Initial commit with base structure

.gitignore

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

LICENSE

+Copyright (c) 2013, Andre Anjos - Idiap Research Institute
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.  Redistributions in binary
+form must reproduce the above copyright notice, this list of conditions and the
+following disclaimer in the documentation and/or other materials provided with
+the distribution.  Neither the name of the Idiap Research Institute nor the
+names of its contributors may be used to endorse or promote products derived
+from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

+include LICENSE README.rst bootstrap.py buildout.cfg
+recursive-include doc conf.py *.rst
+recursive-include xbob *.cpp *.h

README.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Thu 29 Aug 2013 16:07:57 CEST
+
+============================
+ Python bindings for bob.io
+============================
+
+This package contains a set of Pythonic bindings for Bob's io packages and
+functionality.
+
+Installation
+------------
+
+Install it through normal means, via PyPI or use ``zc.buildout`` to bootstrap
+the package and run test units.
+
+Documentation
+-------------
+
+You can generate the documentation for this package, after installation, using
+Sphinx::
+
+  $ sphinx-build -b html doc sphinx
+
+This shall place in the directory ``sphinx``, the current version for the
+documentation of the package.
+
+Testing
+-------
+
+You can run a set of tests using the nose test runner::
+
+  $ nosetests -sv blitz
+
+.. warning::
+
+   If Bob <= 1.2.1 is installed on your python path, nose will automatically
+   load the old version of the insulate plugin available in Bob, which will
+   trigger the loading of incompatible shared libraries (from Bob itself), in
+   to your working binary. This will cause a stack corruption. Either remove
+   the centrally installed version of Bob, or build your own version of Python
+   in which Bob <= 1.2.1 is not installed.
+
+You can run our documentation tests using sphinx itself::
+
+  $ sphinx-build -b doctest doc sphinx
+
+You can test overall test coverage with::
+
+  $ nosetests --with-coverage --cover-package=xbob.io
+
+The ``coverage`` egg must be installed for this to work properly.
+
+Development
+-----------
+
+To develop this package, install using ``zc.buildout``, using the buildout
+configuration found on the root of the package:
+
+  $ python bootstrap.py
+  ...
+  $ ./bin/buildout
+
+Tweak the options in ``buildout.cfg`` to disable/enable verbosity and debug
+builds.

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 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = blitz.array xbob.io scripts
+eggs = xbob.io
+       ipdb
+extensions = mr.developer
+auto-checkout = *
+prefixes = /Users/andre/work/bob/b/dbg
+debug = true
+verbose = true
+
+[sources]
+xbob.buildout = git git@github.com:bioidiap/xbob.buildout
+pypkg = git git@github.com:anjos/pypkg
+
+[blitz.array]
+recipe = xbob.buildout:develop
+setup = src/blitz.array
+eggs = pypkg
+
+[xbob.io]
+recipe = xbob.buildout:develop
+eggs = blitz.array pypkg
+
+[scripts]
+recipe = xbob.buildout:scripts

