first commit

.gitignore

+*~
+*.swp
+*.pyc
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+src
+develop-eggs
+built-docs
+dist
+sphinx
+db.sql3

MANIFEST.in

+include README.rst bootstrap.py buildout.cfg COPYING
+recursive-include docs *.py *.rst
+recursive-include xbob *.sql3

README.rst

+================
+ UTFVP Database
+================
+
+
+This package contains the access API and descriptions for the `UTFVP 
+Database`_. The actual raw data for the database should be downloaded from the original URL. This API is only 
+compatible with the images from the UTFVP English database.  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.utfvp>`_. 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=[
+      ...
+      "bob==1.2.2",  # base signal proc./machine learning library
+      "xbob.db.utfvp",
+    ],
+
+Proceed normally with your ``boostrap/buildout`` steps and you should be all
+set. That means you can now import the ``xbob.db.utfvp`` namespace 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.utfvp
+
+  [sources]
+  xbob.db.utfvp = git https://github.com/bioidiap/xbob.db.utfvp.git
+  ...

bootstrap.py

+##############################################################################
+#
+# Copyright (c) 2006 Zope Foundation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+"""
+
+import os
+import shutil
+import sys
+import tempfile
+
+from optparse import OptionParser
+
+tmpeggs = tempfile.mkdtemp()
+
+usage = '''\
+[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
+
+Bootstraps a buildout-based project.
+
+Simply run this script in a directory containing a buildout.cfg, using the
+Python that you want bin/buildout to use.
+
+Note that by using --find-links to point to local resources, you can keep
+this script from going over the network.
+'''
+
+parser = OptionParser(usage=usage)
+parser.add_option("-v", "--version", help="use a specific zc.buildout version")
+
+parser.add_option("-t", "--accept-buildout-test-releases",
+                  dest='accept_buildout_test_releases',
+                  action="store_true", default=False,
+                  help=("Normally, if you do not specify a --version, the "
+                        "bootstrap script and buildout gets the newest "
+                        "*final* versions of zc.buildout and its recipes and "
+                        "extensions for you.  If you use this flag, "
+                        "bootstrap and buildout will get the newest releases "
+                        "even if they are alphas or betas."))
+parser.add_option("-c", "--config-file",
+                  help=("Specify the path to the buildout configuration "
+                        "file to be used."))
+parser.add_option("-f", "--find-links",
+                  help=("Specify a URL to search for buildout releases"))
+
+
+options, args = parser.parse_args()
+
+######################################################################
+# load/install setuptools
+
+to_reload = False
+try:
+    import pkg_resources
+    import setuptools
+except ImportError:
+    ez = {}
+
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+
+    # XXX use a more permanent ez_setup.py URL when available.
+    exec(urlopen('https://bitbucket.org/pypa/setuptools/raw/0.7.2/ez_setup.py'
+                ).read(), ez)
+    setup_args = dict(to_dir=tmpeggs, download_delay=0)
+    ez['use_setuptools'](**setup_args)
+
+    if to_reload:
+        reload(pkg_resources)
+    import pkg_resources
+    # This does not (always?) update the default working set.  We will
+    # do it.
+    for path in sys.path:
+        if path not in pkg_resources.working_set.entries:
+            pkg_resources.working_set.add_entry(path)
+
+######################################################################
+# Try to best guess the version of buildout given setuptools
+if options.version is None:
+
+  try:
+    from distutils.version import LooseVersion
+    package = pkg_resources.require('setuptools')[0]
+    v = LooseVersion(package.version)
+    if v < LooseVersion('0.7'):
+      options.version = '2.1.1'
+  except:
+    pass
+
+######################################################################
+# Install buildout
+
+ws = pkg_resources.working_set
+
+cmd = [sys.executable, '-c',
+       'from setuptools.command.easy_install import main; main()',
+       '-mZqNxd', tmpeggs]
+
+find_links = os.environ.get(
+    'bootstrap-testing-find-links',
+    options.find_links or
+    ('http://downloads.buildout.org/'
+     if options.accept_buildout_test_releases else None)
+    )
+if find_links:
+    cmd.extend(['-f', find_links])
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+requirement = 'zc.buildout'
+version = options.version
+if version is None and not options.accept_buildout_test_releases:
+    # Figure out the most recent final version of zc.buildout.
+    import setuptools.package_index
+    _final_parts = '*final-', '*final'
+
+    def _final_version(parsed_version):
+        for part in parsed_version:
+            if (part[:1] == '*') and (part not in _final_parts):
+                return False
+        return True
+    index = setuptools.package_index.PackageIndex(
+        search_path=[setuptools_path])
+    if find_links:
+        index.add_find_links((find_links,))
+    req = pkg_resources.Requirement.parse(requirement)
+    if index.obtain(req) is not None:
+        best = []
+        bestv = None
+        for dist in index[req.project_name]:
+            distv = dist.parsed_version
+            if _final_version(distv):
+                if bestv is None or distv > bestv:
+                    best = [dist]
+                    bestv = distv
+                elif distv == bestv:
+                    best.append(dist)
+        if best:
+            best.sort()
+            version = best[-1].version
+if version:
+    requirement = '=='.join((requirement, version))
+cmd.append(requirement)
+
+import subprocess
+if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+    raise Exception(
+        "Failed to execute command:\n%s",
+        repr(cmd)[1:-1])
+
+######################################################################
+# Import and run buildout
+
+ws.add_entry(tmpeggs)
+ws.require(requirement)
+import zc.buildout.buildout
+
+if not [a for a in args if '=' not in a]:
+    args.append('bootstrap')
+
+# if -c was provided, we push it back into args for buildout' main function
+if options.config_file is not None:
+    args[0:0] = ['-c', options.config_file]
+
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)

