pybrainsim-activity Mailing List for PyBrainSim - The Brain Phantom Project (Page 3)
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From: PyBrainSim - T. i. <no...@so...> - 2009-09-02 09:00:04
|
#102: Add a bottom to the 3D halved sphere
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: minor | Milestone: 3D visualization of head model
Component: Simulations | Resolution: duplicate
Keywords: |
-------------------------+--------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => duplicate
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/102#comment:1>
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: PyBrainSim - T. i. <no...@so...> - 2009-09-02 08:58:31
|
#103: Add a bottom to the 3D halved sphere
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: new
Priority: minor | Milestone: 3D visualization of head model
Component: Visualizations | Keywords:
----------------------------+-----------------------------------------------
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/103>
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...> - 2009-09-02 08:58:24
|
#102: Add a bottom to the 3D halved sphere
-------------------------+--------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: new
Priority: minor | Milestone: 3D visualization of head model
Component: Simulations | Keywords:
-------------------------+--------------------------------------------------
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/102>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
|
From: <rg...@us...> - 2009-09-02 08:51:30
|
Revision: 123
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=123&view=rev
Author: rgoj
Date: 2009-09-02 08:51:22 +0000 (Wed, 02 Sep 2009)
Log Message:
-----------
* Changed the 3d object that is presented when testing 3d visualizations to be half a sphere, only for now without a bottom, which looks silly.
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-18 11:07:56 UTC (rev 122)
+++ trunk/src/Head.py 2009-09-02 08:51:22 UTC (rev 123)
@@ -61,17 +61,15 @@
self.headModel = headModel
def displayHead(self):
- dphi, dtheta = pi/250.0, pi/250.0
- [phi,theta] = mgrid[0:pi+dphi*1.5:dphi,0:2*pi+dtheta*1.5:dtheta]
- m0 = 4; m1 = 3; m2 = 2; m3 = 3; m4 = 6; m5 = 2; m6 = 6; m7 = 4;
- r = sin(m0*phi)**m1 + cos(m2*phi)**m3 + sin(m4*theta)**m5 + cos(m6*theta)**m7
+ dphi, dtheta = pi/10.0, pi/10.0
+ #[phi,theta] = mgrid[0:pi+dphi*1.5:dphi,0:2*pi+dtheta*1.5:dtheta]
+ [phi,theta] = mgrid[0:pi/2+dphi:dphi,0:2*pi+dtheta:dtheta]
+ r = 1
x = r*sin(phi)*cos(theta)
- y = r*cos(phi)
- z = r*sin(phi)*sin(theta)
+ y = r*sin(phi)*sin(theta)
+ z = r*cos(phi)
- # View it.
-
- s = mlab.mesh(x, y, z)
+ s = mlab.mesh(x, y, z, opacity=1, color = ( 0.5,0.5,1.0 ))
mlab.show()
def runSimulation(self, duration=1):
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-18 11:10:11
|
#63: Write a 3D view showing a random 3D object
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: 3D visualization of head model
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/63#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...> - 2009-08-18 11:08:04
|
Revision: 122
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=122&view=rev
Author: rgoj
Date: 2009-08-18 11:07:56 +0000 (Tue, 18 Aug 2009)
Log Message:
-----------
* Adding the mayavi import
* Adding displayHead() method, that currently only shows an example of how to use mayavi (from the mayavi wiki), by displaying an object in 3D.
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-18 11:05:08 UTC (rev 121)
+++ trunk/src/Head.py 2009-08-18 11:07:56 UTC (rev 122)
@@ -15,7 +15,8 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
-from numpy import arange
+from numpy import pi, sin, cos, mgrid, arange
+from enthought.mayavi import mlab
__metaclass__ = type # New style classes. Is this necessary?
"""
@@ -59,6 +60,20 @@
def setHeadModel(self, headModel):
self.headModel = headModel
+ def displayHead(self):
+ dphi, dtheta = pi/250.0, pi/250.0
+ [phi,theta] = mgrid[0:pi+dphi*1.5:dphi,0:2*pi+dtheta*1.5:dtheta]
+ m0 = 4; m1 = 3; m2 = 2; m3 = 3; m4 = 6; m5 = 2; m6 = 6; m7 = 4;
+ r = sin(m0*phi)**m1 + cos(m2*phi)**m3 + sin(m4*theta)**m5 + cos(m6*theta)**m7
+ x = r*sin(phi)*cos(theta)
+ y = r*cos(phi)
+ z = r*sin(phi)*sin(theta)
+
+ # View it.
