Initial port of the ATNT database as a satellite package for bob

.gitignore

+*~
+*.swp
+*.pyc
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+src
+develop-eggs
+dist
+sphinx

MANIFEST.in

+include README.rst
+recursive-include docs *.py *.rst
+recursive-include xbob *.txt

README.rst

+===================
+ ATNT/ORL Database
+===================
+
+The ATNT/ORL database is a database of faces.
+
+The actual raw data for the database should be downloaded from the original
+URL. This package only contains the `Bob <http://www.idiap.ch/software/bob/>`_
+accessor methods to use the DB directly from python, with our certified
+protocols.
+
+You would normally not install this package unless you are maintaining it. What
+you would do instead is to tie it in at the package you need to **use** it.
+There are a few ways to achieve this:
+
+1. You can add this package as a requirement at the ``setup.py`` for your own
+   `satellite package
+   <https://github.com/idiap/bob/wiki/Virtual-Work-Environments-with-Buildout>`_
+   or to your Buildout ``.cfg`` file, if you prefer it that way. With this
+   method, this package gets automatically downloaded and installed on your
+   working environment, or
+
+2. You can manually download and install this package using commands like
+   ``easy_install`` or ``pip``.
+
+The package is available in two different distribution formats:
+
+1. You can download it from `PyPI <http://pypi.python.org/pypi>`_, or
+
+2. You can download it in its source form from `its git repository
+   <https://github.com/bioidiap/xbob.db.nuaa>`_. When you download the
+   version at the git repository, you will need to run a command to recreate
+   the backend SQLite file required for its operation. This means that the
+   database raw files must be installed somewhere in this case. With option
+   ``a`` you can run in `dummy` mode and only download the raw data files for
+   the database once you are happy with your setup.
+
+You can mix and match points 1/2 and a/b above based on your requirements. Here
+are some examples:
+
+Modify your setup.py and download from PyPI
+===========================================
+
+That is the easiest. Edit your ``setup.py`` in your satellite package and add
+the following entry in the ``install_requires`` section (note: ``...`` means
+`whatever extra stuff you may have in-between`, don't put that on your
+script)::
+
+    install_requires=[
+      ...
+      "xbob.db.atnt",
+    ],
+
+Proceed normally with your ``boostrap/buildout`` steps and you should be all
+set. That means you can now import the namespace ``xbob.db.atnt`` into your scripts.
+
+Modify your buildout.cfg and download from git
+==============================================
+
+You will need to add a dependence to `mr.developer
+<http://pypi.python.org/pypi/mr.developer/>`_ to be able to install from our
+git repositories. Your ``buildout.cfg`` file should contain the following
+lines::
+
+  [buildout]
+  ...
+  extensions = mr.developer
+  auto-checkout = *
+  eggs = bob
+         ...
+         xbob.db.atnt
+
+  [sources]
+  xbob.db.atnt = git https://github.com/bioidiap/xbob.db.atnt.git
+  ...

buildout.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = external tests sphinx python
+develop = .
+versions = versions
+eggs = bob
+       xbob.db.atnt
+
+[versions]
+;If you would like to pin-down the recipes package version so you are not
+;bothered with eventual updates, do it here. Note that, by pinning the version
+;of the package, you will be also excluded from bug fixes.
+;xbob.buildout = 0.1
+
+[external]
+recipe = xbob.buildout:external
+egg-directories = /idiap/group/torch5spro/nightlies/last/install/linux-x86_64-release/lib
+
+[tests]
+recipe = xbob.buildout:nose
+eggs = ${buildout:eggs}
+script = tests.py
+
+[sphinx]
+recipe = xbob.buildout:sphinx
+eggs = ${buildout:eggs}
+source = ${buildout:directory}/docs
+build = ${buildout:directory}/sphinx
+
+[python]
+recipe = z3c.recipe.scripts
+eggs = ${buildout:eggs}
+interpreter = python
+dependent-scripts = true

docs/conf.py

+#!/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) 2011-2012 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 sys, os
+
+# 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'
+
+# 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',
+  'bob.sphinxext.plot', # ours add source copying to install directory
+  ]
+
+# The viewcode extension appeared only on Sphinx >= 1.0.0
+import sphinx
+if sphinx.__version__ >= "1.0":
+  extensions.append('sphinx.ext.viewcode')
+
+# Always includes todos
+todo_include_todos = 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
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'AT&T/ORL Database (Bob API)'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+from xbob.db.atnt.driver import Interface
+version = Interface().version()
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['**/links.rst']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- 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'
+
+# 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
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#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'
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = ''
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = ''
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'bobdbdoc'
+
+
+# -- 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', 'bobdbman.tex', u'Bob',
+   u'Biometrics Group, Idiap Research Institute', 'manual'),
+]
+
+# 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
+
+# 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', u'AT&T/ORL Database (Bob API) Documentation', [u'Idiap Research Institute'], 1)
+]
+
+
+# We want to remove all private (i.e. _. or __.__) members 
+# that are not in the list of accepted functions
+accepted_private_functions = ['__call__']
+
+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 True
+    else:
+      # test if the method is documented
+      if not hasattr(obj, '__doc__') or not obj.__doc__:
+        return True
+  
+  # Skips selected members in auto-generated documentation. Unfortunately, old
+  # versions of Boost.Python will not generate a __self__ member for static
+  # methods and that screws-up Sphinx processing. 
+  if sphinx.__version__ < "1.0":
+    # We have to remove objects that do not have a __self__ attribute set
+    import types
+    if isinstance(obj, types.BuiltinFunctionType) and \
+      not hasattr(obj, '__self__') and what == 'class':
+        app.warn("Skipping %s %s (no __self__)" % (what, name))
+        return True
+
+    return False
+  
+# Default processing flags for sphinx
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = ['members', 'undoc-members', 'special-members', 'inherited-members', 'show-inheritance']
+
+def setup(app):
+  app.connect('autodoc-skip-member', member_function_test)

