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From: <rg...@us...> - 2010-08-05 17:36:07
|
Revision: 146
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=146&view=rev
Author: rgoj
Date: 2010-08-05 17:35:58 +0000 (Thu, 05 Aug 2010)
Log Message:
-----------
* Minor corrections so that lead field is calculated only once
Modified Paths:
--------------
trunk/src/Head.py
trunk/src/HeadModelDipoleSphere.py
Modified: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py 2010-06-30 08:42:36 UTC (rev 145)
+++ trunk/src/Head.py 2010-08-05 17:35:58 UTC (rev 146)
@@ -80,7 +80,7 @@
recording = []
for i in range(len(self.registrationSiteList)):
recording.append([])
-
+
# Preparing a variable where the output of each of the generators will
# be stored
generatorOutput = []
Modified: trunk/src/HeadModelDipoleSphere.py
===================================================================
--- trunk/src/HeadModelDipoleSphere.py 2010-06-30 08:42:36 UTC (rev 145)
+++ trunk/src/HeadModelDipoleSphere.py 2010-08-05 17:35:58 UTC (rev 146)
@@ -67,7 +67,7 @@
# How many generators and electrodes do we have?
nGenerators = len(self.head.generatorSiteList)
nElectrodes = len(self.head.registrationSiteList)
-
+
# Assuming ideal conductivity
sigma = 1.0
@@ -79,6 +79,7 @@
for iElectrode in range(nElectrodes):
# Calculating the coordinates of the electrode in the Cartesian coordinates associated with the head
+ # The X axis points towards the right ear, while the Y axis points towards the front
electrodeTheta = self.head.registrationSiteList[iElectrode][0]
electrodePhi = self.head.registrationSiteList[iElectrode][1]
xyzElectrodeHead = zeros(3);
@@ -204,30 +205,37 @@
self.leadFieldFrank1952[iElectrode, iGenerator] = cosPsi * (( 1-pow(f,2.0) )/pow( 1+pow(f,2.0)-2*f*cosTheta, 3/2)-1)
self.leadFieldFrank1952[iElectrode, iGenerator] += sinPsi*cosPhi/sinTheta* ( ( 3*f - 3*pow(f,2.0)*cosTheta + pow(f,3.0) - cosTheta )/pow(1+pow(f,2.0)-2*f*cosTheta,3/2) + cosTheta )
self.leadFieldFrank1952[iElectrode, iGenerator] = self.leadFieldFrank1952[iElectrode, iGenerator] / 4 /pi / sigma / self.radius / b
+
+ # This is a nasty trick to make runHeadModel aware that the lead field has already been calculated
+ self.leadField = 1
def runHeadModel(self, generatorOutput, recording):
# Calculating the lead field
- self.calculateLeadField()
+ if self.leadField == 0:
+ self.calculateLeadField()
# Calculating the recording by multyplying the lead field by the generator output
- newRecording = dot(self.leadField, (array([generatorOutput])).transpose())
- newRecordingInfinite = dot(self.leadFieldInfinite, (array([generatorOutput])).transpose())
- newRecordingBrody1973 = dot(self.leadFieldBrody1973, (array([generatorOutput])).transpose())
- newRecordingFrank1952 = dot(self.leadFieldFrank1952, (array([generatorOutput])).transpose())
+ #newRecording = dot(self.leadField, (array([generatorOutput])).transpose())
+ #newRecordingInfinite = dot(self.leadFieldInfinite, (array([generatorOutput])).transpose())
+ newRecordingBrody1973 = dot( self.leadFieldBrody1973, (array([generatorOutput])).transpose())
+ #newRecordingFrank1952 = dot(self.leadFieldFrank1952, (array([generatorOutput])).transpose())
# Converting the new recording to list format for compatibility with rest of the code
- newRecording = list(newRecording[:,0])
- newRecordingInfinite = list(newRecordingInfinite[:,0])
+ #newRecording = list(newRecording[:,0])
+ #newRecordingInfinite = list(newRecordingInfinite[:,0])
newRecordingBrody1973 = list(newRecordingBrody1973[:,0])
- newRecordingFrank1952 = list(newRecordingFrank1952[:,0])
+ #newRecordingFrank1952 = list(newRecordingFrank1952[:,0])
- for i in range(len(newRecording)):
+ # Brody1973 rules, see comments below...
+ newRecording = newRecordingBrody1973
+
+ #for i in range(len(newRecording)):
# All three of the lead field calculation methods implemented above can be used, however
# only Brody1973 and Frank1952 give results in a bounded homogeneous conducting sphere,
# and of these only Brody1973 gives results for all combinations of angles, etc.
# Additionally, due to and arccos in my implementation above, Frank1952 for now gives even
# worse results than it should for many angles...
- newRecording[i] = newRecordingBrody1973[i]
+ #newRecording[i] = newRecordingBrody1973[i]
#newRecording[i] = newRecordingFrank1952[i]
#newRecording[i] = newRecordingInfinite[i]
#newRecording[i] = (newRecordingBrody1973[i])/(newRecordingFrank1952[i])
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|
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From: <rg...@us...> - 2010-06-30 08:42:46
|
Revision: 145
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=145&view=rev
Author: rgoj
Date: 2010-06-30 08:42:36 +0000 (Wed, 30 Jun 2010)
Log Message:
-----------
* Modyfying the example of the use of the spherical head model to showcase it a little better.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2010-06-30 08:36:31 UTC (rev 144)
+++ trunk/src/PyBrainSim.py 2010-06-30 08:42:36 UTC (rev 145)
@@ -296,22 +296,25 @@
head3.setSamplingFrequency(1)
# Adding registration sites
- nElectrodes = 200
+ nElectrodes = 201
angles = []
for i in range(nElectrodes):
angles.append(i*numpy.pi/(nElectrodes-1) - numpy.pi/2)
- head1.addRegistrationSite([angles[-1],numpy.pi/2])
- head2.addRegistrationSite([angles[-1],numpy.pi/2])
- head3.addRegistrationSite([angles[-1],numpy.pi/2])
+ head1.addRegistrationSite([angles[-1],0])
+ head2.addRegistrationSite([angles[-1],0])
+ head3.addRegistrationSite([angles[-1],0])
# Adding a generator
orientation1= 0;
orientation2= numpy.pi/2;
orientation3= numpy.pi/4;
- generator1 = GeneratorNoisy('Gen', head1, position = [ 0.3, 0, orientation1, 0, 0], mean=1, stddev=0.1)
- generator2 = GeneratorNoisy('Gen', head2, position = [ 0.3, 0, orientation2, 0, 0], mean=1, stddev=0.1)
- generator3 = GeneratorNoisy('Gen', head3, position = [ 0.3, 0, orientation3, 0, 0], mean=1, stddev=0.1)
+ generator1 = GeneratorNoisy('Gen', head1, position = [ 4.0, 0, 0, orientation1, numpy.pi/2], mean=1, stddev=0.0)
+ generator2 = GeneratorNoisy('Gen', head2, position = [ 4.0, numpy.pi/4, 0, orientation2, numpy.pi/2], mean=1, stddev=0.0)
+ generator30 = GeneratorNoisy('Gen', head3, position = [ 4.0, 0, 0, orientation1, numpy.pi/2], mean=1, stddev=0.5)
+ generator31 = GeneratorNoisy('Gen', head3, position = [ 4.0, numpy.pi/4, 0, orientation2, numpy.pi/2], mean=3, stddev=0.5)
+ generator32 = GeneratorNoisy('Gen', head3, position = [ 4.0, -numpy.pi/4, 0, orientation3, numpy.pi/2], mean=2, stddev=0.5)
+
# Run the simulation just once (or, equivalently for one second with the sampling rate of 1 Hz)
simulatedData1 = numpy.array(head1.runSimulation(1))
simulatedData2 = numpy.array(head2.runSimulation(1))
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From: <rg...@us...> - 2010-06-30 08:36:37
|
Revision: 144
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=144&view=rev
Author: rgoj
Date: 2010-06-30 08:36:31 +0000 (Wed, 30 Jun 2010)
Log Message:
