pybrainsim-activity Mailing List for PyBrainSim - The Brain Phantom Project (Page 5)
Status: Planning
Brought to you by:
rgoj
Menu
▾
▴
pybrainsim-activity — PyBrainSim commit, issue tracking and other activities mailing list
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(123) |
Aug
(114) |
Sep
(44) |
Oct
|
Nov
|
Dec
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(9) |
Jul
|
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-06 11:52:48
|
#52: Display stimuli on the plot of ongoing activity as a way of visualizing
stimuli/epoch lengths
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/52#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 13:05:13
|
#44: Make the Recording class produce an ERP out of ongoing simulated activity
and information about stimuli
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Simulations | Resolution: fixed
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/44#comment:3>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-05 13:03:19
|
Revision: 88
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=88&view=rev
Author: rgoj
Date: 2009-08-05 13:03:11 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Calculating epoch time points
* Added a commented out line that allows plotting of an ERP signal instead of the continous signal
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-05 13:01:36 UTC (rev 87)
+++ trunk/src/Experiment.py 2009-08-05 13:03:11 UTC (rev 88)
@@ -35,7 +35,10 @@
self.baseline = baseline
self.epochDuration = epochDuration
- self.timePoints = list(arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency ))
+ timeStep = 1.0/self.samplingFrequency
+ self.timePoints = list(arange( timeStep, self.duration + timeStep, timeStep ))
+ epochStartTime = - timeStep * (self.baseline // timeStep)
+ self.epochTimePoints = list(arange( epochStartTime, self.epochDuration + epochStartTime, timeStep))
def setSamplingFrequency(self, samplingFrequency):
self.samplingFrequency = samplingFrequency
@@ -76,7 +79,6 @@
def getRecordingSlice(self, sliceStart, sliceDuration, sliceChannel=0):
startIndex = self.findNearestTimeIndex(sliceStart)
endIndex = self.findNearestTimeIndex(sliceStart + sliceDuration)
- #print str(startIndex) + " " + str(endIndex)
return self.recording[sliceChannel][startIndex:endIndex]
def getERP(self, stimulusNumber=0):
@@ -94,6 +96,7 @@
def plotRecording(self):
plot(self.timePoints, self.recording[0], linewidth=1.0)
+ #plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
xlabel('Time (s)')
ylabel('Amplitude')
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-05 13:01:49
|
Revision: 87
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=87&view=rev
Author: rgoj
Date: 2009-08-05 13:01:36 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Added more stimulus times for fourth example simulation
* In example 3 and 4 the simulation is now correctly run with the duration specified in the Experiment class object
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-05 11:59:20 UTC (rev 86)
+++ trunk/src/PyBrainSim.py 2009-08-05 13:01:36 UTC (rev 87)
@@ -91,7 +91,7 @@
exampleConnection1 = Connection('Con1', exampleHead, exampleStimulus1, exampleGenerator1)
exampleConnection2 = Connection('Con2', exampleHead, exampleStimulus2, exampleGenerator2)
- exampleExperiment.setRecording(exampleHead.runSimulation())
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
elif userChoice == 4:
@@ -99,8 +99,8 @@
exampleHead.setSamplingFrequency(128)
exampleHead.addRegistrationSite([0, 0, 0])
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
- exampleExperiment.setStimulusTimes([[0.3, 0.6]])
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 10.0)
+ exampleExperiment.setStimulusTimes([[0.3, 1.75, 2.16, 3.87, 4.31, 5.183, 6.34, 7.13]])
exampleStimulus = Stimulus('Stim', exampleHead)
print exampleExperiment.getStimulusTimes()[0]
@@ -108,7 +108,7 @@
exampleGenerator = GeneratorSine('Gen', exampleHead)
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
- exampleExperiment.setRecording(exampleHead.runSimulation())
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
exampleExperiment.plotRecording()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-05 11:59:32
|
Revision: 86
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=86&view=rev
Author: rgoj
Date: 2009-08-05 11:59:20 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Changes to Experiment class:
** timePoints is now a member of the class
** added baseline and epochDuration as members
** added the findNearestTimeIndex method
** added the getRecordingSlice method
** added the getERP method
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-05 11:54:07 UTC (rev 85)
