pybrainsim-activity Mailing List for PyBrainSim - The Brain Phantom Project (Page 6)
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From: <rg...@us...> - 2009-08-03 17:31:27
|
Revision: 72
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=72&view=rev
Author: rgoj
Date: 2009-08-03 17:31:21 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* adding getSource and getTarger methods to Connection
Modified Paths:
--------------
trunk/src/Connection.py
Modified: trunk/src/Connection.py
===================================================================
--- trunk/src/Connection.py 2009-08-03 17:27:14 UTC (rev 71)
+++ trunk/src/Connection.py 2009-08-03 17:31:21 UTC (rev 72)
@@ -39,6 +39,12 @@
def getName(self):
return self.name
+ def getSource(self):
+ return self.sourceGenerator
+
+ def getTarget(self):
+ return self.targetGenerator
+
def getSourceName(self):
return self.sourceGenerator.getName()
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From: <rg...@us...> - 2009-08-03 17:27:23
|
Revision: 71
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=71&view=rev
Author: rgoj
Date: 2009-08-03 17:27:14 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Adding another example simulation with two generators and one stimulus for each generator
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 17:05:30 UTC (rev 70)
+++ trunk/src/PyBrainSim.py 2009-08-03 17:27:14 UTC (rev 71)
@@ -43,7 +43,8 @@
Choose the type of simulation you would like to perform:\n\
1. Example dummy simulation\n\
2. Incrementing numbers, one generator and a stimulus\n\
- 3. Sinusoidal generator\n"
+ 3. Incrementing numbers, two generators and a stimulus for one of them\n\
+ 4. Sinusoidal generator\n"
print(welcomeMessage)
userChoice = input("Your choice: ")
@@ -74,6 +75,23 @@
exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
+elif userChoice == 3:
+ exampleHead = Head()
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus1 = Stimulus('Stim1', exampleHead)
+ exampleStimulus2 = Stimulus('Stim2', exampleHead)
+ exampleStimulus1.setStimulusTimes([0.3, 0.6])
+ exampleStimulus2.setStimulusTimes([0.5])
+ exampleGenerator1 = GeneratorNumberIncrementing('Gen1', exampleHead)
+ exampleGenerator2 = GeneratorNumberIncrementing('Gen2', exampleHead)
+ exampleConnection1 = Connection('Con1', exampleHead, exampleStimulus1, exampleGenerator1)
+ exampleConnection2 = Connection('Con2', exampleHead, exampleStimulus2, exampleGenerator2)
+
+ exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
#elif userChoice == 2:
# exampleExperiment = Experiment()
# exampleExperiment.addStimulusTime( 0.2341 )
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-03 17:14:37
|
#100: The Experiment class should allow for different stimulus times for
different stimuli objects
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: new
Priority: major | Milestone: Modelling phase resetting
Component: Simulations | Keywords:
-------------------------+--------------------------------------------------
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/100>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
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From: <rg...@us...> - 2009-08-03 17:05:36
|
Revision: 70
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=70&view=rev
Author: rgoj
Date: 2009-08-03 17:05:30 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Re-adding a second example simulation to the PyBrainSim.py script - using one number incrementing generator with a stimulus
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 17:04:08 UTC (rev 69)
+++ trunk/src/PyBrainSim.py 2009-08-03 17:05:30 UTC (rev 70)
@@ -29,6 +29,7 @@
from Head import Head
from Experiment import Experiment
+from Stimulus import Stimulus
from StimulusDummy import StimulusDummy
from GeneratorDummy import GeneratorDummy
from GeneratorNumberIncrementing import GeneratorNumberIncrementing
@@ -41,7 +42,7 @@
Welcome to this early version of PyBrainSim\n\n\
Choose the type of simulation you would like to perform:\n\
1. Example dummy simulation\n\
- 2. Adding numbers\n\
+ 2. Incrementing numbers, one generator and a stimulus\n\
3. Sinusoidal generator\n"
print(welcomeMessage)
@@ -60,31 +61,20 @@
exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
print(exampleExperiment.getRecording())
+elif userChoice == 2:
+ exampleHead = Head()
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes([0.3, 0.6])
+ exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
#elif userChoice == 2:
-# exampleHead = Head()
-# exampleHead.setSamplingFrequency(32)
-# exampleHead.addRegistrationSite([0, 0, 0])
-# exampleHead.addRegistrationSite([0, 0, 0])
-#
-# exampleGenerator1 = GeneratorDummy()
-# exampleGenerator2 = GeneratorDummy()
-# exampleHead.addGenerator(exampleGenerator1)
