pybrainsim-activity Mailing List for PyBrainSim - The Brain Phantom Project (Page 4)
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From: <rg...@us...> - 2009-08-15 11:14:43
|
Revision: 107
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=107&view=rev
Author: rgoj
Date: 2009-08-15 11:14:34 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Added a few comments
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-15 11:01:16 UTC (rev 106)
+++ trunk/src/Experiment.py 2009-08-15 11:14:34 UTC (rev 107)
@@ -91,11 +91,17 @@
return self.recording[sliceChannel][startIndex:endIndex]
def getERP(self, stimulusNumber=0):
+ # Choosing the stimulus that will be used to make ERPs
stimuli = self.stimulusTimes[stimulusNumber]
+
+ #for channel in range(len(self.recording)):
+ channel = 0
+ # Retrieving slices of recordings around each stimulus (epochs)
epochs = []
for i in range(len(stimuli)):
- epochs.append(self.getRecordingSlice(stimuli[i]))
+ epochs.append(self.getRecordingSlice(stimuli[i], channel))
+ # Making sure all epochs are the same length
for i in range(len(epochs)):
if i == 0:
continue
@@ -158,5 +164,4 @@
#ylabel('Amplitude')
#title('Simulated ERP')
- #show()
show()
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|
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From: <rg...@us...> - 2009-08-15 11:01:24
|
Revision: 106
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=106&view=rev
Author: rgoj
Date: 2009-08-15 11:01:16 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Changed plotRecording so that multiple channels can be plotted at the same time.
* Used advice from the matplotlib cookbook: http://www.scipy.org/Cookbook/Matplotlib/MultilinePlots
* Only the ongoing activity plot is changed, the ERP plots will be reimplemented in the next few commits.
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-14 12:56:59 UTC (rev 105)
+++ trunk/src/Experiment.py 2009-08-15 11:01:16 UTC (rev 106)
@@ -110,17 +110,53 @@
return average
def plotRecording(self):
- subplot(211)
- plot(self.timePoints, self.recording[0], linewidth=1.0)
- for i in range(len(self.stimulusTimes[0])):
- axvline(self.stimulusTimes[0][i], color='r')
- xlabel('Time (s)')
- ylabel('Amplitude')
- title('Simulated EEG recording')
- subplot(212)
- plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
- axvline( 0.0, color='r' )
- xlabel('Time (s)')
- ylabel('Amplitude')
- title('Simulated ERP')
+ # Creating a new matplotlib figure for the plots
+ fig = figure()
+
+ # Each channel will have a plot of the same width and height
+ plotWidth = 0.8
+ plotHeight = 0.4/len(self.recording)
+
+ #
+ # Ongoing activity
+ #
+
+ # Multiple axes will be created, all sharing the same properties
+ axes = []
+ axesProperties = dict([])
+
+ for channel in range(len(self.recording)):
+ # Plotting the recording for each channel
+ axes.append(fig.add_axes([0.1, 0.55 + plotHeight * channel,
+ plotWidth, plotHeight],
+ **axesProperties))
+ axes[channel].plot(self.timePoints, self.recording[channel])
+ axes[channel].set_ylabel("CH " + str(channel+1))
+
+ # All channels must be zoomed in/out and moved at the same time
+ if channel == 0:
+ axesProperties['sharex'] = axes[0]
+ axesProperties['sharey'] = axes[0]
+
+ # Plotting vertical lines to indicate times of stimuli
+ for i in range(len(self.stimulusTimes[0])):
+ axvline(self.stimulusTimes[0][i], color='r')
+
+ # Time values will be printed only for the lowest axis
+ axes[0].set_xlabel("Time")
+ for axis in axes[1:]:
+ setp(axis.get_xticklabels(), visible=False)
+
+ #
+ # Event-related activity
+ #
+
+ #subplot(212)
+ #plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
+ #axvline( 0.0, color='r' )
+ #xlabel('Time (s)')
+ #ylabel('Amplitude')
+ #title('Simulated ERP')
+
+ #show()
show()
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From: <rg...@us...> - 2009-08-14 12:57:16
|
Revision: 105
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=105&view=rev
Author: rgoj
Date: 2009-08-14 12:56:59 +0000 (Fri, 14 Aug 2009)
Log Message:
-----------
* The sixth example now has two registration sites on the opposite sides of the half-shpere
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-14 12:50:53 UTC (rev 104)
+++ trunk/src/PyBrainSim.py 2009-08-14 12:56:59 UTC (rev 105)
@@ -156,6 +156,7 @@
exampleHeadModel = HeadModelHalfSphere(exampleHead)
exampleHead.setSamplingFrequency(128)
exampleHead.addRegistrationSite([0.5, 0, 0.866])
+ exampleHead.addRegistrationSite([-0.5, 0, 0.866])
exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 10.0)
exampleExperiment.setStimulusTimes([[0.3, 1.75, 2.16, 3.87, 4.31, 5.183, 6.34, 7.13]])
@@ -167,8 +168,6 @@
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
exampleExperiment.plotRecording()
else:
print("No such option unfortunately...")