-----------
* Adding implementations of a dipole in a spherical head model
** First, and implementation of a lead field for a homogeneous infinite conductor
** Implementation of formulas from Brody 1973
** Implementation of formulas from Frank 1952 (with problems, however!)
** Implementation can be selected by commenting out appropriate lines of code
** Brody 1973 is selected as the default implementation
** WARNING: All formulas are now being calculated each time a lead field is calculated - this is extremely resource consuming, something should be done about it.
Modified Paths:
--------------
trunk/src/HeadModelDipoleSphere.py
Modified: trunk/src/HeadModelDipoleSphere.py
===================================================================
--- trunk/src/HeadModelDipoleSphere.py 2010-06-27 19:43:32 UTC (rev 143)
+++ trunk/src/HeadModelDipoleSphere.py 2010-06-30 08:36:31 UTC (rev 144)
@@ -15,7 +15,7 @@
# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
-from numpy import arange, array, ones, identity, dot, zeros, sin, cos, pi, sqrt
+from numpy import arange, array, ones, identity, dot, zeros, sin, cos, pi, sqrt, sum, arccos
__metaclass__ = type # New style classes. Is this necessary?
"""
@@ -73,6 +73,9 @@
# The number of electrodes and generators defines the size of the lead field matrix
self.leadField = zeros((nElectrodes,nGenerators))
+ self.leadFieldInfinite = zeros((nElectrodes,nGenerators))
+ self.leadFieldBrody1973 = zeros((nElectrodes,nGenerators))
+ self.leadFieldFrank1952 = zeros((nElectrodes,nGenerators))
for iElectrode in range(nElectrodes):
# Calculating the coordinates of the electrode in the Cartesian coordinates associated with the head
@@ -84,6 +87,10 @@
xyzElectrodeHead[2] = self.radius * cos(electrodeTheta);
for iGenerator in range(nGenerators):
+ #
+ # Infinite homogeneous conductor
+ #
+
# Calculating the coordinates of the dipole in the Cartesian coordinates associated with the head
dipoleRadius = self.radius - self.head.generatorSiteList[iGenerator][0]
dipoleTheta = self.head.generatorSiteList[iGenerator][1]
@@ -102,24 +109,129 @@
distance += pow(xyzElectrodeDipole[1],2.0)
distance += pow(xyzElectrodeDipole[2],2.0)
distance = sqrt(distance)
+
+ # Rotation matrix for translating the coordinates of the electrode in the dipole coordinates parallel
+ # to the reference coordinates at the center of the head to dipole coordinates where the dipole is specified
+ # i.e. where the z axis is radial.
+ rotationMatrix = zeros((3,3));
+ dipoleTheta = self.head.generatorSiteList[iGenerator][1]
+ dipolePhi = self.head.generatorSiteList[iGenerator][2]
+ # Row 1
+ rotationMatrix[0,0] = sin(dipolePhi)
+ rotationMatrix[0,1] = -cos(dipolePhi)
+ rotationMatrix[0,2] = 0
+ # Row 2
+ rotationMatrix[1,0] = cos(dipoleTheta) * cos(dipolePhi)
+ rotationMatrix[1,1] = cos(dipoleTheta) * sin(dipolePhi)
+ rotationMatrix[1,2] = -sin(dipoleTheta)
+ # Row 3
+ rotationMatrix[2,0] = sin(dipoleTheta) * cos(dipolePhi)
+ rotationMatrix[2,1] = sin(dipoleTheta) * sin(dipolePhi)
+ rotationMatrix[2,2] = cos(dipoleTheta)
+
+ rotationMatrixHeadToDipole = rotationMatrix
- self.leadField[iElectrode, iGenerator] = 1.0
+ # The Electrode coordinates in the dipole rotated frame of reference and scaleda
+ xyzElectrodeDipoleRotatedScaled = dot(rotationMatrix, xyzElectrodeDipole) / distance
+ # The Orientation vector
+ orientationTheta = self.head.generatorSiteList[iGenerator][3]
+ orientationPhi = self.head.generatorSiteList[iGenerator][4]
+ xyzOrientationDipoleRotated = zeros(3);
+ xyzOrientationDipoleRotated[0] = sin(orientationTheta) * cos(orientationPhi);
+ xyzOrientationDipoleRotated[1] = sin(orientationTheta) * sin(orientationPhi);
+ xyzOrientationDipoleRotated[2] = cos(orientationTheta);
+
+ # The cosine of the angle between the dipole orientation and the electrode
+ cosAngleOrientationElectrode = sum(xyzElectrodeDipoleRotatedScaled * array(xyzOrientationDipoleRotated))
+
+ # Homogeneous conductor without boundaries
+ self.leadFieldInfinite[iElectrode, iGenerator] = cosAngleOrientationElectrode/distance/distance/4/pi/sigma
+
+ #
+ # Bounded spherical conductor
+ # Brody 1973
+ #
+ rCosPhi = dot(xyzElectrodeHead, xyzDipoleHead) / self.radius
+ #print rCosPhi
+
+ fieldVector = zeros(3);
+ for i in range(3):
+ fieldVector[i] = 2*(xyzElectrodeHead[i] - xyzDipoleHead[i])/pow(distance,2.0)
+ fieldVector[i] += (1/pow(self.radius,2.0)) * (xyzElectrodeHead[i] + (xyzElectrodeHead[i] * rCosPhi - self.radius * xyzDipoleHead[i])/(distance + self.radius - rCosPhi))
+ fieldVector[i] = fieldVector[i] / 4 / pi / sigma / distance
+
+ # Rotation matrix for translating the coordinates in the dipole frame of reference to the
+ # coordinates associated with the dipole parallel to the head coordinates.