-# exampleHead.addGenerator(exampleGenerator2)
-#
-# exampleConnection = ConnectionSimple(exampleGenerator1, exampleGenerator2)
-# exampleHead.addConnection(exampleConnection)
-#
-# exampleStimulus = GeneratorStimulusActivationZeroing()
-# exampleHead.addGenerator(exampleStimulus)
-#
-# exampleStimulusToGeneratorConnection = ConnectionSimple(exampleStimulus, exampleGenerator1)
-# exampleGeneratorToStimulusConnection = ConnectionSimple(exampleGenerator1, exampleStimulus)
-# exampleHead.addConnection(exampleStimulusToGeneratorConnection)
-# exampleHead.addConnection(exampleGeneratorToStimulusConnection)
-#
-# exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
-# print exampleExperiment.getRecording()
-#elif userChoice == 2:
# exampleExperiment = Experiment()
# exampleExperiment.addStimulusTime( 0.2341 )
#
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From: <rg...@us...> - 2009-08-03 17:04:16
|
Revision: 69
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=69&view=rev
Author: rgoj
Date: 2009-08-03 17:04:08 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Correcting mistake: If the stimulus returns a word as it's activation, this should not be counted into the general activation
* Using Numeric.arange to provide the range of time points
* Time points now begin at 1/samplingFrequency and the last point is the end time specified when invoking runSimulation
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-03 17:00:55 UTC (rev 68)
+++ trunk/src/Head.py 2009-08-03 17:04:08 UTC (rev 69)
@@ -15,6 +15,7 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
+from Numeric import arange
__metaclass__ = type # New style classes. Is this necessary?
"""
@@ -57,8 +58,13 @@
# Filling all registration sites with the generators' output
for i in range(len(recording)):
recording[i].append(0)
- for klupek in range(len(self.generatorList)):
- recording[i][-1] += generatorOutput[klupek]
+ for j in range(len(self.generatorList)):
+ # The Stimulus class may return a string variable, we can't add
+ # it to the recording, so we need to look out for it.
+ if isinstance(generatorOutput[j], str):
+ recording[i][-1] += 0
+ else:
+ recording[i][-1] += generatorOutput[j]
return recording
@@ -79,12 +85,14 @@
# Querying all generators and sending generator output through
# connections
- for timePoint in range(duration * self.samplingFrequency):
- print("HEAD, time: " + str(timePoint/self.samplingFrequency))
+ timeStep = 1/self.samplingFrequency
+ timeRange = list(arange(timeStep, duration + timeStep, timeStep))
+ for timePoint in timeRange:
+ print("HEAD, time: " + str(timePoint))
# Recording the output of each generator
for i in range(len(self.generatorList)):
- generatorOutput[i] = (self.generatorList[i]).runGenerator(timePoint/self.samplingFrequency)
+ generatorOutput[i] = (self.generatorList[i]).runGenerator(timePoint)
# Sending the output of generators through connections
for i in range(len(self.connectionList)):
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From: <rg...@us...> - 2009-08-03 17:01:03
|
Revision: 68
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=68&view=rev
Author: rgoj
Date: 2009-08-03 17:00:55 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Correcting mistake: a generator must return it's activation from the runGenerator method
* Correcting mistake: after the end of stimuli in stimulusList the activation would remain unchanged, thus always stimulating the connected generator
* Changing message printed by the runGenerator method
Modified Paths:
--------------
trunk/src/Stimulus.py
Modified: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py 2009-08-03 16:55:34 UTC (rev 67)
+++ trunk/src/Stimulus.py 2009-08-03 17:00:55 UTC (rev 68)
@@ -38,14 +38,14 @@
def runGenerator(self, time):
if self.currentStimulus < len(self.stimulusTimes):
- if self.stimulusTimes[self.currentStimulus] < time:
- print("Stimulus now: BEEEEEEEP! ... Time is: " + str(time) + ", Stimulus list is: " + str(self.stimulusTimes) + " Connected generator phase should have been: " + str(self.connectedGeneratorPhase))
+ if self.stimulusTimes[self.currentStimulus] <= time:
+ print("Stimulus now: BEEEEEEEP! ... Time is: " + str(time) + ", Stimulus list is: " + str(self.stimulusTimes))
self.currentStimulus += 1
-
self.activation = 'Stimulus'
else:
- self.activation = None
+ self.activation = 0
+ else:
+ self.activation = 0
- # The runGenerator method must return a value
- return 0
+ return self.activation
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From: <rg...@us...> - 2009-08-03 16:55:46
|
Revision: 67
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=67&view=rev
Author: rgoj
Date: 2009-08-03 16:55:34 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Correcting a small mistake
Modified Paths:
--------------
trunk/src/GeneratorNumberIncrementing.py
Modified: trunk/src/GeneratorNumberIncrementing.py
===================================================================
--- trunk/src/GeneratorNumberIncrementing.py 2009-08-03 12:07:56 UTC (rev 66)
+++ trunk/src/GeneratorNumberIncrementing.py 2009-08-03 16:55:34 UTC (rev 67)
@@ -29,7 +29,7 @@
print(self.name + ": A GeneratorNumberIncrementing object")
def receiveInput(self, input):
- if activation == 'Stimulus':
+ if input == 'Stimulus':
self.activation = 0
else:
self.activation += input
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From: <rg...@us...> - 2009-08-03 12:40:27
|
Revision: 57
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=57&view=rev
Author: rgoj
Date: 2009-08-03 11:20:21 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Generators now can't be created without a Head class to be attached to, because:
** the __init__ method now needs a Head object as input
** the __init__ method now adds the generator to the specified Head object
* This makes the syntax to use Generators (e.g. in PyBrainSim.py) much, much nicer.
Modified Paths:
--------------
trunk/src/Generator.py
Modified: trunk/src/Generator.py
===================================================================
--- trunk/src/Generator.py 2009-08-03 11:14:11 UTC (rev 56)
+++ trunk/src/Generator.py 2009-08-03 11:20:21 UTC (rev 57)
@@ -22,9 +22,10 @@
"""
class Generator:
- def __init__(self, name):
+ def __init__(self, name, head):
self.name = name
self.activation = 0
+ head.addGenerator(self)
def printInfo(self):
print(self.name + ": A Generator object")
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From: <rg...@us...> - 2009-08-03 12:08:03
|
Revision: 66
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=66&view=rev
Author: rgoj
Date: 2009-08-03 12:07:56 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Adding missing inheritance from the Generator class
Modified Paths:
--------------
trunk/src/GeneratorNumberIncrementing.py
Modified: trunk/src/GeneratorNumberIncrementing.py
===================================================================
--- trunk/src/GeneratorNumberIncrementing.py 2009-08-03 11:59:41 UTC (rev 65)
+++ trunk/src/GeneratorNumberIncrementing.py 2009-08-03 12:07:56 UTC (rev 66)
@@ -22,7 +22,9 @@
integer addition.
"""
-class GeneratorNumberIncrementing:
+from Generator import Generator
+
+class GeneratorNumberIncrementing(Generator):
def printInfo(self):
print(self.name + ": A GeneratorNumberIncrementing object")
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From: <rg...@us...> - 2009-08-03 11:59:48
|
Revision: 65
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=65&view=rev
Author: rgoj
Date: 2009-08-03 11:59:41 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Using StimulusDummy instead of Stimulus for the first example.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 11:58:42 UTC (rev 64)
+++ trunk/src/PyBrainSim.py 2009-08-03 11:59:41 UTC (rev 65)
@@ -29,7 +29,7 @@
from Head import Head
from Experiment import Experiment
-from Stimulus import Stimulus
+from StimulusDummy import StimulusDummy
from GeneratorDummy import GeneratorDummy
from GeneratorNumberIncrementing import GeneratorNumberIncrementing
from Connection import Connection
@@ -53,7 +53,7 @@
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
- exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus = StimulusDummy('Stim', exampleHead)
exampleGenerator = GeneratorDummy('Gen', exampleHead)
exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
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From: <rg...@us...> - 2009-08-03 11:58:49
|
Revision: 64
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=64&view=rev
Author: rgoj
Date: 2009-08-03 11:58:42 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Changing the message printed by StimulusDummy
Modified Paths:
--------------
trunk/src/StimulusDummy.py
Modified: trunk/src/StimulusDummy.py
===================================================================
--- trunk/src/StimulusDummy.py 2009-08-03 11:50:59 UTC (rev 63)
+++ trunk/src/StimulusDummy.py 2009-08-03 11:58:42 UTC (rev 64)
@@ -28,5 +28,5 @@
print(self.name + ": A StimulusDummy object")
def runGenerator(self, time):
- print("[runGenerator] " + self.name + ": Sending out the stimulus")
+ print("[runGenerator] " + self.name + ": Preparing the stimulus")
return Stimulus.runGenerator(self, time)
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From: <rg...@us...> - 2009-08-03 11:51:07
|
Revision: 63
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=63&view=rev
Author: rgoj
Date: 2009-08-03 11:50:59 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Created a StimulusDummy class to print out messages on screen.
