Merge branch 'issue-8-remove-database-configuration' into 'master'

Issue 8 remove database configuration

Continuing the merge with bob.bio.base

bob.bio.base!37

See merge request !14

bob/bio/spear/config/database/banca_audio_G.py

@@ -5,7 +5,7 @@ import bob.db.bio_filelist
 
 banca_wav_directory = "[YOUR_BANCA_WAV_DIRECTORY]"
 
-database = bob.db.bio_filelist.Database(pkg_resources.resource_filename('bob.bio.spear', 'config/database/banca'),
+database = bob.db.bio_filelist.Database(pkg_resources.resource_filename('bob.bio.db', 'default_configs/banca'),
                                         original_directory=banca_wav_directory,
                                         original_extension=".wav")
 

bob/bio/spear/config/database/mobio.py

+#!/usr/bin/env python
+
+from bob.bio.spear.database import MobioBioDatabase
+mobio_wav_directory = "[YOUR_MOBIO_WAV_DIRECTORY]"
+
+mobio_audio_male = MobioBioDatabase(
+    original_directory=mobio_wav_directory,
+    original_extension=".wav",
+    protocol='male',
+    models_depend_on_protocol=True,
+    all_files_options={'gender': 'male'},
+    extractor_training_options={'gender': 'male'},
+    projector_training_options={'gender': 'male'},
+    enroller_training_options={'gender': 'male'},
+    z_probe_options={'gender': 'male'}
+)
+
+mobio_audio_female = MobioBioDatabase(
+    original_directory=mobio_wav_directory,
+    original_extension=".wav",
+    protocol='female',
+    models_depend_on_protocol=True,
+    all_files_options={'gender': 'female'},
+    extractor_training_options={'gender': 'female'},
+    projector_training_options={'gender': 'female'},
+    enroller_training_options={'gender': 'female'},
+    z_probe_options={'gender': 'female'}
+)

bob/bio/spear/config/database/voxforge.py

 #!/usr/bin/env python
 
-import bob.bio.db
-
+from bob.bio.spear.database import VoxforgeBioDatabase
 voxforge_wav_directory = "[YOUR_VOXFORGE_DIRECTORY]"
 
-database = bob.bio.db.VoxforgeBioDatabase(
+database = VoxforgeBioDatabase(
     original_directory=voxforge_wav_directory,
     original_extension=".wav",
 )

bob/bio/spear/database/__init__.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Elie Khoury <Elie.Khoury@idiap.ch>
+# Fri Aug 30 11:42:11 CEST 2013
+#
+# Copyright (C) 2012-2013 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/>.
+
+"""Feature extraction tools"""
+
+from .database import AudioBioFile
+from .mobio import MobioBioDatabase
+from .voxforge import VoxforgeBioDatabase
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/bio/spear/database/database.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+# Wed 20 July 14:43:22 CEST 2016
+
+"""
+  Verification API for bob.db.voxforge
+"""
+
+from bob.bio.base.database.file import BioFile
+import scipy
+import numpy
+
+
+class AudioBioFile(BioFile):
+    def __init__(self, f):
+        """
+        Initializes this File object with an File equivalent for
+        VoxForge database.
+        """
+        super(AudioBioFile, self).__init__(client_id=f.client_id, path=f.path, file_id=f.id)
+
+        self.__f = f
+
+    def load(self, directory=None, extension='.wav'):        
+        rate, audio = scipy.io.wavfile.read(self.make_path(directory, extension))
+        # We consider there is only 1 channel in the audio file => data[0]
+        data= numpy.cast['float'](audio)
+        return rate, data    
+