docs/index.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Mon 13 Aug 2012 12:36:40 CEST 
+
+===================
+ AT&T/ORL Database
+===================
+
+.. automodule:: xbob.db.atnt

setup.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Laurent El Shafey <laurent.el-shafey@idiap.ch>
+
+from setuptools import setup, find_packages
+
+# The only thing we do in this file is to call the setup() function with all
+# parameters that define our package.
+setup(
+
+    name='xbob.db.atnt',
+    version='1.0.0a1',
+    description='ATNT/ORL Database Access API for Bob',
+    url='http://github.com/bioidiap/bob.db.nuaa',
+    license='GPLv3',
+    author='Laurent El Shafey',
+    author_email='laurent.el-shafey@idiap.ch',
+    long_description=open('README.rst').read(),
+
+    # This line is required for any distutils based packaging.
+    packages=find_packages(),
+    include_package_data=True,
+    zip_safe=False,
+
+    install_requires=[
+      'setuptools',
+      'bob',  # base signal proc./machine learning library
+    ],
+
+    namespace_packages = [
+      'xbob',
+      'xbob.db',
+      ],
+
+    entry_points={
+
+      # declare database to bob
+      'bob.db': [
+        'atnt = xbob.db.atnt.driver:Interface',
+        ],
+
+      # declare tests to bob
+      'bob.test': [
+        'atnt = xbob.db.atnt.test:ATNTDatabaseTest',
+        ],
+
+      },
+
+    classifiers = [
+      'Development Status :: 4 - Beta',
+      'Intended Audience :: Developers',
+      'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+      'Natural Language :: English',
+      'Programming Language :: Python',
+      'Topic :: Scientific/Engineering :: Artificial Intelligence',
+      'Topic :: Database :: Front-Ends',
+      ],
+)

xbob/__init__.py

+#see http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
+__import__('pkg_resources').declare_namespace(__name__)

xbob/db/__init__.py

+#see http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
+__import__('pkg_resources').declare_namespace(__name__)

