Update doc for blender sim

doc/source/conf.py

@@ -41,7 +41,8 @@ extensions = ['matplotlib.sphinxext.only_directives',
               'sphinx.ext.todo',
               'sphinx.ext.coverage',
               'sphinx.ext.mathjax',
-              'sphinx.ext.viewcode']
+              'sphinx.ext.viewcode',
+              'sphinxarg.ext']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/source/overview/database.rst

@@ -16,7 +16,7 @@ How to load a database
 ----------------------
 
 .. literalinclude:: examples/get_posorients.py
-      :lines: 8
+   :lines: 8
 
 How to load all position-orientation
 ------------------------------------
@@ -30,7 +30,9 @@ speaking, loading the full table of position-orientaiton.
 .. literalinclude:: examples/get_posorients.py
       :lines: 9-10
 
-.. plot:: overview/examples/get_posorients.py
+.. ipython:: examples/get_posorients.py
+   :verbatim:
+
 
 How to load an image
 --------------------

doc/source/overview/examples/blenddemo_beesampling.py

@@ -3,6 +3,7 @@ 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
 
@@ -25,6 +26,7 @@ bee_samp.create_sampling_grid(
 # will be set to 0
 world_dim = 50 * np.sqrt(2)
 bee_samp.world_dim = world_dim
-# Rendering in a tmp folder
+# Rendering in a temporary folder.
 with tempfile.TemporaryDirectory() as folder:
-    bee_samp.render(folder + '/database.db')
+    filename_db = os.path.join(folder, 'database.db')
+    bee_samp.render(filename_db)

doc/source/overview/examples/blenddemo_cyberbee.py

@@ -4,13 +4,15 @@ from matplotlib.colors import hsv_to_rgb, rgb_to_hsv
 import matplotlib.pyplot as plt
 from navipy.sensors.renderer import BlenderRender
 
-# with tempfile.TemporaryDirectory() as folder:
+# Configure the rendering module
 cyberbee = BlenderRender()
 cyberbee.cycle_samples = 50
 cyberbee.camera_rotation_mode = 'XYZ'
 cyberbee.camera_fov = [[-90, 90], [-180, 180]]
 cyberbee.gaussian_width = 1.5
 cyberbee.camera_resolution = [360, 180]
+
+# Set the position at which to render an image/distance
 posorient = pd.Series(index=['x', 'y', 'z',
                              'alpha_0', 'alpha_1', 'alpha_2'])
 posorient.x = 0
@@ -21,7 +23,7 @@ posorient.alpha_1 = 0
 posorient.alpha_2 = 0
 scene = cyberbee.scene(posorient)
 
-
+# plot
 f, axarr = plt.subplots(2, 1,  sharex=True)
 
 to_plot_im = scene[:, :, :3]

doc/source/overview/rendering.rst

 Rendering
 =========
-"""
+
 Navipy & blender
 ----------------
 What is blender?
@@ -13,69 +13,63 @@ Explain How to create env for navipy
 
 Using navipy in blender
 ~~~~~~~~~~~~~~~~~~~~~~~
-Blender comes with its own python installation. Thus, we need to \
-tell blender to use our virtualenv where the navigation toolbox \
-is installed. To do we need to import the os module
-
-.. literalinclude:: ../blender_run.py
-    :lines: 6 - 7
-
-then activate the environment by using the following function:
 
-.. literalinclude:: ../blender_run.py
-    :lines: 13 - 18
+>>> blendnavipy --blender-world='/path/to/world.blend' --python-script='/path/to/script.py'
 
-here venv_path is the path to the virtual environment within which \
-navipy has been installed.
-
-Now, blender can import all modules used by the navigation toolbox.
-
-How to run python code with blender:
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
->>> blender path/to/world.blend --background --python path/to/code.py
+.. argparse::
+   :filename: ../bin/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: 6
+   :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: 9
-
-.. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 12-19
+   :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 distance to object will be equal to \
+compressed in the database, all distances to object will be equal to \
 zero:
 
 .. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 23-24
+   :lines: 27-28
 
 Finally we can generate the database.
 
 .. literalinclude:: examples/blenddemo_beesampling.py
-   :lines: 28-29
+   :dedent: 4
+   :lines: 31-32
+
+
+(:download:`Source code <examples/blenddemo_beesampling.py>`)
 
 Custom sampling
 ---------------
+.. literalinclude:: examples/blenddemo_cyberbee.py
+   :lines: 5
 
-    .. 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.
 
-    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
 
-    .. 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.
 
-    To render a scene at a given positions we just have to do:
+.. literalinclude:: examples/blenddemo_cyberbee.py
+   :lines: 16-24
 
-    .. literalinclude:: examples/blenddemo_cyberbee.py
-       :lines: 14-22
+(:download:`Source code <examples/blenddemo_cyberbee.py>`)

setup.py

@@ -28,10 +28,18 @@ setup_dict = {'name': 'navipy',
               'author_email': 'olivier.bertrand@uni-bielefeld.de',
               'description': 'Insect Navigation Toolbox',
               'packages': create_package_list("navipy"),
-              'requires': ['numpy', 'pandas', 'matplotlib', 'scipy',
+              'requires': ['numpy',
+                           'pandas',
+                           'matplotlib',
+                           'scipy',
                            'networkx'],
-              'install_requires': ["numpy", 'pandas', 'matplotlib', 'scipy',
-                                   'sphinx_rtd_theme', 'networkx'],
+              'install_requires': ["numpy",
+                                   'pandas',
+                                   'matplotlib',
+                                   'scipy',
+                                   'sphinx_rtd_theme',
+                                   'networkx',
+                                   'sphinx-argparse'],
               'package_data': {'navipy': ['resources/database.db',
                                           'resources/forest_world.blend']},
               'include_package_data': True, }