+ rotationMatrix = zeros((3,3));
+ dipoleTheta = self.head.generatorSiteList[iGenerator][1]
+ dipolePhi = self.head.generatorSiteList[iGenerator][2]
+ # Row 1
+ rotationMatrix[0,0] = sin(dipolePhi)
+ rotationMatrix[0,1] = cos(dipoleTheta) * cos(dipolePhi)
+ rotationMatrix[0,2] = sin(dipoleTheta) * cos(dipolePhi)
+ # Row 2
+ rotationMatrix[1,0] = -cos(dipolePhi)
+ rotationMatrix[1,1] = cos(dipoleTheta) * sin(dipolePhi)
+ rotationMatrix[1,2] = sin(dipoleTheta) * sin(dipolePhi)
+ # Row 3
+ rotationMatrix[2,0] = 0
+ rotationMatrix[2,1] = -sin(dipoleTheta)
+ rotationMatrix[2,2] = cos(dipoleTheta)
+
+ rotationMatrixDipoleToHead = rotationMatrix
+
+ # Rotating Orientation to translated dipole coordinates
+ xyzOrientationDipole = dot(rotationMatrixDipoleToHead, xyzOrientationDipoleRotated)
+
+ self.leadFieldBrody1973[iElectrode, iGenerator] = dot(fieldVector, xyzOrientationDipole)
+
+ #
+ # Bounded spherical conductor
+ # Frank 1952
+ #
+ xyzElectrodeDipoleRotated = dot(rotationMatrixHeadToDipole, xyzElectrodeHead)
+ # The below line causes problems because of arccos!
+ phi = arccos(xyzElectrodeDipoleRotated[0] / xyzElectrodeDipoleRotated[1]) - orientationPhi
+ cosPhi = cos(phi)
+ psi = orientationTheta
+ cosPsi = cos(psi)
+ sinPsi = sin(psi)
+ cosTheta = dot(xyzDipoleHead,xyzElectrodeHead) / sqrt(dot( xyzDipoleHead, xyzDipoleHead )) / sqrt(dot( xyzElectrodeHead, xyzElectrodeHead))
+ sinTheta = sqrt(1-pow(cosTheta,2.0))
+ b = self.radius - self.head.generatorSiteList[iGenerator][0]
+ f = b/self.radius
+ self.leadFieldFrank1952[iElectrode, iGenerator] = cosPsi * (( 1-pow(f,2.0) )/pow( 1+pow(f,2.0)-2*f*cosTheta, 3/2)-1)
+ self.leadFieldFrank1952[iElectrode, iGenerator] += sinPsi*cosPhi/sinTheta* ( ( 3*f - 3*pow(f,2.0)*cosTheta + pow(f,3.0) - cosTheta )/pow(1+pow(f,2.0)-2*f*cosTheta,3/2) + cosTheta )
+ self.leadFieldFrank1952[iElectrode, iGenerator] = self.leadFieldFrank1952[iElectrode, iGenerator] / 4 /pi / sigma / self.radius / b
+
def runHeadModel(self, generatorOutput, recording):
# Calculating the lead field
self.calculateLeadField()
- print self.leadField
- print (array([generatorOutput])).transpose()
-
# Calculating the recording by multyplying the lead field by the generator output
newRecording = dot(self.leadField, (array([generatorOutput])).transpose())
+ newRecordingInfinite = dot(self.leadFieldInfinite, (array([generatorOutput])).transpose())
+ newRecordingBrody1973 = dot(self.leadFieldBrody1973, (array([generatorOutput])).transpose())
+ newRecordingFrank1952 = dot(self.leadFieldFrank1952, (array([generatorOutput])).transpose())
# Converting the new recording to list format for compatibility with rest of the code
newRecording = list(newRecording[:,0])
+ newRecordingInfinite = list(newRecordingInfinite[:,0])
+ newRecordingBrody1973 = list(newRecordingBrody1973[:,0])
+ newRecordingFrank1952 = list(newRecordingFrank1952[:,0])
- print newRecording
-
+ for i in range(len(newRecording)):
+ # All three of the lead field calculation methods implemented above can be used, however
+ # only Brody1973 and Frank1952 give results in a bounded homogeneous conducting sphere,
+ # and of these only Brody1973 gives results for all combinations of angles, etc.
+ # Additionally, due to and arccos in my implementation above, Frank1952 for now gives even
+ # worse results than it should for many angles...
+ newRecording[i] = newRecordingBrody1973[i]
+ #newRecording[i] = newRecordingFrank1952[i]
+ #newRecording[i] = newRecordingInfinite[i]
+ #newRecording[i] = (newRecordingBrody1973[i])/(newRecordingFrank1952[i])
+
for channel in range(len(recording)):
recording[channel].append(newRecording[channel])
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From: <rg...@us...> - 2010-06-27 19:43:38
|
Revision: 143
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=143&view=rev
Author: rgoj
Date: 2010-06-27 19:43:32 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Preparing for the presentation of dipoles with different rotations in the dipolar model example.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2010-06-27 17:14:44 UTC (rev 142)
+++ trunk/src/PyBrainSim.py 2010-06-27 19:43:32 UTC (rev 143)
@@ -281,33 +281,51 @@
def menuButton9(self, control):
# head will hold sources, registrations sites and the head model
- head = Head()
+ head1 = Head()
+ head2 = Head()
+ head3 = Head()
# headModel will be our single sphere head model
- headModel = HeadModelDipoleSphere(head, 10.0)
+ headModel1 = HeadModelDipoleSphere(head1, 10.0)
+ headModel2 = HeadModelDipoleSphere(head2, 10.0)
+ headModel3 = HeadModelDipoleSphere(head3, 10.0)
# We need only one data point per simulation
- head.setSamplingFrequency(1)
+ head1.setSamplingFrequency(1)
+ head2.setSamplingFrequency(1)
+ head3.setSamplingFrequency(1)
# Adding registration sites
nElectrodes = 200
angles = []
for i in range(nElectrodes):
angles.append(i*numpy.pi/(nElectrodes-1) - numpy.pi/2)
- head.addRegistrationSite([angles[-1],numpy.pi/2])
+ head1.addRegistrationSite([angles[-1],numpy.pi/2])
+ head2.addRegistrationSite([angles[-1],numpy.pi/2])
+ head3.addRegistrationSite([angles[-1],numpy.pi/2])
# Adding a generator
- orientation = 0;
- generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, orientation, 0, 0], mean=1, stddev=0.1)
+ orientation1= 0;
+ orientation2= numpy.pi/2;
+ orientation3= numpy.pi/4;
+ generator1 = GeneratorNoisy('Gen', head1, position = [ 0.3, 0, orientation1, 0, 0], mean=1, stddev=0.1)
+ generator2 = GeneratorNoisy('Gen', head2, position = [ 0.3, 0, orientation2, 0, 0], mean=1, stddev=0.1)
+ generator3 = GeneratorNoisy('Gen', head3, position = [ 0.3, 0, orientation3, 0, 0], mean=1, stddev=0.1)
# Run the simulation just once (or, equivalently for one second with the sampling rate of 1 Hz)
- simulatedData = numpy.array(head.runSimulation(1))
+ simulatedData1 = numpy.array(head1.runSimulation(1))
+ simulatedData2 = numpy.array(head2.runSimulation(1))
+ simulatedData3 = numpy.array(head3.runSimulation(1))
- print(simulatedData)
- pylab.plot(angles,simulatedData)
+ pylab.subplot(311)
+ pylab.plot(angles,simulatedData1)
+ pylab.title("Potential from superficial dipoles of different orientations")
+ pylab.subplot(312)
+ pylab.plot(angles,simulatedData2)
+ pylab.subplot(313)
+ pylab.plot(angles,simulatedData3)
pylab.xlabel("Location of measurement on scalp [radians]")
- pylab.ylabel("Potential on scalp [arbitrary units]")