+++ trunk/src/Experiment.py 2009-08-05 11:59:20 UTC (rev 86)
@@ -27,12 +27,16 @@
from pylab import *
class Experiment:
- def __init__(self, samplingFrequency = 128, duration = 1, recording = [], stimulusTimes = []):
+ def __init__(self, samplingFrequency = 128, duration = 1, recording = [], stimulusTimes = [], baseline = 0.1, epochDuration = 0.3):
self.samplingFrequency = samplingFrequency
self.duration = duration
self.recording = recording
self.stimulusTimes = stimulusTimes
+ self.baseline = baseline
+ self.epochDuration = epochDuration
+ self.timePoints = list(arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency ))
+
def setSamplingFrequency(self, samplingFrequency):
self.samplingFrequency = samplingFrequency
@@ -52,14 +56,44 @@
return self.recording
def setStimulusTimes(self, stimulusTimes):
+ #TODO: If dimension of stimulusTimes is 1... it needs to be two :/
self.stimulusTimes = stimulusTimes
def getStimulusTimes(self):
return self.stimulusTimes
+ def findNearestTimeIndex(self, timePoint):
+ """ Returns the index of the closest time point within timePoints that
+ is smaller than the given value timePoint"""
+ if timePoint in self.timePoints:
+ return self.timePoints.index(timePoint)
+ else:
+ for i in range(len(self.timePoints)):
+ if timePoint < self.timePoints[i]:
+ if timePoint > self.timePoints[i-1]:
+ return i-1
+
+ def getRecordingSlice(self, sliceStart, sliceDuration, sliceChannel=0):
+ startIndex = self.findNearestTimeIndex(sliceStart)
+ endIndex = self.findNearestTimeIndex(sliceStart + sliceDuration)
+ #print str(startIndex) + " " + str(endIndex)
+ return self.recording[sliceChannel][startIndex:endIndex]
+
+ def getERP(self, stimulusNumber=0):
+ stimuli = self.stimulusTimes[stimulusNumber]
+ epochs = []
+ for i in range(len(stimuli)):
+ epochs.append(self.getRecordingSlice(stimuli[i] - self.baseline, self.epochDuration))
+
+ average = list(zeros(len(epochs[0])))
+ for i in range(len(epochs)):
+ for j in range(len(epochs[i])):
+ average[j] += epochs[i][j]
+
+ return average
+
def plotRecording(self):
- timePoints = arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency )
- plot(timePoints, self.recording[0], linewidth=1.0)
+ plot(self.timePoints, self.recording[0], linewidth=1.0)
xlabel('Time (s)')
ylabel('Amplitude')
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-05 11:54:15
|
Revision: 85
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=85&view=rev
Author: rgoj
Date: 2009-08-05 11:54:07 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* The fourth example now also uses the Experiment class to set the stimulus times
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-05 10:23:11 UTC (rev 84)
+++ trunk/src/PyBrainSim.py 2009-08-05 11:54:07 UTC (rev 85)
@@ -98,13 +98,17 @@
exampleHead = Head()
exampleHead.setSamplingFrequency(128)
exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
+ exampleExperiment.setStimulusTimes([[0.3, 0.6]])
exampleStimulus = Stimulus('Stim', exampleHead)
- exampleStimulus.setStimulusTimes([0.3, 0.6])
+ print exampleExperiment.getStimulusTimes()[0]
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
exampleGenerator = GeneratorSine('Gen', exampleHead)
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ exampleExperiment.setRecording(exampleHead.runSimulation())
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
exampleExperiment.plotRecording()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 10:25:20
|
#44: Make the Recording class produce an ERP out of ongoing simulated activity
and information about stimuli
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: new
Priority: major | Milestone: Activity plots
Component: Simulations | Keywords:
-------------------------+--------------------------------------------------
Changes (by rgoj):
* milestone: Modelling phase resetting => Activity plots
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/44#comment:2>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 10:23:52
|
#51: Enable the user to choose the scale of the plots
-----------------------+----------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Interface | Resolution: fixed
Keywords: |
-----------------------+----------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/51#comment:2>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 10:23:20
|
#50: Write a scrolling activity viewer
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/50#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-05 10:23:17
