Initial version of the package

.gitignore

+*~
+.idea
+.DS_Store
+*.swp
+*.pyc
+*.so
+*.dylib
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+develop-eggs
+sphinx
+dist
+.nfs*
+.gdb_history
+build
+*.egg
+src/
+*.sql3

MANIFEST.in

+include README.rst bootstrap-buildout.py buildout.cfg COPYING version.txt requirements.txt
+recursive-include doc *.py *.rst
+recursive-include bob/bio/base/test/data *-dev*

README.rst

+.. vim: set fileencoding=utf-8 :
+.. Pavel Korshunov <pavel.korshunov@idiap.ch>
+.. Wed 30 Sep 23:36:23 2015 CET
+
+========================================
+Scripts to run anti-spoofing experiments
+========================================
+
+This package is part of the ``bob.spoof`` packages, which allow to run comparable and reproducible anti-spoofing experiments on publicly available databases.
+
+This package contains basic functionality to run anti-spoofing experiments.
+It provides a generic ``./bin/spoof.py`` script that takes several parameters, including:
+
+* A database and its evaluation protocol
+* A data preprocessing algorithm
+* A feature extraction algorithm
+* An anti-spoofing algorithm
+
+All these steps of the biometric recognition system are given as configuration files.
+
+In this base class implementation, only a core functionality is implemented. The specialized algorithms should be provided by other packages, which are usually in the ``bob.spoof`` namespace, such as:
+
+* `bob.spoof.speech for speech anti-spoofing set of algorithms
+
+
+Installation
+------------
+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.
+
+.. _bob: https://www.idiap.ch/software/bob

bob/__init__.py

+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

bob/pad/__init__.py

+# see https://docs.python.org/3/library/pkgutil.html
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)

