Merge simplified euler to optic flow

.coveragerc

+# .coveragerc to control coverage.py
+[run]
+omit =
+    # Omit all test_ functions
+    **/test_*
+    # Omit blender functions / can be only tested with blender files
+    **/blend*
+source = navipy
+
+[html]
+directory = coverage_html_report
\ No newline at end of file

.gitlab-ci.yml

+image: python:latest
+
+stages:
+  - build
+  - test
+  - coverage
+  - doc_build
+
+navipy_install:
+  stage: build
+  before_script:
+  - python3 -V # Print out python version for debugging
+
+  script:
+  - pip3 install virtualenv
+  - virtualenv -p python3 venv
+  - source venv/bin/activate
+  - pip3 install .
+  - python navipy/scripts/config_matplotlib_server.py # because no interactive backend
+
+  artifacts:
+    paths:
+      - venv
+    expire_in: 2 hours
+
+  artifacts:
+    paths:
+      - venv
+
+flake8:
+  stage: test
+  dependencies:
+  - navipy_install
+
+  script:
+  - source $CI_PROJECT_DIR/venv/bin/activate
+  - python3 -m flake8 navipy/*.py
+  
+navipy_unittest:
+  stage: test
+  dependencies: 
+  - navipy_install
+
+  script:
+  - source $CI_PROJECT_DIR/venv/bin/activate
+  - python3 -m coverage run -m unittest discover navipy
+
+  artifacts:
+    paths:
+      - .coverage
+    expire_in: 1 hours
+
+coverage:
+  stage: coverage
+  dependencies: 
+  - navipy_install
+  - navipy_unittest
+  
+  script:
+  - source $CI_PROJECT_DIR/venv/bin/activate
+  - python3 -m coverage html
+
+  artifacts:
+    paths:
+      - coverage_html_report
+    expire_in: 1 day
+
+doc_build:
+  stage: doc_build
+  dependencies:
+  - navipy_install
+  - coverage
+
+  script:
+  - source $CI_PROJECT_DIR/venv/bin/activate
+  - cd doc ; make html
+
+  artifacts:
+    paths:
+    - doc/build
+    
+    expire_in: 1 week
\ No newline at end of file

CONTRIBUTING.md

+We are glad that you are considering contributing to navipy, and are
+looking forward to your contribution.
+
+# Pre-requisit
+We strongly recommand you to download, install, test, and compile the documentation
+
+## Installation
+```
+git clone git@gitlab.ub.uni-bielefeld.de:olivier.bertrand/navipy.git
+cd navipy
+python setup.py install
+```
+
+## Unittesting
+From the root directory of the repository
+
+```
+python -m unittest discover navipy
+```
+
+## Blend-unittesting
+Several functionalty of navipy requires Blender, and thus code has to be run within blender (see doc for details). Unittesting of function requiring blender can be done as follow
+
+```
+blendunittest
+```
+
+Note: this command require blender to be installed
+
+## Doc building
+The doc is contained in doc/source
+
+```
+cd doc
+make html
+```
+
+# Convention
+We follow the PEP8 recommendation and the code should be formatted as such.
+
+# Testing
+Ideally every function should be properly tested. Test file should match the pattern 'test*.py' here the * should match the module to be tested. For example to test function within maths.py, a file named test_maths.py should be created and stored in the same folder than maths.py
+
+Certain functionalities require the use of blender. Such test need to be stored in a file 'blendtest*.py'. Note that the blendunittest command uses the blender environment navipy/resources/twocylinders_world.blend. Therefore your test function should use this environment as well.
+
+# Documentation
+The documentation is based on Sphinx syntax. Although documenting functions is a must, tutorial is a bonus that will strongly encourage.

README.md

@@ -11,9 +11,67 @@ The navigation toolbox aims to bring in an intuitive python toolbox different me
 -    Avoid re-rendering by using grid constrained motion.
 