|
Revision: 84
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=84&view=rev
Author: rgoj
Date: 2009-08-05 10:23:11 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* The plotRecording function now plots the first channel of the recording
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-05 10:06:51 UTC (rev 83)
+++ trunk/src/Experiment.py 2009-08-05 10:23:11 UTC (rev 84)
@@ -58,13 +58,11 @@
return self.stimulusTimes
def plotRecording(self):
- t = arange( 0.0, 2.0, 0.01 )
- #t = arange( 1.0/128, 1.0 + 1.0/128, 1.0/128 )
- s = sin(2*pi*t)
- plot(t, s, linewidth=1.0)
+ timePoints = arange( 1.0/self.samplingFrequency, self.duration + 1.0/self.samplingFrequency, 1.0/self.samplingFrequency )
+ plot(timePoints, self.recording[0], linewidth=1.0)
- xlabel('time (s)')
- ylabel('voltage (mV)')
+ xlabel('Time (s)')
+ ylabel('Amplitude')
title('Simulated EEG recording')
grid(True)
show()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 10:22:18
|
#49: Write a function that would take care of displaying a simple plot
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/49#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-05 10:06:59
|
Revision: 83
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=83&view=rev
Author: rgoj
Date: 2009-08-05 10:06:51 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* All examples in PyBrainSim.py updated to use the new Experiment class
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-05 10:03:30 UTC (rev 82)
+++ trunk/src/PyBrainSim.py 2009-08-05 10:06:51 UTC (rev 83)
@@ -57,7 +57,7 @@
exampleGenerator = GeneratorDummy('Gen', exampleHead)
exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
- exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
print("\nSimulations resulted in the following recording:")
print(exampleExperiment.getRecording())
elif userChoice == 2:
@@ -70,7 +70,7 @@
exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
- exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
elif userChoice == 3:
@@ -78,7 +78,7 @@
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
- exampleExperiment = Experiment()
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
exampleStimulus1 = Stimulus('Stim1', exampleHead)
@@ -91,7 +91,7 @@
exampleConnection1 = Connection('Con1', exampleHead, exampleStimulus1, exampleGenerator1)
exampleConnection2 = Connection('Con2', exampleHead, exampleStimulus2, exampleGenerator2)
- exampleExperiment.setRecording(exampleHead.runSimulation( 1 ))
+ exampleExperiment.setRecording(exampleHead.runSimulation())
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
elif userChoice == 4:
@@ -107,7 +107,6 @@
exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
-
exampleExperiment.plotRecording()
else:
print("No such option unfortunately...")
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-05 10:03:39
|
Revision: 82
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=82&view=rev
Author: rgoj
Date: 2009-08-05 10:03:30 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* added getSamplingFrequency()
* removed an outdated comment
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-05 10:02:26 UTC (rev 81)
+++ trunk/src/Head.py 2009-08-05 10:03:30 UTC (rev 82)
@@ -36,9 +36,10 @@
def setSamplingFrequency(self, samplingFrequency):
self.samplingFrequency = samplingFrequency
+ def getSamplingFrequency(self):
+ return self.samplingFrequency
+
def addGenerator(self, generator):
- # TODO: We must check for equal generator names - two identical names
- # can't currently be allowed to happen!
self.generatorList.append(generator)
self.generatorSiteList.append([0, 0, 0])
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-05 10:02:36
|
Revision: 81
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=81&view=rev
Author: rgoj
Date: 2009-08-05 10:02:26 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Experiment class now has duration and samplingFrequency parameters
* Experiment class now holds a method for plotting the recording... which for now holds the matplotlib example of plotting a sinusoid, to be used for plotting the real recording soon.
* The fourth example in PyBrainSim is updated to use the updated Experiment class
Modified Paths:
--------------
trunk/src/Experiment.py
trunk/src/PyBrainSim.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-05 07:14:20 UTC (rev 80)
+++ trunk/src/Experiment.py 2009-08-05 10:02:26 UTC (rev 81)
@@ -24,11 +24,27 @@
interface to Neuroscan, e.g. by providing an export to .cnt files feature.
"""
+from pylab import *
+
class Experiment:
- def __init__(self, recording = [], stimulusTimes = []):
+ def __init__(self, samplingFrequency = 128, duration = 1, recording = [], stimulusTimes = []):
+ self.samplingFrequency = samplingFrequency
+ self.duration = duration
self.recording = recording
self.stimulusTimes = stimulusTimes
+ def setSamplingFrequency(self, samplingFrequency):
+ self.samplingFrequency = samplingFrequency
+
+ def getSamplingFrequency(self):
+ return self.samplingFrequency
+
+ def setDuration(self, duration):
+ self.duration = duration
+
+ def getDuration(self):
+ return self.duration
+
def setRecording(self, recording):
self.recording = recording
@@ -38,9 +54,17 @@
def setStimulusTimes(self, stimulusTimes):
self.stimulusTimes = stimulusTimes
- def addStimulusTime(self, stimulusTime):
- self.stimulusTimes.append(stimulusTime)
- self.stimulusTimes.sort()
-
def getStimulusTimes(self):
return self.stimulusTimes
+
+ def plotRecording(self):
+ t = arange( 0.0, 2.0, 0.01 )
+ #t = arange( 1.0/128, 1.0 + 1.0/128, 1.0/128 )
+ s = sin(2*pi*t)
+ plot(t, s, linewidth=1.0)
+
+ xlabel('time (s)')
+ ylabel('voltage (mV)')
+ title('Simulated EEG recording')
+ grid(True)
+ show()
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-05 07:14:20 UTC (rev 80)
+++ trunk/src/PyBrainSim.py 2009-08-05 10:02:26 UTC (rev 81)
@@ -104,8 +104,10 @@
exampleGenerator = GeneratorSine('Gen', exampleHead)
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
- exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
+
+ exampleExperiment.plotRecording()
else:
print("No such option unfortunately...")
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 09:01:44
|
#48: Decide on a library that could be used to produce the desired plots
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Activity plots
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
Comment:
This will of course have to be matplotlib - which seems to be the standard
for Python scientific computing, when it comes to plotting 2D figures...
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/48#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 08:50:41
|
#100: The Experiment class should allow for different stimulus times for
different stimuli objects
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Modelling phase resetting
Component: Simulations | Resolution: fixed
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/100#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-05 07:14:27
|
Revision: 80
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=80&view=rev
Author: rgoj
Date: 2009-08-05 07:14:20 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Example 3 now also shows how the Experiment class can be used to keep track of stimulus times for two separate stimulus objects. This is more of a hack for now, but should take more shape later.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-05 06:58:57 UTC (rev 79)
+++ trunk/src/PyBrainSim.py 2009-08-05 07:14:20 UTC (rev 80)
@@ -78,16 +78,20 @@
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
+ exampleExperiment = Experiment()
+ exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
+
exampleStimulus1 = Stimulus('Stim1', exampleHead)
exampleStimulus2 = Stimulus('Stim2', exampleHead)
- exampleStimulus1.setStimulusTimes([0.3, 0.6])
- exampleStimulus2.setStimulusTimes([0.5])
+ exampleStimulus1.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ exampleStimulus2.setStimulusTimes(exampleExperiment.getStimulusTimes()[1])
+
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 ))
+ exampleExperiment.setRecording(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
elif userChoice == 4:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-08-05 06:59:36
|
#39: Write a simple phase-resetting stimulus for the sinusoidal generator
--------------------+-------------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Modelling phase resetting
Component: Design | Resolution: fixed
Keywords: |
--------------------+-------------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/39#comment:1>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-05 06:59:09
|
Revision: 79
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=79&view=rev
Author: rgoj
Date: 2009-08-05 06:58:57 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
* Reworking GeneratorSine:
** added printInfo method
** corrected the receiveInput method
** the runGenerator method is now much cleaner
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-03 18:36:14 UTC (rev 78)
+++ trunk/src/GeneratorSine.py 2009-08-05 06:58:57 UTC (rev 79)
@@ -23,28 +23,29 @@
stimulus.
