]
+rst_epilog = """
+.. |project| replace:: Bob
+.. |version| replace:: %s
+.. |current-year| date:: %%Y
+""" % (version,)
# Default processing flags for sphinx
-autoclass_content = 'both'
+autoclass_content = 'class'
autodoc_member_order = 'bysource'
-autodoc_default_flags = ['members', 'inherited-members', 'show-inheritance']
+autodoc_default_flags = [
+ 'members',
+ 'undoc-members',
+ 'inherited-members',
+ 'show-inheritance',
+ ]
# For inter-documentation mapping:
from bob.extension.utils import link_documentation
-intersphinx_mapping = link_documentation(['python', 'numpy', 'bob.bio.face', 'bob.bio.speaker', 'bob.bio.gmm', 'bob.bio.video', 'bob.bio.csu', 'bob.bio.spear', 'gridtk', 'bob.db.youtube'])
-
-
-def skip(app, what, name, obj, skip, options):
- # Do not skip the __call__ and the __str__ functions as we have special implementations for them.
- if name in ("__str__", "__call__"):
- return False
- return skip
-
-# getting dictionaries printed nicely.
-# see: http://stackoverflow.com/questions/7250659/python-code-to-generate-part-of-sphinx-documentation-is-it-possible/18143318#18143318
-try:
- from StringIO import StringIO
-except ImportError:
- from io import StringIO
-
-from sphinx.util.compat import Directive
-from docutils import nodes, statemachine
-
-class ExecDirective(Directive):
- """Execute the specified python code and insert the output into the document"""
- has_content = True
-
- def run(self):
- oldStdout, sys.stdout = sys.stdout, StringIO()
-
- tab_width = self.options.get('tab-width', self.state.document.settings.tab_width)
- source = self.state_machine.input_lines.source(self.lineno - self.state_machine.input_offset - 1)
-
- try:
- exec('\n'.join(self.content))
- text = sys.stdout.getvalue()
- lines = statemachine.string2lines(text, tab_width, convert_whitespace=True)
- self.state_machine.insert_input(lines, source)
- return []
- except Exception:
- return [nodes.error(None, nodes.paragraph(text = "Unable to execute python code at %s:%d:" % (os.path.basename(source), self.lineno)), nodes.paragraph(text = str(sys.exc_info()[1])))]
- finally:
- sys.stdout = oldStdout
+intersphinx_mapping = link_documentation()
+
+# We want to remove all private (i.e. _. or __.__) members
+# that are not in the list of accepted functions
+accepted_private_functions = ['__array__']
+
+def member_function_test(app, what, name, obj, skip, options):
+ # test if we have a private function
+ if len(name) > 1 and name[0] == '_':
+ # test if this private function should be allowed
+ if name not in accepted_private_functions:
+ # omit privat functions that are not in the list of accepted private functions
+ return skip
+ else:
+ # test if the method is documented
+ if not hasattr(obj, '__doc__') or not obj.__doc__:
+ return skip
+ return False
def setup(app):
- app.connect("autodoc-skip-member", skip)
- app.add_directive('exec', ExecDirective)
+ app.connect('autodoc-skip-member', member_function_test)
diff --git a/doc/img/logo.png b/doc/img/logo.png
index b9dd573a01019afd1af58a881996930e5212699d..b60858a7068bf45c1ed8e3da12fe244ccdcfe85d 100644
Binary files a/doc/img/logo.png and b/doc/img/logo.png differ
diff --git a/doc/implementation.rst b/doc/implementation.rst
index d60db9b39d9992f4855bb7250fa9bae6f4197acc..984742d6b8be59c719b7bd9d98929b211f8d2a6f 100644
--- a/doc/implementation.rst
+++ b/doc/implementation.rst
@@ -218,13 +218,13 @@ Verification Database Interface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
For most of the data sets, we rely on the database interfaces from Bob_.
-Particularly, all databases that are derived from the :py:class:`bob.db.verification.utils.Database` (click :ref:`here <verification_databases>` for a list of implemented databases) are supported by a special derivation of the databases from above.
+Particularly, all databases that are derived from the :py:class:`bob.bio.db.BioDatabase` (click :ref:`here <verification_databases>` for a list of implemented databases) are supported by a special derivation of the databases from above.