- pylab.title("Potential from superficial dipole of orientation " + str(orientation))
+ pylab.ylabel("Scalp potential [relative]")
pylab.show()
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From: <rg...@us...> - 2010-06-27 17:14:50
|
Revision: 142
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=142&view=rev
Author: rgoj
Date: 2010-06-27 17:14:44 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Added a plot to the dipole spherical head model example.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2010-06-27 16:41:28 UTC (rev 141)
+++ trunk/src/PyBrainSim.py 2010-06-27 17:14:44 UTC (rev 142)
@@ -290,17 +290,25 @@
head.setSamplingFrequency(1)
# Adding registration sites
- nElectrodes = 20
+ nElectrodes = 200
+ angles = []
for i in range(nElectrodes):
- head.addRegistrationSite([i*numpy.pi/(nElectrodes-1),numpy.pi/2])
+ angles.append(i*numpy.pi/(nElectrodes-1) - numpy.pi/2)
+ head.addRegistrationSite([angles[-1],numpy.pi/2])
- # Adding generators
- generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
+ # Adding a generator
+ orientation = 0;
+ generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, orientation, 0, 0], mean=1, stddev=0.1)
# Run the simulation just once (or, equivalently for one second with the sampling rate of 1 Hz)
simulatedData = numpy.array(head.runSimulation(1))
print(simulatedData)
+ pylab.plot(angles,simulatedData)
+ pylab.xlabel("Location of measurement on scalp [radians]")
+ pylab.ylabel("Potential on scalp [arbitrary units]")
+ pylab.title("Potential from superficial dipole of orientation " + str(orientation))
+ pylab.show()
def menuButtonQuit(self, control):
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From: <rg...@us...> - 2010-06-27 16:41:35
|
Revision: 141
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=141&view=rev
Author: rgoj
Date: 2010-06-27 16:41:28 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Changes to dipole source example:
** No noise at level of electrode
** Easy to specify number of evenly spaced electrodes
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2010-06-27 16:33:45 UTC (rev 140)
+++ trunk/src/PyBrainSim.py 2010-06-27 16:41:28 UTC (rev 141)
@@ -290,24 +290,16 @@
head.setSamplingFrequency(1)
# Adding registration sites
- head.addRegistrationSite([-numpy.pi/2, numpy.pi/2])
- head.addRegistrationSite([-numpy.pi/4, numpy.pi/2])
- head.addRegistrationSite([0, numpy.pi/2])
- head.addRegistrationSite([numpy.pi/4, numpy.pi/2])
- head.addRegistrationSite([numpy.pi/2, numpy.pi/2])
+ nElectrodes = 20
+ for i in range(nElectrodes):
+ head.addRegistrationSite([i*numpy.pi/(nElectrodes-1),numpy.pi/2])
# Adding generators
generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
- generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
- generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
# Run the simulation just once (or, equivalently for one second with the sampling rate of 1 Hz)
- simulatedData = numpy.array(head.runSimulation(5))
+ simulatedData = numpy.array(head.runSimulation(1))
- # Add Gaussian noise with mean 0 and variance 1
- electrodeNoise = numpy.random.normal(0, 0.0000001, simulatedData.shape);
- simulatedData = simulatedData + electrodeNoise
-
print(simulatedData)
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From: <rg...@us...> - 2010-06-27 16:33:51
|
Revision: 140
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=140&view=rev
Author: rgoj
Date: 2010-06-27 16:33:45 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Added an example usage of the work in progress dipole single sphere head model. This example will be modified later to actually show something interesting.
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2010-06-27 15:56:09 UTC (rev 139)
+++ trunk/src/PyBrainSim.py 2010-06-27 16:33:45 UTC (rev 140)
@@ -38,11 +38,13 @@
from Head import Head
from HeadModel import HeadModel
from HeadModelHalfSphere import HeadModelHalfSphere
+from HeadModelDipoleSphere import HeadModelDipoleSphere
from Experiment import Experiment
from Stimulus import Stimulus
from StimulusDummy import StimulusDummy
from GeneratorDummy import GeneratorDummy
from GeneratorNumberIncrementing import GeneratorNumberIncrementing
+from GeneratorNoisy import GeneratorNoisy
from GeneratorSine import GeneratorSine
from Connection import Connection
from ConnectionDummy import ConnectionDummy
@@ -61,6 +63,7 @@
self.frame.Bind(wx.EVT_BUTTON, self.menuButton6, id=xrc.XRCID("menuButton6"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButton7, id=xrc.XRCID("menuButton7"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton9, id=xrc.XRCID("menuButton9"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
self.frame.Show()
@@ -276,6 +279,38 @@
pylab.plot(recording[i][firstPointToDisplay:])
pylab.show()
+ def menuButton9(self, control):
+ # head will hold sources, registrations sites and the head model
+ head = Head()
+
+ # headModel will be our single sphere head model
+ headModel = HeadModelDipoleSphere(head, 10.0)
+
+ # We need only one data point per simulation
+ head.setSamplingFrequency(1)
+
+ # Adding registration sites
+ head.addRegistrationSite([-numpy.pi/2, numpy.pi/2])
+ head.addRegistrationSite([-numpy.pi/4, numpy.pi/2])
+ head.addRegistrationSite([0, numpy.pi/2])
+ head.addRegistrationSite([numpy.pi/4, numpy.pi/2])
+ head.addRegistrationSite([numpy.pi/2, numpy.pi/2])
+
+ # Adding generators
+ generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
+ generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
+ generator = GeneratorNoisy('Gen', head, position = [ 0.3, 0, 0, 0, 0], mean=1, stddev=0.1)
+
+ # Run the simulation just once (or, equivalently for one second with the sampling rate of 1 Hz)
+ simulatedData = numpy.array(head.runSimulation(5))
+
+ # Add Gaussian noise with mean 0 and variance 1
+ electrodeNoise = numpy.random.normal(0, 0.0000001, simulatedData.shape);
+ simulatedData = simulatedData + electrodeNoise
+
+ print(simulatedData)
+
+
def menuButtonQuit(self, control):
self.Exit()
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|
|
From: <rg...@us...> - 2010-06-27 15:56:15
|
Revision: 139
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=139&view=rev
Author: rgoj
Date: 2010-06-27 15:56:09 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Adding a new menu button to the PyBrainSim.py script for showcasing the new work in progress dipole model, this doesn't do anything yet.