 # How to install the navigation toolbox
+The rendering from the insect point of view is done with the blender rendering engine. Thus, you will need to first install Blender
+https://www.blender.org/
+
+## Windows
+We recommend using Anaconda (https://www.anaconda.com/) and create a virtual environment within it before installing the toolbox. 
+
+Start the Anaconda Prompt, and then enter
+```
+conda update conda
+```
+Upadate any packages if necessary by typing y to proceed
+
+Then, create a virtual environment for your project
+```
+conda create -n yourenvname python=x.x anaconda
+```
+here `yourenvname` is the name of your project (without special characters and spaces), and `python=x.x` the version of python
+to use, for example `python=3.5.3` (see table below to install a version matching with blender)
+
+You can now activate your environment. 
+```
+activate yourenvname
+```
+
+and install navipy by going the root folder of the toolbox (use cd to change directory and dir to list the content of a directory), and typing
+```
+python setup.py install
+```
+
+You can now use the navigation toolbox. 
+
+## Linux (Ubuntu)
+From the terminal 
+```
+pip install update
+```
+Upadate any packages if necessary by typing y to proceed
+
+Then, create a virtual environment for your project
+```
+mkvirtualenv yourenvname
+```
+here `yourenvname` is the name of your project (without special characters and spaces)
+
+You can now activate your environment. 
+```
+workon yourenvname
+```
+
+and install navipy by going the root folder of the toolbox (use cd to change directory and ls to list the content of a directory), and typing
+```
+python setup.py install
+```
+
+## Blender-python version
+| Blender version | Python version |
+| --------------- | -------------- |
+| 2.79b           | 3.5.3          |
+
 
->>> python setup.py install
 
 # Code of conduct
 
-In the interest of fostering an open and welcoming environment, we as students and teachers pledge to making participation in this class a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
\ No newline at end of file
+In the interest of fostering an open and welcoming environment, we as users and developers pledge to making participation with this project a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
\ No newline at end of file

doc/source/conf.py

@@ -19,9 +19,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../src/'))
-sys.path.insert(0, os.path.abspath('../../src/database/'))
-
+sys.path.insert(0, os.path.abspath('../../tutorials'))
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -34,7 +32,6 @@ sys.path.insert(0, os.path.abspath('../../src/database/'))
 extensions = ['matplotlib.sphinxext.only_directives',
               'matplotlib.sphinxext.plot_directive',
               'IPython.sphinxext.ipython_directive',
-              'IPython.sphinxext.ipython_console_highlighting',
               'sphinx.ext.autodoc',
               'sphinx.ext.doctest',
               'sphinx.ext.intersphinx',
@@ -42,7 +39,8 @@ extensions = ['matplotlib.sphinxext.only_directives',
               'sphinx.ext.coverage',
               'sphinx.ext.mathjax',
               'sphinx.ext.viewcode',
-              'sphinxarg.ext']
+              'sphinx.ext.inheritance_diagram',
+              'nbsphinx']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -80,7 +78,7 @@ language = None
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = []
+exclude_patterns = ['**/.ipynb_checkpoints/*']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

doc/source/gettingstarted.rst

@@ -3,6 +3,10 @@ Getting started
 
 Installing navipy
 -----------------
+It is recommanded to install navipy in a \
+`virtual environment <https://virtualenvwrapper.readthedocs.io/en/latest/install.html>`_ . By doing \
+so, the python version installed on the system and the one used by \
+navipy may differ, and ease the use of blender rendering engine. 
 
 .. code-block:: bash
 
@@ -15,6 +19,16 @@ Testing navipy
 
    python -m unittest discover navipy
 
+Testing blender
+---------------
+
+Navipy comes with a command line tool to run your script under blender. \
+It is however required that the python version used by blender, and the one use by navipy matche. To test your installation of blender and navipy you can download the (:download:`script <../../navipy/sensors/blendnavipy_test.py>`) and run it under blender with the following command:
+
+ .. code-block:: bash
+		 
+   blendnavipy --python-script='blendnavipy_test.py' 
+
 
 The core modules
 ----------------

doc/source/index.rst

@@ -26,7 +26,7 @@ Content
    overview/index
    tutorials/index
    references/index
-
+   tests/index
 
 Indices and tables
 ==================

doc/source/overview/database.rst

@@ -4,11 +4,12 @@ Database
 Database are generated by the rendering module, and contains all \
 images and there corresponding position-orientations.
 
-* position_orientation: containing all position and orientation of where \
-images were rendered. The position-orientation is described by \
-['x','y','z','alpha_0','alpha_1','alpha_2']
-* image: containing all images ever rendered. Each channel of each image \
-are normalised, so to use the full coding range.
+* position_orientation: containing all position and orientation \
+  of where images were rendered. The position-orientation is \
+  described by ['x','y','z','alpha_0','alpha_1','alpha_2']
+* image: containing all images ever rendered. \
+  Each channel of each image are normalised, so to use the \
+  full coding range.
 * normalisation: the normalisation constantes
 
