diff --git a/doc/implementation.rst b/doc/implementation.rst
index ed0d4bc1261a48d76e9202f5ace44d059f1adb69..77686756fe9aa5477da5b253ac8405f3cac1eeac 100644
--- a/doc/implementation.rst
+++ b/doc/implementation.rst
@@ -218,56 +218,58 @@ 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.bio.base.database.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.BioDatabase` 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.bio.base.database.BioDatabase` interface.
+For Bob_'s ZT-norm databases, we provide the :py:class:`bob.bio.base.database.ZTBioDatabase` interface.
Defining your own Database
~~~~~~~~~~~~~~~~~~~~~~~~~~
+..
+ If you have your own database that you want to execute the recognition experiments on, you should first check if you could use the :ref:`Verifcation File List Database <bob.db.bio_filelist>` interface by defining appropriate file lists for the training set, the model set, and the probes.
+ In most of the cases, the :py:class:`bob.db.bio_filelist.Database` should be sufficient to run experiments.
+ Please refer to the documentation :ref:`Documentation <bob.db.bio_filelist>` of this database for more instructions on how to configure this database.
-If you have your own database that you want to execute the recognition experiments on, you should first check if you could use the :ref:`Verifcation FileList Database <bob.db.verification.filelist>` interface by defining appropriate file lists for the training set, the model set, and the probes.
-In most of the cases, the :py:class:`bob.db.verification.filelist.Database` should be sufficient to run experiments.
-Please refer to the documentation :ref:`Documentation <bob.db.verification.filelist>` of this database for more instructions on how to configure this database.
+To "plug" your own database in this framework you have to write your own database class by deriving :py:class:`bob.bio.base.database.BioDatabase`.
+In this case, you have to derive your class from the :py:class:`bob.bio.base.database.BioDatabase`, and provide the following functions:
-In case you want to have a more complicated interface to your database, you are welcome to write your own database wrapper class.
-In this case, you have to derive your class from the :py:class:`bob.bio.base.database.Database`, and provide the following functions:
-* ``__init__(self, <your-parameters>, **kwargs)``: Constructor of your database interface.
- Please call the base class constructor, providing all the required parameters, e.g. by ``bob.bio.base.database.Database.__init__(self, **kwargs)``.
-* ``all_files(self)``: Returns a list of all :py:class:`bob.bio.base.database.File` objects of the database.
- 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.File` objects that is used for training.
- If ``arrange_by_clients`` is enabled, you might want to use the :py:meth:`bob.bio.base.database.Database.arrange_by_client` function to perform the job.
-* ``model_ids(self, group = 'dev'): The ids for the models (usually, there is only one model per client and, thus, you can simply use the client ids) for the given group.
+* ``__init__(self, <your-parameters>, **kwargs)`` Constructor of your database interface.
+ Please call the base class constructor, providing all the required parameters, e.g. by ``super(<your_db>,self).__init__(self, **kwargs)``.
Usually, providing ids for the group ``'dev'`` should be sufficient.
-* ``client_id_from_model_id(self, model_id)``: Returns the client id for the given model id.
-* ``enroll_files(self, model_id, group='dev')``: Returns the list of model :py:class:`bob.bio.base.database.File` objects for the given model id.
-* ``probe_files(self, model_id=None, group='dev')``: Returns the list of probe files, the given model_id should be compared with.
- Usually, all probe files are compared with all model files.
- In this case, you can just ignore the ``model_id``.
- If the ``model_id`` is ``None``, this function is supposed to return *all* probe files for all models of the given group.
+
+* ``objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs)``
+ This function must return a list of ``bob.db.base.database.BioFile`` objects with your data.
+ The keyword arguments are possible filters that you may use.
+
+* ``model_ids_with_protocol(self, groups, protocol, **kwargs)``
+ This function must return a list of model ids for the given groups and given protocol.
+ In this context models are basically them "templates" used for enrollment.
Additionally, you can define more lists that can be used for ZT score normalization.
-In this case, derive you class from :py:class:`bob.bio.base.database.DatabaseZT` instead, and additionally overwrite the following functions:
+If you don't know what ZT score normalization is, just forget about it and move on.
+If you know and want to use it, just derive your class from :py:class:`bob.bio.base.database.ZTBioDatabase` instead, and additionally overwrite the following functions:
-* ``t_model_ids(self, group = 'dev')``: The ids for the T-Norm models for the given group.
