diff --git a/doc/source/example/processing/apcv.py b/doc/source/example/processing/apcv.py
index 494936458450c16355a08e2be8026b5cc3abce33..2d5433d9d820e50694363b5da85b0efa9604b127 100644
--- a/doc/source/example/processing/apcv.py
+++ b/doc/source/example/processing/apcv.py
@@ -1,20 +1,20 @@
import matplotlib.pyplot as plt
from navipy.database import DataBaseLoad
import navipy.processing as processing
-from navipy.sensors import Senses
+from navipy import Brain
import pkg_resources
# 1) Connect to the database
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
+mybrain = Brain(renderer=mydb)
# 2) Define the position-orinetation at which
# we want the image
posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
-my_apcv = processing.pcode.apcv(mysenses.vision.scene,
- mysenses.vision.viewing_directions)
+mybrain.update(posorient)
+my_apcv = processing.pcode.apcv(mybrain.vision.scene,
+ mybrain.vision.viewing_directions)
my_apcv_sph = processing.tools.cartesian_to_spherical(x=my_apcv[..., 0],
y=my_apcv[..., 1],
diff --git a/doc/source/example/processing/contrast_weighted_nearness.py b/doc/source/example/processing/contrast_weighted_nearness.py
index 614d6675c9473386666ec6653174c3742b2e7548..283580c4345a0c5be2f7442e6340dcedc2c59b7c 100644
--- a/doc/source/example/processing/contrast_weighted_nearness.py
+++ b/doc/source/example/processing/contrast_weighted_nearness.py
@@ -1,7 +1,7 @@
import matplotlib.pyplot as plt
from navipy.database import DataBaseLoad
import navipy.processing as processing
-from navipy.sensors import Senses
+from navipy import Brain
import pkg_resources
@@ -9,13 +9,13 @@ import pkg_resources
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
+mybrain = Brain(renderer=mydb)
# 2) Define the position-orinetation at which
# we want the image
posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
+mybrain.update(posorient)
my_contrast = processing.pcode.contrast_weighted_nearness(
- mysenses.vision.scene)
+ mybrain.vision.scene)
f, axarr = plt.subplots(2, 2, figsize=(15, 8))
axarr = axarr.flatten()
diff --git a/doc/source/example/processing/michelson_contrast.py b/doc/source/example/processing/michelson_contrast.py
index 9d6e12c0b2dcea90e0a6738934de42724047f767..c5681b904ef0f5cfaba14c9e71cdedb50e46baf4 100644
--- a/doc/source/example/processing/michelson_contrast.py
+++ b/doc/source/example/processing/michelson_contrast.py
@@ -1,19 +1,19 @@
import matplotlib.pyplot as plt
from navipy.database import DataBaseLoad
import navipy.processing as processing
-from navipy.sensors import Senses
+from navipy import Brain
import pkg_resources
# 1) Connect to the database
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
+mybrain = Brain(renderer=mydb)
# 2) Define the position-orinetation at which
# we want the image
posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
-my_contrast = processing.pcode.michelson_contrast(mysenses.vision.scene)
+mybrain.update(posorient)
+my_contrast = processing.pcode.michelson_contrast(mybrain.vision.scene)
f, axarr = plt.subplots(2, 2, figsize=(15, 8))
axarr = axarr.flatten()
diff --git a/doc/source/example/processing/pcv.py b/doc/source/example/processing/pcv.py
index 325d61952fe5357578362b837b6477505d9e9c5c..19d517fd4e63415ad4f35b32cde3a179db414ddc 100644
--- a/doc/source/example/processing/pcv.py
+++ b/doc/source/example/processing/pcv.py
@@ -1,17 +1,17 @@
# import matplotlib.pyplot as plt
from navipy.database import DataBaseLoad
import navipy.processing as processing
-from navipy.sensors import Senses
+from navipy import Brain
import pkg_resources
# 1) Connect to the database
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
+mybrain = Brain(renderer=mydb)
# 2) Define the position-orinetation at which
# we want the image
posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
-my_pcv = processing.pcode.pcv(mysenses.vision.scene,
- mysenses.vision.viewing_directions)
+mybrain.update(posorient)
+my_pcv = processing.pcode.pcv(mybrain.vision.scene,