 

doc/source/overview/examples/blenddemo_beesampling.py

-"""
-Example on how to use the rendering module
-"""
-import tempfile
-import numpy as np
-import os
-from navipy.sensors.bee_sampling import BeeSampling
-from navipy.sensors.renderer import BlenderRender
-
-# create a bee sampling
-cyberbee = BlenderRender()
-cyberbee.cycle_samples = 5
-bee_samp = BeeSampling(cyberbee)
-# Create a list of point from which we want to render images
-# Careful three d meshing grow quickly.
-x = np.linspace(-5, 5, 3)
-y = np.linspace(-5, 5, 3)
-z = np.linspace(1.8, 1.8, 1)
-alpha_1 = np.array([0]) + np.pi / 2
-alpha_2 = np.array([0])
-alpha_3 = np.array([0])
-bee_samp.create_sampling_grid(
-    x, y, z, alpha1=alpha_1, alpha2=alpha_2, alpha3=alpha_3)
-# Assign maximum world dimension. Otherwise the distance
-# will go to infinity, and the distance to objects after compression
-# will be set to 0
-world_dim = 50 * np.sqrt(2)
-bee_samp.world_dim = world_dim
-# Rendering in a temporary folder.
-with tempfile.TemporaryDirectory() as folder:
-    filename_db = os.path.join(folder, 'database.db')
-    bee_samp.render(filename_db)

doc/source/overview/moving.rst

@@ -8,3 +8,8 @@ Overview
 Summary
 *******
 .. automodule:: navipy.moving.agent
+
+Inheritance
+***********
+.. inheritance-diagram:: navipy.moving.agent
+

doc/source/overview/rendering.rst

@@ -17,59 +17,6 @@ Using navipy in blender
 >>> blendnavipy --blender-world='/path/to/world.blend' --python-script='/path/to/script.py'
 
 .. argparse::
-   :filename: ../bin/blendnavipy.py
+   :filename: ../navipy/sensors/blendnavipy.py
    :func: parser_blendnavipy	      
    :prog: blendnavipy
-
-How to generate a database using blender
-----------------------------------------
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 7, 8
-
-First we configure the rendering module
-
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 11, 12
-
-With the toolbox at disposition we just need to configure the \
-BeeSampling to render images on a regular 3D grid.
-
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 13,16-23
-
-If we want to use the distance to objects, we need to tell the \
-BeeSampling what is the maximum distance to objects in the environment.\
- Otherwise the distance can go until infinity, and since the image are \
-compressed in the database, all distances to object will be equal to \
-zero:
-
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 27-28
-
-Finally we can generate the database.
-
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :dedent: 4
-   :lines: 31-32
-
-
-(:download:`Source code <examples/blenddemo_beesampling.py>`)
-
-Custom sampling
----------------
-.. literalinclude:: examples/blenddemo_cyberbee.py
-   :lines: 5
-
-With the toolbox at disposition we just need to configure the \
-Cyberbee to render images at desired positions.
-
-.. literalinclude:: examples/blenddemo_cyberbee.py
-   :lines: 8-13
-
-To render a scene at a given positions, we assign position orientation \
-to and then tell the cyberbee to get the scene at that point.
-
-.. literalinclude:: examples/blenddemo_cyberbee.py
-   :lines: 16-24
-
-(:download:`Source code <examples/blenddemo_cyberbee.py>`)

doc/source/references/index.rst

@@ -10,3 +10,4 @@ References
    comparing
    moving
    database
+   maths

doc/source/references/maths.rst

+Maths
+=====
+
+.. automodule:: navipy.maths
+   :members:
+      
+Constants
+---------
+
+.. automodule:: navipy.maths.constants
+   :members:
+      
+Coordinates
+-----------
+
+.. automodule:: navipy.maths.coordinates
+   :members:
+      
+Homogeneous transformations
+---------------------------
+
+.. automodule:: navipy.maths.homogeneous_transformations
+   :members:
+      
+Euler
+~~~~~
+
+.. automodule:: navipy.maths.euler
+   :members:
+      
+Quaternions
+~~~~~~~~~~~
+
+.. automodule:: navipy.maths.quaternion
+   :members:
+      
+Random generator
+----------------
+
+.. automodule:: navipy.maths.random
+   :members:
+      
+Tools
+-----
+
+.. automodule:: navipy.maths.tools
+   :members:

doc/source/references/processing.rst

 Processing
-----------
+==========
 
 .. automodule:: navipy.processing
 
 Place code
-~~~~~~~~~~
+----------
 
 .. automodule:: navipy.processing.pcode
    :members:

doc/source/tests/brain.rst

+Brain
+=====
+
+No test...

doc/source/tests/comparing.rst

+Comparing
+=========
+
+.. automodule:: navipy.comparing.test
+   :members:

doc/source/tests/database.rst

+Database
+========
+
+.. automodule:: navipy.database.test
+   :members: