First commit

.gitignore

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

README.rst

+.. vim: set fileencoding=utf-8 :
+.. Sat Aug 20 07:33:55 CEST 2016
+
+.. image:: https://img.shields.io/badge/docs-stable-yellow.svg
+   :target: https://www.idiap.ch/software/bob/docs/bob/bob.paper.tifs2018_dsu/stable/index.html
+.. image:: http://img.shields.io/badge/docs-latest-orange.svg
+   :target: https://www.idiap.ch/software/bob/docs/bob/bob.paper.tifs2018_dsu/master/index.html
+.. image:: https://gitlab.idiap.ch/bob/bob.paper.tifs2018_dsu/badges/master/build.svg
+   :target: https://gitlab.idiap.ch/bob/bob.paper.tifs2018_dsu/commits/master
+.. image:: https://gitlab.idiap.ch/bob/bob.paper.tifs2018_dsu/badges/master/coverage.svg
+   :target: https://gitlab.idiap.ch/bob/bob.paper.tifs2018_dsu/commits/master
+.. image:: https://img.shields.io/badge/gitlab-project-0000c0.svg
+   :target: https://gitlab.idiap.ch/bob/bob.paper.tifs2018_dsu
+.. image:: https://img.shields.io/pypi/v/bob.paper.tifs2018_dsu.svg
+   :target: https://pypi.python.org/pypi/bob.paper.tifs2018_dsu
+
+=======================================================================================================================
+Python package to reproduce the experiments from the paper "Heterogeneous Face Recognition Using Domain Specific Units"
+=======================================================================================================================
+
+This package is part of the signal-processing and machine learning toolbox
+Bob_.
+This package is part of the ``bob.bio`` packages, which allow to run comparable and reproducible biometric recognition experiments on publicly available databases.
+
+
+Installation
+------------
+
+Follow our `installation`_ instructions. Then, using the Python interpreter
+provided by the distribution, bootstrap and buildout this package::
+
+  $ conda install bob.thesis.tiago
+  $ bob bio htface --help
+
+
+Contact
+-------
+
+For questions or reporting issues to this software package, contact our
+development `mailing list`_.
+
+
+.. Place your references here:
+.. _bob: https://www.idiap.ch/software/bob
+.. _installation: https://gitlab.idiap.ch/bob/bob/wikis/Installation
+.. _mailing list: https://groups.google.com/forum/?fromgroups#!forum/bob-devel

bob/__init__.py

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

bob/paper/__init__.py

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

bob/paper/tifs2018_dsu/__init__.py

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

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
+
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
+
+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("--version",
+                  action="store_true", default=False,
+                  help=("Return bootstrap.py 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("--buildout-version",
+                  help="Use a specific zc.buildout version")
+parser.add_option("--setuptools-version",
+                  help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+                  help=("Allow for re-use of existing directory of "
+                        "setuptools versions"))
+
+options, args = parser.parse_args()
+if options.version:
+    print("bootstrap.py version %s" % __version__)
+    sys.exit(0)
+
+
+######################################################################
+# load/install setuptools
+
+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+ez = {}
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    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():
+            # Strip all site-packages directories from sys.path that
+            # are not sys.prefix; this is because on Windows
+            # sys.prefix is a site-package directory.
+            if sitepackage_path != sys.prefix:
+                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
+if options.setuptools_to_dir is not None:
+    setup_args['to_dir'] = options.setuptools_to_dir
+
+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
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
+cmd = [sys.executable, '-c',
+       'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
+       '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])
+
+requirement = 'zc.buildout'
+version = options.buildout_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) != 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 :
+; Sat Aug 20 07:33:55 CEST 2016
+
+[buildout]
+parts = scripts
+eggs = bob.paper.tifs2018_dsu
+       bob.bio.face_ongoing
+       bob.bio.htface
+
+extensions = bob.buildout
+             mr.developer
+auto-checkout = *
+
+develop = src/bob.bio.face_ongoing
+          src/bob.bio.htface
+          .
+
+newest = false
+verbose = true
+
+
+[sources]
+bob.bio.face_ongoing = git git@gitlab.idiap.ch:bob/bob.bio.face_ongoing
+bob.bio.htface = git git@gitlab.idiap.ch:bob/bob.bio.htface
+
+[scripts]
+recipe = bob.buildout:scripts
+dependent-scripts = true