+
+ s = mlab.mesh(x, y, z)
+ mlab.show()
+
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"""
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From: <rg...@us...> - 2009-08-18 11:05:16
|
Revision: 121
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=121&view=rev
Author: rgoj
Date: 2009-08-18 11:05:08 +0000 (Tue, 18 Aug 2009)
Log Message:
-----------
* Added a new example to the PyBrainSim.py scritpt, that will be used to showcase the 3d head model display features.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-18 11:04:12 UTC (rev 120)
+++ trunk/src/PyBrainSim.py 2009-08-18 11:05:08 UTC (rev 121)
@@ -49,7 +49,8 @@
4. A single sinusoidal generator\n\
5. A hundred sinusoidal generators with random frequencies, some connected\
to a stimulus.\n\
- 6. A single sinusoidal generator but with two registration sites"
+ 6. A single sinusoidal generator but with two registration sites\n\
+ 7. A presentation of the 3d head model."
print(welcomeMessage)
userChoice = input("Your choice: ")
@@ -170,5 +171,8 @@
exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
exampleExperiment.plotRecording()
+elif userChoice == 7:
+ exampleHead = Head()
+ exampleHead.displayHead()
else:
print("No such option unfortunately...")
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From: <rg...@us...> - 2009-08-18 11:04:21
|
Revision: 120
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=120&view=rev
Author: rgoj
Date: 2009-08-18 11:04:12 +0000 (Tue, 18 Aug 2009)
Log Message:
-----------
* Changning from Numeric to from numpy, because Numeric is obsolete (works under Debian Lenny, doesn't work under Ubuntuy Jaunty Jackalope...)
Modified Paths:
--------------
trunk/src/Head.py
trunk/src/HeadModel.py
trunk/src/HeadModelHalfSphere.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-15 16:15:42 UTC (rev 119)
+++ trunk/src/Head.py 2009-08-18 11:04:12 UTC (rev 120)
@@ -15,7 +15,7 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
-from Numeric import arange
+from numpy import arange
__metaclass__ = type # New style classes. Is this necessary?
"""
Modified: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py 2009-08-15 16:15:42 UTC (rev 119)
+++ trunk/src/HeadModel.py 2009-08-18 11:04:12 UTC (rev 120)
@@ -15,7 +15,7 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
-from Numeric import arange
+from numpy import arange
__metaclass__ = type # New style classes. Is this necessary?
"""
Modified: trunk/src/HeadModelHalfSphere.py
===================================================================
--- trunk/src/HeadModelHalfSphere.py 2009-08-15 16:15:42 UTC (rev 119)
+++ trunk/src/HeadModelHalfSphere.py 2009-08-18 11:04:12 UTC (rev 120)
@@ -15,7 +15,7 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
-from Numeric import arange
+from numpy import arange
__metaclass__ = type # New style classes. Is this necessary?
"""
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From: PyBrainSim - T. i. <no...@so...> - 2009-08-16 13:06:51
|
#62: Which library to use for 3D visualizations?
----------------------------+-----------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: 3D visualization of head model
Component: Visualizations | Resolution: fixed
Keywords: |
----------------------------+-----------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
Comment:
Mayavi2... of course.
