added user-guide

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',
+    'matplotlib.sphinxext.plot_directive'
+    ]
+
+import sphinx
+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
+
+# 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.ip.qualitymeasure'
+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'Extraction of image quality measures for face-PAD 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.
+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',
+  'inherited-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()
+
+
+# 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
+    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', member_function_test)

doc/guide.rst

+.. py:currentmodule:: bob.ip.qualitymeasure
+
+.. testsetup:: *
+
+   from __future__ import print_function
+   import math
+   import os, sys
+   import argparse
+
+   import bob.io.image #remove this if possible
+   import bob.io.base
+   import bob.io.video
+   import bob.ip.color
+   import numpy as np
+   from bob.ip.qualitymeasure import galbally_iqm_features as iqm
+   from bob.ip.qualitymeasure import msu_iqa_features as iqa
+
+   import bob.io.base.test_utils #remove this if possible
+
+   import pkg_resources
+   video_file = bob.io.base.test_utils.datafile('real_client001_android_SD_scene01.mp4', 'bob.ip.qualitymeasure', 'data')
+   video4d = bob.io.video.reader(video_file)
+
+=============
+ User Guide
+=============
+
+You can used this Bob package to extract image-quality features for face-PAD applications.
+Two sets of quality-features are implemented in this package:
+
+1. The image-quality measures proposed by Galbally et al. (TIFS 2014), and
+
+2. The image-quality features proposed by Wen et al. (TIFS 2015).
+
+The package includes separate modules for implementing the two feature-sets.
+The module ``galbally_iqm_features`` implements the features proposed by Gabally et al., and the module ``msu_iqa_features`` implements the features proposed by Wen et al. 
+In each module, a single function needs to be called, to retrieve all the features implemented in the module.
+The examples below show how to use the functions in the two modules.
+
+Note that both feature-sets are extracted from still-images. However, in face-PAD experiments, we typically process videos.
+Therefore, the examples below use a video as input, but show how to extract image-quality features for a single frame.
+
+Computing Galbally's image-quality measures
+-------------------------------------------
+The function ``compute_quality_features()`` (in the module galbally_iqm_features) can be used to compute 18 image-quality measures 
+proposed by Galbally et al. Note that Galbally et al. proposed 25 features in their paper. This package implements the following
+18 features from their paper, namely: 
+[mse, psnr, ad, sc, nk, md, lmse, nae, snrv, ramdv, mas, mams, sme, gme, gpe, ssim, vif, hlfi].
+Therefore, the function ``galbally_iqm_features::compute_quality_features()`` returns a tuple of 18 scalars, in the order listed above.
+
+.. doctest::
+
+
+   >>> from bob.ip.qualitymeasure import galbally_iqm_features as iqm
+   >>> video4d = bob.io.video.reader(video_file) # doctest: +SKIP
+   >>> rgb_frame = video4d[0]
+   >>> print(len(rgb_frame))
+   [3, 480, 720]
+   >>> gf_set = iqm.compute_quality_features(rgb_frame)
+   >>> print(len(gf_set))
+   18
+
+In the example-code above, we have used a color (RGB) image as input to the function ``compute_quality_features()``.
+In fact, the features proposed by Galbally et al. are computed over gray-level images.
+Therefore, the function ``galbally_iqm_features::compute_quality_features()`` takes as input either a RGB color-image,
+or a gray-level image.
+(The input image should be a numpy-array. RGB color-images should be in the format expected by Bob_.)
+When the input image is 3-dimensional, the first dimension being '3' (as is the case in the example above), the input
+is considered to represent a color RGB image, and is first converted to a gray-level image.
+If the input is 2-dimensional (say, a numpy array of shape [480, 720]), then it is considered to represent a gray-level
+image, and the RGB-to-gray conversion step is skipped. 
+
+Computing Wen's image-quality measures
+--------------------------------------
+The code below shows how to compute the image-quality features proposed by Wen et al. (Here, we refer to these features as
+'MSU features'.)
+These features are computed from a RGB color-image. The 2 feature-types (image-blur, color-diversity) all together form
+a 118-D feature-vector.
+The function ``compute_msu_iqa_features()`` (from the module ``msu_iqa_features``) returns a 1D numpy array of length 118.
+
+.. doctest::
+
+   >>> from bob.ip.qualitymeasure import msu_iqa_features as iqa
+   >>> video4d = bob.io.video.reader(video_file) # doctest: +SKIP
+   >>> rgb_frame = video4d[0]
+   >>> msuf_set = iqa.compute_msu_iqa_features(rgb_frame)
+   >>> print(len(msuf_set))
+   118
+
+
+.. _Bob: https://www.idiap.ch/software/bob/ 
+.. _documentation: https://menpofit.readthedocs.io/en/stable/

doc/index.rst

+.. vim: set fileencoding=utf-8 :
+.. Sushil Bhattacharjee <sushil.bhattacharjee@idiap.ch>
+.. Tue 08 Mar 2017 15:42:29 CET
+
+===============================================================
+ Bob's Routines for Image-Quality Measures for PAD Applications
+===============================================================
+
+.. todolist::
+
+This package provides functions for extracting image-quality features for still, color images.
+Two sets of features are computed: the set of features proposed by Galbally et al.(TIFS2014),
+and the set of features proposed by Wen et al. (TIFS2015).
+Note that not all features proposed by the authors of the papers are available in this package.
+
+
+Documentation
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   guide
+   py_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
+..
+.. Place here references to all citations in lower case
+
+.. _bob: https://www.idiap.ch/software/bob/

doc/py_api.rst

+.. vim: set fileencoding=utf-8 :
+
+============
+ Python API
+============
+
+Detailed Information
+--------------------
+
+.. automodule:: bob.ip.qualitymeasure