doc/c_cpp_api.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.dos.anjos@gmail.com>
+.. Tue 15 Oct 14:59:05 2013
+
+=========
+ C++ API
+=========
+
+The C++ API of ``xbob.core`` allows users to leverage from automatic converters
+for classes in :py:class:`xbob.core.random`.  To use the C API, clients should
+first, include the header file ``<xbob.core/random.h>`` on their compilation
+units and then, make sure to call once ``import_xbob_core_random()`` at their
+module instantiation, as explained at the `Python manual
+<http://docs.python.org/2/extending/extending.html#using-capsules>`_.
+
+Here is a dummy C example showing how to include the header and where to call
+the import function:
+
+.. code-block:: c++
+
+   #include <xbob.core/random.h>
+
+   PyMODINIT_FUNC initclient(void) {
+
+     PyObject* m Py_InitModule("client", ClientMethods);
+
+     if (!m) return;
+
+     // imports the NumPy C-API 
+     import_array();
+
+     // imports blitz.array C-API
+     import_blitz_array();
+
+     // imports xbob.core.random C-API
+     import_xbob_core_random();
+
+   }
+
+.. note::
+
+  The include directory can be discovered using
+  :py:func:`xbob.core.get_include`.
+
+Mersenne Twister Random Number Generator (mt19937)
+--------------------------------------------------
+
+This package contains bindings to ``boost::random::mt19937``, which is a
+powerful random number generator available within the Boost_ C++ library.
+
+.. cpp:type:: PyBoostMt19937Object
+
+   The pythonic object representation for a ``boost::random::mt19937`` object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        boost::random::mt19937* rng;
+      } PyBoostMt19937Object;
+   
+   .. c:member:: boost::random::mt19937* rng
+
+      A direct pointer to the boost random number generator. You can use this
+      pointer in your C/C++ code if required.
+
+
+.. cpp:function:: int PyBoostMt19937_Check(PyObject* o)
+
+   Checks if the input object ``o`` is a ``PyBoostMt19937Object``. Returns
+   ``1`` if it is, and ``0`` otherwise.
+
+
+.. cpp:function:: int PyBoostMt19937_Converter(PyObject* o, PyBoostMt19937Object** a)
+
+   This function is meant to be used with :c:func:`PyArg_ParseTupleAndKeywords`
+   family of functions in the Python C-API. It checks the input
+   object to be of type ``PyBoostMt19937Object`` and sets a **new
+   reference** to it (in ``*a``) if it is the case. Returns ``0`` in case of
+   failure, ``1`` in case of success.
+
+.. cpp:function:: PyObject* PyBoostMt19937_SimpleNew()
+
+   Creates a new instance of :cpp:type:`PyBoostMt19937Object`, with the default
+   seed. Returns a **new reference**.
+
+.. cpp:function:: PyObject* PyBoostMt19937_NewWithSeed(Py_ssize_t seed)
+
+   Creates a new instance of :cpp:type:`PyBoostMt19937Object`, with a user
+   given seed. Returns a **new reference**.
+
+Distribution API
+----------------
+
+Together with the boost random number generator ``mt19937``, this package
+provides bindings to these ``boost::random`` distributions:
+
+  * Uniform
+  * Normal (or Gaussian)
+  * Log-normal
+  * Gamma
+  * Binomial
+
+Distributions wrap the random number generator, skewing the distribution of
+numbers according to their parametrization. Distributions are *templated*
+according to the scalar data types they produce. Different distributions
+support a different set of scalar types:
+
+  ============== =================================================
+   Distribution   Scalars supported
+  ============== =================================================
+    Uniform       bool, int8/16/32/64, uint8/16/32/64, float32/64
+    Normal        float32/64
+    Log-normal    float32/64
+    Gamma         float32/64
+    Binomial      float32/64 (internally using int64)
+  ============== =================================================
+
+.. cpp:type:: PyBoostUniformObject
+
+   The pythonic object representation for a ``boost::random::uniform_*``
+   object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        int type_num;
+        boost::shared_ptr<void> distro;
+      } PyUniformObject;
+
+   .. c:member:: int type_num;
+
+      The NumPy type number of scalars produced by this distribution. Accepted
+      values match the scalar type produced:
+
+       ============= ========================================
+        Scalar type   NumPy scalar type number (enumeration)
+       ============= ========================================
+          bool        ``NPY_BOOL``
+          int8        ``NPY_INT8``
+          int16       ``NPY_INT16``
+          int32       ``NPY_INT32``
+          int64       ``NPY_INT64``
+          int8        ``NPY_INT8``
+          int16       ``NPY_INT16``
+          int32       ``NPY_INT32``
+          int64       ``NPY_INT64``
+          float32     ``NPY_FLOAT32``
+          float64     ``NPY_FLOAT64``
+       ============= ========================================
+
+   .. c:member:: boost::shared_ptr<void> distro
+