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/62#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...> - 2009-08-15 16:39:20
|
#61: Write an example of using the SphericalHeadModel in the PyBrainSim.py
script
-------------------------+--------------------------------------------------
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/61#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...> - 2009-08-15 16:16:59
|
#60: Make the recorded activity be lower depending on distance from a given
generator
-------------------------+--------------------------------------------------
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/60#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...> - 2009-08-15 16:16:02
|
#59: Write a SphericalHeadModel class with 3D positions and limits for positions
-------------------------+--------------------------------------------------
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/59#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...> - 2009-08-15 16:15:49
|
Revision: 119
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=119&view=rev
Author: rgoj
Date: 2009-08-15 16:15:42 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Added a third registration site in example 6 in PyBrainSim, to showcase the new functionality (HeadModelHalfSphere) even better.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-15 16:12:35 UTC (rev 118)
+++ trunk/src/PyBrainSim.py 2009-08-15 16:15:42 UTC (rev 119)
@@ -155,8 +155,9 @@
exampleHead = Head()
exampleHeadModel = HeadModelHalfSphere(exampleHead)
exampleHead.setSamplingFrequency(128)
- exampleHead.addRegistrationSite([0.5, 0, 0.866])
- exampleHead.addRegistrationSite([-0.5, 0, 0.866])
+ exampleHead.addRegistrationSite([ 0.5, 0.0, 0.866])
+ exampleHead.addRegistrationSite([ 0.0, 0.0, 0.866])
+ exampleHead.addRegistrationSite([-0.5, 0.0, 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]])
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From: <rg...@us...> - 2009-08-15 16:12:44
|
Revision: 118
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=118&view=rev
Author: rgoj
Date: 2009-08-15 16:12:35 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Correcting error in example 5 from PyBrainSim.py caused by changing the GeneratorSine __init__() method: a new parameter was added and this was not correctly set by the example.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-15 16:04:26 UTC (rev 117)
+++ trunk/src/PyBrainSim.py 2009-08-15 16:12:35 UTC (rev 118)
@@ -143,9 +143,9 @@
exampleGenerators = []
exampleConnections = []
for i in range(100):
- frequency = 2.0 + random() * 18
- phaseShift = random()
- exampleGenerators.append(GeneratorSine('Gen', exampleHead, frequency, phaseShift))
+ randomFrequency = 2.0 + random() * 18
+ randomPhaseShift = random()
+ exampleGenerators.append(GeneratorSine('Gen', exampleHead, frequency=randomFrequency, phaseShift=randomPhaseShift))
if(random() > 0.75):
exampleConnections.append(Connection('Con', exampleHead, exampleStimulus, exampleGenerators[i]))
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From: <rg...@us...> - 2009-08-15 16:04:38
|
Revision: 117
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=117&view=rev
Author: rgoj
Date: 2009-08-15 16:04:26 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Changed the example for HeadModelHalfSphere to show off that activity is now recorded differently depending on distance between recording site and generator
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-15 16:02:11 UTC (rev 116)
+++ trunk/src/PyBrainSim.py 2009-08-15 16:04:26 UTC (rev 117)
@@ -163,7 +163,8 @@
exampleStimulus = Stimulus('Stim', exampleHead)
exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
- exampleGenerator = GeneratorSine('Gen', exampleHead)
+ exampleGenerator = GeneratorSine('Gen', exampleHead, position = [0.5, 0, 0.366], frequency = 7)
+ exampleGenerator = GeneratorSine('Gen', exampleHead, position = [-0.5, 0, 0.366], frequency = 4)
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
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From: <rg...@us...> - 2009-08-15 16:02:19
|
Revision: 116
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=116&view=rev
Author: rgoj
Date: 2009-08-15 16:02:11 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Adding a new class: HeadModelHalfSphere that makes it possible to add generators and registration sites in a half sphere of radius 1. The recorded activity is lowered depending on distance between generator and registration site.
Added Paths:
-----------
trunk/src/HeadModelHalfSphere.py
Added: trunk/src/HeadModelHalfSphere.py
===================================================================
--- trunk/src/HeadModelHalfSphere.py (rev 0)
+++ trunk/src/HeadModelHalfSphere.py 2009-08-15 16:02:11 UTC (rev 116)
@@ -0,0 +1,71 @@
+# 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?
