From 2947bfcefea928758f872074196e26cadabef8ac Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <bolirev@hotmail.com>
Date: Wed, 3 Jan 2018 15:27:10 +0100
Subject: [PATCH] Update the doc of database
---
doc/source/example/database/get_posorients.py | 13 ++++++++
.../example/database/load_image_posorient.py | 8 +++--
.../example/database/load_image_rowid.py | 8 +++--
doc/source/moving.rst | 12 ++++---
navipy/database/__init__.py | 33 +++++--------------
5 files changed, 39 insertions(+), 35 deletions(-)
create mode 100644 doc/source/example/database/get_posorients.py
diff --git a/doc/source/example/database/get_posorients.py b/doc/source/example/database/get_posorients.py
new file mode 100644
index 0000000..89b3f2a
--- /dev/null
+++ b/doc/source/example/database/get_posorients.py
@@ -0,0 +1,13 @@
+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)
diff --git a/doc/source/example/database/load_image_posorient.py b/doc/source/example/database/load_image_posorient.py
index 6b22ef1..43b4206 100644
--- a/doc/source/example/database/load_image_posorient.py
+++ b/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()
diff --git a/doc/source/example/database/load_image_rowid.py b/doc/source/example/database/load_image_rowid.py
index e67ab2a..fcd1fca 100644
--- a/doc/source/example/database/load_image_rowid.py
+++ b/doc/source/example/database/load_image_rowid.py
@@ -1,17 +1,19 @@
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()
diff --git a/doc/source/moving.rst b/doc/source/moving.rst
index f6d1353..1163efd 100644
--- a/doc/source/moving.rst
+++ b/doc/source/moving.rst
@@ -1,11 +1,13 @@
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:
diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index cd90192..c4bd1d6 100644
--- a/navipy/database/__init__.py
+++ b/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
"""
--
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