"""
-import math
+from math import pi
+from math import sin
+
from Generator import Generator
class GeneratorSine(Generator):
def __init__(self, name, head, frequency = 2, phaseShift = 0):
Generator.__init__(self, name, head)
self.frequency = frequency
- self.phaseShift = phaseShift
+ self.currentPhase = phaseShift
+ self.lastTimePoint = 0
+
+ def printInfo(self):
+ print(self.name + ": A GeneratorSine object")
def receiveInput(self, input):
if input == 'Stimulus':
- self.phaseShift = -self.activation
- else:
- self.activation += input
+ self.currentPhase = 0
def runGenerator(self, time):
-# self.phase = (2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) \
-# % (2 * math.pi / self.frequency) / (2 * math.pi)
- self.phase = ((2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) \
- % (2 * math.pi)) / (2 * math.pi)
-# self.activation += math.sin(self.phase * 2 * math.pi)
- self.activation = math.sin(self.phase * 2 * math.pi)
- print("Output is now: " + str(self.activation))
-
+ timeStep = time - self.lastTimePoint
+ self.lastTimePoint = time
+ self.currentPhase += self.frequency * timeStep
+ self.activation = sin(self.currentPhase * 2 * pi)
+
return self.activation
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 18:36:27
|
Revision: 78
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=78&view=rev
Author: rgoj
Date: 2009-08-03 18:36:14 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Corrected mistake: __init__ must be also called with the head argument
* Corrected mistake: the phase of the sine is now correctly calculated
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-03 18:14:42 UTC (rev 77)
+++ trunk/src/GeneratorSine.py 2009-08-03 18:36:14 UTC (rev 78)
@@ -27,8 +27,8 @@
from Generator import Generator
class GeneratorSine(Generator):
- def __init__(self, name, frequency = 2, phaseShift = 0):
- Generator.__init__(self, name)
+ def __init__(self, name, head, frequency = 2, phaseShift = 0):
+ Generator.__init__(self, name, head)
self.frequency = frequency
self.phaseShift = phaseShift
@@ -39,6 +39,12 @@
self.activation += input
def runGenerator(self, time):
- self.phase = (2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) % (2 * math.pi / self.frequency) / (2 * math.pi)
- print("Phase is now: " + str(self.phase))
- return math.sin(self.phase * 2 * math.pi)
+# self.phase = (2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) \
+# % (2 * math.pi / self.frequency) / (2 * math.pi)
+ self.phase = ((2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) \
+ % (2 * math.pi)) / (2 * math.pi)
+# self.activation += math.sin(self.phase * 2 * math.pi)
+ self.activation = math.sin(self.phase * 2 * math.pi)
+ print("Output is now: " + str(self.activation))
+
+ return self.activation
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 18:14:49
|
Revision: 77
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=77&view=rev
Author: rgoj
Date: 2009-08-03 18:14:42 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Removed the obsolete sendOutput() method
* Wrote a proper receiveInput() method, so that a stimulus will reset the phase of the generated sine
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-03 18:10:19 UTC (rev 76)
+++ trunk/src/GeneratorSine.py 2009-08-03 18:14:42 UTC (rev 77)
@@ -32,12 +32,11 @@
self.frequency = frequency
self.phaseShift = phaseShift
- def sendOutput(self):
- print("Sending output: " + str(self.phase))
- return self.phase
-
- def receiveInput(self, newPhaseShift):
- self.phaseShift = newPhaseShift
+ def receiveInput(self, input):
+ if input == 'Stimulus':
+ self.phaseShift = -self.activation
+ else:
+ self.activation += input
def runGenerator(self, time):
self.phase = (2 * math.pi * self.frequency * time + 2 * math.pi * self.phaseShift) % (2 * math.pi / self.frequency) / (2 * math.pi)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 18:10:27
|
Revision: 76
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=76&view=rev
Author: rgoj
Date: 2009-08-03 18:10:19 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Made a better __init__ method, invoking the parent class
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-03 18:07:46 UTC (rev 75)
+++ trunk/src/GeneratorSine.py 2009-08-03 18:10:19 UTC (rev 76)
@@ -24,12 +24,12 @@
"""
import math
+from Generator import Generator
-class GeneratorSine:
- def __init__(self, frequency = 1, phaseShift = 0):
- self.activation = 0
+class GeneratorSine(Generator):
+ def __init__(self, name, frequency = 2, phaseShift = 0):
+ Generator.__init__(self, name)
self.frequency = frequency
- self.phase = phaseShift
self.phaseShift = phaseShift
def sendOutput(self):
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 18:07:55
|
Revision: 75
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=75&view=rev
Author: rgoj
Date: 2009-08-03 18:07:46 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Proper column width of license and beginning commentary
Modified Paths:
--------------
trunk/src/GeneratorSine.py
trunk/src/PyBrainSim.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-03 17:57:45 UTC (rev 74)
+++ trunk/src/GeneratorSine.py 2009-08-03 18:07:46 UTC (rev 75)
@@ -3,23 +3,24 @@
#
# 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 GeneratorSine class is an example generator that simply generates a single sine.
+The GeneratorSine class is a reimplementation of the Generator class. It
+provides a sine generator and allows the phase of the sine to be zeroed by a
+stimulus.