Modified Paths:
--------------
trunk/src/PyBrainSimGUI1.xrc
Modified: trunk/src/PyBrainSimGUI1.xrc
===================================================================
--- trunk/src/PyBrainSimGUI1.xrc 2010-06-27 15:31:45 UTC (rev 138)
+++ trunk/src/PyBrainSimGUI1.xrc 2010-06-27 15:56:09 UTC (rev 139)
@@ -1,103 +1,113 @@
<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<resource xmlns="http://www.wxwindows.org/wxxrc" version="2.3.0.1">
- <object class="wxFrame" name="menuFrame">
- <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
- <size>450,390</size>
- <title>PyBrainSim: Choose example simulation</title>
- <object class="wxPanel" name="menuPanel">
- <style>wxTAB_TRAVERSAL</style>
- <object class="wxBoxSizer">
- <orient>wxVERTICAL</orient>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton1">
- <label>Example dummy simulation</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton2">
- <label>Number generator and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton3">
- <label>Two number generators and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton4">
- <label>Sine generator and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton5">
- <label>Random sine generators and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton6">
- <label>Two sine generators, two recording sites and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton7">
- <label>Dummy 3D head model</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton8">
- <label>Neural mass model of a single cortical area</label>
- <default>1</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxEXPAND | wxALL</flag>
- <border>5</border>
- <object class="wxStaticLine" name="m_staticline2">
- <style>wxLI_HORIZONTAL</style>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL</flag>
- <border>5</border>
- <object class="wxButton" name="menuButtonQuit">
- <label>Quit</label>
- <default>0</default>
- </object>
- </object>
- </object>
- </object>
- </object>
+ <object class="wxFrame" name="menuFrame">
+ <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
+ <size>449,450</size>
+ <title>PyBrainSim: Choose example simulation</title>
+ <object class="wxPanel" name="menuPanel">
+ <style>wxTAB_TRAVERSAL</style>
+ <object class="wxBoxSizer">
+ <orient>wxVERTICAL</orient>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton1">
+ <label>Example dummy simulation</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton2">
+ <label>Number generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton3">
+ <label>Two number generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton4">
+ <label>Sine generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton5">
+ <label>Random sine generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton6">
+ <label>Sine generator, stimuli and two recording sites</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton7">
+ <label>Dummy 3D head model</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton8">
+ <label>Neural mass model of a single cortical area</label>
+ <default>1</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton9">
+ <label>Dipole sources in a conducting sphere</label>
+ <default>1</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxEXPAND | wxALL</flag>
+ <border>5</border>
+ <object class="wxStaticLine" name="m_staticline2">
+ <style>wxLI_HORIZONTAL</style>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButtonQuit">
+ <label>Quit</label>
+ <default>0</default>
+ </object>
+ </object>
+ </object>
+ </object>
+ </object>
</resource>
+
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|
|
From: <rg...@us...> - 2010-06-27 15:31:51
|
Revision: 138
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=138&view=rev
Author: rgoj
Date: 2010-06-27 15:31:45 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Adding a work in progress of a single conducting sphere head model with generators as dipoles at last!
Added Paths:
-----------
trunk/src/HeadModelDipoleSphere.py
Added: trunk/src/HeadModelDipoleSphere.py
===================================================================
--- trunk/src/HeadModelDipoleSphere.py (rev 0)
+++ trunk/src/HeadModelDipoleSphere.py 2010-06-27 15:31:45 UTC (rev 138)
@@ -0,0 +1,126 @@
+# 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 numpy import arange, array, ones, identity, dot, zeros, sin, cos, pi, sqrt
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+This reimplemenation of the HeadModel class models the head as a single
+conductant sphere containing dipolar sources.
+"""
+
+from HeadModel import HeadModel
+
+class HeadModelDipoleSphere(HeadModel):
+ def __init__(self, head, radius):
+ HeadModel.__init__(self, head)
+ self.head = head
+ self.radius = radius # Radius of the head in [cm]
+ self.leadField = 0;
+
+ def checkPosition(self,position):
+ # Checking if position is a list of two or five numbers
+ # The position of each registration site is given in spherical coordinates
+ # associated with the center of the spherical head. The radial coordinate of the electrode
+ # is always equal to the radius of the head, hence it doesn't need to be specified.
+ # The only two parameters that need to be specified are the angles theta and phi in this
+ # order.
+ # For each generator, all three cordinates must be given: the depth of the dipole and the
+ # theta and phi angles. Additionaly, angles specyfying the orientation of the dipole in
+ # the spherical coordinates of the dipole must also be given. The theta angle is then the
+ # orientation with respect to the surface of the head - i.e. theta = 0 means a radial
+ # dipole, while theta = pi/2 means a tangential dipole. Only values in this range are
+ # allowed! The specification of the phi angle is considered less important and should be
+ # explained more thoroughly in other documentation.
+ if not isinstance(position, list):
+ return False
+ if len(position) != 2 and len(position) != 5:
+ return False
+ # Check the radial coordinate (depth) of the dipole
+ if len(position) == 5 and (position[0] <= 0 or position[0] >= self.radius):
+ return False
+ # Check the theta angle of the orientation of the dipole
+ if len(position) == 5 and (position[3] < 0 or position[3] > pi/2):
+ return False
+ for i in range(len(position)):
+ if (not isinstance(position[i], float)) and (not isinstance(position[i], int)):
+ return False
+
+ # If none of the conditions above fail, the position is correct
+ return True
+
+ def calculateLeadField(self):
+ # How many generators and electrodes do we have?
+ nGenerators = len(self.head.generatorSiteList)
+ nElectrodes = len(self.head.registrationSiteList)
+
+ # Assuming ideal conductivity
+ sigma = 1.0
+
+ # The number of electrodes and generators defines the size of the lead field matrix
+ self.leadField = zeros((nElectrodes,nGenerators))
+
+ for iElectrode in range(nElectrodes):
+ # Calculating the coordinates of the electrode in the Cartesian coordinates associated with the head
+ electrodeTheta = self.head.registrationSiteList[iElectrode][0]
+ electrodePhi = self.head.registrationSiteList[iElectrode][1]
+ xyzElectrodeHead = zeros(3);
+ xyzElectrodeHead[0] = self.radius * sin(electrodeTheta) * cos(electrodePhi);
+ xyzElectrodeHead[1] = self.radius * sin(electrodeTheta) * sin(electrodePhi);
+ xyzElectrodeHead[2] = self.radius * cos(electrodeTheta);
+
+ for iGenerator in range(nGenerators):
+ # Calculating the coordinates of the dipole in the Cartesian coordinates associated with the head
+ dipoleRadius = self.radius - self.head.generatorSiteList[iGenerator][0]
+ dipoleTheta = self.head.generatorSiteList[iGenerator][1]
+ dipolePhi = self.head.generatorSiteList[iGenerator][2]
+ xyzDipoleHead = zeros(3);
+ xyzDipoleHead[0] = dipoleRadius * sin(dipoleTheta) * cos(dipolePhi);
+ xyzDipoleHead[1] = dipoleRadius * sin(dipoleTheta) * sin(dipolePhi);
+ xyzDipoleHead[2] = dipoleRadius * cos(dipoleTheta);
+
+ # Calculating the coordinates of the electrode in the coordinates associated with the dipole
+ xyzElectrodeDipole = xyzElectrodeHead - xyzDipoleHead;
+
+ # Calculating the distance between the dipole and the electrode
+ distance = 0;
+ distance += pow(xyzElectrodeDipole[0],2.0)
+ distance += pow(xyzElectrodeDipole[1],2.0)
+ distance += pow(xyzElectrodeDipole[2],2.0)
+ distance = sqrt(distance)
+
+ self.leadField[iElectrode, iGenerator] = 1.0
+
+ def runHeadModel(self, generatorOutput, recording):
+ # Calculating the lead field
+ self.calculateLeadField()
+
+ print self.leadField
+ print (array([generatorOutput])).transpose()
+
+ # Calculating the recording by multyplying the lead field by the generator output
+ newRecording = dot(self.leadField, (array([generatorOutput])).transpose())
+
+ # Converting the new recording to list format for compatibility with rest of the code
+ newRecording = list(newRecording[:,0])
+
+ print newRecording
+
+ for channel in range(len(recording)):
+ recording[channel].append(newRecording[channel])
+
+ return recording
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|
|
From: <rg...@us...> - 2010-06-27 15:30:04
|
Revision: 137
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=137&view=rev
Author: rgoj
Date: 2010-06-27 15:29:58 +0000 (Sun, 27 Jun 2010)
Log Message:
-----------
* Added a Generator that returns a normally distributed number every time it is ran.