bob/bio/spear/database/mobio.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Amir Mohammadi <amir.mohammadi@idiap.ch>
+# Wed 13 Jul 16:43:22 CEST 2016
+
+"""
+  MOBIO database implementation of bob.bio.db.ZTDatabase interface.
+  It is an extension of an SQL-based database interface, which directly talks to Mobio database, for
+  verification experiments (good to use in bob.bio.base framework).
+"""
+
+
+from .database import AudioBioFile
+from bob.bio.base.database import ZTBioDatabase, BioFile
+
+
+class MobioBioDatabase(ZTBioDatabase):
+    """
+    Implements verification API for querying Mobio database.
+    """
+
+    def __init__(
+            self,
+            **kwargs
+    ):
+        # call base class constructors to open a session to the database
+        super(MobioBioDatabase, self).__init__(name='mobio',
+                                               **kwargs)
+
+        from bob.db.mobio.query import Database as LowLevelDatabase
+        self.__db = LowLevelDatabase()
+
+    def model_ids_with_protocol(self, groups=None, protocol=None, gender=None):
+        return self.__db.model_ids(groups=groups, protocol=protocol, gender=gender)
+
+    def tmodel_ids_with_protocol(self, protocol=None, groups=None, **kwargs):
+        return self.__db.tmodel_ids(protocol=protocol, groups=groups, **kwargs)
+
+    def objects(self, groups=None, protocol=None, purposes=None, model_ids=None, **kwargs):
+        retval = self.__db.objects(groups=groups, protocol=protocol, purposes=purposes, model_ids=model_ids, **kwargs)
+        return [AudioBioFile(f) for f in retval]
+
+    def tobjects(self, groups=None, protocol=None, model_ids=None, **kwargs):
+        retval = self.__db.tobjects(groups=groups, protocol=protocol, model_ids=model_ids, **kwargs)
+        return [AudioBioFile(f) for f in retval]
+
+    def zobjects(self, groups=None, protocol=None, **kwargs):
+        retval = self.__db.zobjects(groups=groups, protocol=protocol, **kwargs)
+        return [AudioBioFile(f) for f in retval]

bob/bio/spear/database/voxforge.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+# Wed 20 July 14:43:22 CEST 2016
+
+"""
+  Verification API for bob.db.voxforge
+"""
+
+from .database import AudioBioFile
+from bob.bio.base.database import BioDatabase, BioFile
+
+class VoxforgeBioDatabase(BioDatabase):
+    """
+    Implements verification API for querying Voxforge database.
+    """
+
+    def __init__(self, original_directory=None, original_extension=None, **kwargs):
+        # call base class constructors to open a session to the database
+        super(VoxforgeBioDatabase, self).__init__(
+            name='voxforge', protocol='',
+            original_directory=original_directory,
+            original_extension=original_extension, **kwargs)
+
+        from bob.db.voxforge.query import Database as LowLevelDatabase
+        self.__db = LowLevelDatabase(original_directory=original_directory, original_extension=original_extension)
+
+    def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
+        """Returns a set of models ids for the specific query by the user.
+
+        Keyword Parameters:
+
+        protocol
+            Protocol is ignored in this context, since its choice has no influence on models.
+
+        groups
+            The groups to which the subjects attached to the models belong ('dev', 'eval', 'world')
+
+        Returns: A list containing the ids of all models belonging to the given groups.
+        """
+        return [client.id for client in self.__db.clients(groups=groups, protocol=protocol)]
+
+    def objects(self, protocol=None, purposes=None, model_ids=None,
+                groups=None, gender=None):
+        """Returns a set of Files for the specific query by the user.
+
+        Keyword Parameters:
+
+        protocol
+            Not applicable. VoxForge has only one protocol
+
+        purposes
+            The purposes can be either 'enroll', 'probe', or their tuple.
+            If 'None' is given (this is the default), it is
+            considered the same as a tuple with both possible values.
+
+        model_ids
+            Only retrieves the files for the provided list of model ids (claimed
+            client id).  If 'None' is given (this is the default), no filter over
+            the model_ids is performed.
+
+        groups
+            One of the groups ('dev', 'eval', 'world') or a tuple with several of them.
+            If 'None' is given (this is the default), it is considered the same as a
+            tuple with all possible values.
+
+        gender
+            Not applicable
+
+        Returns: A set of Files with the specified properties.
+        """
+
+        # now, query the actual Voxforge database
+        objects = self.__db.objects(groups=groups,
+                                    model_ids=model_ids, purposes=purposes)
+
+        # make sure to return BioFile representation of a file, not the database one
+        return [AudioBioFile(BioFile(client_id=f.client_id, path=f.path, file_id=f.id)) for f in objects]