+ mybrain.vision.viewing_directions)
diff --git a/doc/source/example/processing/skyline.py b/doc/source/example/processing/skyline.py
index 8846f93e37ef579bcb7a58bb712b24fc25874985..d8b2440714fefcd121c9fa6c8c57da05bbf0ca74 100644
--- a/doc/source/example/processing/skyline.py
+++ b/doc/source/example/processing/skyline.py
@@ -1,19 +1,19 @@
import matplotlib.pyplot as plt
from navipy.database import DataBaseLoad
import navipy.processing as processing
-from navipy.sensors import Senses
+from navipy import Brain
import pkg_resources
# 1) Connect to the database
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
+mybrain = Brain(renderer=mydb)
# 2) Define the position-orinetation at which
# we want the image
posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
-my_skyline = processing.pcode.skyline(mysenses.vision.scene)
+mybrain.update(posorient)
+my_skyline = processing.pcode.skyline(mybrain.vision.scene)
f, axarr = plt.subplots(1, 2, figsize=(15, 4))
for chan_i, chan_n in enumerate(mydb.channels):
diff --git a/doc/source/example/tutorials/asv_homing_grid.py b/doc/source/example/tutorials/asv_homing_grid.py
index 8d3124c5b6bd524409373ecdad206a3a3e312b3c..5f75e8346f17be0729c350521a1b534ac2756e02 100644
--- a/doc/source/example/tutorials/asv_homing_grid.py
+++ b/doc/source/example/tutorials/asv_homing_grid.py
@@ -5,27 +5,41 @@ import pkg_resources
from navipy.database import DataBaseLoad
from navipy.processing.pcode import apcv
from navipy.moving.agent import GridAgent
-from navipy.sensors import Senses
-
+from navipy import Brain
+
+
+# 0) Define a class heriting from Brain
+class ASVBrain(Brain):
+ def __init__(self, renderer=None):
+ Brain.__init__(self,renderer=renderer)
+ # Init memory
+ posorient = mydb.posorients.loc[12, :]
+ mybrain.update(posorient)
+ self.memory = apcv(mybrain.vision.scene,
+ mybrain.vision.viewing_directions)
+
+ def velocity(self):
+ asv = apcv(self.vision.scene,
+ self.vision.viewing_directions)
+ homing_vector = self.memory - asv
+ homing_vector = np.squeeze(homing_vector[..., 0, :])
+ velocity = pd.Series(data=0,
+ index=['dx', 'dy', 'dz',
+ 'dalpha_0', 'dalpha_1', 'dalpha_2'])
+ velocity[['dx', 'dy', 'dz']] = homing_vector
+ return velocity
+
# 1) Connect to the database
mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
mydb = DataBaseLoad(mydb_filename)
-mysenses = Senses(renderer=mydb)
-# 2) Define the position-orinetation at which
-# we want the image
-posorient = mydb.posorients.loc[12, :]
-mysenses.update(posorient)
-memory = apcv(mysenses.vision.scene,
- mysenses.vision.viewing_directions)
-
-
+mybrain = ASVBrain(renderer=mydb)
# Create a grid agent
-my_agent = GridAgent(mydb_filename)
+my_agent = GridAgent(mybrain)
# init position
rowid = 1
-initpos = mydb.posorients.loc[rowid]
+initpos = mybrain.posorients.loc[rowid]
my_agent.posorient = initpos
# Mode of motion
@@ -35,23 +49,6 @@ mode_of_motion['param'] = dict()
mode_of_motion['param']['grid_spacing'] = 1
my_agent.mode_of_motion = mode_of_motion
-# Define a motion function
-
-
-def asv_homing(posorient_vel, senses, memory):
- asv = apcv(senses.vision.scene,
- senses.vision.viewing_directions)
- homing_vector = memory - asv
- homing_vector = np.squeeze(homing_vector[..., 0, :])
- velocity = pd.Series(data=0,
- index=['dx', 'dy', 'dz',
- 'dalpha_0', 'dalpha_1', 'dalpha_2'])
- velocity[['dx', 'dy', 'dz']] = homing_vector
- return velocity
-
-
-my_agent.motion = asv_homing
-my_agent.motion_param = {'memory': memory}
# Run
max_nstep = 100
trajectory = my_agent.fly(max_nstep, return_tra=True)
diff --git a/navipy/__init__.py b/navipy/__init__.py
index 99e6fe839c8d6ded6fd96f768b1e3f07f7394df3..8c0854c94e0d2d77b520b36f7b33a3e41af889d5 100644
--- a/navipy/__init__.py
+++ b/navipy/__init__.py
@@ -20,12 +20,8 @@ Then the senses can be updated at a new position orientation:
.. literalinclude:: example/processing/apcv.py
:lines: 15
-Renderer
---------
-.. automodule:: navipy.sensors.renderer
-
"""
-from database import DataBaseLoad