For these databases, the special :py:class:`bob.bio.base.database.DatabaseBob` interface is provided, which takes the Bob_ database as parameter.
Several such databases are defined in the according packages, i.e., :ref:`bob.bio.spear <bob.bio.spear>`, :ref:`bob.bio.face <bob.bio.face>` and :ref:`bob.bio.video <bob.bio.video>`.
For Bob_'s ZT-norm databases, we provide the :py:class:`bob.bio.base.database.DatabaseBobZT` interface.
Additionally, a generic database interface, which is derived from :py:class:`bob.bio.base.database.DatabaseBobZT`, is the :py:class:`bob.bio.base.database.DatabaseFileList`.
-This database interfaces with the :py:class:`bob.db.verification.filelist.Database`, which is a generic database based on file lists, implementing the :py:class:`bob.db.verification.utils.Database` interface.
+This database interfaces with the :py:class:`bob.db.verification.filelist.Database`, which is a generic database based on file lists, implementing the :py:class:`bob.bio.db.BioDatabase` interface.
Defining your own Database
~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/requirements.txt b/requirements.txt
index 71eba5d0fcc37c4bceaa124f02d6e95bcfcb255a..97c8574647adf403007f648acb78b847d8d1fa1a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,18 +1,14 @@
-setuptools
-scipy
-bob.extension
+bob.bio.db
bob.blitz
bob.core
+bob.db.base
+bob.extension
bob.io.base
bob.learn.activation
-bob.math
-bob.learn.linear
-bob.sp
bob.learn.em
+bob.learn.linear
+bob.math
bob.measure
-bob.db.base
-bob.db.verification.utils
-bob.db.verification.filelist
-bob.db.atnt # for test purposes
-bob.io.image # for test purposes
-matplotlib # for plotting
+bob.sp
+scipy
+setuptools
diff --git a/setup.py b/setup.py
index 92304c24a2572edb49367ccf96c58f490099534a..f10b8155a0fcb8c951a4fcd5cc398304436d5249 100644
--- a/setup.py
+++ b/setup.py
@@ -1,37 +1,6 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
-# Andre Anjos <andre.anjos@idiap.ch>
# Mon 16 Apr 08:18:08 2012 CEST
-#
-# Copyright (C) Idiap Research Institute, Martigny, Switzerland
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, version 3 of the License.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# This file contains the python (distutils/setuptools) instructions so your
-# package can be installed on **any** host system. It defines some basic
-# information like the package name for instance, or its homepage.
-#
-# It also defines which other packages this python package depends on and that
-# are required for this package's operation. The python subsystem will make
-# sure all dependent packages are installed or will install them for you upon
-# the installation of this package.
-#
-# The 'buildout' system we use here will go further and wrap this package in
-# such a way to create an isolated python working environment. Buildout will
-# make sure that dependencies which are not yet installed do get installed, but
-# **without** requiring administrative privileges on the host system. This
-# allows you to test your package with new python dependencies w/o requiring
-# administrative interventions.
from setuptools import setup, dist
dist.Distribution(dict(setup_requires=['bob.extension']))
@@ -47,10 +16,10 @@ setup(
# information before releasing code publicly.
name = 'bob.bio.base',
version = open("version.txt").read().rstrip(),
- description = 'Basic tools for running biometric recognition experiments',
+ description = 'Tools for running biometric recognition experiments',
- url = 'https://www.github.com/bioidiap/bob.bio.base',
- license = 'GPLv3',
+ url = 'https://www.gitlab.idiap.ch/bob/bob.bio.base',
+ license = 'BSD',
author = 'Manuel Gunther',
author_email = 'siebenkopf@googlemail.com',
keywords = 'bob, biometric recognition, evaluation',
@@ -157,7 +126,7 @@ setup(
'Framework :: Bob',
'Development Status :: 3 - Alpha',
'Intended Audience :: Developers',
- 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+ 'License :: OSI Approved :: BSD License',
'Natural Language :: English',
'Programming Language :: Python',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
diff --git a/test-requirements.txt b/test-requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89e63d6ac71191c42c61748db750825d0f213b62
--- /dev/null
+++ b/test-requirements.txt
@@ -0,0 +1,4 @@
+bob.db.atnt
+bob.io.image
+matplotlib
+gridtk