buildout-dev.cfg

@@ -25,7 +25,6 @@ develop = src/bob.extension
           src/bob.measure
           src/bob.db.base
           src/bob.bio.base
-          src/bob.bio.db
           src/bob.db.bio_filelist
           src/bob.db.voxforge
           .
@@ -36,23 +35,24 @@ 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.ap = git https://github.com/bioidiap/bob.ap
-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.bio.base = git https://github.com/bioidiap/bob.bio.base
-bob.bio.db = git git@gitlab.idiap.ch:biometric/bob.bio.db
-bob.db.bio_filelist = git git@github.com:bioidiap/bob.db.bio_filelist
-bob.db.voxforge = git git@github.com:bioidiap/bob.db.voxforge
+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.ap = git https://gitlab.idiap.ch/bob/bob.ap
+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.base = git https://gitlab.idiap.ch/bob/bob.bio.base branch=issue-8-remove-database-configuration
+bob.db.bio_filelist = git git@gitlab.idiap.ch:bob/bob.db.bio_filelist
+bob.db.voxforge = git git@gitlab.idiap.ch:bob/bob.db.voxforge
 
 [scripts]
 recipe = bob.buildout:scripts
 dependent-scripts = true
+
+

develop.cfg

-; vim: set fileencoding=utf-8 :
-; Elie Khoury <Elie.Khoury@idiap.ch>
-; Thu 11 Jun 18:07:26 CEST 2015
-
-[buildout]
-parts = scripts
-eggs = bob.bio.spear
-       bob.bio.db
-       bob.db.base
-       bob.db.bio_filelist
-       bob.db.voxforge
-       bob.bio.base
-       bob.db.asvspoof
-       gridtk
-
-extensions = bob.buildout
-             mr.developer
-auto-checkout = *
-develop = src/bob.bio.db
-          src/bob.db.bio_filelist
-          src/bob.db.voxforge
-          src/bob.bio.base
-          src/bob.db.asvspoof
-          .
-
-; options for bob.buildout
-debug = false
-verbose = true
-newest = false
-
-[sources]
-bob.db.base = git git@gitlab.idiap.ch:bob/bob.db.base
-bob.bio.db = git git@gitlab.idiap.ch:bob/bob.bio.db
-bob.db.bio_filelist = git git@gitlab.idiap.ch:bob/bob.db.bio_filelist
-bob.db.voxforge = git git@gitlab.idiap.ch:bob/bob.db.voxforge
-bob.bio.base = git git@gitlab.idiap.ch:bob/bob.bio.base
-bob.db.asvspoof = git git@gitlab.idiap.ch:bob/bob.db.asvspoof
-
-
-[scripts]
-recipe = bob.buildout:scripts
-dependent-scripts = true

requirements.txt

@@ -12,5 +12,4 @@ bob.learn.em
 bob.measure 
 bob.db.base
 bob.bio.base
-bob.bio.db
 matplotlib   # for plotting

setup.py

@@ -100,9 +100,11 @@ setup(
     entry_points = {
 
       'bob.bio.database': [
-        'voxforge            = bob.bio.spear.config.database.voxforge:database',
+        'voxforge         = bob.bio.spear.config.database.voxforge:database',
         'banca-audio      = bob.bio.spear.config.database.banca_audio_G:database',
-        'timit                   = bob.bio.spear.config.database.timit:database',
+        'timit            = bob.bio.spear.config.database.timit:database',
+        'mobio-male       = bob.bio.spear.config.database.mobio:mobio_audio_male',
+        'mobio-female       = bob.bio.spear.config.database.mobio:mobio_audio_female',
       ],
 
       'bob.bio.preprocessor': [