Added Paths:
-----------
trunk/src/GeneratorNoisy.py
Added: trunk/src/GeneratorNoisy.py
===================================================================
--- trunk/src/GeneratorNoisy.py (rev 0)
+++ trunk/src/GeneratorNoisy.py 2010-06-27 15:29:58 UTC (rev 137)
@@ -0,0 +1,45 @@
+# PyBrainSim
+# Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# PyBrainSim is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
+
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+The GeneratorNoisy class is a reimplementation of the Generator class. It
+provides a simple generator which, whenever required, generates a number
+generated from a Gaussian distribution with specified mean and variance.
+"""
+
+from numpy.random import normal
+
+from Generator import Generator
+
+class GeneratorNoisy(Generator):
+ def __init__(self, name, head, position = [0,0,0], mean = 0, stddev = 0):
+ Generator.__init__(self, name, head, position)
+ self.mean = mean
+ self.stddev = stddev
+
+ def printInfo(self):
+ print(self.name + ": A GeneratorNoisy object")
+
+ def runGenerator(self, time):
+ if self.stddev == 0:
+ self.activation = self.mean
+ else:
+ self.activation = normal(self.mean, self.stddev)
+
+ return self.activation
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|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-09-14 00:52:21
|
#109: Make the text displayed to standard output display in a graphical log
-----------------------+----------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Simple graphical user interface
Component: Interface | Resolution: fixed
Keywords: |
-----------------------+----------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/109#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...> - 2009-09-14 00:50:56
|
Revision: 136
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=136&view=rev
Author: rgoj
Date: 2009-09-14 00:50:41 +0000 (Mon, 14 Sep 2009)
Log Message:
-----------
* Simulations that presented their output via stdandard output, now print to the output log window.
* Removed simulation progress information from the neural mass simulation, because somehow it just won't get displayed in the log window...
Modified Paths:
--------------
trunk/src/PyBrainSim.py
Modified: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-09-14 00:48:51 UTC (rev 135)
+++ trunk/src/PyBrainSim.py 2009-09-14 00:50:41 UTC (rev 136)
@@ -49,9 +49,10 @@
class PyBrainSimGUI(wx.App):
def OnInit(self):
- self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
+ self.res1 = xrc.XmlResource("PyBrainSimGUI1.xrc")
+ self.res2 = xrc.XmlResource("PyBrainSimGUI2.xrc")
- self.frame = self.res.LoadFrame(None, "menuFrame")
+ self.frame = self.res1.LoadFrame(None, "menuFrame")
self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButton2, id=xrc.XRCID("menuButton2"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButton3, id=xrc.XRCID("menuButton3"))
@@ -62,6 +63,10 @@
self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
self.frame.Show()
+
+ self.logWindow = self.res2.LoadFrame(None, "outputWindow")
+ self.log = xrc.XRCCTRL(self.logWindow, "outputLog")
+
return True
def menuButton1(self, control):
@@ -75,8 +80,9 @@
exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print(exampleExperiment.getRecording())
+ output = str(exampleExperiment.getRecording())
+ self.log.SetValue(output)
+ self.logWindow.Show()
def menuButton2(self, control):
exampleHead = Head()
@@ -90,8 +96,9 @@
exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
+ output = str(exampleExperiment.getRecording())
+ self.log.SetValue(output)
+ self.logWindow.Show()
def menuButton3(self, control):
exampleHead = Head()
@@ -113,8 +120,9 @@
exampleConnection2 = Connection('Con2', exampleHead, exampleStimulus2, exampleGenerator2)
exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
+ output = str(exampleExperiment.getRecording())
+ self.log.SetValue(output)
+ self.logWindow.Show()
def menuButton4(self, control):
exampleHead = Head()
@@ -126,14 +134,11 @@
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()
def menuButton5(self, control):
@@ -230,7 +235,6 @@
cC3=0.25*cC1
cC4=0.25*cC1
noise = noiseObject.getNoise(t)
- #print("Time: " + str(t) + " Noise: " + str(noise))
return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
@@ -251,7 +255,7 @@
r = []
recording = [ [], [], [], [], [], [] ]
parameter = [ 68, 128, 135, 270, 675, 1350 ]
-
+
# Differential equation integration
for i in range(len(parameter)):
# Preparing the integration
@@ -259,7 +263,6 @@
r[i].set_initial_value(y0, t0)
r[i].set_f_params( someNoise, parameter[i] )
# Integrating
- print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
while r[i].successful() and r[i].t < timeSpan:
r[i].integrate(r[i].t+dtime)
recording[i].append(r[i].y[2] - r[i].y[4])
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|
|
From: <rg...@us...> - 2009-09-14 00:48:58
|
Revision: 135
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=135&view=rev
Author: rgoj
Date: 2009-09-14 00:48:51 +0000 (Mon, 14 Sep 2009)
Log Message:
-----------
* Adding a renamed version of PyBrainSimGUI.xrc
* Corrected description of one of the simulations
Added Paths:
-----------
trunk/src/PyBrainSimGUI1.xrc
Added: trunk/src/PyBrainSimGUI1.xrc
===================================================================
--- trunk/src/PyBrainSimGUI1.xrc (rev 0)
+++ trunk/src/PyBrainSimGUI1.xrc 2009-09-14 00:48:51 UTC (rev 135)
@@ -0,0 +1,103 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<resource xmlns="http://www.wxwindows.org/wxxrc" version="2.3.0.1">
+ <object class="wxFrame" name="menuFrame">
+ <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
+ <size>450,390</size>
+ <title>PyBrainSim: Choose example simulation</title>
+ <object class="wxPanel" name="menuPanel">
+ <style>wxTAB_TRAVERSAL</style>
+ <object class="wxBoxSizer">
+ <orient>wxVERTICAL</orient>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton1">
+ <label>Example dummy simulation</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton2">
+ <label>Number generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton3">
+ <label>Two number generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton4">
+ <label>Sine generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton5">
+ <label>Random sine generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton6">
+ <label>Two sine generators, two recording sites and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton7">
+ <label>Dummy 3D head model</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton8">
+ <label>Neural mass model of a single cortical area</label>
+ <default>1</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxEXPAND | wxALL</flag>
+ <border>5</border>
+ <object class="wxStaticLine" name="m_staticline2">
+ <style>wxLI_HORIZONTAL</style>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButtonQuit">
+ <label>Quit</label>
+ <default>0</default>
+ </object>
+ </object>
+ </object>
+ </object>
+ </object>
+</resource>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-09-14 00:48:01
|
Revision: 134
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=134&view=rev
Author: rgoj
Date: 2009-09-14 00:47:55 +0000 (Mon, 14 Sep 2009)
Log Message:
-----------
* Removing, because of name change.