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From: <rg...@us...> - 2009-08-14 12:51:00
|
Revision: 104
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=104&view=rev
Author: rgoj
Date: 2009-08-14 12:50:53 +0000 (Fri, 14 Aug 2009)
Log Message:
-----------
* Added a sixth example to PyBrainSim.py that for now replicates a singe sine generator example, but will soon be changed to showcase multi-recording-site functionality.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-13 17:20:12 UTC (rev 103)
+++ trunk/src/PyBrainSim.py 2009-08-14 12:50:53 UTC (rev 104)
@@ -30,6 +30,7 @@
from Head import Head
from HeadModel import HeadModel
+from HeadModelHalfSphere import HeadModelHalfSphere
from Experiment import Experiment
from Stimulus import Stimulus
from StimulusDummy import StimulusDummy
@@ -47,7 +48,8 @@
3. Incrementing numbers, two generators and a stimulus for one of them\n\
4. A single sinusoidal generator\n\
5. A hundred sinusoidal generators with random frequencies, some connected\
- to a stimulus.\n"
+ to a stimulus.\n\
+ 6. A single sinusoidal generator but with two registration sites"
print(welcomeMessage)
userChoice = input("Your choice: ")
@@ -149,5 +151,24 @@
exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
exampleExperiment.plotRecording()
+elif userChoice == 6:
+ exampleHead = Head()
+ exampleHeadModel = HeadModelHalfSphere(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([0.5, 0, 0.866])
+
+ 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]
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ exampleGenerator = GeneratorSine('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+ exampleExperiment.plotRecording()
else:
print("No such option unfortunately...")
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-14 12:44:02
|
#101: Display recordings from multiple channels in the plotRecording() method
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: new
Priority: major | Milestone: Spherical head model
Component: Simulations | Keywords:
-------------------------+--------------------------------------------------
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/101>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-08-13 17:20:23
|
Revision: 103
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=103&view=rev
Author: rgoj
Date: 2009-08-13 17:20:12 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* With a simple one line change the HeadModel class now is aware of it's "governing class" Head object, so that it's information about positions can be used in the HeadModel.
Modified Paths:
--------------
trunk/src/HeadModel.py
Modified: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py 2009-08-13 11:55:33 UTC (rev 102)
+++ trunk/src/HeadModel.py 2009-08-13 17:20:12 UTC (rev 103)
@@ -25,6 +25,7 @@
class HeadModel:
def __init__(self, head):
+ self.head = head
head.setHeadModel(self)
def checkPosition(self,position):
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-13 17:18:25
|
#57: Implement the notion of positions for generators and recording sites in the
DummyHeadModel class
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Spherical head model
Component: Simulations | Resolution: fixed
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
Comment:
Will be covered by simply using the Head class and it's notion of
positions...
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/57#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...> - 2009-08-13 11:56:42
|
#58: Implement a mechanism for cheching whether a position is correct in the
DummyHeadModel
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Spherical head model
Component: Simulations | Resolution: fixed
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/58#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...> - 2009-08-13 11:55:42
|
Revision: 102
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=102&view=rev
Author: rgoj
Date: 2009-08-13 11:55:33 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* Adding a checkPosition function in the HeadModel
* Using the new function in the PyBrainSim scripts
* Correcting comments
Modified Paths:
--------------
trunk/src/Head.py
trunk/src/HeadModel.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-13 09:14:46 UTC (rev 101)
+++ trunk/src/Head.py 2009-08-13 11:55:33 UTC (rev 102)
@@ -40,21 +40,22 @@
def getSamplingFrequency(self):
return self.samplingFrequency
- def addGenerator(self, generator):
+ def addGenerator(self, generator, position = [0,0,0]):
+ if self.headModel.checkPosition(position):
+ self.generatorSiteList.append(position)
+ else:
+ print("Wrong position of generator!")
