diff --git a/doc/source/analysing.rst b/doc/source/analysing.rst
deleted file mode 100644
index e8147d2c15ea0153cce7c01ab9a64db302226542..0000000000000000000000000000000000000000
--- a/doc/source/analysing.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-Analysing
-=========
-
-Finding catchment areas
------------------------
-
-Attractor type
---------------
-
-Does my agent go home?
-----------------------
-
-Catchment area around a or few goals
-------------------------------------
diff --git a/doc/source/comparing.rst b/doc/source/comparing.rst
index 1eebda9175fc53bc1d83af08b008049b743f6442..7d9a4add49cbcd4bdeb06fdf5ed439f9786c1c5f 100644
--- a/doc/source/comparing.rst
+++ b/doc/source/comparing.rst
@@ -1,14 +1,27 @@
Comparing
=========
-Talk about memory
+.. automodule:: navipy.comparing
-Image difference (IDF)
-----------------------
+Place code
+----------
+
+Image diff
+~~~~~~~~~~
+.. autofunction:: navipy.comparing.simple_imagediff
-Rotational image difference (rIDF)
-----------------------------------
+Euclidian image diff
+~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: navipy.comparing.imagediff
-Familiarity network (Infomax)
------------------------------
+Rotational image difference function
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: navipy.comparing.rot_imagediff
+Differential optic flow
+~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: navipy.comparing.diff_optic_flow
+
+
+Memory in networks
+------------------
diff --git a/doc/source/computing.rst b/doc/source/computing.rst
deleted file mode 100644
index 05619e1d98c71a6a9b8d2d63eb46f52296276bc3..0000000000000000000000000000000000000000
--- a/doc/source/computing.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-Computing
-=========
-
-From rotational image differences
----------------------------------
-
-From average place-code vector
-------------------------------
-
-From familiarity network
-------------------------
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 8a2e022b56bc762d9eb5c1b27fe460a88ff57f36..33bcd90d2adf718b78202fec9c611981d2ef9739 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -42,7 +42,7 @@ extensions = ['matplotlib.sphinxext.only_directives',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
- 'sphinx.ext.githubpages']
+ 'sphinx.ext.graphviz']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -94,7 +94,7 @@ todo_include_todos = True
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
-html_theme = 'alabaster'
+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
diff --git a/doc/source/gettingstarted.rst b/doc/source/gettingstarted.rst
index a13831da0574965dea1d55c2ae7e56d42fe22459..5a07d027e29563b52970aaa39f1d9cfe0c298c4f 100644
--- a/doc/source/gettingstarted.rst
+++ b/doc/source/gettingstarted.rst
@@ -1,2 +1,25 @@
Getting started
===============
+
+Installing navipy
+-----------------
+
+.. code-block:: bash
+
+ python setup.py install
+
+Testing navipy
+--------------
+
+.. code-block:: bash
+
+ python -m unittest discover navipy
+
+
+The core modules
+----------------
+
+* Rendering
+* Processing
+* Comparing
+* Moving
diff --git a/doc/source/index.rst b/doc/source/index.rst
index a034d2d37d62a7b6e214855d89c6ae49df5c0308..d4217a2f25a53b78de22a85a93576009d71f793a 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -3,19 +3,30 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to Navigation Toolbox's documentation!
-==============================================
+About navipy
+============
+Navipy is a package providing method to simulate a navigating agent in realistic environment. Navipy make use of the blender rendering engine and its python API. Therefore any environment that can be realised with blender, can be used by navipy. Blender rendering may however be too slow to test different model of navigation or the different parameters of a given model. To speed up the simulation, the scene at relevant location in the environment can be stored in a database. Then, instead of rendering the scene again, it is simply loaded from the database. The agent can, thus, jump from relevant location to the next (i.e. move on a grid) without the need to use the blender API. Moreover, certain models of navigation do not depend on the history of the agent, but instead associate a moving direction to the current agent location. With such model, a graph can be created from the moving direction at each location on a grid of relevant places. The graph make use of the package networkx, thus attracting points or loop can be found, the possible connection from one point on the grid to another can be assessed, the number of independent sub graph can be calculated, etc.
+
+Goals
+=====
+The navigation toolbox aims to bring in an intuitive python toolbox different methods to model the visual navigation of a virtual agent.
+
+* Keep the interface simple
+* Allow complex environments and realistic world scenario
+* Implement the most popular model of insect navigation
+* Avoid re-rendering by using grid constrained motion.
+
+Content
+=======
.. toctree::
:maxdepth: 1
-
+
gettingstarted
rendering
processing
comparing
- computing
moving
- analysing
database
diff --git a/navipy/comparing/__init__.py b/navipy/comparing/__init__.py
index 703cb552f4d603eed2ebcc9feb4c6a68db04f59a..a871b809565e865f0d88376fd0a84906cb90d40d 100644
--- a/navipy/comparing/__init__.py
+++ b/navipy/comparing/__init__.py
@@ -75,6 +75,7 @@ the current and memorised place code.
Current opinion in neurobiology
..note: assume that the image is periodic along the x axis
(the left-right axis)
+
"""
if not is_ibpc(current): # and not is_obpc(current):
raise TypeError('The current and memory place code\
diff --git a/setup.py b/setup.py
index 05847f7b69666d7590467a15d8e3aff2eb26d091..8a43804f718cd9589aa4c38701e92245e7c1d7e9 100644
--- a/setup.py
+++ b/setup.py
@@ -29,7 +29,7 @@ setup_dict = {'name': 'navipy',
'description': 'Insect Navigation Toolbox',
'packages': create_package_list("navipy"),
'requires': ['numpy', 'pandas', 'matplotlib', 'scipy'],
- 'install_requires': ["numpy", 'pandas', 'matplotlib', 'scipy'],
+ 'install_requires': ["numpy", 'pandas', 'matplotlib', 'scipy', 'sphinx_rtd_theme', 'pydot'],
'package_data': {'navipy': ['resources/database.db']},
'include_package_data': True, }