Removed Paths:
-------------
trunk/src/PyBrainSimGUI.xrc
Deleted: trunk/src/PyBrainSimGUI.xrc
===================================================================
--- trunk/src/PyBrainSimGUI.xrc 2009-09-14 00:45:53 UTC (rev 133)
+++ trunk/src/PyBrainSimGUI.xrc 2009-09-14 00:47:55 UTC (rev 134)
@@ -1,104 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
-<resource xmlns="http://www.wxwindows.org/wxxrc" version="2.3.0.1">
- <object class="wxFrame" name="menuFrame">
- <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
- <size>450,390</size>
- <title>PyBrainSim: Choose example simulation</title>
- <object class="wxPanel" name="menuPanel">
- <style>wxTAB_TRAVERSAL</style>
- <object class="wxBoxSizer">
- <orient>wxVERTICAL</orient>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton1">
- <label>Example dummy simulation</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton2">
- <label>Number generator and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton3">
- <label>Two number generators and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton4">
- <label>Sine generator and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton5">
- <label>Random sine generators and stimuli</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton6">
- <label>Sine generator, stimuli and two recording sites</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton7">
- <label>Dummy 3D head model</label>
- <default>0</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
- <border>5</border>
- <object class="wxButton" name="menuButton8">
- <label>Neural mass model of a single cortical area</label>
- <default>1</default>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxEXPAND | wxALL</flag>
- <border>5</border>
- <object class="wxStaticLine" name="m_staticline2">
- <style>wxLI_HORIZONTAL</style>
- </object>
- </object>
- <object class="sizeritem">
- <option>0</option>
- <flag>wxALL|wxALIGN_CENTER_HORIZONTAL</flag>
- <border>5</border>
- <object class="wxButton" name="menuButtonQuit">
- <label>Quit</label>
- <default>0</default>
- </object>
- </object>
- </object>
- </object>
- </object>
-</resource>
-
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|
|
From: <rg...@us...> - 2009-09-14 00:45:58
|
Revision: 133
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=133&view=rev
Author: rgoj
Date: 2009-09-14 00:45:53 +0000 (Mon, 14 Sep 2009)
Log Message:
-----------
* Added XML resources for a second window, for the output log.
Added Paths:
-----------
trunk/src/PyBrainSimGUI2.xrc
Added: trunk/src/PyBrainSimGUI2.xrc
===================================================================
--- trunk/src/PyBrainSimGUI2.xrc (rev 0)
+++ trunk/src/PyBrainSimGUI2.xrc 2009-09-14 00:45:53 UTC (rev 133)
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<resource xmlns="http://www.wxwindows.org/wxxrc" version="2.3.0.1">
+ <object class="wxFrame" name="outputWindow">
+ <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
+ <size>500,86</size>
+ <title>PyBrainSim: Simulation results</title>
+ <object class="wxPanel" name="outputWindowPanel">
+ <style>wxTAB_TRAVERSAL</style>
+ <object class="wxBoxSizer">
+ <orient>wxVERTICAL</orient>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxTextCtrl" name="outputLog">
+ <style>wxTE_MULTILINE</style>
+ <value></value>
+ <maxlength>0</maxlength>
+ </object>
+ </object>
+ </object>
+ </object>
+ </object>
+</resource>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-09-13 23:40:43
|
Revision: 132
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=132&view=rev
Author: rgoj
Date: 2009-09-13 23:40:34 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* PyBrainSimGUI.py becomes PyBrainSim.py
* We now have a graphical interface!
Added Paths:
-----------
trunk/src/PyBrainSim.py
Removed Paths:
-------------
trunk/src/PyBrainSimGUI.pyw
Copied: trunk/src/PyBrainSim.py (from rev 130, trunk/src/PyBrainSimGUI.pyw)
===================================================================
--- trunk/src/PyBrainSim.py (rev 0)
+++ trunk/src/PyBrainSim.py 2009-09-13 23:40:34 UTC (rev 132)
@@ -0,0 +1,281 @@
+#!/usr/bin/python
+
+# 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/>.
+
+"""
+PyBrainSim is an interactive tool for the simulation and visualization of the
+electromagnetic activity of the brain, currently under development.
+
+This script allows you to choose from a few example simulations, ranging from
+adding numbers to neural mass models.
+
+pybrainsim.sourceforge.net
+"""
+
+import wx
+from wx import xrc
+
+import numpy
+import pylab
+from random import random
+from scipy.integrate import ode
+
+from Head import Head
+from HeadModel import HeadModel
+from HeadModelHalfSphere import HeadModelHalfSphere
+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
+
+class PyBrainSimGUI(wx.App):
+ def OnInit(self):
+ self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
+
+ self.frame = self.res.LoadFrame(None, "menuFrame")
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton2, id=xrc.XRCID("menuButton2"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton3, id=xrc.XRCID("menuButton3"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton4, id=xrc.XRCID("menuButton4"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton5, id=xrc.XRCID("menuButton5"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton6, id=xrc.XRCID("menuButton6"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton7, id=xrc.XRCID("menuButton7"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
+ self.frame.Show()
+ return True
+
+ def menuButton1(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = StimulusDummy('Stim', exampleHead)
+ exampleGenerator = GeneratorDummy('Gen', exampleHead)
+ exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print(exampleExperiment.getRecording())
+
+ def menuButton2(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes([0.3, 0.6])
+ exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton3(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
+ exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
+
+ exampleStimulus1 = Stimulus('Stim1', exampleHead)
+ exampleStimulus2 = Stimulus('Stim2', exampleHead)
+ 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.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton4(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ 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()
+
+ def menuButton5(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ 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):
+ 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]))
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ exampleExperiment.plotRecording()
+
+ def menuButton6(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModelHalfSphere(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ 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]])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ 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()))
+ exampleExperiment.plotRecording()
+
+ def menuButton7(self, control):
+ exampleHead = Head()
+ exampleHead.displayHead()
+
+ def menuButton8(self, control):
+ # This class will produce noise that will be fed into the modelled
+ # cortical area as input.