Added Paths:
-----------
trunk/src/StimulusDummy.py
Added: trunk/src/StimulusDummy.py
===================================================================
--- trunk/src/StimulusDummy.py (rev 0)
+++ trunk/src/StimulusDummy.py 2009-08-03 11:50:59 UTC (rev 63)
@@ -0,0 +1,32 @@
+# PyBrainSim Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# PyBrainSim is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
+
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+This is a reimplementation of the Stimulus class (child of the Generator class)
+that prints messages from inside of the interesting methods.
+"""
+
+from Stimulus import Stimulus
+
+class StimulusDummy(Stimulus):
+ def printInfo(self):
+ print(self.name + ": A StimulusDummy object")
+
+ def runGenerator(self, time):
+ print("[runGenerator] " + self.name + ": Sending out the stimulus")
+ return Stimulus.runGenerator(self, time)
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From: <rg...@us...> - 2009-08-03 11:39:16
|
Revision: 62
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=62&view=rev
Author: rgoj
Date: 2009-08-03 11:39:06 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Adding a Stimulus object to the first dummy example simulation in PyBrainSim.py
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 11:37:53 UTC (rev 61)
+++ trunk/src/PyBrainSim.py 2009-08-03 11:39:06 UTC (rev 62)
@@ -29,14 +29,13 @@
from Head import Head
from Experiment import Experiment
+from Stimulus import Stimulus
from GeneratorDummy import GeneratorDummy
from GeneratorNumberIncrementing import GeneratorNumberIncrementing
from Connection import Connection
from ConnectionDummy import ConnectionDummy
#from GeneratorSine import GeneratorSine
-#from GeneratorStimulusActivationZeroing import GeneratorStimulusActivationZeroing
-#from GeneratorStimulusPhaseReset import GeneratorStimulusPhaseReset
welcomeMessage = "\n\
Welcome to this early version of PyBrainSim\n\n\
@@ -54,9 +53,9 @@
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
- exampleGenerator1 = GeneratorDummy('Gen1', exampleHead)
- exampleGenerator2 = GeneratorDummy('Gen2', exampleHead)
- exampleConnection = ConnectionDummy('Con', exampleHead, exampleGenerator1, exampleGenerator2)
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleGenerator = GeneratorDummy('Gen', exampleHead)
+ exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
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From: <rg...@us...> - 2009-08-03 11:38:02
|
Revision: 61
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=61&view=rev
Author: rgoj
Date: 2009-08-03 11:37:53 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Making Stimulus look more like a generator - running the Generator's init method in the Stimulus init method.
Modified Paths:
--------------
trunk/src/Stimulus.py
Modified: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py 2009-08-03 11:27:10 UTC (rev 60)
+++ trunk/src/Stimulus.py 2009-08-03 11:37:53 UTC (rev 61)
@@ -25,9 +25,13 @@
from Generator import Generator
class Stimulus(Generator):
- def __init__(self):
- self.activation = None
+ def __init__(self, name, head):
+ Generator.__init__(self, name, head)
self.stimulusTimes = []
+ self.currentStimulus = 0
+
+ def printInfo(self):
+ print(self.name + ": A Stimulus object")
def setStimulusTimes(self, stimulusTimes):
self.stimulusTimes = stimulusTimes
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From: <rg...@us...> - 2009-08-03 11:27:19
|
Revision: 60
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=60&view=rev
Author: rgoj
Date: 2009-08-03 11:27:10 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* No need for a separate call to addConnection, removing it, because it is now implemented in the init method of the Connection class.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 11:24:07 UTC (rev 59)
+++ trunk/src/PyBrainSim.py 2009-08-03 11:27:10 UTC (rev 60)
@@ -56,9 +56,7 @@
exampleGenerator1 = GeneratorDummy('Gen1', exampleHead)
exampleGenerator2 = GeneratorDummy('Gen2', exampleHead)
-
- exampleConnection = ConnectionDummy('Con', exampleGenerator1, exampleGenerator2)
- exampleHead.addConnection(exampleConnection)
+ exampleConnection = ConnectionDummy('Con', exampleHead, exampleGenerator1, exampleGenerator2)
exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
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From: <rg...@us...> - 2009-08-03 11:24:14
|
Revision: 59
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=59&view=rev
Author: rgoj
Date: 2009-08-03 11:24:07 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* The init method of the Connection class now adds itself to the specified Head object.