self.generatorList.append(generator)
- self.generatorSiteList.append([0, 0, 0])
+ self.generatorSiteList.append(position)
def addConnection(self, connection):
self.connectionList.append(connection)
def addRegistrationSite(self, position):
- # We should be checking whether the position is within the boundaries
- # of the brain, which need to be defined somewhere somehow. The class
- # must somehow provide a means to accessing the size of the brain, the
- # available positions, etc. One interesting thing to do would be to
- # implement a method returning a position for a name of a given
- # brain/scalp region...
- self.registrationSiteList.append(position)
+ if self.headModel.checkPosition(position):
+ self.registrationSiteList.append(position)
+ else:
+ print("Wrong position of registration site!")
def setHeadModel(self, headModel):
self.headModel = headModel
Modified: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py 2009-08-13 09:14:46 UTC (rev 101)
+++ trunk/src/HeadModel.py 2009-08-13 11:55:33 UTC (rev 102)
@@ -26,14 +26,16 @@
class HeadModel:
def __init__(self, head):
head.setHeadModel(self)
+
+ def checkPosition(self,position):
+ return position == [0,0,0]
def runHeadModel(self, generatorOutput, recording):
# Filling all registration sites with the generators' output
for i in range(len(recording)):
recording[i].append(0)
for j in range(len(generatorOutput)):
- # The Stimulus class may return a string variable, we can't add
- # it to the recording, so we need to look out for it.
+ # Rejecting generator output that isn't a number
if isinstance(generatorOutput[j], str):
recording[i][-1] += 0
else:
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-13 09:15:31
|
#45: Separate head model from the head class, making a new class DummyHeadModel
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Spherical head model
Component: Simulations | Resolution: fixed
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/45#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...> - 2009-08-13 09:14:53
|
Revision: 101
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=101&view=rev
Author: rgoj
Date: 2009-08-13 09:14:46 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* Using the HeadModel in the PyBrainSim.py examples - creating a HeadModel object in each example
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-13 09:04:53 UTC (rev 100)
+++ trunk/src/PyBrainSim.py 2009-08-13 09:14:46 UTC (rev 101)
@@ -29,6 +29,7 @@
from random import random
from Head import Head
+from HeadModel import HeadModel
from Experiment import Experiment
from Stimulus import Stimulus
from StimulusDummy import StimulusDummy
@@ -54,6 +55,7 @@
if userChoice == 1:
exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
@@ -66,6 +68,7 @@
print(exampleExperiment.getRecording())
elif userChoice == 2:
exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
@@ -79,6 +82,7 @@
print exampleExperiment.getRecording()
elif userChoice == 3:
exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
exampleHead.setSamplingFrequency(10)
exampleHead.addRegistrationSite([0, 0, 0])
@@ -100,6 +104,7 @@
print exampleExperiment.getRecording()
elif userChoice == 4:
exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
exampleHead.setSamplingFrequency(128)
exampleHead.addRegistrationSite([0, 0, 0])
@@ -118,6 +123,7 @@
exampleExperiment.plotRecording()
elif userChoice == 5:
exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
exampleHead.setSamplingFrequency(256)
exampleHead.addRegistrationSite([0, 0, 0])
exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 100.0)
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From: <rg...@us...> - 2009-08-13 09:05:01
|
Revision: 100
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=100&view=rev
Author: rgoj
Date: 2009-08-13 09:04:53 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* Added an __init__ method, where the HeadModel is attached to a given Head...
