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Commit b17111bc authored by Amir Mohammadi's avatar Amir Mohammadi
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update docs

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1 merge request!2First Alpha release
bob.fusion.base.algorithm package
=================================
Submodules
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bob.fusion.base.algorithm.Algorithm module
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.. automodule:: bob.fusion.base.algorithm.Algorithm
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.algorithm.AlgorithmBob module
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.. automodule:: bob.fusion.base.algorithm.AlgorithmBob
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.algorithm.LLR module
------------------------------------
.. automodule:: bob.fusion.base.algorithm.LLR
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.algorithm.MLP module
------------------------------------
.. automodule:: bob.fusion.base.algorithm.MLP
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.algorithm.Weighted_Sum module
---------------------------------------------
.. automodule:: bob.fusion.base.algorithm.Weighted_Sum
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.algorithm.mlp_train_helper module
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.. automodule:: bob.fusion.base.algorithm.mlp_train_helper
:members:
:undoc-members:
:show-inheritance:
Module contents
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.. automodule:: bob.fusion.base.algorithm
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config.algorithm package
========================================
Submodules
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bob.fusion.base.config.algorithm.llr module
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.. automodule:: bob.fusion.base.config.algorithm.llr
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config.algorithm.llr_skl module
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.. automodule:: bob.fusion.base.config.algorithm.llr_skl
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config.algorithm.mean module
--------------------------------------------
.. automodule:: bob.fusion.base.config.algorithm.mean
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config.algorithm.mlp module
-------------------------------------------
.. automodule:: bob.fusion.base.config.algorithm.mlp
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config.algorithm.plr_2 module
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.. automodule:: bob.fusion.base.config.algorithm.plr_2
:members:
:undoc-members:
:show-inheritance:
Module contents
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.. automodule:: bob.fusion.base.config.algorithm
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.config package
==============================
Subpackages
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.. toctree::
bob.fusion.base.config.algorithm
Module contents
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.. automodule:: bob.fusion.base.config
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base package
=======================
Subpackages
-----------
.. toctree::
bob.fusion.base.algorithm
bob.fusion.base.config
bob.fusion.base.script
bob.fusion.base.tools
Module contents
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.. automodule:: bob.fusion.base
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.script package
==============================
Submodules
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bob.fusion.base.script.bob_fuse module
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.. automodule:: bob.fusion.base.script.bob_fuse
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.script.plot_fusion_decision_boundary module
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.. automodule:: bob.fusion.base.script.plot_fusion_decision_boundary
:members:
:undoc-members:
:show-inheritance:
Module contents
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.. automodule:: bob.fusion.base.script
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.tools package
=============================
Submodules
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bob.fusion.base.tools.command_line module
-----------------------------------------
.. automodule:: bob.fusion.base.tools.command_line
:members:
:undoc-members:
:show-inheritance:
bob.fusion.base.tools.plotting module
-------------------------------------
.. automodule:: bob.fusion.base.tools.plotting
:members:
:undoc-members:
:show-inheritance:
Module contents
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.. automodule:: bob.fusion.base.tools
:members:
:undoc-members:
:show-inheritance:
bob.fusion package
==================
Subpackages
-----------
.. toctree::
bob.fusion.base
Module contents
---------------
.. automodule:: bob.fusion
:members:
:undoc-members:
:show-inheritance:
#!/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'
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.pngmath',
'sphinx.ext.ifconfig',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.doctest',
'sphinx.ext.graphviz',
'sphinx.ext.intersphinx',
'sphinx.ext.napoleon',
'sphinx.ext.viewcode',
#'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')
if sphinx.__version__ >= "1.4.1":
extensions.append('sphinx.ext.imgmath')
imgmath_image_format = 'svg'
else:
extensions.append('sphinx.ext.pngmath')
# 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
......@@ -58,12 +80,12 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
project = u'Bobs interface for running score fusion in biometric recognition experiments'
project = u'bob.fusion.base'
import time
copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
# Grab the setup entry
distribution = pkg_resources.require('bob.fusion.base')[0]
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
......@@ -108,13 +130,18 @@ 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'Score fusion in biometric experiments'
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.