+from navipy.database import DataBaseLoad
class Bunch:
def __init__(self, **kwds):
@@ -48,6 +44,7 @@ class Brain():
raise NotImplementedError("Subclasses should implement this")
def update(self, posorient):
+ self.posorient = posorient
if self.renderer is not None:
self.vision.scene = self.renderer.scene(posorient)
diff --git a/navipy/moving/agent.py b/navipy/moving/agent.py
index 6a8acb54d9706912c62ae1ab78a46749264be93b..53dae2fc93a40d09092d5c3fb4b54f14a0cfe27d 100644
--- a/navipy/moving/agent.py
+++ b/navipy/moving/agent.py
@@ -11,13 +11,14 @@
"""
import numpy as np
import pandas as pd
+import copy
import networkx as nx
import multiprocessing
from multiprocessing import Queue, JoinableQueue, Process
import inspect
from navipy.database import DataBaseLoad
import navipy.moving.maths as navimomath
-from navipy.sensors import Senses
+from navipy import Brain
version = float(nx.__version__)
@@ -27,18 +28,20 @@ def defaultcallback(*args, **kwargs):
raise NameError('No Callback')
-class DefaultSensors():
+class DefaultBrain():
def __init__(self):
pass
def update(self, posorient):
raise NameError('No Callback')
+ def velocity(self):
+ raise NameError('No Callback')
+
class AbstractAgent():
def __init__(self):
- self._brian = DefaultSensors()
- self._motion_param = None
+ self._brain = DefaultBrain()
self._alter_posorientvel = defaultcallback
self._posorient_col = ['x', 'y', 'z',
'alpha_0', 'alpha_1', 'alpha_2']
@@ -93,7 +96,7 @@ class AbstractAgent():
def move(self):
self._brain.update(self.posorient)
- self.velocity = self._brian.velocity()
+ self.velocity = self._brain.velocity()
alteredpos = self._alter_posorientvel(self._posorient_vel)
self.posorient = alteredpos
self.velocity = alteredpos
@@ -193,7 +196,7 @@ GridAgent is a close loop agent here its position is snap to a grid.
move_mode=self._mode_move['mode'],
move_param=self._mode_move['param'])
tmp = navimomath.closest_pos(
- posorient_vel, self._posorients)
+ posorient_vel, self._brain.posorients)
posorient_vel.loc[self._posorient_col] = \
tmp.loc[self._posorient_col]
posorient_vel.name = tmp.name
@@ -248,8 +251,8 @@ the agent motion, or
2. pre-computed agent-motion
"""
- def __init__(self, brian):
- self._brain = copy.deepcopy(brain)
+ def __init__(self, brain):
+ self._brain = copy.copy(brain)
# Init the graph
self._graph = nx.DiGraph()
for row_id, posor in self._brain.posorients.iterrows():
@@ -284,7 +287,7 @@ the agent motion, or
# Start ndatabase loader
num_agents = ncpu
- agents = [GridAgent(copy.deepcopy(self._brain),
+ agents = [GridAgent(copy.copy(self._brain),
posorients_queue=posorients_queue,
results_queue=results_queue)
for _ in range(num_agents)]
diff --git a/navipy/moving/test_agent.py b/navipy/moving/test_agent.py
index 0247b407359794581950d17b79712943844394a7..ace9b780245bfab309908e4a5f3f0fedd92b1cab 100644
--- a/navipy/moving/test_agent.py
+++ b/navipy/moving/test_agent.py
@@ -6,6 +6,7 @@ import pandas as pd
import networkx as nx
import navipy.moving.agent as naviagent
import navipy.database as navidb
+from navipy import Brain
import pkg_resources
import unittest
@@ -13,18 +14,29 @@ import unittest
version = float(nx.__version__)
-class TestNavipyMovingAgent(unittest.TestCase):
+class BrainTest(Brain):
+ def __init__(self, renderer=None):
+ Brain.__init__(self,renderer=renderer)
+ self.__posorient_col = ['x', 'y', 'z',
+ 'alpha_0', 'alpha_1', 'alpha_2']
+ self.__velocity_col = ['d' + col for col in self.__posorient_col]
+ self.__posorient_vel_col = self.__posorient_col
+ self.__posorient_vel_col.extend(self.__velocity_col)
+
+ def velocity(self):
+ return pd.Series(data=0,index=self.__posorient_vel_col)
+class TestNavipyMovingAgent(unittest.TestCase):
def setUp(self):
self.mydb_filename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
self.mydb = navidb.DataBaseLoad(self.mydb_filename)
+ self.brain = BrainTest(self.mydb)
self.__posorient_col = ['x', 'y', 'z',
'alpha_0', 'alpha_1', 'alpha_2']
self.__velocity_col = ['d' + col for col in self.__posorient_col]