* Corrected a small mistake
Modified Paths:
--------------
trunk/src/HeadModel.py
Modified: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py 2009-08-13 09:03:49 UTC (rev 99)
+++ trunk/src/HeadModel.py 2009-08-13 09:04:53 UTC (rev 100)
@@ -24,11 +24,14 @@
"""
class HeadModel:
+ def __init__(self, head):
+ head.setHeadModel(self)
+
def runHeadModel(self, generatorOutput, recording):
# Filling all registration sites with the generators' output
for i in range(len(recording)):
recording[i].append(0)
- for j in range(len(self.generatorList)):
+ for j in range(len(generatorOutput)):
# 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):
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From: <rg...@us...> - 2009-08-13 09:04:01
|
Revision: 99
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=99&view=rev
Author: rgoj
Date: 2009-08-13 09:03:49 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* Removed the runHeadModel code
* Added a setHeadModel method
* Using the new HeadModel object in runSimulation
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-13 08:34:43 UTC (rev 98)
+++ trunk/src/Head.py 2009-08-13 09:03:49 UTC (rev 99)
@@ -32,6 +32,7 @@
self.generatorSiteList = []
self.connectionList = []
self.registrationSiteList = []
+ self.headModel = None
def setSamplingFrequency(self, samplingFrequency):
self.samplingFrequency = samplingFrequency
@@ -55,20 +56,9 @@
# brain/scalp region...
self.registrationSiteList.append(position)
- def runHeadModel(self, generatorOutput, recording):
- # Filling all registration sites with the generators' output
- for i in range(len(recording)):
- recording[i].append(0)
- 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]
+ def setHeadModel(self, headModel):
+ self.headModel = headModel
- return recording
-
def runSimulation(self, duration=1):
"""Queries all generators, sends the generators' output to connections,
to the head model and then to the specified registration sites"""
@@ -100,6 +90,6 @@
self.connectionList[i].runConnection(generatorOutput[sourceGeneratorIndex])
# Passing the output of the generators through to the head model
- recording = self.runHeadModel(generatorOutput, recording)
+ recording = self.headModel.runHeadModel(generatorOutput, recording)
return recording
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From: <rg...@us...> - 2009-08-13 08:34:52
|
Revision: 98
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=98&view=rev
Author: rgoj
Date: 2009-08-13 08:34:43 +0000 (Thu, 13 Aug 2009)
Log Message:
-----------
* Adding the HeadModel class to replace the corresponding code in Head.py
Added Paths:
-----------
trunk/src/HeadModel.py
Added: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py (rev 0)
+++ trunk/src/HeadModel.py 2009-08-13 08:34:43 UTC (rev 98)
@@ -0,0 +1,39 @@
+# 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/>.
+
+from __future__ import division
+from Numeric import arange
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+The HeadModel class takes care of what happens to the generators' activity on
+it's way to the registration sites - i.e. with impedance of the skull.
+"""
+
+class HeadModel:
+ def runHeadModel(self, generatorOutput, recording):
+ # Filling all registration sites with the generators' output
+ for i in range(len(recording)):
+ recording[i].append(0)
+ 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
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-07 10:40:59
|
#47: Write a presentation of phase resetting in the PyBrainSim.py script
-------------------------+--------------------------------------------------
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/47#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...> - 2009-08-07 10:39:40
|
Revision: 97
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=97&view=rev
Author: rgoj
Date: 2009-08-07 10:39:26 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Added a fifth simulation example to the PyBrainSim.py script, with a hundred generators of random frequency and initial phase, some connected to a stimulus. This gives very nice results in the form of an ongoing signal that looks very similar to EEG and an ERP that has some nice peaks, and completes a milestone!
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-07 10:21:20 UTC (rev 96)
+++ trunk/src/PyBrainSim.py 2009-08-07 10:39:26 UTC (rev 97)
@@ -26,6 +26,8 @@
pybrainsim.sourceforge.net
"""
+from random import random
+
from Head import Head
from Experiment import Experiment
from Stimulus import Stimulus
@@ -42,7 +44,9 @@
1. Example dummy simulation\n\
2. Incrementing numbers, one generator and a stimulus\n\
3. Incrementing numbers, two generators and a stimulus for one of them\n\
- 4. Sinusoidal generator\n"
+ 4. A single sinusoidal generator\n\
+ 5. A hundred sinusoidal generators with random frequencies, some connected\
+ to a stimulus.\n"
print(welcomeMessage)
userChoice = input("Your choice: ")
@@ -112,5 +116,32 @@
print("\nSimulations resulted in the following recording:")
print exampleExperiment.getRecording()
exampleExperiment.plotRecording()
+elif userChoice == 5:
+ exampleHead = Head()
+ exampleHead.setSamplingFrequency(256)
+ exampleHead.addRegistrationSite([0, 0, 0])
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 100.0)
+
+ # Randomizing stimuli times
+ stimuli = []
+ for i in range(100):
+ stimuli.append( i + 0.2 +random()/2 )
+ exampleExperiment.setStimulusTimes([stimuli])
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+
+ # Creating many generators with random frequencies in the range 2-20 Hz and
+ # random phases. Connecting some of them to the stimulus generator
+ exampleGenerators = []
+ exampleConnections = []
+ for i in range(100):
+ frequency = 2.0 + random() * 18
+ phaseShift = random()
+ exampleGenerators.append(GeneratorSine('Gen', exampleHead, frequency, phaseShift))
+ if(random() > 0.75):
+ exampleConnections.append(Connection('Con', exampleHead, exampleStimulus, exampleGenerators[i]))
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ exampleExperiment.plotRecording()
else:
print("No such option unfortunately...")