+      A direct pointer to the boost distribution. The underlying allocated type
+      changes with the scalar that is produced by the distribution:
+
+       ============= ==============================================
+        Scalar type   C++ data type
+       ============= ==============================================
+          bool        ``boost::random::uniform_smallint<uint8_t>``
+          int8        ``boost::random::uniform_int<int8_t>``
+          int16       ``boost::random::uniform_int<int16_t>``
+          int32       ``boost::random::uniform_int<int32_t>``
+          int64       ``boost::random::uniform_int<int64_t>``
+          uint8       ``boost::random::uniform_int<uint8_t>``
+          uint16      ``boost::random::uniform_int<uint16_t>``
+          uint32      ``boost::random::uniform_int<uint32_t>``
+          uint64      ``boost::random::uniform_int<uint64_t>``
+          float32     ``boost::random::uniform_real<float>``
+          float64     ``boost::random::uniform_real<double>``
+       ============= ==============================================
+
+   In order to use the distribution in your C/C++ code, you must first cast the
+   shared pointer using ``boost::static_pointer_cast<D>``, with ``D`` matching
+   one of the distributions listed above, depending on the value of
+
+.. cpp:type:: PyBoostNormalObject
+
+   The pythonic object representation for a
+   ``boost::random::normal_distribution`` object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        int type_num;
+        boost::shared_ptr<void> distro;
+      } PyUniformObject;
+
+   .. c:member:: int type_num;
+
+      The NumPy type number of scalars produced by this distribution. Accepted
+      values match the scalar type produced:
+
+       ============= ========================================
+        Scalar type   NumPy scalar type number (enumeration)
+       ============= ========================================
+          float32     ``NPY_FLOAT32``
+          float64     ``NPY_FLOAT64``
+       ============= ========================================
+
+   .. c:member:: boost::shared_ptr<void> distro
+
+      A direct pointer to the boost distribution. The underlying allocated type
+      changes with the scalar that is produced by the distribution:
+
+       ============= ================================================
+        Scalar type   C++ data type
+       ============= ================================================
+          float32     ``boost::random::normal_distribution<float>``
+          float64     ``boost::random::normal_distribution<double>``
+       ============= ================================================
+
+.. cpp:type:: PyBoostLogNormalObject
+
+   The pythonic object representation for a
+   ``boost::random::lognormal_distribution`` object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        int type_num;
+        boost::shared_ptr<void> distro;
+      } PyUniformObject;
+
+   .. c:member:: int type_num;
+
+      The NumPy type number of scalars produced by this distribution. Accepted
+      values match the scalar type produced:
+
+       ============= ========================================
+        Scalar type   NumPy scalar type number (enumeration)
+       ============= ========================================
+          float32     ``NPY_FLOAT32``
+          float64     ``NPY_FLOAT64``
+       ============= ========================================
+
+   .. c:member:: boost::shared_ptr<void> distro
+
+      A direct pointer to the boost distribution. The underlying allocated type
+      changes with the scalar that is produced by the distribution:
+
+       ============= ===================================================
+        Scalar type   C++ data type
+       ============= ===================================================
+          float32     ``boost::random::lognormal_distribution<float>``
+          float64     ``boost::random::lognormal_distribution<double>``
+       ============= ===================================================
+
+.. cpp:type:: PyBoostGammaObject
+
+   The pythonic object representation for a
+   ``boost::random::gamma_distribution`` object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        int type_num;
+        boost::shared_ptr<void> distro;
+      } PyUniformObject;
+
+   .. c:member:: int type_num;
+
+      The NumPy type number of scalars produced by this distribution. Accepted
+      values match the scalar type produced:
+
+       ============= ========================================
+        Scalar type   NumPy scalar type number (enumeration)
+       ============= ========================================
+          float32     ``NPY_FLOAT32``
+          float64     ``NPY_FLOAT64``
+       ============= ========================================
+
+   .. c:member:: boost::shared_ptr<void> distro
+
+      A direct pointer to the boost distribution. The underlying allocated type
+      changes with the scalar that is produced by the distribution:
+
+       ============= ===============================================
+        Scalar type   C++ data type
+       ============= ===============================================
+          float32     ``boost::random::gamma_distribution<float>``
+          float64     ``boost::random::gamma_distribution<double>``
+       ============= ===============================================
+
+.. cpp:type:: PyBoostBinomialObject
+
+   The pythonic object representation for a
+   ``boost::random::binomial_distribution`` object.
+
+   .. code-block:: c
+
+      typedef struct {
+        PyObject_HEAD
+        int type_num;
+        boost::shared_ptr<void> distro;
+      } PyUniformObject;
+
+   .. c:member:: int type_num;
+
+      The NumPy type number of scalars produced by this distribution. Accepted
+      values match the scalar type produced:
+
+       ============= ========================================
+        Scalar type   NumPy scalar type number (enumeration)
+       ============= ========================================
+          float32     ``NPY_FLOAT32``
+          float64     ``NPY_FLOAT64``
+       ============= ========================================
+
+   .. c:member:: boost::shared_ptr<void> distro
+
+      A direct pointer to the boost distribution. The underlying allocated type
+      changes with the scalar that is produced by the distribution:
+
+       ============= ==========================================================
+        Scalar type   C++ data type
+       ============= ==========================================================
+          float32     ``boost::random::binomial_distribution<int64_t,float>``
+          float64     ``boost::random::binomial_distribution<int64_t,double>``
+       ============= ==========================================================
+
+.. cpp:function:: int PyBoostUniform_Check(PyObject* o)
+
+.. cpp:function:: int PyBoostNormal_Check(PyObject* o)
+
+.. cpp:function:: int PyBoostLogNormal_Check(PyObject* o)
+
+.. cpp:function:: int PyBoostGamma_Check(PyObject* o)
+
+.. cpp:function:: int PyBoostBinomial_Check(PyObject* o)
+
+   Checks if the input object ``o`` is a ``PyBoost<Distribution>Object``.
+   Returns ``1`` if it is, and ``0`` otherwise.
+
+.. cpp:function:: int PyBoostUniform_Converter(PyObject* o, PyBoostUniformObject** a)
+
+.. cpp:function:: int PyBoostNormal_Converter(PyObject* o, PyBoostNormalObject** a)
+
+.. cpp:function:: int PyBoostLogNormal_Converter(PyObject* o, PyBoostLogNormalObject** a)
+
+.. cpp:function:: int PyBoostGamma_Converter(PyObject* o, PyBoostGammaObject** a)
+
+.. cpp:function:: int PyBoostBinomial_Converter(PyObject* o, PyBoostBinomialObject** a)
+
+   This function is meant to be used with :c:func:`PyArg_ParseTupleAndKeywords`
+   family of functions in the Python C-API. It checks the input object to be of
+   type ``PyBoost<Distribution>Object`` and returns a **new reference** to it
+   (in ``*a``) if it is the case. Returns ``0`` in case of failure, ``1`` in
+   case of success.
+
+.. cpp:function:: PyObject* PyBoostUniform_SimpleNew(int type_num, PyObject* min, PyObject* max)
+
+   Creates a new instance of :cpp:type:`PyBoostUniformObject`, with the input
+   scalar establishing the minimum and the maximum of the distribution. Note
+   that ``bool`` distributions will raise an exception if one tries to set the
+   minimum and the maximum, since that is non-sensical.
+
+   The parameter ``type_num`` may be set to one of the supported ``NPY_``
+   enumeration values (e.g. ``NPY_UINT16``).
+
+   .. warning::
+
+     For integral uniform distributions the range of numbers produced is
+     defined as :math:`[min, max]`. For real-valued distributions, the range of
+     numbers produced lies on the interval :math:`[min, max[`.
+
+.. cpp:function:: PyObject* PyBoostNormal_SimpleNew(int type_num, PyObject* mean, PyObject* sigma)
+
+.. cpp:function:: PyObject* PyBoostLogNormal_SimpleNew(int type_num, PyObject* mean, PyObject* sigma)
+
+.. cpp:function:: PyObject* PyBoostGamma_SimpleNew(int type_num, PyObject* alpha, PyObject* beta)
+
+.. cpp:function:: PyObject* PyBoostBinomial_SimpleNew(int type_num, PyObject* t, PyObject* p)
+
+   Depending on the distribution, which may be one of ``Normal``,
+   ``LogNormal``, ``Gamma`` or ``Binomial``, each of the parameters assume a
+   different function:
+
+     ============== ============= ============================
+      Distribution   Parameter 1   Parameter 2
+     ============== ============= ============================
+      Normal         mean          sigma (standard deviation)
+      LogNormal      mean          sigma (standard deviation)
+      Gamma          alpha         beta
+      Binomial       t             p
+     ============== ============= ============================
+
+   The parameter ``type_num`` may be set to one of the supported ``NPY_``
+   enumeration values (e.g. ``NPY_FLOAT64``).
+
+.. include:: links.rst