bob/pad/base/__init__.py

+from . import algorithm
+from . import tools
+#from . import grid # only one file, not complete directory
+
+from . import script
+from . import test
+
+def get_config():
+  """Returns a string containing the configuration information.
+  """
+  import bob.extension
+  return bob.extension.get_config(__name__)
+
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/pad/base/algorithm/Algorithm.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Pavel Korshunov <pavel.korshunov@idiap.ch>
+# @date: Wed 19 Aug 13:43:21 2015
+#
+# 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
+from bob.bio.base import utils
+
+
+class Algorithm:
+    """This is the base class for all anti-spoofing algorithms.
+    It defines the minimum requirements for all derived algorithm classes.
+
+    Call the constructor in derived class implementations.
+    If your derived algorithm performs feature projection, please register this here.
+    If it needs training for the projector, please set this here, too.
+
+    **Parameters:**
+
+    performs_projection : bool
+      Set to ``True`` if your derived algorithm performs a projection.
+      Also implement the :py:meth:`project` function, and the :py:meth:`load_projector` if necessary.
+
+    requires_projector_training : bool
+      Only valid, when ``performs_projection = True``.
+      Set this flag to ``False``, when the projection is applied, but the projector does not need to be trained.
+
+    kwargs : ``key=value`` pairs
+      A list of keyword arguments to be written in the :py:meth:`__str__` function.
+
+    """
+
+    def __init__(
+            self,
+            performs_projection=False,  # enable if your tool will project the features
+            requires_projector_training=True,  # by default, the projector needs training, if projection is enabled
+            **kwargs  # parameters from the derived class that should be reported in the __str__() function
+    ):
+        self.performs_projection = performs_projection
+        self.requires_projector_training = performs_projection and requires_projector_training
+        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.
+        """
+        return "%s(%s)" % (str(self.__class__), ", ".join(
+            ["%s=%s" % (key, value) for key, value in self._kwargs.items() if value is not None]))
+
+    def project(self, feature):
+        """project(feature) -> projected
+
+        This function will project the given feature.
+        It must be overwritten by derived classes, as soon as ``performs_projection = True`` was set in the constructor.
+        It is assured that the :py:meth:`load_projector` was called once before the ``project`` function is executed.
+
+        **Parameters:**
+
+        feature : object
+          The feature to be projected.
+
+        **Returns:**
+
+        projected : object
+          The projected features.
+          Must be writable with the :py:meth:`write_feature` function and readable with the :py:meth:`read_feature` function.
+
+        """
+        raise NotImplementedError("Please overwrite this function in your derived class")
+
+    def score(self, toscore):
+        """score(toscore) -> score
+
+        This function will compute the score for the given object ``toscore``.
+        It must be overwritten by derived classes.
+
+        **Parameters:**
+
+        toscore : object
+          The object to compute the score for.
+
+        **Returns:**
+
+        score : float
+          A score value for the object ``toscore``.
+        """
+        raise NotImplementedError("Please overwrite this function in your derived class")
+
+    def score_for_multiple_projections(self, toscore):
+        """scorescore_for_multiple_projections(toscore) -> score
+
+        This function will compute the score for a list of objects in ``toscore``.
+        It must be overwritten by derived classes.
+
+        **Parameters:**
+
+        toscore : [object]
+          A list of objects to compute the score for.
+
+        **Returns:**
+
+        score : float
+          A score value for the object ``toscore``.
+        """
+        raise NotImplementedError("Please overwrite this function in your derived class")
+
+    ############################################################
+    ### Special functions that might be overwritten on need
+    ############################################################
+
+    def write_feature(self, feature, feature_file):
+        """Saves the given *projected* feature to a file with the given name.
+        In this base class implementation:
+
+        - If the given feature has a ``save`` attribute, it calls ``feature.save(bob.io.base.HDF5File(feature_file), 'w')``.
+          In this case, the given feature_file might be either a file name or a bob.io.base.HDF5File.
+        - Otherwise, it uses :py:func:`bob.io.base.save` to do that.
+
+        If you have a different format, please overwrite this function.
+
+        Please register 'performs_projection = True' in the constructor to enable this function.
+
+        **Parameters:**
+
+        feature : object
+          A feature as returned by the :py:meth:`project` function, which should be written.
+
+        feature_file : str or :py:class:`bob.io.base.HDF5File`
+          The file open for writing, or the file name to write to.
+        """
+        utils.save(feature, feature_file)
+
+    def read_feature(self, feature_file):
+        """read_feature(feature_file) -> feature
+
+        Reads the *projected* feature from file.
+        In this base class implementation, it uses :py:func:`bob.io.base.load` to do that.
+        If you have different format, please overwrite this function.
+
+        Please register ``performs_projection = True`` in the constructor to enable this function.
+
+        **Parameters:**
+
+        feature_file : str or :py:class:`bob.io.base.HDF5File`
+          The file open for reading, or the file name to read from.
+
+        **Returns:**
+
+        feature : object
+          The feature that was read from file.
+        """
+        return utils.load(feature_file)
+
+    def read_toscore_object(self, toscore_object_file):
+        """read_toscore_object(toscore_object_file) -> toscore_object
+
+        Reads the toscore_object feature from a file.
+        By default, the toscore_object feature is identical to the projected feature.
+        Hence, this base class implementation simply calls :py:meth:`read_feature`.
+
+        If your algorithm requires different behavior, please overwrite this function.
+
+        **Parameters:**
+
+        toscore_object_file : str or :py:class:`bob.io.base.HDF5File`
+          The file open for reading, or the file name to read from.
+
+        **Returns:**
+
+        toscore_object : object
+          The toscore_object that was read from file.
+        """
+        return self.read_feature(toscore_object_file)
+
+    def train_projector(self, training_features, projector_file):
+        """This function can be overwritten to train the feature projector.
+        If you do this, please also register the function by calling this base class constructor
+        and enabling the training by ``requires_projector_training = True``.
+
+        **Parameters:**
+
+        training_features : [object] or [[object]]
+          A list of *extracted* features that can be used for training the projector.
+          Features will be provided in a single list
+
+        projector_file : str
+          The file to write.
+          This file should be readable with the :py:meth:`load_projector` function.
+        """
+        raise NotImplementedError(
+            "Please overwrite this function in your derived class, or unset the 'requires_projector_training' option in the constructor.")
+
+    def load_projector(self, projector_file):
+        """Loads the parameters required for feature projection from file.
+        This function usually is useful in combination with the :py:meth:`train_projector` function.
+        In this base class implementation, it does nothing.
+
+        Please register `performs_projection = True` in the constructor to enable this function.
+
+        **Parameters:**
+
+        projector_file : str
+          The file to read the projector from.
+        """
+        pass

bob/pad/base/algorithm/__init__.py

+from .Algorithm import Algorithm
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/pad/base/config/grid/demanding.py

+import bob.bio.base
+
+# define a queue with demanding parameters
+grid = bob.bio.base.grid.Grid(
+    number_of_scoring_jobs=1,
+    number_of_enrollment_jobs=1,
+    training_queue='32G',
+    # preprocessing
+    preprocessing_queue='4G',
+    # feature extraction
+    extraction_queue='8G',
+    # feature projection
+    projection_queue='8G',
+    # model enrollment
+    enrollment_queue='8G',
+    # scoring
+    scoring_queue='8G'
+)