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From: <rg...@us...> - 2009-08-07 10:21:28
|
Revision: 96
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=96&view=rev
Author: rgoj
Date: 2009-08-07 10:21:20 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* getRecordingSlice now needs only stimulus time as input
* Changed the way start and end indices are calculated in getRecordingSlice
* Added a warning to getERP that prints out a message if epochs are of different length
* Corrected a mistake that caused the average to not be an average, but just a sum
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-07 10:16:59 UTC (rev 95)
+++ trunk/src/Experiment.py 2009-08-07 10:21:20 UTC (rev 96)
@@ -82,22 +82,31 @@
if timePoint > self.timePoints[i-1]:
return i
- def getRecordingSlice(self, sliceStart, sliceDuration, sliceChannel=0):
- startIndex = self.findNearestTimeIndex(sliceStart)
- endIndex = self.findNearestTimeIndex(sliceStart + sliceDuration)
+ def getRecordingSlice(self, stimulus, sliceChannel=0):
+ stimulusIndex = self.findNearestTimeIndex(stimulus)
+ timeStep = 1.0 / self.samplingFrequency
+ startIndex = int(stimulusIndex - (self.baseline // timeStep))
+ endIndex = int(stimulusIndex + 1 + ((self.epochDuration - self.baseline) // timeStep))
+
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))
+ epochs.append(self.getRecordingSlice(stimuli[i]))
+ for i in range(len(epochs)):
+ if i == 0:
+ continue
+ elif (len(epochs[i]) != len(epochs[i-1])):
+ print str(len(epochs[i])) + " " + str(len(epochs[i-1]))
+ print "EPOCHS OF DIFFERENT LENGTHS!!!"
+
average = list(zeros(len(epochs[0])))
for i in range(len(epochs)):
for j in range(len(epochs[i])):
- average[j] += epochs[i][j]
-
+ average[j] += epochs[i][j] / len(epochs)
return average
def plotRecording(self):
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From: <rg...@us...> - 2009-08-07 10:17:07
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Revision: 95
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=95&view=rev
Author: rgoj
Date: 2009-08-07 10:16:59 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Chagned the method epochTimePoints is calculated in Experiment.__init__()
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-07 10:11:53 UTC (rev 94)
+++ trunk/src/Experiment.py 2009-08-07 10:16:59 UTC (rev 95)
@@ -38,8 +38,10 @@
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))
+
+ startIndex = int( - (self.baseline // timeStep))
+ endIndex = int(1 + ((self.epochDuration - self.baseline) // timeStep))
+ self.epochTimePoints = list((arange(endIndex - startIndex) - (self.baseline // timeStep)) * timeStep)
def setSamplingFrequency(self, samplingFrequency):
self.samplingFrequency = samplingFrequency
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From: <rg...@us...> - 2009-08-07 10:12:04
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Revision: 94
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=94&view=rev
Author: rgoj
Date: 2009-08-07 10:11:53 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* A warning is printed when findNearestTimeIndex invoked with out of bounds arguments.
