populating the directory with initial files

MANIFEST.in

+include README.rst bootstrap-buildout.py buildout.cfg COPYING version.txt requirements.txt
+recursive-include doc *.py *.rst

bob/__init__.py

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

bob/ip/__init__.py

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

bob/ip/skincolorfilter/__init__.py

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

bob/ip/skincolorfilter/script/test.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.dos.anjos@gmail.com>
+# Wed 15 Aug 09:59:33 2012
+#
+# 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/>.
+
+"""Test Units
+"""
+
+def test_version():
+  from .script import version
+  assert version.main() == 0

bob/ip/skincolorfilter/skin_color_filter.py

+#!/usr/bin/env python
+# encoding: utf-8
+# Guillaume HEUSCH <guillaume.heusch@idiap.ch>
+# Wed 29 Jul 09:27:26 CEST 2015
+
+import sys
+import numpy
+
+class SkinColorFilter():
+  """
+  This class implements a number of functions to perform skin color filtering. It is based on the work published in 
+  "Adaptive skin segmentation via feature-based face detection", M.J. Taylor and T. Morris, Proc SPIE Photonics Europe, 2014
+  """
+  def __init__(self):
+    self.mean = numpy.array([0.0, 0.0])
+    self.covariance = numpy.zeros((2, 2), 'float64')
+    self.covariance_inverse = numpy.zeros((2, 2), 'float64')
+
+  def generate_circular_mask(self, image, radius_ratio=0.4):
+    """
+    This function will generate a circular mask to be applied to the image. 
+    The mask will be true for the pixels contained in a circle centered in the image center,
+    and with radius equals to radius_ratio * the image's height.
+
+    :param image: the (face) image to mask
+    """
+    x_center = image.shape[1] / 2
+    y_center = image.shape[2] / 2
+
+    # arrays with the image coordinates
+    x = numpy.zeros((image.shape[1], image.shape[2]))
+    x[:] = range(0, x.shape[1])
+    y = numpy.zeros((image.shape[2], image.shape[1]))
+    y[:] = range(0, y.shape[1])
+    y = numpy.transpose(y)
+
+    # translate s.t. the center is the origin
+    x -= x_center
+    y -= y_center
+
+    # condition to be inside of a circle: x^2 + y^2 < r^2
+    radius = radius_ratio*image.shape[2]
+    self.circular_mask = (x**2 + y**2) < (radius**2)
+
+
+  def remove_luma(self, image):
+    """
+    This function remove pixels that are considered as non-skin according to their luma values.
+    The luma value for all pixels inside a provided circular mask is calculated. Pixels for which the
+    luma value deviates more than 1.5 * standard deviation are pruned. 
+
+    :param image: the (face) image to process
+    """
+    # compute the mean and std of luma values on non-masked pixels only
+    luma = 0.299*image[0, self.circular_mask] + 0.587*image[1, self.circular_mask] + 0.114*image[2, self.circular_mask]
+    m = numpy.mean(luma)
+    s = numpy.std(luma)
+
+    # apply the filtering to the whole image to get the luma mask
+    luma = 0.299*image[0, :, :] + 0.587*image[1, :, :] + 0.114*image[2, :, :]
+    self.luma_mask = numpy.logical_and((luma > (m - 1.5*s)), (luma < (m + 1.5*s)))
+
+
+  def get_gaussian_parameters(self, image):
+    """
+    This function computes the mean and covariance matrix of the skin pixels in the normalised rg colorspace.
+    Note that only the pixels for which both the circular and the luma mask is 'True' are considered. 
+
+    :param image: the (face) image out of which skin color characteristics will be extracted.
+    """
+    self.generate_circular_mask(image)
+    self.remove_luma(image)
+    mask = numpy.logical_and(self.luma_mask, self.circular_mask)
+
+    # get the mean
+    channel_sum = image[0].astype('float64') + image[1] + image[2]
+    nonzero_mask = numpy.logical_or(numpy.logical_or(image[0] > 0, image[1] > 0), image[2] > 0)
+    r = numpy.zeros((image.shape[1], image.shape[2]))
+    r[nonzero_mask] = image[0, nonzero_mask] / channel_sum[nonzero_mask]
+    g = numpy.zeros((image.shape[1], image.shape[2]))
+    g[nonzero_mask] = image[1, nonzero_mask] / channel_sum[nonzero_mask]
+    self.mean = numpy.array([numpy.mean(r[mask]), numpy.mean(g[mask])])
+    
+    # get the covariance
+    r_minus_mean = r[mask] - self.mean[0]
+    g_minus_mean = g[mask] - self.mean[1]
+    samples = numpy.vstack((r_minus_mean, g_minus_mean))
+    samples = samples.T
+    cov = sum([numpy.outer(s,s) for s in samples])
+    self.covariance = cov / float(samples.shape[0] - 1) 
+    
+    # store the inverse covariance matrix (no need to recompute)
+    if numpy.linalg.det(self.covariance) != 0:
+      self.covariance_inverse = numpy.linalg.inv(self.covariance)
+    else:
+      self.covariance_inverse = numpy.zeros_like(self.covariance)
+
+
+  def get_skin_pixels(self, image, threshold):
+    """
+    This function computes the probability of skin-color for each pixel in the image.
+    the distribution of skin color is considered to be gaussian in the rg colorspace.
+    
+    :param image: the image to process
+    :param threshold: the threshold on the probability of a pixel to be of skin color.
+    """
+    skin_map = numpy.zeros((image.shape[1], image.shape[2]), 'float64')
+    
+    # get the image in rg colorspace
+    channel_sum = image[0].astype('float64') + image[1] + image[2]
+    nonzero_mask = numpy.logical_or(numpy.logical_or(image[0] > 0, image[1] > 0), image[2] > 0)
+    r = numpy.zeros((image.shape[1], image.shape[2]), 'float64')
+    r[nonzero_mask] = image[0, nonzero_mask] / channel_sum[nonzero_mask]
+    g = numpy.zeros((image.shape[1], image.shape[2]), 'float64')
+    g[nonzero_mask] = image[1, nonzero_mask] / channel_sum[nonzero_mask]
+    
+    # compute the skin probability map
+    r_minus_mean = r - self.mean[0]
+    g_minus_mean = g - self.mean[1]
+    v = numpy.dstack((r_minus_mean, g_minus_mean))
+    v = v.reshape((r.shape[0]*r.shape[1], 2))
+    probs = [numpy.dot(k, numpy.dot(self.covariance_inverse, k)) for k in v]
+    probs = numpy.array(probs).reshape(r.shape)
+    skin_map = numpy.exp(-0.5 * probs)
+
+    return skin_map > threshold