buildout.cfg

+; vim: set fileencoding=utf-8 :
+
+[buildout]
+parts = scripts
+develop = .
+eggs = xbob.db.utfvp
+newest = false
+
+[scripts]
+recipe = xbob.buildout:scripts
+dependent-scripts = true

setup.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Pedro Tome <Pedro.Tome@idiap.ch>
+#
+# Copyright (C) 2014 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 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.utfvp',
+    version='1.0.0',
+    description='UTFVP Database Access API for Bob',
+    url='https://pypi.python.org/pypi/xbob.db.utfvp',
+    license='GPLv3',
+    author='',
+    author_email='',
+    keywords='vein recognition, bob, xbob, xbob.db, UTFVP',
+    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',
+      'six',  # py2/3 compatibility library
+      'bob==1.2.2',  # base signal proc./machine learning library
+      'xbob.db.verification.utils>=1.0.0' # defines a set of utilities for face verification databases like this one.
+    ],
+
+    namespace_packages = [
+      'xbob',
+      'xbob.db',
+      ],
+
+    entry_points = {
+      # bob database declaration
+      'bob.db': [
+        'utfvp = xbob.db.utfvp.driver:Interface',
+        ],
+
+      # bob unittest declaration
+      'bob.test': [
+        'utfvp = xbob.db.utfvp.test:UTFVPDatabaseTest',
+        ],
+      },
+
+    classifiers = [
+      'Development Status :: 3 - Beta',
+      'Environment :: Console',
+      'Intended Audience :: Developers',
+      'Intended Audience :: Education',
+      'Intended Audience :: Science/Research',
+      'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+      'Natural Language :: English',
+      'Programming Language :: Python',
+      'Programming Language :: Python :: 3',
+      '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/utfvp/__init__.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Laurent El Shafey <laurent.el-shafey@idiap.ch>
+#
+# Copyright (C) 2014 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 UTFVP Database for finger verification
+"""
+
+from .query import Database
+from .models import Client, File, Protocol, Model, ProtocolPurpose
+
+__all__ = dir()