doc/conf.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.anjos@idiap.ch>
+# Tue 15 Oct 16:37:18 2013 CEST
+#
+# Copyright (C) 2011-2013 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/>.
+
+import os
+import sys
+import glob
+import pkg_resources
+
+# 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',
+  'matplotlib.sphinxext.plot_directive',
+  ]
+
+# 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'xbob.io'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# Grab the setup entry
+distribution = pkg_resources.require('xbob.io')[0]
+
+# 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.
+version = distribution.version
+# The full version, including alpha/beta/rc tags.
+release = distribution.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 = 'xbob_io'
+
+# 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 = 'xbob_io_doc'
+
+
+# -- 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', 'xbob_io.tex', u'Bob I/O Routines',
+   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 = """
+.. |version| replace:: %s
+""" % (version,)
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'xbob_io', u'Bob I/O Routines Documentation', [u'Idiap Research Institute'], 1)
+]
+
+# Default processing flags for sphinx
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = ['members', 'undoc-members', 'inherited-members', 'show-inheritance']
+
+def smaller_than(v1, v2):
+  """Compares scipy/numpy version numbers"""
+
+  c1 = v1.split('.')
+  c2 = v2.split('.')[:len(c1)] #clip to the compared version
+  for i, k in enumerate(c2):
+    n1 = c1[i]
+    n2 = c2[i]
+    try:
+      n1 = int(n1)
+      n2 = int(n2)
+    except ValueError:
+      n1 = str(n1)
+      n2 = str(n2)
+    if n1 > n2: return False
+  return True
+
+# Some name mangling to find the correct sphinx manuals for some packages
+numpy_version = __import__('numpy').version.version
+if smaller_than(numpy_version, '1.5.z'):
+  numpy_version = '.'.join(numpy_version.split('.')[:-1]) + '.x'
+else:
+  numpy_version = '.'.join(numpy_version.split('.')[:-1]) + '.0'
+numpy_manual = 'http://docs.scipy.org/doc/numpy-%s/' % numpy_version
+
+# For inter-documentation mapping:
+intersphinx_mapping = {
+  'http://docs.python.org/%d.%d/' % sys.version_info[:2]: None,
+  numpy_manual: None,
+  }
+
+def setup(app):
+  pass

