7 files changed, 489 insertions, 0 deletions
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100755
index 0000000..4801716
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = docs/build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+\ No newline at end of file
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100755
index 0000000..f88c76c
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=docs/build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100755
index 0000000..406877b
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,187 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'CCPi-Framework'
+copyright = '2019, Edoardo Pasca'
+author = 'Edoardo Pasca'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '19.02'
+
+
+# -- 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.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['docstemplates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+#source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'classic'
+
+# 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 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 = ['docsstatic']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'CCPi-Frameworkdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'CCPi-Framework.tex', 'CCPi-Framework Documentation',
+     'Edoardo Pasca', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'ccpi-framework', 'CCPi-Framework Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'CCPi-Framework', 'CCPi-Framework Documentation',
+     author, 'CCPi-Framework', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
diff --git a/docs/source/framework.rst b/docs/source/framework.rst
new file mode 100644
index 0000000..4da0d6a
--- /dev/null
+++ b/docs/source/framework.rst
@@ -0,0 +1,20 @@
+DataContainers and Geometry
+========================================
+|
+
+.. autoclass:: ccpi.framework.DataContainer
+   :members:
+.. autoclass:: ccpi.framework.ImageData
+   :members:
+.. autoclass:: ccpi.framework.AcquisitionData
+   :members:
+.. autoclass:: ccpi.framework.AcquisitionGeometry
+   :members:
+.. autoclass:: ccpi.framework.ImageGeometry
+   :members:
+.. autoclass:: ccpi.framework.DataProcessor
+   :members:
+
+|
+
+:ref:`Return Home <mastertoc>`
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100755
index 0000000..4342bec
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,23 @@
+.. CCPi-Framework documentation master file, created by
+   sphinx-quickstart on Tue Mar 19 15:12:44 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CCPi-Framework's documentation!
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :name: mastertoc
+
+
+   framework
+   optimisation
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/optimisation.md b/docs/source/optimisation.md
new file mode 100755
index 0000000..a3b9039
--- /dev/null
+++ b/docs/source/optimisation.md
@@ -0,0 +1,113 @@
+Optimisation framework
+======================
+
+This package allows rapid prototyping of optimisation-based
+reconstruction problems, i.e. defining and solving different
+optimization problems to enforce different properties on the
+reconstructed image.
+
+Firstly, it provides an object-oriented framework for defining
+mathematical operators and functions as well a collection of useful
+example operators and functions. Both smooth and non-smooth functions
+can be used.
+
+Further, it provides a number of high-level generic implementations of
+optimisation algorithms to solve genericlly formulated optimisation
+problems constructed from operator and function objects.
+
+The fundamental components are:
+
+-   Operator: A class specifying a (currently linear) operator
+-   Function: A class specifying mathematical functions such as a least
+    squares data fidelity.
+-   Algorithm: Implementation of an iterative optimisation algorithm to
+    solve a particular generic optimisation problem. Algorithms are
+    iterable Python object which can be run in a for loop. Can be
+    stopped and warm restarted.
+
+Algorithm
+---------
+
+A number of generic algorithm implementations are provided including
+Gradient Descent CGLS and FISTA. An algorithm is designed for a
+particular generic optimisation problem accepts and number of Functions
+and/or Operators as input to define a specific instance of the generic
+optimisation problem to be solved. They are iterable objects which can
+be run in a for loop. The user can provide a stopping criterion
+different than the default max\_iteration.
+
+New algorithms can be easily created by extending the Algorithm class.
+The user is required to implement only 4 methods: set\_up, \_\_init\_\_,
+update and update\_objective.
+
+-   `set_up` and `__init__` are used to configure the algorithm
+-   `update` is the actual iteration updating the solution
+-   `update_objective` defines how the objective is calculated.
+
+For example, the implementation of the update of the Gradient Descent
+algorithm to minimise a Function will only be:
+
+The `Algorithm` provides the infrastructure to continue iteration, to
+access the values of the objective function in subsequent iterations,
+the time for each iteration.
+
+::: {.autoclass members="" private-members="" special-members=""}
+ccpi.optimisation.algorithms.Algorithm
+:::
+
+::: {.autoclass members=""}
+ccpi.optimisation.algorithms.GradientDescent
+:::
+
+::: {.autoclass members=""}
+ccpi.optimisation.algorithms.CGLS
+:::
+
+::: {.autoclass members=""}
+ccpi.optimisation.algorithms.FISTA
+:::
+
+Operator
+--------
+
+The two most important methods are `direct` and `adjoint` methods that
+describe the result of applying the operator, and its adjoint
+respectively, onto a compatible `DataContainer` input. The output is
+another `DataContainer` object or subclass hereof. An important special
+case is to represent the tomographic forward and backprojection
+operations.