bootstrap-buildout.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"))
+parser.add_option("--allow-site-packages",
+                  action="store_true", default=False,
+                  help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--setuptools-version",
+                  help="use a specific setuptools version")
+
+
+options, args = parser.parse_args()
+
+######################################################################
+# load/install setuptools
+
+try:
+    if options.allow_site_packages:
+        import setuptools
+        import pkg_resources
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+ez = {}
+exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+
+if not options.allow_site_packages:
+    # ez_setup imports site, which adds site packages
+    # this will remove them from the path to ensure that incompatible versions
+    # of setuptools are not in the path
+    import site
+    # inside a virtualenv, there is no 'getsitepackages'.
+    # We can't remove these reliably
+    if hasattr(site, 'getsitepackages'):
+        for sitepackage_path in site.getsitepackages():
+            sys.path[:] = [x for x in sys.path if sitepackage_path not in x]
+
+setup_args = dict(to_dir=tmpeggs, download_delay=0)
+
+if options.setuptools_version is not None:
+    setup_args['version'] = options.setuptools_version
+
+ez['use_setuptools'](**setup_args)
+import setuptools
+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)
+
+######################################################################
+# 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):
+        try:
+            return not parsed_version.is_prerelease
+        except AttributeError:
+            # Older setuptools
+            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

+# Guillaume HEUSCH <guillaume.heusch@idiap.ch>
+# Wed 30 Mar 14:24:00 CEST 2016
+
+[buildout]
+parts = scripts
+eggs = bob.ip.skincolorfilter
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+develop = src/bob.extension
+          src/bob.blitz
+          src/bob.core
+          src/bob.io.base
+          src/bob.io.image
+          src/bob.ip.base
+          src/bob.ip.facedetect
+          .
+
+; options for bob.buildout
+debug = true
+verbose = true
+newest = false
+
+[sources]
+bob.extension = git https://github.com/bioidiap/bob.extension
+bob.blitz = git https://github.com/bioidiap/bob.blitz
+bob.core = git https://github.com/bioidiap/bob.core
+bob.io.base = git https://github.com/bioidiap/bob.io.base
+bob.io.image = git https://github.com/bioidiap/bob.io.image
+bob.ip.base = git https://github.com/bioidiap/bob.ip.base
+bob.ip.facedetect = git https://github.com/bioidiap/bob.ip.facedetect
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true

doc/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) 2011-2014 Idiap Research Institute, Martigny, Switzerland
+
+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',
+  ]
+
+# 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'Bob Example Project'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# Grab the setup entry
+distribution = pkg_resources.require('bob.example.project')[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 = '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 = 'bob_example_project_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', 'bob_example_project.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 = ''
+