conda/meta.yaml

+{% set name = 'bob.paper.tifs2018_dsu' %}
+{% set project_dir = environ.get('RECIPE_DIR') + '/..' %}
+
+package:
+  name: {{ name }}
+  version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
+
+build:
+  skip: true  # [not linux]
+  entry_points:
+  number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
+  run_exports:
+    - {{ pin_subpackage(name) }}
+  script:
+    - cd {{ project_dir }}
+    {% if environ.get('BUILD_EGG') %}
+    - python setup.py sdist --formats=zip
+    {% endif %}
+    - python setup.py install --single-version-externally-managed --record record.txt
+
+requirements:
+  host:
+    - python {{ python }}
+    - setuptools {{ setuptools }}
+    - bob.bio.htface
+    - bob.bio.face_ongoing
+    - bob.db.cuhk_cufs
+    - bob.db.cuhk_cufsf
+    - bob.db.pola_thermal
+    - bob.db.nivl
+    - bob.db.cbsr_nir_vis_2
+  run:
+    - python
+    - setuptools
+    - matplotlib
+    - six
+    - wheel
+    - tensorflow
+    - numpy
+      
+test:
+  imports:
+    - {{ name }}
+  commands:
+    - bob bio htface --help
+    - bob bio face_ongoing --help
+    - nosetests --with-coverage --cover-package=bob.bio.htface -sv bob.bio.htface
+    - sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
+    - sphinx-build -aEb doctest {{ project_dir }}/doc sphinx
+    - conda inspect linkages -p $PREFIX {{ name }}  # [not win]
+    - conda inspect objects -p $PREFIX {{ name }}  # [osx]
+  requires:
+    - bob-devel {{ bob_devel }}.*
+    - nose
+    - coverage
+    - sphinx
+    - sphinx_rtd_theme
+    - gridtk
+
+about:
+  home: https://www.idiap.ch/software/bob/
+  license: BSD License
+  summary: Tools to reproduce the experiments of the Ph.D. thesis from Tiago de Freitas Pereira
+  license_family: BSD
+

doc/FAQ.rst

+.. vim: set fileencoding=utf-8 :
+.. Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+
+
+====
+ FAQ
+====
+
+

doc/conf.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+import os
+import sys
+import glob
+import pkg_resources
+
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+needs_sphinx = '1.3'
+
+# 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.ifconfig',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.mathjax',
+    'matplotlib.sphinxext.plot_directive'
+    ]
+
+# Be picky about warnings
+nitpicky = True
+
+# Ignores stuff we can't easily resolve on other project's sphinx manuals
+nitpick_ignore = []
+
+# Allows the user to override warnings from a separate file
+if os.path.exists('nitpick-exceptions.txt'):
+    for line in open('nitpick-exceptions.txt'):
+        if line.strip() == "" or line.startswith("#"):
+            continue
+        dtype, target = line.split(None, 1)
+        target = target.strip()
+        try: # python 2.x
+            target = unicode(target)
+        except NameError:
+            pass
+        nitpick_ignore.append((dtype, target))
+
+# Always includes todos
+todo_include_todos = True
+
+# Generates auto-summary automatically
+autosummary_generate = True
+
+# Create numbers on figures with captions
+numfig = 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.thesis.tiago'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# Grab the setup entry
+distribution = pkg_resources.require(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 = []
+
+# Some variables which are useful for generated material
+project_variable = project.replace('.', '_')
+short_description = u'Learning how to recognize faces in heterogeneous environments Ph.D. thesis'
+owner = [u'Idiap Research Institute']
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'
+
+# 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 = [sphinx_rtd_theme.get_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 = project_variable
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = 'img/logo.png'
+
+# 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 = 'img/favicon.ico'
+
+# 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 = project_variable + u'_doc'
+
+
+# -- Post configuration --------------------------------------------------------
+
+# Included after all input documents
+rst_epilog = """
+.. |project| replace:: Bob
+.. |version| replace:: %s
+.. |current-year| date:: %%Y
+""" % (version,)
+
+# Default processing flags for sphinx
+autoclass_content = 'class'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = [
+  'members',
+  'undoc-members',
+  'show-inheritance',
+  ]
+
+# For inter-documentation mapping:
+from bob.extension.utils import link_documentation, load_requirements
+sphinx_requirements = "extra-intersphinx.txt"
+if os.path.exists(sphinx_requirements):
+  intersphinx_mapping = link_documentation(
+      additional_packages=['python','numpy'] + \
+          load_requirements(sphinx_requirements)
+          )
+else:
+  intersphinx_mapping = link_documentation()
+