+
+::: {.autoclass members=""}
+ccpi.optimisation.operators.Operator
+:::
+
+::: {.autoclass members=""}
+ccpi.optimisation.operators.LinearOperator
+:::
+
+::: {.autoclass members=""}
+ccpi.optimisation.operators.ScaledOperator
+:::
+
+Function
+--------
+
+A `Function` represents a mathematical function of one or more inputs
+and is intended to accept `DataContainers` as input as well as any
+additional parameters.
+
+Fixed parameters can be passed in during the creation of the function
+object. The methods of the function reflect the properties of it, for
+example, if the function represented is differentiable the function
+should contain a method `gradient` which should return the gradient of
+the function evaluated at an input point. If the function is not
+differentiable but allows a simple proximal operator, the method
+`proximal` should return the proximal operator evaluated at an input
+point. The function value is evaluated by calling the function itself,
+e.g. `f(x)` for a `Function f` and input point `x`.
+
+::: {.autoclass members=""}
+ccpi.optimisation.functions.Function
+:::
+
+`Return Home <mastertoc>`{.interpreted-text role="ref"}
diff --git a/docs/source/optimisation.rst b/docs/source/optimisation.rst
new file mode 100644
index 0000000..7c1eda6
--- /dev/null
+++ b/docs/source/optimisation.rst
@@ -0,0 +1,92 @@
+Optimisation framework
+**********************
+This package allows rapid prototyping of optimisation-based reconstruction problems, i.e. defining and solving different optimization problems to enforce different properties on the reconstructed image.
+
+Firstly, it provides an object-oriented framework for defining mathematical operators and functions as well a collection of useful example operators and functions. Both smooth and non-smooth functions can be used.
+
+Further, it provides a number of high-level generic implementations of optimisation algorithms to solve genericlly formulated optimisation problems constructed from operator and function objects.
+
+The fundamental components are:
+
++ Operator: A class specifying a (currently linear) operator
++ Function: A class specifying mathematical functions such as a least squares data fidelity.
++ Algorithm: Implementation of an iterative optimisation algorithm to solve a particular generic optimisation problem. Algorithms are iterable Python object which can be run in a for loop. Can be stopped and warm restarted.
+
+Algorithm
+=========
+
+A number of generic algorithm implementations are provided including 
+Gradient Descent CGLS and FISTA. An algorithm is designed for a 
+particular generic optimisation problem accepts and number of 
+Functions and/or Operators as input to define a specific instance of 
+the generic optimisation problem to be solved.
+They are iterable objects which can be run in a for loop. 
+The user can provide a stopping criterion different than the default max_iteration.
+
+New algorithms can be easily created by extending the Algorithm class. The user is required to implement only 4 methods: set_up, __init__, update and update_objective.
+
++ :code:`set_up` and :code:`__init__` are used to configure the algorithm
++ :code:`update` is the actual iteration updating the solution
++ :code:`update_objective` defines how the objective is calculated.
+
+For example, the implementation of the update of the Gradient Descent 
+algorithm to minimise a Function will only be:
+
+.. code-block :: python
+
+    def update(self):
+        self.x += -self.rate * self.objective_function.gradient(self.x)
+    def update_objective(self):
+        self.loss.append(self.objective_function(self.x))
+
+The :code:`Algorithm` provides the infrastructure to continue iteration, to access the values of the objective function in subsequent iterations, the time for each iteration.
+
+.. autoclass:: ccpi.optimisation.algorithms.Algorithm
+   :members:
+   :private-members:
+   :special-members:
+.. autoclass:: ccpi.optimisation.algorithms.GradientDescent
+   :members:
+.. autoclass:: ccpi.optimisation.algorithms.CGLS
+   :members:
+.. autoclass:: ccpi.optimisation.algorithms.FISTA
+   :members:
+
+Operator
+========
+The two most important methods are :code:`direct` and :code:`adjoint` 
+methods that describe the result of applying the operator, and its 
+adjoint respectively, onto a compatible :code:`DataContainer` input. 
+The output is another :code:`DataContainer` object or subclass 
+hereof. An important special case is to represent the tomographic 
+forward and backprojection operations.
+
+.. autoclass:: ccpi.optimisation.operators.Operator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.LinearOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.ScaledOperator
+   :members:
+
+Function
+========
+
+A :code:`Function` represents a mathematical function of one or more inputs 
+and is intended to accept :code:`DataContainers` as input as well as any 
+additional parameters. 
+
+Fixed parameters can be passed in during the creation of the function object. 
+The methods of the function reflect the properties of it, for example, if the function
+represented is differentiable the function should contain a method :code:`gradient` 
+which should return the gradient of the function evaluated at an input point. 
+If the function is not differentiable but allows a simple proximal operator, 
+the method :code:`proximal` should return the proximal operator evaluated at an
+input point. The function value is evaluated by calling the function itself, 
+e.g. :code:`f(x)` for a :code:`Function f` and input point :code:`x`.
+
+
+.. autoclass:: ccpi.optimisation.functions.Function
+   :members:
+
+
+:ref:`Return Home <mastertoc>`