Modified Paths:
--------------
trunk/src/Connection.py
Modified: trunk/src/Connection.py
===================================================================
--- trunk/src/Connection.py 2009-08-03 11:21:36 UTC (rev 58)
+++ trunk/src/Connection.py 2009-08-03 11:24:07 UTC (rev 59)
@@ -27,10 +27,11 @@
"""
class Connection:
- def __init__(self, name, sourceGenerator, targetGenerator):
+ def __init__(self, name, head, sourceGenerator, targetGenerator):
self.name = name
self.sourceGenerator = sourceGenerator
self.targetGenerator = targetGenerator
+ head.addConnection(self)
def printInfo(self):
print(self.name + " A Connection object")
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From: <rg...@us...> - 2009-08-03 11:21:42
|
Revision: 58
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=58&view=rev
Author: rgoj
Date: 2009-08-03 11:21:36 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Generators are now added to the Head object during generator initialization, no need for a separate call to Head.addGenerator(generator)
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 11:20:21 UTC (rev 57)
+++ trunk/src/PyBrainSim.py 2009-08-03 11:21:36 UTC (rev 58)
@@ -54,10 +54,8 @@
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
- exampleGenerator1 = GeneratorDummy('Gen1')
- exampleGenerator2 = GeneratorDummy('Gen2')
- exampleHead.addGenerator(exampleGenerator1)
- exampleHead.addGenerator(exampleGenerator2)
+ exampleGenerator1 = GeneratorDummy('Gen1', exampleHead)
+ exampleGenerator2 = GeneratorDummy('Gen2', exampleHead)
exampleConnection = ConnectionDummy('Con', exampleGenerator1, exampleGenerator2)
exampleHead.addConnection(exampleConnection)
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From: <rg...@us...> - 2009-08-03 11:14:23
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Revision: 56
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=56&view=rev
Author: rgoj
Date: 2009-08-03 11:14:11 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Only existing, rechecked and correct imports are left, the rest is commented out during refactoring.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 11:06:58 UTC (rev 55)
+++ trunk/src/PyBrainSim.py 2009-08-03 11:14:11 UTC (rev 56)
@@ -30,11 +30,13 @@
from Experiment import Experiment
from GeneratorDummy import GeneratorDummy
+from GeneratorNumberIncrementing import GeneratorNumberIncrementing
+from Connection import Connection
from ConnectionDummy import ConnectionDummy
-from GeneratorSine import GeneratorSine
-from GeneratorStimulusActivationZeroing import GeneratorStimulusActivationZeroing
-from GeneratorStimulusPhaseReset import GeneratorStimulusPhaseReset
+#from GeneratorSine import GeneratorSine
+#from GeneratorStimulusActivationZeroing import GeneratorStimulusActivationZeroing
+#from GeneratorStimulusPhaseReset import GeneratorStimulusPhaseReset
welcomeMessage = "\n\
Welcome to this early version of PyBrainSim\n\n\
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From: <rg...@us...> - 2009-08-03 11:07:08
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Revision: 55
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=55&view=rev
Author: rgoj
Date: 2009-08-03 11:06:58 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* GeneratorNumberIncrementing now reacts to input 'Stimulus' from a Stimulus class object by zeroing it's activation, making instantaneous zeroing of activation possible.