"""
import math
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-03 17:57:45 UTC (rev 74)
+++ trunk/src/PyBrainSim.py 2009-08-03 18:07:46 UTC (rev 75)
@@ -28,16 +28,14 @@
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 GeneratorSine import GeneratorSine
from Connection import Connection
from ConnectionDummy import ConnectionDummy
-#from GeneratorSine import GeneratorSine
-
welcomeMessage = "\n\
Welcome to this early version of PyBrainSim\n\n\
Choose the type of simulation you would like to perform:\n\
@@ -92,27 +90,18 @@
exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
-#elif userChoice == 2:
-# exampleExperiment = Experiment()
-# exampleExperiment.addStimulusTime( 0.2341 )
-#
-# exampleHead = Head()
-# exampleHead.setSamplingFrequency( 10 )
-# exampleHead.addRegistrationSite([0, 0, 0])
-#
-# exampleGenerator1 = GeneratorSine()
-# exampleHead.addGenerator(exampleGenerator1)
-#
-# exampleStimulus = GeneratorStimulusPhaseReset()
-# exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes())
-# exampleHead.addGenerator(exampleStimulus)
-#
-# exampleStimulusToGeneratorConnection = ConnectionSimple(exampleStimulus, exampleGenerator1)
-# exampleGeneratorToStimulusConnection = ConnectionSimple(exampleGenerator1, exampleStimulus)
-# exampleHead.addConnection(exampleGeneratorToStimulusConnection)
-# exampleHead.addConnection(exampleStimulusToGeneratorConnection)
-#
-# exampleExperiment.setRecording(exampleHead.runSimulation( 1.1 ))
-# print exampleExperiment.getRecording()
+elif userChoice == 4:
+ exampleHead = Head()
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes([0.3, 0.6])
+ exampleGenerator = GeneratorSine('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.runSimulation( 1 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
else:
print("No such option unfortunately...")
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 17:57:52
|
Revision: 74
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=74&view=rev
Author: rgoj
Date: 2009-08-03 17:57:45 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Removing the no longer needed methods:
** getSourceName()
** getTargetName()
* Instead it is now possible to run Connection.getSource().getName()
Modified Paths:
--------------
trunk/src/Connection.py
Modified: trunk/src/Connection.py
===================================================================
--- trunk/src/Connection.py 2009-08-03 17:56:27 UTC (rev 73)
+++ trunk/src/Connection.py 2009-08-03 17:57:45 UTC (rev 74)
@@ -45,11 +45,5 @@
def getTarget(self):
return self.targetGenerator
- def getSourceName(self):
- return self.sourceGenerator.getName()
-
- def getTargetName(self):
- return self.targetGenerator.getName()
-
def runConnection(self, sourceGeneratorOutput):
self.targetGenerator.receiveInput(sourceGeneratorOutput)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-08-03 17:56:35
|
Revision: 73
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=73&view=rev
Author: rgoj
Date: 2009-08-03 17:56:27 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
* Prepared a new method for checking which generator's output must a connection recieve in the runSimulation method, using the new getSource() method in the Connection class
* Removed the old method
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-03 17:31:21 UTC (rev 72)
+++ trunk/src/Head.py 2009-08-03 17:56:27 UTC (rev 73)
@@ -96,26 +96,11 @@
# Sending the output of generators through connections
for i in range(len(self.connectionList)):
- # All the generator names are checked against names of the
- # source generators of all the connections, to find which
- # generator's output should be passed on to the connection.
- # There must be a better way to do this...
- sourceGeneratorIndex = 0
- for j in range(len(self.generatorList)):
- if self.connectionList[i].getSourceName() == self.generatorList[j].getName():
- sourceGeneratorIndex = j
-
- # Perhaps this is a nicer method of doing the same thing as
- # above... but leaving this here for further testing. Besides
- # it breaks the encapsulation of the connection class -
- # directly communicating with one of it's members...
- sourceGeneratorIndex2 = self.generatorList.index(self.connectionList[i].sourceGenerator)
- print("Established method: " + str(sourceGeneratorIndex) + ", new method: " + str(sourceGeneratorIndex2))
-
+ # Checking which generator's output must a connection recieve
+ sourceGeneratorIndex = self.generatorList.index(self.connectionList[i].getSource())
self.connectionList[i].runConnection(generatorOutput[sourceGeneratorIndex])
- # Passing the output of the generators through to the head model to
- # get the recording
+ # Passing the output of the generators through to the head model
recording = self.runHeadModel(generatorOutput, recording)
return recording
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