+
+"""
+This reimplemenation of the HeadModel class provides a half sphere model of a
+head. The checkPosition() and runHeadModel() methods have been modified, so
+that only positions within one half of a sphere of radius 1 are allowed and
+recorded activity is smaller when generator is further from registration site.
+"""
+
+from HeadModel import HeadModel
+
+class HeadModelHalfSphere(HeadModel):
+ def __init__(self, head):
+ HeadModel.__init__(self, head)
+ self.head = head
+
+ def checkPosition(self,position):
+ # Checking if position is a list of three numbers
+ if not isinstance(position, list):
+ return False
+ if len(position) != 3:
+ return False
+ for i in range(3):
+ if (not isinstance(position[i], float)) and (not isinstance(position[i], int)):
+ return False
+ # Checking if position is smaller than the sphere radius of 1
+ positionLength = position[0] ** 2 + position[1] ** 2 + position[2] ** 2
+ if positionLength > 1:
+ return False
+ # If none of the conditions above fail, the position is correct
+ return True
+
+ def runHeadModel(self, generatorOutput, recording):
+ # Filling all registration sites with the generators' output
+ for channel in range(len(recording)):
+ recording[channel].append(0)
+ for generator in range(len(generatorOutput)):
+ # Rejecting generator output that isn't a number
+ if isinstance(generatorOutput[generator], str):
+ recording[channel][-1] += 0
+ else:
+ distance = 0
+ # Distance between generator and registration site
+ for dimension in range(3):
+ distance += ((self.head.generatorSiteList[generator][dimension]
+ -
+ self.head.registrationSiteList[channel][dimension])
+ ** 2)
+ # The recorded activity is smaller when the generator is
+ # far from the registration site.
+ recording[channel][-1] += generatorOutput[generator] / distance
+
+ return recording
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From: <rg...@us...> - 2009-08-15 15:57:41
|
Revision: 115
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=115&view=rev
Author: rgoj
Date: 2009-08-15 15:57:34 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* It is now possible to set position of GeneratorSine upon initialization.
Modified Paths:
--------------
trunk/src/GeneratorSine.py
Modified: trunk/src/GeneratorSine.py
===================================================================
--- trunk/src/GeneratorSine.py 2009-08-15 15:56:42 UTC (rev 114)
+++ trunk/src/GeneratorSine.py 2009-08-15 15:57:34 UTC (rev 115)
@@ -29,8 +29,8 @@
from Generator import Generator
class GeneratorSine(Generator):
- def __init__(self, name, head, frequency = 2, phaseShift = 0):
- Generator.__init__(self, name, head)
+ def __init__(self, name, head, position = [0,0,0], frequency = 2, phaseShift = 0):
+ Generator.__init__(self, name, head, position)
self.frequency = frequency
self.phaseShift = phaseShift
self.currentPhase = self.phaseShift
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From: <rg...@us...> - 2009-08-15 15:56:49
|
Revision: 114
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=114&view=rev
Author: rgoj
Date: 2009-08-15 15:56:42 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* It is now possible to define position of generator upon initialization, this is forwarded to the addGenerator method in the Head object passed upon initialization.
Modified Paths:
--------------
trunk/src/Generator.py
Modified: trunk/src/Generator.py
===================================================================
--- trunk/src/Generator.py 2009-08-15 15:55:24 UTC (rev 113)
+++ trunk/src/Generator.py 2009-08-15 15:56:42 UTC (rev 114)
@@ -22,10 +22,10 @@
"""
class Generator:
- def __init__(self, name, head):
+ def __init__(self, name, head, position = [0, 0, 0]):
self.name = name
self.activation = 0
- head.addGenerator(self)
+ head.addGenerator(self, position)
def printInfo(self):
print(self.name + ": A Generator object")
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From: <rg...@us...> - 2009-08-15 15:55:37
|
Revision: 113
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=113&view=rev
Author: rgoj
Date: 2009-08-15 15:55:24 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Correcting a mistake that would cause an uncorrect position to be added to position list anyway
Modified Paths:
--------------
trunk/src/Head.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2009-08-15 15:06:17 UTC (rev 112)
+++ trunk/src/Head.py 2009-08-15 15:55:24 UTC (rev 113)
@@ -43,10 +43,9 @@
def addGenerator(self, generator, position = [0,0,0]):
if self.headModel.checkPosition(position):
self.generatorSiteList.append(position)
+ self.generatorList.append(generator)
else:
print("Wrong position of generator!")