Modified Paths:
--------------
trunk/src/GeneratorNumberIncrementing.py
Modified: trunk/src/GeneratorNumberIncrementing.py
===================================================================
--- trunk/src/GeneratorNumberIncrementing.py 2009-08-03 10:56:16 UTC (rev 54)
+++ trunk/src/GeneratorNumberIncrementing.py 2009-08-03 11:06:58 UTC (rev 55)
@@ -23,14 +23,14 @@
"""
class GeneratorNumberIncrementing:
- def __init__(self):
- self.activation = 0
+ def printInfo(self):
+ print(self.name + ": A GeneratorNumberIncrementing object")
- def sendOutput(self):
- return self.activation
-
def receiveInput(self, input):
- self.activation += input
+ if activation == 'Stimulus':
+ self.activation = 0
+ else:
+ self.activation += input
def runGenerator(self, time):
self.activation = self.activation + 1
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From: <rg...@us...> - 2009-08-03 10:56:23
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Revision: 54
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=54&view=rev
Author: rgoj
Date: 2009-08-03 10:56:16 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Prepared a better documentation comment
* Corrected column width of comments
Modified Paths:
--------------
trunk/src/GeneratorNumberIncrementing.py
Modified: trunk/src/GeneratorNumberIncrementing.py
===================================================================
--- trunk/src/GeneratorNumberIncrementing.py 2009-08-03 10:46:29 UTC (rev 53)
+++ trunk/src/GeneratorNumberIncrementing.py 2009-08-03 10:56:16 UTC (rev 54)
@@ -1,25 +1,25 @@
-# PyBrainSim
-# Copyright 2009 Roman Goj
+# PyBrainSim Copyright 2009 Roman Goj
#
# This file is part of PyBrainSim.
#
-# PyBrainSim is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# PyBrainSim is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
#
-# PyBrainSim is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
+# PyBrainSim is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
-# You should have received a copy of the GNU General Public License
-# along with PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU General Public License along with
+# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
__metaclass__ = type # New style classes. Is this necessary?
"""
-The GeneratorNumberIncrementing class serves as a starting point for creating complex classes simulation populations of neurons. Although currently all it does is adding integers.
+The GeneratorNumberIncrementing class is a reimplementation of the Generator
+class. It provides an elementary example of how the methods could be used to do
+integer addition.
"""
class GeneratorNumberIncrementing:
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From: <rg...@us...> - 2009-08-03 10:46:50
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Revision: 53
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=53&view=rev
Author: rgoj
Date: 2009-08-03 10:46:29 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* One empty line too many.
Modified Paths:
--------------
trunk/src/Stimulus.py
Modified: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py 2009-08-03 10:42:32 UTC (rev 52)
+++ trunk/src/Stimulus.py 2009-08-03 10:46:29 UTC (rev 53)
@@ -43,6 +43,5 @@
else:
self.activation = None
-
# The runGenerator method must return a value
return 0
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From: <rg...@us...> - 2009-08-03 10:42:40
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Revision: 52
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=52&view=rev
Author: rgoj
Date: 2009-08-03 10:42:32 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Removing the obsolete class GeneratorStimulusPhaseReset.
Removed Paths:
-------------
trunk/src/GeneratorStimulusPhaseReset.py
Deleted: trunk/src/GeneratorStimulusPhaseReset.py
===================================================================
--- trunk/src/GeneratorStimulusPhaseReset.py 2009-08-03 10:41:45 UTC (rev 51)
+++ trunk/src/GeneratorStimulusPhaseReset.py 2009-08-03 10:42:32 UTC (rev 52)
@@ -1,49 +0,0 @@
-# PyBrainSim
-# Copyright 2009 Roman Goj
-#
-# This file is part of PyBrainSim.
-#
-# PyBrainSim is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# PyBrainSim is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
-
-__metaclass__ = type # New style classes. Is this necessary?
-
-"""
-"""
-
-from GeneratorDummy import GeneratorDummy
-
-class GeneratorStimulusPhaseReset(GeneratorDummy):
- def __init__(self):
- self.activation = 0
- self.connectedGeneratorPhase = 0
- self.stimulusTimes = []
- self.currentStimulus = 0
-
- def setStimulusTimes(self, stimulusTimes):
- self.stimulusTimes = stimulusTimes
-
- def receiveInput(self, input):
- self.connectedGeneratorPhase = input
- print("Received input: " + str(self.connectedGeneratorPhase))
-
- def runGenerator(self, time):
- if self.currentStimulus < len(self.stimulusTimes):
- if self.stimulusTimes[self.currentStimulus] < time:
- print("Stimulus now: BEEEEEEEP! ... Time is: " + str(time) + ", Stimulus list is: " + str(self.stimulusTimes) + " Connected generator phase should have been: " + str(self.connectedGeneratorPhase))
- self.activation = -self.connectedGeneratorPhase
- self.currentStimulus += 1
- else:
- self.activation = 0
-
- return 0
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From: <rg...@us...> - 2009-08-03 10:41:54
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Revision: 51
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=51&view=rev
Author: rgoj
Date: 2009-08-03 10:41:45 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* The Stimulus class now also implements stimulusTimes from the phase resetting stimulus class, which will now be removed.