-* ``t_enroll_files(self, model_id, group='dev')``: Returns the list of model :py:class:`bob.bio.base.database.File` objects for the given T-Norm model id.
-* ``z_probe_files(self, group='dev')``: Returns the list of Z-probe :py:class:`bob.bio.base.database.File` objects, with which all the models and T-Norm models are compared.
+* ``tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs)``
+ This function must return a list of ``bob.db.base.database.BioFile`` objects used for `T` normalization.
+
+* ``zobjects(self, groups=None, protocol=None, **kwargs)``
+ This function must return a list of ``bob.db.base.database.BioFile`` objects used for `Z` normalization.
+
+* ``tmodel_ids_with_protocol(self, protocol=None, groups=None, **kwargs)``
+ The ids for the T norm models for the given group and protocol.
.. note:
For a proper biometric recognition protocol, the identities from the models and the T-Norm models, as well as the Z-probes should be different.
-For some protocols, a single probe consists of several features, see :ref:`bob.bio.base.algorithms` about strategies how to incorporate several probe files into one score.
-If your database should provide this functionality, please overwrite:
-
-* ``uses_probe_file_sets(self)``: Return ``True`` if the current protocol of the database provides multiple files for one probe.
-* ``probe_file_sets(self, model_id=None, group='dev')``: Returns a list of lists of :py:class:`bob.bio.base.database.FileSet` objects.
-* ``z_probe_file_sets(self, model_id=None, group='dev')``: Returns a list of lists of Z-probe :py:class:`bob.bio.base.database.FileSet` objects (only needed if the base class is :py:class:`bob.bio.base.database.DatabaseZT`).
+..
+ For some protocols, a single probe consists of several features, see :ref:`bob.bio.base.algorithms` about strategies how to incorporate several probe files into one score.
+ If your database should provide this functionality, please overwrite:
+ * ``uses_probe_file_sets(self)``: Return ``True`` if the current protocol of the database provides multiple files for one probe.
+ * ``probe_file_sets(self, model_id=None, group='dev')``: Returns a list of lists of :py:class:`bob.bio.base.database.FileSet` objects.
+ * ``z_probe_file_sets(self, model_id=None, group='dev')``: Returns a list of lists of Z-probe :py:class:`bob.bio.base.database.FileSet` objects (only needed if the base class is :py:class:`bob.bio.base.database.DatabaseZT`).
.. _bob.bio.base.configuration-files:
@@ -282,7 +284,7 @@ In ``bob.bio`` this is achieved by providing these parameters in configuration f
In these files, an *instance* of one of the tools is generated, and assigned to a variable with a specific name.
These variable names are:
-* ``database`` for an instance of a (derivation of a) :py:class:`bob.bio.base.database.Database`
+* ``database`` for an instance of a (derivation of a) :py:class:`bob.bio.base.database.BioDatabase`
* ``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`
* ``algorithm`` for an instance of a (derivation of a) :py:class:`bob.bio.base.algorithm.Algorithm`
diff --git a/doc/installation.rst b/doc/installation.rst
index a63e64c43896684d7c6f4bba7a08e84436429c47..6fd14c3c3bb4314a6bfc089a93a9223c9153cb21 100644
--- a/doc/installation.rst
+++ b/doc/installation.rst
@@ -18,7 +18,7 @@ Please make sure that you have read the `Dependencies <https://github.com/idiap/
However, we found that running Bob_ in a virtual Unix environment such as the one provided by VirtualBox_ is a good alternative.
Installation via conda
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
The most simple and most convenient way to use the ``bob.bio`` tools is to install it using `conda <http://conda.pydata.org/docs/intro.html>`_.
We offer pre-compiled binary installations of Bob_ and ``bob.bio`` with conda.
@@ -32,7 +32,7 @@ first search the ``bob.bio`` in the conda-forge channel and then install it.
Installation via zc.buildout
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+----------------------------
Another convenient way to use the ``bob.bio`` tools is to use a ``zc.buildout`` package, as explained in more detail `here <https://github.com/idiap/bob/wiki/Installation#using-zcbuildout-for-production>`__.
There, in the ``eggs`` section of the ``buildout.cfg`` file, simply list the ``bob.bio`` packages that you want, like:
@@ -121,6 +121,7 @@ In case any of the tests fail for unexplainable reasons, please file a bug repor
In other versions, some of the tests may fail.
+
Generate this documentation
---------------------------