[sphinx] Fixing warnings

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......@@ -63,7 +63,7 @@ These five options are:
* ``--sub-directory``: A descriptive name for your experiment, which will serve as a sub-directory
The first four parameters, i.e., the ``database``, the ``preprocessor``, the ``extractor`` and the ``algorithm`` can be specified in several different ways.
For the start, we will use only the registered :ref:`Resources <bob.bio.base.resources>`.
For the start, we will use only the registered `Resources <bob.bio.base_legacy.resources>`.
These resources define the source code that will be used to compute the experiments, as well as all the meta-parameters of the algorithms (which we will call the *configuration*).
To get a list of registered resources, please call:
......@@ -112,8 +112,8 @@ After the experiment has finished successfully, one or more text file containing
all the scores are written. In this section, commands that helps to quickly
evaluate a set of scores by generating metrics or plots are presented here.
The scripts take as input either a 4-column or 5-column data format as specified
in the documentation of :py:func:`bob.bio.base.score.load.four_column` or
:py:func:`bob.bio.base.score.load.five_column`.
in the documentation of :py:func:`bob.bio.base_legacy.score.load.four_column` or
:py:func:`bob.bio.base_legacy.score.load.five_column`.
Two sets of commands, ``bob pad`` and ``bob vuln`` are available for
Presentation Attack Detection and
......
......@@ -4,10 +4,10 @@ gridtk
bob.io.base
bob.db.base
bob.db.avspoof
bob.bio.base
bob.bio.base_legacy
bob.pad.voice
bob.db.voicepa
bob.bio.spear
bob.bio.face
bob.bio.face_legacy
bob.pad.face
bob.learn.linear
\ No newline at end of file
......@@ -98,7 +98,7 @@ The high-level Database Interface
---------------------------------
the low-level FileList database interface is extended, so that filelist databases can be used to run both types:
vulnerability analysis experiments using :ref:`bob.bio.base <bob.bio.base>` verification framework
vulnerability analysis experiments using `bob.bio.base_legacy <bob.bio.base_legacy>` verification framework
and PAD experiments using ``bob.pad.base`` framework.
For instance, provided the lists of files for database ``example_db`` in the correct format are located
......
......@@ -12,7 +12,7 @@ The *high level database interface* (HLDI) is needed to run biometric experiment
This tutorial explains how to create a *high level* database
interface, using as an example ``bob.pad.*`` framework (e.g.
``bob.pad.face``). The process is similar for ``bob.bio`` frameworks,
e.g. ``bob.bio.face``, ``bob.bio.vein``). High level database interface
e.g. ``bob.bio.face_legacy``, ``bob.bio.vein``). High level database interface
is a link between low level database interface/package (e.g. ``bob.db.replay``) and a
corresponding framework used to run biometric experiments (e.g.
``bob.pad.face``). Generally speaking, the low level interface has lot's
......@@ -90,7 +90,7 @@ structure of the class. For the ``ReplayPadFile`` class it looks as
follows:
- ``ReplayPadFile`` -> ``bob.pad.base.database.PadFile`` ->
``bob.bio.base.database.BioFile`` -> ``bob.db.base.File``
``bob.bio.base_legacy.database.BioFile`` -> ``bob.db.base.File``
Here the notation ``A`` -> ``B`` means ``A`` inherits from ``B``. Well,
the inheritance is pretty deep, but no need to worry about this. The
......@@ -171,11 +171,11 @@ Let's consider an example of the ``ReplayPadDatabase`` class. The implementation
Instead, let's try to understand why the implementation looks like this. Again, the methods to be implemented are defined by the corresponding base class of our ``*Database`` class.
In the case of PAD ``*Database`` the inheritance structure is as follows:
- ``ReplayPadDatabase`` -> ``bob.pad.base.database.PadDatabase`` -> ``bob.bio.base.database.BioDatabase`` -> ``bob.db.base.Database``
- ``ReplayPadDatabase`` -> ``bob.pad.base.database.PadDatabase`` -> ``bob.bio.base_legacy.database.BioDatabase`` -> ``bob.db.base.Database``
For the verification database the inheritance would be:
- ``bob.pad.base.database.PadDatabase`` -> ``bob.bio.base.database.BioDatabase`` -> ``bob.db.base.Database``
- ``bob.pad.base.database.PadDatabase`` -> ``bob.bio.base_legacy.database.BioDatabase`` -> ``bob.db.base.Database``
For other biometric experiments it might look differently.