self.__posorient_vel_col = self.__posorient_col
self.__posorient_vel_col.extend(self.__velocity_col)
-
#
# AbstractAgent
#
@@ -42,15 +54,12 @@ class TestNavipyMovingAgent(unittest.TestCase):
# GridAgent
#
def test_move_gridagent(self):
- agent = naviagent.GridAgent(self.mydb_filename)
- initposorient = agent.db.posorients.loc[13, :]
+ agent = naviagent.GridAgent(self.brain)
+ initposorient = self.brain.posorients.loc[13, :]
initposovel = pd.Series(data=0,
index=self.__posorient_vel_col)
initposovel.loc[initposorient.index] = initposorient
agent.posorient = initposovel
- agent.motion = lambda posorient, scene:\
- pd.Series(data=0,
- index=self.__posorient_vel_col)
with self.assertRaises(AttributeError):
agent.move()
mode_move = {'mode': 'on_cubic_grid',
@@ -64,15 +73,12 @@ class TestNavipyMovingAgent(unittest.TestCase):
obtained, initposorient.loc[obtained.index]))
def test_fly_gridagent(self):
- agent = naviagent.GridAgent(self.mydb_filename)
- initposorient = agent.db.posorients.loc[13, :]
+ agent = naviagent.GridAgent(self.brain)
+ initposorient = self.brain.posorients.loc[13, :]
initposovel = pd.Series(data=0,
index=self.__posorient_vel_col)
initposovel.loc[initposorient.index] = initposorient
agent.posorient = initposovel
- agent.motion = lambda posorient, scene:\
- pd.Series(data=0,
- index=self.__posorient_vel_col)
with self.assertRaises(AttributeError):
agent.fly(max_nstep=10)
mode_move = {'mode': 'on_cubic_grid',
@@ -90,7 +96,7 @@ class TestNavipyMovingAgent(unittest.TestCase):
#
def test_init_graphagent(self):
- agent = naviagent.GraphAgent(self.mydb_filename)
+ agent = naviagent.GraphAgent(self.brain)
if version < 2:
graph_nodes = list(agent.graph.nodes())
else:
@@ -100,7 +106,7 @@ class TestNavipyMovingAgent(unittest.TestCase):
'Init of graph failed. Node missmatch')
def test_graph_setter(self):
- agent = naviagent.GraphAgent(self.mydb_filename)
+ agent = naviagent.GraphAgent(self.brain)
if version < 2:
graph_nodes = list(agent.graph.nodes())
else:
@@ -128,7 +134,7 @@ class TestNavipyMovingAgent(unittest.TestCase):
3 Two loops attractors
"""
# Test all node to first
- agent = naviagent.GraphAgent(self.mydb_filename)
+ agent = naviagent.GraphAgent(self.brain)
if version < 2:
graph_nodes = list(agent.graph.nodes())
@@ -193,7 +199,7 @@ class TestNavipyMovingAgent(unittest.TestCase):
2. Saddle points
3. Local minima
"""
- agent = naviagent.GraphAgent(self.mydb_filename)
+ agent = naviagent.GraphAgent(self.brain)
# Local maxima
if version < 2:
graph_nodes = list(agent.graph.nodes())
diff --git a/navipy/sensors/__init__.py b/navipy/sensors/__init__.py
index 3928b27c6bdf132d56924146838d7cfd9e88e83e..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/navipy/sensors/__init__.py
+++ b/navipy/sensors/__init__.py
@@ -1,47 +0,0 @@
-"""
-Every agent comes with a battery of senses (biological agent) \
-or sensors (technical agent). The senses of agents in navipy are limited
-to:
-
-* 4d vision (brighness + depth)
-
-The 4d vision sense is controlled by rendering module, either an \
-online rendering or loaded from a database containing pre-rendered images.
-
-For example to use pre-rendered images from a database:
-
-.. literalinclude:: example/processing/apcv.py
- :lines: 10-11
-
-Then the senses can be updated at a new position orientation:
-
-.. literalinclude:: example/processing/apcv.py
- :lines: 15
-
-Renderer
---------
-.. automodule:: navipy.sensors.renderer
-
-"""
-
-
-class Bunch:
- def __init__(self, **kwds):
- self.__dict__.update(kwds)
-
-
-class Senses():
- def __init__(self,
- renderer=None):
- self.vision = Bunch(scene=None,
- viewing_directions=None,
- channels=None)
- self.renderer = renderer
- if self.renderer is not None:
- self.vision.scene = None
- self.vision.viewing_directions = renderer.viewing_directions
- self.vision.channels = renderer.channels
-
- def update(self, posorient):
- if self.renderer is not None:
- self.vision.scene = self.renderer.scene(posorient)