Update the doc of database

doc/source/example/database/get_posorients.py

+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+from navipy.database import DataBaseLoad
+import pkg_resources
+
+
+# 1) Connect to the database
+mydb_filename = pkg_resources.resource_filename(
+    'navipy', 'resources/database.db')
+mydb = DataBaseLoad(mydb_filename)
+posorients = mydb.posorients
+posorients.head(n=5)

doc/source/example/database/load_image_posorient.py

@@ -2,11 +2,12 @@ import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
 from navipy.database import DataBaseLoad
-import os
+import pkg_resources
 
 
 # 1) Connect to the database
-mydb_filename = os.path.abspath('../database.db')
+mydb_filename = pkg_resources.resource_filename(
+    'navipy', 'resources/database.db')
 mydb = DataBaseLoad(mydb_filename)
 # 2) Define the position-orinetation at which
 # we want the image
@@ -19,7 +20,8 @@ posorient.alpha_0 = np.pi / 2
 posorient.alpha_1 = 0
 posorient.alpha_2 = 0
 # 3) Load the image
-image = mydb.read_image(posorient=posorient)
+image = mydb.scene(posorient=posorient)
+image = image[...,0]
 # 4) plot the image
 to_plot_im = image[:, :, :3]
 to_plot_im -= to_plot_im.min()

doc/source/example/database/load_image_rowid.py

 import numpy as np
 import matplotlib.pyplot as plt
 from navipy.database import DataBaseLoad
-import os
+import pkg_resources
 
 
 # 1) Connect to the database
-mydb_filename = os.path.abspath('../database.db')
+mydb_filename = pkg_resources.resource_filename(
+    'navipy', 'resources/database.db')
 mydb = DataBaseLoad(mydb_filename)
 # 2) Define the position-orinetation at which
 # we want the image
 rowid = 12
 # 3) Load the image
-image = mydb.read_image(rowid=rowid)
+image = mydb.scene(rowid=rowid)
+image = image[...,0]
 # 4) plot the image
 to_plot_im = image[:, :, :3]
 to_plot_im -= to_plot_im.min()

doc/source/moving.rst

 Moving
 ======
 
-Moving on a grid
-----------------
+.. automodule:: navipy.moving
 
-Moving between grid points
---------------------------
-Interpolation of neighbouring images
+.. autoclass:: navipy.moving.agent.CyberBeeAgent
+    :members:
 
+.. autoclass:: navipy.moving.agent.GridAgent
+    :members:
 
+.. autoclass:: navipy.moving.agent.GraphAgent
+    :members:

navipy/database/__init__.py

@@ -13,11 +13,8 @@ are normalised, so to use the full coding range.
 How to load a database
 ----------------------
 
-.. code-block:: python
-
-   from database import DataBaseLoad
-   mydb_filename = 'database.db'
-   mydb = DataBaseLoad(mydb_filename)
+.. literalinclude:: example/database/get_posorients.py
+      :lines: 11
 
 How to load all position-orientation
 ------------------------------------
@@ -28,10 +25,10 @@ situation, it may be usefull to know all \
 position-orientation in the database. More technically \
 speaking, loading the full table of position-orientaiton.
 
-.. code-block:: python
+.. literalinclude:: example/database/get_posorients.py
+      :lines: 12-13
 
-   posorients = mydb.get_posorients()
-   posorients.head()
+.. plot:: example/database/get_posorients.py
 
 How to load an image
 --------------------
@@ -44,17 +41,8 @@ the position-orientation can be given. The DataBaseLoader will \
 look if this position-orientation has been rendered. If it is \
 the case, the image will be returned.
 
-.. code-block:: python
-
-   posorient = pd.Series(index=['x', 'y', 'z',
-                             'alpha_0', 'alpha_1', 'alpha_2'])
-   posorient.x = -0.6
-   posorient.y = -7.2
-   posorient.z = 2.35
-   posorient.alpha_0 = np.pi / 2
-   posorient.alpha_1 = 0
-   posorient.alpha_2 = 0
-   image = mydb.read_image(posorient=posorient)
+.. literalinclude:: example/database/load_image_posorient.py
+      :lines: 14-23
 
 .. plot:: example/database/load_image_posorient.py
 
@@ -65,15 +53,12 @@ Indeed each position-orientation can be identified by a unique row \
 number. This number is consistant through the entire database. Thus, \
 an image can be loaded by providing the row number.
 
-.. code-block:: python
-
-   rowid = 1000
-   image = mydb.read_image(rowid=rowid)
+.. literalinclude:: example/database/load_image_rowid.py
+      :lines: 13-15
 
 .. plot:: example/database/load_image_rowid.py
 
 
-
 .. todo: channels as part of database
 
 """