doc/index.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Mon  4 Nov 20:58:04 2013 CET
+.. 
+.. Copyright (C) 2011-2013 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/>.
+
+.. Master file, created by sphinx-quickstart on Mon Mar 21 18:07:34 2011.  You
+   can adapt this file completely to your liking, but it should at least contain
+   the root `toctree` directive.
+
+=====================
+ Bob's Core Routines
+=====================
+
+This module contains base functionality from Bob bound to Python, available in
+the C++ counter-part ``bob::core``. It includes basic conversion routines,
+random number generation and central logging facilities.
+
+Reference
+---------
+
+.. toctree::
+   :maxdepth: 2
+
+   py_api
+   c_cpp_api
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. include:: links.rst

doc/links.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Tue 20 Mar 2012 08:57:32 CET 
+.. 
+.. Copyright (C) 2011-2013 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/>.
+
+.. This file contains all links we use for documentation in a centralized place
+
+.. Place here references to all citations in lower case
+
+.. _boost: http://www.boost.org
+.. _buildout: http://pypi.python.org/pypi/zc.buildout/
+.. _c++: http://www2.research.att.com/~bs/C++.html
+.. _numpy: http://numpy.scipy.org
+.. _nose: http://nose.readthedocs.org
+.. _pypi: http://pypi.python.org
+.. _scipy: http://www.scipy.org
+.. _setuptools: http://trac.edgewall.org/wiki/setuptools
+.. _sphinx: http://sphinx.pocoo.org
+
+.. Place here references to licenses
+
+.. _apache-2.0: http://www.opensource.org/licenses/Apache-2.0
+.. _artistic-2.0: http://www.opensource.org/licenses/Artistic-2.0
+.. _bsd-2-clause: http://www.opensource.org/licenses/BSD-2-Clause
+.. _bsd-3-clause: http://www.opensource.org/licenses/BSD-3-Clause
+.. _bsl-1.0: http://www.opensource.org/licenses/BSL-1.0
+.. _gpl-2.0: http://www.opensource.org/licenses/GPL-2.0
+.. _gpl-3.0: http://www.opensource.org/licenses/GPL-3.0
+.. _hdf5 license: ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/COPYING
+.. _lgpl-2.1: http://www.opensource.org/licenses/LGPL-2.1
+.. _libpng license: http://www.libpng.org/pub/png/src/libpng-LICENSE.txt
+.. _mit: http://www.opensource.org/licenses/MIT
+.. _python-2.0: http://www.opensource.org/licenses/Python-2.0

doc/py_api.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.dos.anjos@gmail.com>
+.. Tue 15 Oct 17:41:52 2013
+
+.. testsetup:: coretest
+
+   import numpy
+   import xbob.core
+
+============
+ User Guide
+============
+
+Array Conversion
+----------------
+
+The function :py:func:`xbob.core.convert` allows you to convert objects of type
+:py:class:`numpy.ndarray` between different types, with range compression or
+decompression. For example, here we demonstrate a conversion using default
+ranges. In this type of conversion, our implementation will assume that the
+source array contains values within the range of ``uint8_t`` numbers and will
+expand it to the range of ``uint16_t`` numbers, as desired by the programmer:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> x = numpy.array([0,255,0,255,0,255], 'uint8').reshape(2,3)
+   >>> x
+   array([[  0, 255,   0],
+          [255,   0, 255]], dtype=uint8)
+   >>> xbob.core.convert(x, 'uint16')
+   array([[    0, 65535,     0],
+          [65535,     0, 65535]], dtype=uint16)
+
+
+The user can optionally specify source, destination ranges or both. For
+example:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> x = numpy.array([0, 10, 20, 30, 40], 'uint8')
+   >>> xbob.core.convert(x, 'float64', source_range=(0,40), dest_range=(0.,1.))
+   array([ 0.  ,  0.25,  0.5 ,  0.75,  1.  ])
+
+Any range not specified is assumed to default on the type range.
+
+
+Random Number Generation
+------------------------
+
+You can build a new random number generator (RNG) of type
+:py:class:`xbob.core.random.mt19937` using one of two possible ways:
+
+1. Use the default constructor, which initializes with the default seed:
+
+   .. doctest:: coretest
+      :options: +NORMALIZE_WHITESPACE
+
+      >>> xbob.core.random.mt19937()
+      xbob.core.random.mt19937()
+
+2. Pass a seed while initializing:
+
+   .. doctest:: coretest
+      :options: +NORMALIZE_WHITESPACE
+
+      >>> rng = xbob.core.random.mt19937(34)
+
+RNGs can be compared for equality. The ``==`` operator checks if both
+generators are on the exact same state and would generate the same sequence of
+numbers when exposed to the same distributions. For example:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> rng1 = xbob.core.random.mt19937(111)
+   >>> rng2 = xbob.core.random.mt19937(111)
+   >>> rng1 == rng2
+   True
+   >>> rng3 = xbob.core.random.mt19937(12)
+   >>> rng1 == rng3
+   False
+
+The seed can be re-initialized at any point in time, which can be used to sync
+two RNGs:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> rng3.seed(111)
+   >>> rng1 == rng3
+   True
+
+Distributions skew numbers produced by the RNG so they look like the
+parameterized distribution. By calling a distribution with an RNG, one
+effectively generates random numbers:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> rng = xbob.core.random.mt19937()
+   >>> # creates an uniform distribution of integers inside [0, 10]
+   >>> u = xbob.core.random.uniform(int, 0, 10)
+   >>> u(rng) # doctest: +SKIP
+   8
+
+At our reference guide (see below), you will find more implemented
+distributions you can use on your programs. To simplify the task of generating
+random numbers, we provide a class that mimics the behavior of
+``boost::random::variate_generator``, in Python:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> ugen = xbob.core.random.variate_generator(rng, u)
+   >>> ugen() # doctest: +SKIP
+   6
+
+You can also pass an optional shape when you call the variate generator, in
+which case it generates a :py:class:`numpy.ndarray` of the specified size:
+
+.. doctest:: coretest
+   :options: +NORMALIZE_WHITESPACE
+
+   >>> ugen((3,3)) # doctest: +SKIP
+   array([[ 3,  1,  6],
+          [ 3,  2,  6],
+          [10, 10, 10]])
+
+Reference
+---------
+
+This section includes information for using the pure Python API of
+``xbob.core``.
+
+.. autofunction:: xbob.core.get_include
+
+.. autofunction:: xbob.core.convert
+
+.. autoclass:: xbob.core.random.mt19937
+
+.. autoclass:: xbob.core.random.uniform
+
+.. autoclass:: xbob.core.random.normal
+
+.. autoclass:: xbob.core.random.lognormal
+
+.. autoclass:: xbob.core.random.gamma
+
+.. autoclass:: xbob.core.random.binomial
+
+.. autoclass:: xbob.core.random.variate_generator

setup.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.anjos@idiap.ch>
+# Mon 16 Apr 08:18:08 2012 CEST
+
+from setuptools import setup, find_packages, dist
+from distutils.extension import Extension
+from distutils.version import LooseVersion
+
+dist.Distribution(dict(setup_requires=['pypkg', 'numpy', 'blitz.array']))
+import pypkg
+import numpy
+import blitz
+import platform
+
+# Minimum version requirements for pkg-config packages
+MINIMAL_BLITZ_VERSION_REQUIRED = '0.10'
+MINIMAL_BOB_VERSION_REQUIRED = '1.3'
+
+# Pkg-config dependencies
+blitz_pkg = pypkg.pkgconfig('blitz')
+if blitz_pkg < MINIMAL_BLITZ_VERSION_REQUIRED:
+  raise RuntimeError("This package requires Blitz++ %s or superior, but you have %s" % (MINIMAL_BLITZ_VERSION_REQUIRED, blitz_pkg.version))
+
+bob_pkg = pypkg.pkgconfig('bob-io')
+if bob_pkg < MINIMAL_BOB_VERSION_REQUIRED:
+  raise RuntimeError("This package requires Bob %s or superior, but you have %s" % (MINIMAL_BOB_VERSION_REQUIRED, bob_pkg.version))
+
+# Make-up the names of versioned Bob libraries we must link against
+if platform.system() == 'Darwin':
+  bob_libraries=['%s.%s' % (k, bob_pkg.version) for k in bob_pkg.libraries()]
+elif platform.system() == 'Linux':
+  bob_libraries=[':lib%s.so.%s' % (k, bob_pkg.version) for k in bob_pkg.libraries()]
+else:
+  raise RuntimeError("This package currently only supports MacOSX and Linux builds")
+
+# Add system include directories
+extra_compile_args = []
+system_includes = \
+    [blitz.get_include()] + \
+    blitz_pkg.include_directories() + \
+    [numpy.get_include()]
+for k in system_includes: extra_compile_args += ['-isystem', k]
+
+# NumPy API macros necessary?
+define_macros=[
+    ("PY_ARRAY_UNIQUE_SYMBOL", "XBOB_IO_PY_ARRAY_API"),
+    ("NO_IMPORT_ARRAY", "1"),
+    ]
+
+import numpy
+from distutils.version import StrictVersion
+if StrictVersion(numpy.__version__) >= StrictVersion('1.7'):
+  define_macros.append(("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"))
+
+# Compilation options
+if platform.system() == 'Darwin':
+  extra_compile_args += ['-std=c++11', '-Wno-#warnings']
+else:
+  extra_compile_args += ['-std=c++11']
+
+# Local include directory
+import os
+package_dir = os.path.dirname(os.path.realpath(__file__))
+package_dir = os.path.join(package_dir, 'xbob', 'io', 'include')
+include_dirs = [package_dir]
+
+# Define package version
+version = '2.0.0a0'
+define_macros += [
+    ("XBOB_CORE_VERSION", version),
+    ]
+
+setup(
+
+    name='xbob.io',
+    version=version,
+    description='Bindings for bob.io',
+    url='http://github.com/anjos/xbob.io',
+    license='BSD',
+    author='Andre Anjos',
+    author_email='andre.anjos@idiap.ch',
+
+    long_description=open('README.rst').read(),
+
+    packages=find_packages(),
+    include_package_data=True,
+
+    install_requires=[
+      'setuptools',
+      'blitz.array',
+    ],
+
+    namespace_packages=[
+      "xbob",
+      ],
+
+    ext_modules = [
+      Extension("xbob.io._library",
+        [
+          "xbob/io/file.cpp",
+          ],
+        define_macros=define_macros,
+        include_dirs=include_dirs + bob_pkg.include_directories(),
+        extra_compile_args=extra_compile_args,
+        library_dirs=bob_pkg.library_directories(),
+        runtime_library_dirs=bob_pkg.library_directories(),
+        libraries=bob_libraries,
+        language="c++",
+        ),
+      ],
+
+    classifiers = [
+      'Development Status :: 3 - Alpha',
+      'Intended Audience :: Developers',
+      'License :: OSI Approved :: BSD License',
+      'Natural Language :: English',
+      'Programming Language :: Python',
+      'Programming Language :: Python :: 3',
+      'Topic :: Software Development :: Libraries :: Python Modules',
+      ],
+
+    )

xbob/__init__.py

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

xbob/io/__init__.py

+from ._convert import convert
+from . import log
+from . import random
+
+def get_include():
+  """Returns the directory containing the C/C++ API include directives"""
+
+  return __import__('pkg_resources').resource_filename(__name__, 'include')
+
+__all__ = ['convert', 'log', 'random']

xbob/io/include/xbob.io/config.h

+/**
+ * @author Andre Anjos <andre.anjos@idiap.ch>
+ * @date Fri  1 Nov 07:10:59 2013 
+ *
+ * @brief General directives for all modules in xbob.core
+ */
+
+#ifndef XBOB_CORE_CONFIG_H
+#define XBOB_CORE_CONFIG_H
+
+/* Macros that define versions and important names */
+#define XBOB_IO_API_VERSION 0x0200
+
+#endif /* XBOB_CORE_CONFIG_H */