- self.generatorList.append(generator)
- self.generatorSiteList.append(position)
def addConnection(self, connection):
self.connectionList.append(connection)
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From: <rg...@us...> - 2009-08-15 15:06:25
|
Revision: 112
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=112&view=rev
Author: rgoj
Date: 2009-08-15 15:06:17 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Removing unused self.head member
Modified Paths:
--------------
trunk/src/HeadModel.py
Modified: trunk/src/HeadModel.py
===================================================================
--- trunk/src/HeadModel.py 2009-08-15 14:54:55 UTC (rev 111)
+++ trunk/src/HeadModel.py 2009-08-15 15:06:17 UTC (rev 112)
@@ -25,7 +25,6 @@
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...> - 2009-08-15 14:57:55
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#101: Display recordings from multiple channels in the plotRecording() method
-------------------------+--------------------------------------------------
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/101#comment:1>
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...> - 2009-08-15 14:55:06
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Revision: 111
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=111&view=rev
Author: rgoj
Date: 2009-08-15 14:54:55 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Moved the matplotlib functions responsible for multiple axes, plotting, etc. to a new plotChannels() method.
* The plotChannels() method is now called from plotRecording() to plot both ongoing and event-related activity.
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-15 11:32:34 UTC (rev 110)
+++ trunk/src/Experiment.py 2009-08-15 14:54:55 UTC (rev 111)
@@ -118,28 +118,21 @@
return channelERPs
- def plotRecording(self):
- # Creating a new matplotlib figure for the plots
- fig = figure()
+ def plotChannels(self, channelData, time, stimuli, fig, bottom, height):
+ # Multiple axes will be created, all sharing the same properties
+ axes = []
+ axesProperties = dict([])
# Each channel will have a plot of the same width and height
plotWidth = 0.8
- plotHeight = 0.4/len(self.recording)
+ plotHeight = height/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)):
+ for channel in range(len(channelData)):
# Plotting the recording for each channel
- axes.append(fig.add_axes([0.1, 0.55 + plotHeight * channel,
+ axes.append(fig.add_axes([0.1, bottom + plotHeight * channel,
plotWidth, plotHeight],
**axesProperties))
- axes[channel].plot(self.timePoints, self.recording[channel])
+ axes[channel].plot(time, channelData[channel])
axes[channel].set_ylabel("CH " + str(channel+1))
# All channels must be zoomed in/out and moved at the same time
@@ -148,25 +141,32 @@
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')
+ if isinstance(stimuli, float):
+ axvline(stimuli, color='r')
+ else:
+ for i in range(len(stimuli)):
+ axvline(stimuli[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)
+
+ def plotRecording(self):
+ # Creating a new matplotlib figure for the plots
+ fig = figure()
+
+ # Ongoing activity
+ self.plotChannels(self.recording, self.timePoints,
+ self.stimulusTimes[0], fig, 0.55, 0.4)
+ figtext( 0.93, 0.75, 'Ongoing activity', rotation = 'vertical',
+ verticalalignment = 'center')
- #
# Event-related activity
- #
+ self.plotChannels(self.getERP(), self.epochTimePoints,
+ 0.0, fig, 0.075, 0.4)
+ figtext( 0.93, 0.275, 'Event-related activity', rotation = 'vertical',
+ verticalalignment = 'center' )
- print self.getERP()
-
- #subplot(212)
- #plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
- #axvline( 0.0, color='r' )
- #xlabel('Time (s)')
- #ylabel('Amplitude')
- #title('Simulated ERP')
-
+ # Showing the prepared figure
show()
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From: <rg...@us...> - 2009-08-15 11:32:41
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Revision: 110
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=110&view=rev
Author: rgoj
Date: 2009-08-15 11:32:34 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* The getERP() method now returns a list of ERPs for each channel instead of just the ERP of channel 0.