if sphinx.__version__ >= "1.0":
html_theme = 'nature'
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
......@@ -122,14 +149,14 @@ if sphinx.__version__ >= "1.0":
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
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 = 'bob'
#html_short_title = project_variable
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
......@@ -187,105 +214,56 @@ html_favicon = 'img/favicon.ico'
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'bob_bio_base_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_bio_base.tex', u'Bob',
u'Biometrics Group, Idiap Research Institute', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = ''
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
htmlhelp_basename = project_variable + u'_doc'
# 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
# -- Post configuration --------------------------------------------------------
# Included after all input documents
rst_epilog = ''
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'bob.bio.base', u'Base tools to run biometric recognition experiments', [u'Idiap Research Institute'], 1)
]
rst_epilog = """
.. |project| replace:: Bob
.. |version| replace:: %s
.. |current-year| date:: %%Y
""" % (version,)
# Default processing flags for sphinx
autoclass_content = 'both'
autoclass_content = 'class'
autodoc_member_order = 'bysource'
autodoc_default_flags = ['members', 'inherited-members', 'show-inheritance']
autodoc_default_flags = [
'members',
'undoc-members',
'inherited-members',
'show-inheritance',
]
# For inter-documentation mapping:
from bob.extension.utils import link_documentation
intersphinx_mapping = link_documentation(['python', 'numpy', 'bob.bio.face', 'bob.bio.speaker', 'bob.bio.gmm', 'bob.bio.video', 'bob.bio.csu', 'bob.bio.spear', 'gridtk', 'bob.db.youtube'])
def skip(app, what, name, obj, skip, options):
# Do not skip the __call__ and the __str__ functions as we have special implementations for them.
if name in ("__str__", "__call__"):
return False
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()
# We want to remove all private (i.e. _. or __.__) members
# that are not in the list of accepted functions
accepted_private_functions = ['__array__']
def member_function_test(app, what, name, obj, skip, options):
# test if we have a private function
if len(name) > 1 and name[0] == '_':
# test if this private function should be allowed
if name not in accepted_private_functions:
# omit privat functions that are not in the list of accepted private functions
return skip
# getting dictionaries printed nicely.
# see: http://stackoverflow.com/questions/7250659/python-code-to-generate-part-of-sphinx-documentation-is-it-possible/18143318#18143318
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
from sphinx.util.compat import Directive
from docutils import nodes, statemachine
class ExecDirective(Directive):
"""Execute the specified python code and insert the output into the document"""
has_content = True
def run(self):
oldStdout, sys.stdout = sys.stdout, StringIO()
tab_width = self.options.get('tab-width', self.state.document.settings.tab_width)
source = self.state_machine.input_lines.source(self.lineno - self.state_machine.input_offset - 1)
try:
exec('\n'.join(self.content))
text = sys.stdout.getvalue()
lines = statemachine.string2lines(text, tab_width, convert_whitespace=True)
self.state_machine.insert_input(lines, source)
return []
except Exception:
return [nodes.error(None, nodes.paragraph(text = "Unable to execute python code at %s:%d:" % (os.path.basename(source), self.lineno)), nodes.paragraph(text = str(sys.exc_info()[1])))]
finally:
sys.stdout = oldStdout
else:
# test if the method is documented
if not hasattr(obj, '__doc__') or not obj.__doc__:
return skip
return False
def setup(app):
app.connect("autodoc-skip-member", skip)
app.add_directive('exec', ExecDirective)
app.connect('autodoc-skip-member', member_function_test)
......@@ -20,6 +20,6 @@ Using ``sklearn`` classifiers and pre-processors you can implement different fus
There are two scripts available in the package as of now and they work for verification scenarios.
Spoofing and Anti-spoofing scenarios are not considered yet **in the scripts** however the Python API allows for easy extension.
Also take a look at the scripts ``bob_fuse.py`` and ``plot_fusion_decision_boundary.py`` and use them for your actual fusion experiments.
Also take a look at the scripts ``bob_fuse.py`` and ``bob_fusion_decision_boundary.py`` and use them for your actual fusion experiments.
.. include:: links.rst
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