xbob/db/atnt/__init__.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# @author: Manuel Guenther <Manuel.Guenther@idiap.ch> 
+# @date: Fri Apr 20 12:04:44 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/>.
+
+"""
+The AT&T "Database of Faces" is a small free facial image database to test face 
+recognition and verification algorithms on. It is also known by its former name
+"The ORL Database of Faces". You can download the AT&T database from:
+http://www.cl.cam.ac.uk/research/dtg/attarchive/facedatabase.html
+"""
+import os
+import sys
+import numpy
+from bob.db import utils
+
+__all__ = ['Database',]
+
+class Database(object):
+  """Wrapper class for the AT&T (aka ORL) database of faces (http://www.cl.cam.ac.uk/research/dtg/attarchive/facedatabase.html).
+  This class defines a simple protocol for training, enrollment and probe by splitting the few images of the database in a reasonable manner.""" 
+
+  def __init__(self):
+    self.m_groups = ('world', 'dev')
+    self.m_purposes = ('enrol', 'probe')
+    self.m_client_ids = set(range(1, 41))
+    self.m_files = set(range(1, 11))
+    self.m_training_clients = set([1,2,5,6,10,11,12,14,16,17,20,21,24,26,27,29,33,34,36,39])
+    self.m_enrol_files = set([2,4,5,7,9])
+
+  def dbname(self):
+    """Calculates my own name automatically."""
+    return os.path.basename(os.path.dirname(__file__))
+
+
+  def __check_validity__(self, l, obj, valid, default):
+    """Checks validity of user input data against a set of valid values."""
+    if not l: return default
+    elif isinstance(l, str) or isinstance(l, int): return self.__check_validity__([l], obj, valid, default) 
+    for k in l:
+      if k not in valid:
+        raise RuntimeError, 'Invalid %s "%s". Valid values are %s, or lists/tuples of those' % (obj, k, valid)
+    return l
+
+  def __make_path__(self, client_id, file_id, directory, extension):
+    """Generates the file name for the given client id and file id of the AT&T database."""
+    stem = os.path.join("s" + str(client_id), str(file_id))
+    if not extension: extension = ''
+    if directory: return os.path.join(directory, stem + extension)
+    return stem + extension
+
+
+  def clients(self, groups = None):
+    """Returns the vector of ids of the clients used in a given purpose
+    
+    Keyword Parameters:
+
+    groups
+      One of the groups 'world', 'dev' or a tuple with both of them (which is the default).
+    """
+
+    VALID_GROUPS = self.m_groups
+    groups = self.__check_validity__(groups, "group", VALID_GROUPS, VALID_GROUPS)
+    
+    ids = set()
+    if 'world' in groups:
+      ids |= self.m_training_clients
+    if 'dev' in groups:
+      ids |= self.m_client_ids - self.m_training_clients
+      
+    return list(sorted(ids))
+  
+
+  def models(self, groups = None):
+    """Returns the vector of ids of the models used in a given purpose
+    
+    Keyword Parameters:
+
+    groups
+      One of the groups 'world', 'dev' or a tuple with both of them (which is the default).
+    """
+
+    VALID_GROUPS = self.m_groups
+    groups = self.__check_validity__(groups, "group", VALID_GROUPS, VALID_GROUPS)
+    
+    ids = set()
+    if 'world' in groups:
+      ids |= self.m_training_clients
+    if 'dev' in groups:
+      ids |= self.m_client_ids - self.m_training_clients
+      
+    return list(sorted(ids))
+
+  
+  def get_client_id_from_file_id(self, file_id):
+    """Returns the client id from the given image id"""
+    return (file_id-1) / len(self.m_files) + 1
+    
+
+  def files(self, directory=None, extension=None, client_ids=None, groups=None, purposes=None):
+    """Returns a set of filenames for the specific query by the user.
+
+    Keyword Parameters:
+
+    directory
+      A directory name that will be prepended to the final filepath returned
+
+    extension
+      A filename extension that will be appended to the final filepath returned
+
+    client_ids
+      The ids of the clients whose files need to be retrieved. Should be a list of integral numbers from [1,40]
+
+    groups
+      One of the groups 'world' or 'dev' or a list with both of them (which is the default).
+
+    purposes
+      One of the purposes 'enrol' or 'probe' or a list with both of them (which is the default).
+      This field is ignored when the group 'train' is selected.
+
+    """
+
+    # check if groups set are valid
+    VALID_GROUPS = self.m_groups
+    groups = self.__check_validity__(groups, "group", VALID_GROUPS, VALID_GROUPS)
+
+    # collect the ids to retrieve
+    ids = set(self.clients(groups))
+
+    # check the desired client ids for sanity
+    VALID_IDS = self.m_client_ids
+    client_ids = set(self.__check_validity__(client_ids, "client id", VALID_IDS, VALID_IDS))
+
+    # calculate the intersection between the ids and the desired client ids
+    ids = ids & client_ids
+
+    # check that the groups are valid
+    VALID_PURPOSES = self.m_purposes
+    if 'dev' in groups:
+      purposes = self.__check_validity__(purposes, "purpose", VALID_PURPOSES, VALID_PURPOSES)
+    else:
+      purposes = VALID_PURPOSES
+      
+    file_ids = set()
+    if 'enrol' in purposes:
+      file_ids |= self.m_enrol_files
+    if 'probe' in purposes:
+      file_ids |= self.m_files - self.m_enrol_files
+    
+    # go through the dataset and collect all desired files
+    files = {}
+    for client_id in ids:
+      for file_id in file_ids:
+        files[(client_id-1) * len(self.m_files) + file_id] = self.__make_path__(client_id, file_id, directory, extension)
+              
+    return files
+ 

xbob/db/atnt/driver.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# @author: Manuel Guenther <Manuel.Guenther@idiap.ch> 
+# @date: Fri Apr 20 12:04:44 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/>.
+
+"""Commands the AT&T database can respond to.
+"""
+
+import os
+import sys 
+from bob.db.driver import Interface as BaseInterface
+
+def dumplist(args):
+  """Dumps lists of files based on your criteria."""
+
+  from .__init__ import Database
+  db = Database()
+
+  r = db.files(directory=args.directory, extension=args.extension, groups=args.groups, purposes=args.purposes)
+
+  output = sys.stdout
+  if args.selftest:
+    from bob.db.utils import null
+    output = null()
+
+  for id, f in r.items():
+    output.write('%s\n' % (f,))
+
+  return 0
+
+def checkfiles(args):
+  """Checks the existence of the files based on your criteria.""" 
+    
+  from .__init__ import Database
+  db = Database()
+
+  r = db.files(directory=args.directory, extension=args.extension)
+
+  # go through all files, check if they are available
+  good = {}
+  bad = {}
+  for id, f in r.items():
+    if os.path.exists(f): good[id] = f
+    else: bad[id] = f
+
+  # report
+  output = sys.stdout
+  if args.selftest:
+    from bob.db.utils import null
+    output = null()
+
+  if bad:
+    for id, f in bad.items():
+      output.write('Cannot find file "%s"\n' % (f,))
+    output.write('%d files (out of %d) were not found at "%s"\n' % \
+        (len(bad), len(r), args.directory))
+
+  return 0
+
+class Interface(BaseInterface):
+   
+  def name(self):
+    return 'atnt'
+  
+  def version(self):
+    import pkg_resources  # part of setuptools