bob/pad/base/database/DatabaseBobSpoof.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# @author: Pavel Korshunov <pavel.korshunov@idiap.ch>
+# @date: Wed 19 Aug 13:43:21 2015
+#
+# 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 bob.bio.base.database.Database import Database
+import os
+
+import antispoofing.utils.db
+
+
+class DatabaseBobSpoof(Database):
+    """This class can be used whenever you have a database that follows the Bob
+    antispoofing database interface, which is defined in :py:class:`antispoofing.utils.db.Database`
+
+    **Parameters:**
+
+    database : derivative of :py:class:`antispoofing.utils.db.Database`
+      The database instance that provides the actual interface, see :ref:`antispoofing_databases` for a list.
+
+    all_files_options : dict
+      Dictionary of options passed to the :py:meth:`antispoofing.utils.db.Database.objects` database query when retrieving all data.
+
+    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`` 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
+            original_directory=None,  # the directory where the data files are located
+            check_original_files_for_existence=False,
+            **kwargs  # The default parameters of the base class
+    ):
+
+        Database.__init__(
+            self,
+            **kwargs
+        )
+
+        assert isinstance(database, antispoofing.utils.db.Database), \
+            "Only databases derived from antispoofing.utils.db.Database are supported by this interface. " \
+            "Please implement your own bob.bio.base.database.Database interface for anti-spoofing experiments."
+
+        self.database = database
+        if original_directory is None:
+            self.original_directory = database.original_directory
+        else:
+            self.original_directory = original_directory
+
+        self.all_files_options = all_files_options
+        self.check_existence = check_original_files_for_existence
+
+        self._kwargs = kwargs
+
+    def set_protocol(self, protocol):
+        """
+        Sets the protocol for the database. The protocol can be specified via command line to spoof.py
+        script with option -P
+        :param protocol: name of the protocol
+        :return: None
+        """
+        self.protocol = protocol
+        self.database.set_kwargs({'protocol': protocol})
+
+    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" % (self.original_directory)
+        if self.all_files_options: params += ", all_files_options=%s" % self.all_files_options
+
+        return "%s(%s)" % (str(self.__class__), params)
+
+
+    def replace_directories(self, replacements=None):
+        """This helper function replaces the ``original_directory`` of the database with
+        the directory 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.
+
+        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
+
+           original/path/to/data = /path/to/your/data
+
+        **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 = self.original_directory
+
+
+    def all_files(self, groups=('train', 'dev', 'eval')):
+        """all_files(groups=('train', 'dev', 'eval')) -> files
+
+        Returns all files of the database, respecting the current protocol.
+
+        **Parameters:**
+
+        groups : some of ``('train', 'dev', 'eval')`` or ``None``
+          The groups to get the data for.
+          If ``None``, data for all groups is returned.
+
+        **Returns:**
+
+        files : [:py:class:`antispoofing.utils.db.File`]
+          The sorted and unique list of all files of the database.
+        """
+        realset = []
+        attackset = []
+        if 'train' in groups:
+            real, attack = self.database.get_train_data()
+            realset += real
+            attackset += attack
+        if 'dev' in groups:
+            real, attack = self.database.get_devel_data()
+            realset += real
+            attackset += attack
+        if 'eval' in groups:
+            real, attack = self.database.get_test_data()
+            realset += real
+            attackset += attack
+        return [realset, attackset]
+
+    def training_files(self, step=None, arrange_by_client=False):
+        """training_files(step = None, arrange_by_client = False) -> files
+
+        Returns all training File objects
+        This function needs to be implemented in derived class implementations.
+
+        **Parameters:**
+            The parameters are not applicable in this version of anti-spoofing experiments
+
+        **Returns:**
+
+        files : [:py:class:`File`] or [[:py:class:`File`]]
+          The (arranged) list of files used for the training.
+        """
+        return self.database.get_train_data()
+
+    def original_file_names(self, files):
+        """original_file_names(files) -> paths
+
+        Returns the full paths of the real and attack data of the given File objects.
+
+        **Parameters:**
+
+        files : [[:py:class:`antispoofing.utils.db.File`], [:py:class:`antispoofing.utils.db.File`]]
+          The list of lists ([real, attack]]) of file object to retrieve the original data file names for.
+
+        **Returns:**
+
+        paths : [str]
+          The paths extracted for the concatenated real+attack files, in the preserved order.
+        """
+        realfiles = files[0]
+        attackfiles = files[1]
+        realpaths = [file.make_path(directory=self.original_directory, extension=self.original_extension) for file in
+                     realfiles]
+        attackpaths = [file.make_path(directory=self.original_directory, extension=self.original_extension) for file in
+                       attackfiles]
+        return realpaths + attackpaths

bob/pad/base/database/__init__.py

+#from .utils import File, FileSet
+
+# from bob.bio.base.database.Database import Database
+from .DatabaseBobSpoof import DatabaseBobSpoof
+
+# gets sphinx autodoc done right - don't remove it
+__all__ = [_ for _ in dir() if not _.startswith('_')]

bob/pad/base/script/__init__.py

+from . import spoof

bob/pad/base/script/spoof.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# @author: Pavel Korshunov <pavel.korshunov@idiap.ch>
+# @date: Wed 19 Aug 13:43:21 2015
+#
+# 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 sys
+import argparse
+import os.path
+
+import logging
+
+logger = logging.getLogger("bob.pad.base")
+
+from .. import tools
+import bob.bio.base.tools as biotools
+
+
+# from bob.bio.base.tools import grid
+
+def parse_arguments(command_line_parameters, exclude_resources_from=[]):
+    """This function parses the given options (which by default are the command line options).
+    If exclude_resources_from is specified (as a list), the resources from the given packages are
+    not listed in the help message."""
+    # set up command line parser
+    parsers = tools.command_line_parser(exclude_resources_from=exclude_resources_from)
+
+    # Add sub-tasks that can be executed by this script
+    parser = parsers['main']
+    parser.add_argument('--sub-task',