* Corrected a small mistake in findNearestTimeIndex - it would return the wrong number
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-07 10:09:11 UTC (rev 93)
+++ trunk/src/Experiment.py 2009-08-07 10:11:53 UTC (rev 94)
@@ -71,11 +71,14 @@
is smaller than the given value timePoint"""
if timePoint in self.timePoints:
return self.timePoints.index(timePoint)
+ elif (timePoint > max(self.timePoints)) | (timePoint < min(self.timePoints)):
+ print("findNearestTimeIndex: Something is WRONG! timePoint: " + str(timePoint) )
+ return -1
else:
for i in range(len(self.timePoints)):
if timePoint < self.timePoints[i]:
if timePoint > self.timePoints[i-1]:
- return i-1
+ return i
def getRecordingSlice(self, sliceStart, sliceDuration, sliceChannel=0):
startIndex = self.findNearestTimeIndex(sliceStart)
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From: <rg...@us...> - 2009-08-07 10:09:20
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Revision: 93
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=93&view=rev
Author: rgoj
Date: 2009-08-07 10:09:11 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Importing division from python 3.0
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-07 09:50:49 UTC (rev 92)
+++ trunk/src/Experiment.py 2009-08-07 10:09:11 UTC (rev 93)
@@ -14,7 +14,8 @@
#
# You should have received a copy of the GNU General Public License along with
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
-
+
+from __future__ import division
__metaclass__ = type # New style classes. Is this necessary?
"""
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From: <rg...@us...> - 2009-08-07 09:50:55
|
Revision: 92
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=92&view=rev
Author: rgoj
Date: 2009-08-07 09:50:49 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Upon phase reset sine generators now return to their initial phase, instead of zero phase.
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-07 09:49:12 UTC (rev 91)
+++ trunk/src/GeneratorSine.py 2009-08-07 09:50:49 UTC (rev 92)
@@ -32,7 +32,8 @@
def __init__(self, name, head, frequency = 2, phaseShift = 0):
Generator.__init__(self, name, head)
self.frequency = frequency
- self.currentPhase = phaseShift
+ self.phaseShift = phaseShift
+ self.currentPhase = self.phaseShift
self.lastTimePoint = 0
def printInfo(self):
@@ -40,7 +41,7 @@
def receiveInput(self, input):
if input == 'Stimulus':
- self.currentPhase = 0
+ self.currentPhase = self.phaseShift
def runGenerator(self, time):
timeStep = time - self.lastTimePoint
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From: <rg...@us...> - 2009-08-07 09:49:22
|
Revision: 91
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=91&view=rev
Author: rgoj
Date: 2009-08-07 09:49:12 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Removing small debugging print() call
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-07 09:48:31 UTC (rev 90)
+++ trunk/src/Head.py 2009-08-07 09:49:12 UTC (rev 91)
@@ -89,8 +89,6 @@
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)
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From: <rg...@us...> - 2009-08-07 09:48:38
|
Revision: 90
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=90&view=rev
Author: rgoj
Date: 2009-08-07 09:48:31 +0000 (Fri, 07 Aug 2009)
Log Message:
-----------
* Removing small debugging print() call
Modified Paths:
--------------
trunk/src/Stimulus.py
Modified: trunk/src/Stimulus.py
===================================================================
--- trunk/src/Stimulus.py 2009-08-06 12:13:46 UTC (rev 89)
+++ trunk/src/Stimulus.py 2009-08-07 09:48:31 UTC (rev 90)
@@ -39,8 +39,6 @@
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))
-
self.currentStimulus += 1
self.activation = 'Stimulus'
else:
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From: <rg...@us...> - 2009-08-06 12:16:03
|
Revision: 89
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=89&view=rev
Author: rgoj
Date: 2009-08-06 12:13:46 +0000 (Thu, 06 Aug 2009)
Log Message:
-----------
* Experiment.plotRecording() now has two plots - one with the ongoing EEG activity and another with the ERP.
* Both plots have vertical lines to indicate stimulus times
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-05 13:03:11 UTC (rev 88)
+++ trunk/src/Experiment.py 2009-08-06 12:13:46 UTC (rev 89)
@@ -95,11 +95,17 @@
return average
def plotRecording(self):
+ subplot(211)
plot(self.timePoints, self.recording[0], linewidth=1.0)
- #plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
-
+ for i in range(len(self.stimulusTimes[0])):
+ axvline(self.stimulusTimes[0][i], color='r')
xlabel('Time (s)')
ylabel('Amplitude')
title('Simulated EEG recording')
- grid(True)
+ subplot(212)
+ plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
+ axvline( 0.0, color='r' )
+ xlabel('Time (s)')
+ ylabel('Amplitude')
+ title('Simulated ERP')
show()
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-06 12:01:30
|
#53: Write a simple "signal browser function" that could easily be used to look
at any signal
-----------------------+----------------------------------------------------
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/53#comment:2>
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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