In the given example the behavior of the ``ReplayPadDatabase`` class is defined by the ``bob.pad.base.database.PadDatabase`` base class, which sates that two methods must be implemented in the high level database implementation: ``objects()`` and ``annotations()``. The ``objects()`` method returns a list of instances of ``ReplayPadFile`` class. The ``annotations()`` method is empty, since the developer of the code decided to return the annotations in the ``*File`` class. Note: you are not obliged to do it that way, it's just a matter of taste.
......
......@@ -12,7 +12,7 @@ Therefore, python is used to implement tools such as preprocessors, feature extr
Everything is file based so any tool can implement its own way of reading and writing data, features or models.
Configurations are stored in configuration files, so it should be easy to test different parameters of your algorithms without modifying the code.
Also, it is important to note that ``bob.pad.base`` reuses concept, design, and large parts of code from :ref:`bob.bio.base <bob.bio.base>` package,
Also, it is important to note that ``bob.pad.base`` reuses concept, design, and large parts of code from `bob.bio.base_legacy <bob.bio.base_legacy>` package,
which is designed for recognition experiments.
......@@ -38,8 +38,8 @@ If you plan to write your own tools, please assure that you are following the fo
Preprocessors and Extractors
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
All preprocessor and extractor classes are based on the empty base classess implemented in :ref:`bob.bio.base <bob.bio.base>`, specifically,
on :py:class:`bob.bio.base.preprocessor.Preprocessor` and :py:class:`bob.bio.base.extractor.Extractor` classes.
All preprocessor and extractor classes are based on the empty base classess implemented in `bob.bio.base_legacy <bob.bio.base_legacy>`, specifically,
on :py:class:`bob.bio.base_legacy.preprocessor.Preprocessor` and :py:class:`bob.bio.base_legacy.extractor.Extractor` classes.
.. _bob.pad.base.algorithms:
......@@ -135,7 +135,7 @@ and provide only the following functions:
Please call the base class constructor, providing all the required parameters, e.g. by ``bob.pad.base.database.PadDatabase.__init__(self, **kwargs)``.
* ``objects(self, , groups=None, protocol=None, purposes=None, model_ids=None, **kwargs)``: Expected to return a list of :py:class:`bob.pad.base.database.PadFile` objects of the database given the specified parameters.
The list needs to be sorted by the file id (you can use the ``self.sort(files)`` function for sorting).
* ``training_files(self, step, arrange_by_client = False)``: A sorted list of the :py:class:`bob.bio.base.database.BioFile` objects that is used for training.
* ``training_files(self, step, arrange_by_client = False)``: A sorted list of the :py:class:`bob.bio.base_legacy.database.BioFile` objects that is used for training.
You should have ``arrange_by_clients`` disabled.
......@@ -152,10 +152,10 @@ In these files, an *instance* of one of the tools is generated, and assigned to
These variable names are:
* ``database`` for an instance of a (derivation of a) :py:class:`bob.pad.base.database.PadDatabase`
* ``preprocessor`` for an instance of a (derivation of a) :py:class:`bob.bio.base.preprocessor.Preprocessor`
* ``extractor`` for an instance of a (derivation of a) :py:class:`bob.bio.base.extractor.Extractor`
* ``preprocessor`` for an instance of a (derivation of a) :py:class:`bob.bio.base_legacy.preprocessor.Preprocessor`
* ``extractor`` for an instance of a (derivation of a) :py:class:`bob.bio.base_legacy.extractor.Extractor`
* ``algorithm`` for an instance of a (derivation of a) :py:class:`bob.pad.base.algorithm.Algorithm`
* ``grid`` for an instance of the :py:class:`bob.bio.base.grid.Grid`
* ``grid`` for an instance of the :py:class:`bob.bio.base_legacy.grid.Grid`
.. _bob.pad.base.resources:
......@@ -171,10 +171,10 @@ We use the SetupTools_ mechanism of registering so-called entry points in the ``
Particularly, we use a specific list of entry points, which are:
* ``bob.pad.base.database.PadDatabase`` to register an instance of a (derivation of a) :py:class:`bob.pad.base.database.PadDatabase`
* ``bob.bio.preprocessor`` to register an instance of a (derivation of a) :py:class:`bob.bio.base.preprocessor.Preprocessor`
* ``bob.bio.extractor`` to register an instance of a (derivation of a) :py:class:`bob.bio.base.extractor.Extractor`
* ``bob.bio.preprocessor`` to register an instance of a (derivation of a) :py:class:`bob.bio.base_legacy.preprocessor.Preprocessor`
* ``bob.bio.extractor`` to register an instance of a (derivation of a) :py:class:`bob.bio.base_legacy.extractor.Extractor`
* ``bob.pad.algorithm`` to register an instance of a (derivation of a) :py:class:`bob.pad.base.algorithm.Algorithm`
* ``bob.bio.grid`` to register an instance of the :py:class:`bob.bio.base.grid.Grid`
* ``bob.bio.grid`` to register an instance of the :py:class:`bob.bio.base_legacy.grid.Grid`
For each of the tools, several resources are defined, which you can list with the ``./bin/resources.py`` command line.