* Now we are ready to plot ERPs with the plotRecording function.
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-15 11:20:44 UTC (rev 109)
+++ trunk/src/Experiment.py 2009-08-15 11:32:34 UTC (rev 110)
@@ -91,27 +91,32 @@
return self.recording[sliceChannel][startIndex:endIndex]
def getERP(self, stimulusNumber=0):
+ # We will be returning a list of ERPs for each channel
+ channelERPs = []
+
# 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], channel))
+ for channel in range(len(self.recording)):
+ # Retrieving slices of recordings around each stimulus (epochs)
+ epochs = []
+ for i in range(len(stimuli)):
+ epochs.append(self.getRecordingSlice(stimuli[i], channel))
+
+ # Making sure all epochs are of the same length
+ for i in range(len(epochs))[1:]:
+ if (len(epochs[i]) != len(epochs[i-1])):
+ print("Not all epochs are of the same length: " +
+ str(len(epochs[i])) + " " + str(len(epochs[i-1])))
+
+ # Calculating the average of all the epochs
+ average = list(zeros(len(epochs[0])))
+ for i in range(len(epochs)):
+ for j in range(len(epochs[i])):
+ average[j] += epochs[i][j] / len(epochs)
+ channelERPs.append(average)
- # Making sure all epochs are of the same length
- for i in range(len(epochs))[1:]:
- if (len(epochs[i]) != len(epochs[i-1])):
- print("Not all epochs are of the same length: " +
- str(len(epochs[i])) + " " + str(len(epochs[i-1])))
-
- average = list(zeros(len(epochs[0])))
- for i in range(len(epochs)):
- for j in range(len(epochs[i])):
- average[j] += epochs[i][j] / len(epochs)
- return average
+ return channelERPs
def plotRecording(self):
# Creating a new matplotlib figure for the plots
@@ -154,6 +159,8 @@
#
# Event-related activity
#
+
+ print self.getERP()
#subplot(212)
#plot(self.epochTimePoints, self.getERP(), linewidth=1.0)
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From: <rg...@us...> - 2009-08-15 11:20:51
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Revision: 109
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=109&view=rev
Author: rgoj
Date: 2009-08-15 11:20:44 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Simplified the code for comparing epoch lengths
Modified Paths:
--------------
trunk/src/Experiment.py
Modified: trunk/src/Experiment.py
===================================================================
--- trunk/src/Experiment.py 2009-08-15 11:15:50 UTC (rev 108)
+++ trunk/src/Experiment.py 2009-08-15 11:20:44 UTC (rev 109)
@@ -101,14 +101,12 @@
for i in range(len(stimuli)):
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
- elif (len(epochs[i]) != len(epochs[i-1])):
- print str(len(epochs[i])) + " " + str(len(epochs[i-1]))
- print "EPOCHS OF DIFFERENT LENGTHS!!!"
-
+ # Making sure all epochs are of the same length
+ for i in range(len(epochs))[1:]:
+ if (len(epochs[i]) != len(epochs[i-1])):
+ print("Not all epochs are of the same length: " +
+ str(len(epochs[i])) + " " + str(len(epochs[i-1])))
+
average = list(zeros(len(epochs[0])))
for i in range(len(epochs)):
for j in range(len(epochs[i])):
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From: <rg...@us...> - 2009-08-15 11:15:57
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Revision: 108
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=108&view=rev
Author: rgoj
Date: 2009-08-15 11:15:50 +0000 (Sat, 15 Aug 2009)
Log Message:
-----------
* Removed a print command left over from some testing
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-08-15 11:14:34 UTC (rev 107)
+++ trunk/src/PyBrainSim.py 2009-08-15 11:15:50 UTC (rev 108)
@@ -162,7 +162,6 @@
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)
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