xbob/db/utfvp/create.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Laurent El Shafey <Laurent.El-Shafey@idiap.ch>
+# Wed Feb 19 10:53:53 CET 2014
+#
+# Copyright (C) 2014 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/>.
+
+"""This script creates the UTFVP database in a single pass.
+"""
+
+import os
+
+from .models import *
+
+def nodot(item):
+  """Can be used to ignore hidden files, starting with the . character."""
+  return item[0] != '.'
+
+def add_files(session, imagedir, verbose):
+  """Add files (and clients) to the UTFVP database."""
+
+  def add_file(session, subdir, filename, client_dict, model_dict, file_dict, verbose):
+    """Parse a single filename and add it to the list.
+       Also add a client entry if not already in the database."""
+
+    v = os.path.splitext(os.path.basename(filename))[0].split('_')
+    subclient_id = int(v[0])
+    finger_id = int(v[1])
+    client_id = "%d_%d" % (subclient_id, finger_id)
+    if not (client_id in client_dict):
+      c = Client(client_id, subclient_id)
+      session.add(c)
+      session.flush()
+      session.refresh(c)
+      client_dict[client_id] = True
+    session_id = int(v[2])
+    base_path = os.path.join(subdir, os.path.basename(filename).split('.')[0])
+    sgroup = 'dev'
+    if subclient_id <= 36:
+      if subclient_id < 19:
+        if finger_id == ((subclient_id-1) % 6) + 1:
+          sgroup = 'world'
+      elif subclient_id > 19:
+        if finger_id == ((subclient_id-2) % 6) + 1:
+          sgroup = 'world'
+    if verbose>1: print("  Adding file '%s'..." %(base_path, ))
+    cfile = File(client_id, base_path, sgroup, finger_id, session_id)
+    session.add(cfile)
+    session.flush()
+    session.refresh(cfile)
+    file_dict[sgroup][cfile.id] = cfile
+    if sgroup == 'dev':
+      model_id = "%d_%d_%d" % (subclient_id, finger_id, session_id)
+      if verbose>1: print("  Adding Model '%s'..." %(model_id, ))
+      model = Model(model_id, client_id, cfile.id)
+      session.add(model)
+      session.flush()
+      session.refresh(model)
+      model_dict[model_id] = model
+    return [client_dict, model_dict, file_dict]
+
+  if verbose: print("Adding files...")
+  subdir_list = list(filter(nodot, os.listdir(imagedir)))
+  client_dict = {}
+  model_dict = {}
+  file_dict = {}
+  file_dict['world'] = {}
+  file_dict['dev'] = {}
+  for subdir in subdir_list:
+    file_list = list(filter(nodot, os.listdir(os.path.join(imagedir, subdir))))
+    for filename in file_list:
+      filename_, extension = os.path.splitext(filename)
+      if extension == '.png':
+        client_dict, model_dict, file_dict = add_file(session, subdir, os.path.join(imagedir, filename), client_dict, model_dict, file_dict, verbose)
+
+  return [client_dict, model_dict, file_dict]
+
+def add_protocols(session, client_dict, model_dict, file_dict, verbose):
+  """Adds protocols"""
+  # 2. ADDITIONS TO THE SQL DATABASE
+  protocol_list = ['master', 'paper']
+  protocolPurpose_list = [('world', 'train'), ('dev', 'enrol'), ('dev', 'probe')]
+  for proto in protocol_list:
+    p = Protocol(proto)
+    # Add protocol
+    if verbose: print("Adding protocol %s..." % (proto))
+    session.add(p)
+    session.flush()
+    session.refresh(p)
+   
+    for purpose in protocolPurpose_list:
+      pu = ProtocolPurpose(p.id, purpose[0], purpose[1])
+      if verbose>1: print(" Adding protocol purpose ('%s', '%s','%s')..." % (p.name, purpose[0], purpose[1]))
+      session.add(pu)
+      session.flush()
+      session.refresh(pu)
+
+      cfile_dict = file_dict[purpose[0]]
+      for f_id, f_file in cfile_dict.iteritems():
+        if f_file.client.subclient_id == 19 and proto == 'master':
+          continue
+        if verbose>1: print("   Adding file ('%s') to protocol purpose ('%s', '%s','%s')..." % (f_file.path, p.name, purpose[0], purpose[1]))
+        pu.files.append(f_file)
+    
+    for m_id, model in model_dict.iteritems():
+      if model.client.subclient_id == 19 and proto == 'master':
+        continue
+      p.models.append(model)
+
+
+def create_tables(args):
+  """Creates all necessary tables (only to be used at the first time)"""
+
+  from bob.db.utils import create_engine_try_nolock
+
+  engine = create_engine_try_nolock(args.type, args.files[0], echo=(args.verbose > 2))
+  Base.metadata.create_all(engine)
+
+# Driver API
+# ==========
+
+def create(args):
+  """Creates or re-creates this database"""
+
+  from bob.db.utils import session_try_nolock
+
+  dbfile = args.files[0]
+
+  if args.recreate:
+    if args.verbose and os.path.exists(dbfile):
+      print('unlinking %s...' % dbfile)
+    if os.path.exists(dbfile): os.unlink(dbfile)
+
+  if not os.path.exists(os.path.dirname(dbfile)):
+    os.makedirs(os.path.dirname(dbfile))
+
+  # the real work...
+  create_tables(args)
+  s = session_try_nolock(args.type, args.files[0], echo=(args.verbose > 2))
+  client_dict, model_dict, file_dict = add_files(s, args.imagedir, args.verbose)
+  add_protocols(s, client_dict, model_dict, file_dict, args.verbose)
+  s.commit()
+  s.close()
+
+def add_command(subparsers):
+  """Add specific subcommands that the action "create" can use"""
+
+  parser = subparsers.add_parser('create', help=create.__doc__)
+
+  parser.add_argument('-R', '--recreate', action='store_true', help="If set, I'll first erase the current database")
+  parser.add_argument('-v', '--verbose', action='count', help='Do SQL operations in a verbose way')
+  parser.add_argument('-D', '--imagedir', metavar='DIR', default='/idiap/resource/database/UTFVP/data', help="Change the relative path to the directory containing the images of the UTFVP database (defaults to %(default)s)")
+
+  parser.set_defaults(func=create) #action

xbob/db/utfvp/driver.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Laurent El Shafey <laurent.el-shafey@idiap.ch>
+# Wed Feb 19 12:31:20 CET 2014
+#
+# Copyright (C) 2014 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/>.
+
+"""Bob Database Driver entry-point for the UTFVP
+"""
+
+import os
+import sys
+from bob.db.driver import Interface as BaseInterface
+
+
+def dumplist(args):
+  """Dumps lists of files based on your criteria"""
+
+  from .query import Database
+  db = Database()
+
+  r = db.objects(
+      protocol=args.protocol,
+      purposes=args.purpose,
+      model_ids=(args.models,),
+      groups=args.group,
+      classes=args.sclass
+  )
+
+  output = sys.stdout
+  if args.selftest:
+    from bob.db.utils import null
+    output = null()
+
+  for f in r:
+    output.write('%s\n' % (f.make_path(args.directory, args.extension),))
+
+  return 0
+
+
+def checkfiles(args):