......
......@@ -4,7 +4,7 @@
Tools implemented in bob.pad.base
===================================
Please not that some parts of the code in this package are dependent on and reused from :ref:`bob.bio.base <bob.bio.base>` package.
Please not that some parts of the code in this package are dependent on and reused from `bob.bio.base_legacy <bob.bio.base_legacy>` package.
Summary
-------
......@@ -12,7 +12,7 @@ Summary
Base Classes
~~~~~~~~~~~~
Most of the base classes are reused from :ref:`bob.bio.base <bob.bio.base>`.
Most of the base classes are reused from `bob.bio.base_legacy <bob.bio.base_legacy>`.
Only one base class that is presentation attack detection specific, ``Algorithm`` is implemented in this package.
.. autosummary::
......@@ -29,9 +29,9 @@ Implementations
Preprocessors and Extractors
----------------------------
Preprocessors and Extractors from the :ref:`bob.bio.base <bob.bio.base>`
Preprocessors and Extractors from the `bob.bio.base_legacy <bob.bio.base_legacy>`
package can also be used in this package. Please see
:any:`bob.bio.base.implemented` for more details.
`bob.bio.base_legacy.implemented` for more details.
Algorithms
----------
......@@ -46,7 +46,7 @@ Databases
Grid Configuration
------------------
Code related to grid is reused from :ref:`bob.bio.base <bob.bio.base>` package. Please see the corresponding documentation.
Code related to grid is reused from `bob.bio.base_legacy <bob.bio.base_legacy>` package. Please see the corresponding documentation.
.. include:: links.rst
......@@ -25,7 +25,7 @@ This results in a nearly infinite amount of possible experiments that can be run
But it is also possible to use your own database, preprocessor, feature extractor, or PAD algorithm and test this against the baseline algorithms implemented in the our packages.
.. note::
The ``bob.pad.*`` packages are derived from the `bob.bio.* <http://pypi.python.org/pypi/bob.bio.base>`__, packages that are designed for biometric recognition experiments.
The ``bob.pad.*`` packages are derived from the `bob.bio.* <http://pypi.python.org/pypi/bob.bio.base_legacy>`__, packages that are designed for biometric recognition experiments.
This package :py:mod:`bob.pad.base` includes the basic definition of a PAD experiment, as well as a generic script, which can execute the full experiment in a single command line.
Changing the employed tools such as the database, protocol, preprocessor, feature extractor or a PAD algorithm is as simple as changing a command line parameter.
......
......@@ -43,7 +43,7 @@ command line below will install all the required packages:
.. code-block:: sh
$ source activate <bob_conda_environment>
$ conda install bob.bio.base \
$ conda install bob.bio.base_legacy \
bob.bio.spear \
bob.pad.base \
bob.pad.voice \
......@@ -61,7 +61,7 @@ please refer to the `spoofing_databases <https://gitlab.idiap.ch/bob/bob/wikis/P
After downloading the original data for the databases, you will need to tell ``bob.pad``, where these databases can be found.
For this purpose, we have decided to implement a special file, where you can set your directories.
Similar to ``bob.bio.base``, by default, this file is located in ``~/.bob_bio_databases.txt``, and it contains several lines, each line looking somewhat like:
Similar to ``bob.bio.base_legacy``, by default, this file is located in ``~/.bob_bio_databases.txt``, and it contains several lines, each line looking somewhat like:
.. code-block:: text
......
......@@ -34,7 +34,7 @@ Scoring
~~~~~~~
.. autosummary::
bob.bio.base.tools.compute_scores
bob.bio.base_legacy.tools.compute_scores
Details
-------
......
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