Modified Paths:
--------------
trunk/src/Stimulus.py
Modified: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py 2009-08-03 10:32:34 UTC (rev 50)
+++ trunk/src/Stimulus.py 2009-08-03 10:41:45 UTC (rev 51)
@@ -27,15 +27,22 @@
class Stimulus(Generator):
def __init__(self):
self.activation = None
- self.counter = 0
+ self.stimulusTimes = []
+
+ def setStimulusTimes(self, stimulusTimes):
+ self.stimulusTimes = stimulusTimes
def runGenerator(self, time):
- if self.counter == 5:
- self.activation = 'Stimulus'
- self.counter = 0
- else:
- self.activation = None
- self.counter += 1
+ if self.currentStimulus < len(self.stimulusTimes):
+ if self.stimulusTimes[self.currentStimulus] < time:
+ print("Stimulus now: BEEEEEEEP! ... Time is: " + str(time) + ", Stimulus list is: " + str(self.stimulusTimes) + " Connected generator phase should have been: " + str(self.connectedGeneratorPhase))
+
+ self.currentStimulus += 1
+
+ self.activation = 'Stimulus'
+ else:
+ self.activation = None
+
# The runGenerator method must return a value
return 0
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From: <rg...@us...> - 2009-08-03 10:32:46
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Revision: 50
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=50&view=rev
Author: rgoj
Date: 2009-08-03 10:32:34 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Adding a new stimulus class which should be used from now on for any Stimulus reimplementation.
Added Paths:
-----------
trunk/src/Stimulus.py
Added: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py (rev 0)
+++ trunk/src/Stimulus.py 2009-08-03 10:32:34 UTC (rev 50)
@@ -0,0 +1,41 @@
+# PyBrainSim Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# PyBrainSim is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
+
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+The Stimulus class is a child class of the Generatorc lass. It reimplements the
+runGenerator method, so that a stimulus can be periodically sent to all
+connected generators.
+"""
+
+from Generator import Generator
+
+class Stimulus(Generator):
+ def __init__(self):
+ self.activation = None
+ self.counter = 0
+
+ def runGenerator(self, time):
+ if self.counter == 5:
+ self.activation = 'Stimulus'
+ self.counter = 0
+ else:
+ self.activation = None
+ self.counter += 1
+
+ # The runGenerator method must return a value
+ return 0
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From: <rg...@us...> - 2009-08-03 10:31:24
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Revision: 49
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=49&view=rev
Author: rgoj
Date: 2009-08-03 10:31:15 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Removing old stimulus class, which won't be used any more.
Removed Paths:
-------------
trunk/src/GeneratorStimulusActivationZeroing.py
Deleted: trunk/src/GeneratorStimulusActivationZeroing.py
===================================================================
--- trunk/src/GeneratorStimulusActivationZeroing.py 2009-08-03 10:20:38 UTC (rev 48)
+++ trunk/src/GeneratorStimulusActivationZeroing.py 2009-08-03 10:31:15 UTC (rev 49)
@@ -1,46 +0,0 @@
-# PyBrainSim
-# Copyright 2009 Roman Goj
-#
-# This file is part of PyBrainSim.
-#
-# PyBrainSim is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# PyBrainSim is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
-
-__metaclass__ = type # New style classes. Is this necessary?
-
-"""
-The GeneratorStimulusActivationZeroing class is a child class of the Generator class. It reimplements the runGenerator method, so that a stimulus can be periodically sent to all connected generators.
-
-Currently the GeneratorStimulusActivationZeroing class only keeps a counter to remember the number of times it was called.
-"""
-
-from GeneratorDummy import GeneratorDummy
-
-class GeneratorStimulusActivationZeroing(GeneratorDummy):
- def __init__(self):
- self.activation = 0
- self.connectedGeneratorOutput = 0
- self.counter = 0
-
- def receiveInput(self, input):
- self.connectedGeneratorOutput = input
-
- def runGenerator(self, time):
- if self.counter == 10:
- self.activation = -self.connectedGeneratorOutput
- self.counter = 0
- else:
- self.activation = 0
- self.counter += 1
-
- return 0 # This is necessary, because the activation of this function is added to the recording in Head.py
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