+ class NeuralNoise:
+ def __init__(self, timeSpan, dtime):
+ self.noise = []
+ self.dtime = dtime
+ self.timePoints = range( int(timeSpan//dtime+1) )
+ # Random noise distributed evenly between 120 and 320
+ for i in self.timePoints:
+ self.noise.append( 120+200*random() )
+ def getNoise(self, time):
+ # Searching for the appropriate time point
+ for i in self.timePoints:
+ if time < self.timePoints[i]*self.dtime:
+ # Interpolating between the randomly generated values
+ return self.noise[i] + \
+ (self.noise[i+1]-self.noise[i]) \
+ * ((self.timePoints[i]*self.dtime-time)/self.dtime)
+
+ # The sigmoid function
+ def sigmoidFunction(v):
+ """Constants taken from Jansen and Rit 1995, p. 360"""
+ cEzero = 2.5
+ cR = 0.56
+ cVzero = 6
+
+ """Sigmoid function taken from Jansen and Rit 1995, p. 360"""
+ return 2*cEzero / ( 1 + numpy.exp( cR*( cVzero - v ) ) )
+
+ # Defining the equations
+ def f(t, y, noiseObject, cC):
+ cA=3.25
+ ca=100.0
+ cB=22.0
+ cb=50.0
+ cC1=cC
+ cC2=0.8*cC1
+ cC3=0.25*cC1
+ cC4=0.25*cC1
+ noise = noiseObject.getNoise(t)
+ #print("Time: " + str(t) + " Noise: " + str(noise))
+ return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
+ ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
+ 2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
+ ) - 2*cb*y[5] - cb**2*y[4]]
+
+ # How many seconds should be modelled and how accurately
+ timeSpan = 3
+ dtime = 0.001
+ firstPointToDisplay = 1000
+
+ # A noise object that will be used as input into the equations
+ someNoise = NeuralNoise(timeSpan+1, dtime*10)
+
+ # Initial conditions
+ y0, t0 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 0
+
+ # Preparing for simulations
+ r = []
+ recording = [ [], [], [], [], [], [] ]
+ parameter = [ 68, 128, 135, 270, 675, 1350 ]
+
+ # Differential equation integration
+ for i in range(len(parameter)):
+ # Preparing the integration
+ r.append(ode(f).set_integrator('vode', method='bdf'))
+ r[i].set_initial_value(y0, t0)
+ r[i].set_f_params( someNoise, parameter[i] )
+ # Integrating
+ print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
+ while r[i].successful() and r[i].t < timeSpan:
+ r[i].integrate(r[i].t+dtime)
+ recording[i].append(r[i].y[2] - r[i].y[4])
+
+ # Show results of simulations
+ for i in range(len(parameter)):
+ pylab.subplot( len(parameter), 1, i+1)
+ if i==0:
+ pylab.title("Simulations based on Fig. 3 from Jansen and Rit 1995")
+ pylab.ylabel( "C = " + str(parameter[i]) )
+ pylab.plot(recording[i][firstPointToDisplay:])
+ pylab.show()
+
+ def menuButtonQuit(self, control):
+ self.Exit()
+
+if __name__ == '__main__':
+ app = PyBrainSimGUI(0)
+ app.MainLoop()
Property changes on: trunk/src/PyBrainSim.py
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mergeinfo
+
Deleted: trunk/src/PyBrainSimGUI.pyw
===================================================================
--- trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:39:27 UTC (rev 131)
+++ trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:40:34 UTC (rev 132)
@@ -1,281 +0,0 @@
-#!/usr/bin/python
-
-# 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/>.
-
-"""
-PyBrainSim is an interactive tool for the simulation and visualization of the
-electromagnetic activity of the brain, currently under development.
-
-This script allows you to choose from a few example simulations, ranging from
-adding numbers to neural mass models.
-
-pybrainsim.sourceforge.net
-"""
-
-import wx
-from wx import xrc
-
-import numpy
-import pylab
-from random import random
-from scipy.integrate import ode
-
-from Head import Head
-from HeadModel import HeadModel
-from HeadModelHalfSphere import HeadModelHalfSphere
-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
-
-class PyBrainSimGUI(wx.App):
- def OnInit(self):
- self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
-
- self.frame = self.res.LoadFrame(None, "menuFrame")
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton2, id=xrc.XRCID("menuButton2"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton3, id=xrc.XRCID("menuButton3"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton4, id=xrc.XRCID("menuButton4"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton5, id=xrc.XRCID("menuButton5"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton6, id=xrc.XRCID("menuButton6"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton7, id=xrc.XRCID("menuButton7"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
- self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
- self.frame.Show()
- return True
-
- def menuButton1(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleStimulus = StimulusDummy('Stim', exampleHead)
- exampleGenerator = GeneratorDummy('Gen', exampleHead)
- exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print(exampleExperiment.getRecording())
-
- def menuButton2(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleStimulus = Stimulus('Stim', exampleHead)
- exampleStimulus.setStimulusTimes([0.3, 0.6])
- exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
- exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
-
- def menuButton3(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
- exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
-
- exampleStimulus1 = Stimulus('Stim1', exampleHead)
- exampleStimulus2 = Stimulus('Stim2', exampleHead)
- 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.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
-
- def menuButton4(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(128)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- 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()
-
- def menuButton5(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- 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):
- 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]))
-
- exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
- exampleExperiment.plotRecording()
-
- def menuButton6(self, control):
- exampleHead = Head()
- exampleHeadModel = HeadModelHalfSphere(exampleHead)
- exampleHead.setSamplingFrequency(128)
- 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]])
-
- exampleStimulus = Stimulus('Stim', exampleHead)
- exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
- 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()))
- exampleExperiment.plotRecording()
-
- def menuButton7(self, control):
- exampleHead = Head()
- exampleHead.displayHead()
-
- def menuButton8(self, control):
- # This class will produce noise that will be fed into the modelled
- # cortical area as input.
- class NeuralNoise:
- def __init__(self, timeSpan, dtime):
- self.noise = []
- self.dtime = dtime
- self.timePoints = range( int(timeSpan//dtime+1) )
- # Random noise distributed evenly between 120 and 320
- for i in self.timePoints:
- self.noise.append( 120+200*random() )
- def getNoise(self, time):
- # Searching for the appropriate time point
- for i in self.timePoints:
- if time < self.timePoints[i]*self.dtime:
- # Interpolating between the randomly generated values
- return self.noise[i] + \
- (self.noise[i+1]-self.noise[i]) \
- * ((self.timePoints[i]*self.dtime-time)/self.dtime)
-
- # The sigmoid function
- def sigmoidFunction(v):
- """Constants taken from Jansen and Rit 1995, p. 360"""
- cEzero = 2.5
- cR = 0.56
- cVzero = 6
-
- """Sigmoid function taken from Jansen and Rit 1995, p. 360"""
- return 2*cEzero / ( 1 + numpy.exp( cR*( cVzero - v ) ) )
-
- # Defining the equations
- def f(t, y, noiseObject, cC):
- cA=3.25
- ca=100.0
- cB=22.0
- cb=50.0
- cC1=cC
- cC2=0.8*cC1
- cC3=0.25*cC1
- cC4=0.25*cC1
- noise = noiseObject.getNoise(t)
- #print("Time: " + str(t) + " Noise: " + str(noise))
- return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
- ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
- 2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
- ) - 2*cb*y[5] - cb**2*y[4]]
-
- # How many seconds should be modelled and how accurately
- timeSpan = 3
- dtime = 0.001
- firstPointToDisplay = 1000
-
- # A noise object that will be used as input into the equations
- someNoise = NeuralNoise(timeSpan+1, dtime*10)
-
- # Initial conditions
- y0, t0 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 0
-
- # Preparing for simulations
- r = []
- recording = [ [], [], [], [], [], [] ]
- parameter = [ 68, 128, 135, 270, 675, 1350 ]
-
- # Differential equation integration
- for i in range(len(parameter)):
- # Preparing the integration
- r.append(ode(f).set_integrator('vode', method='bdf'))
- r[i].set_initial_value(y0, t0)
- r[i].set_f_params( someNoise, parameter[i] )
- # Integrating
- print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
- while r[i].successful() and r[i].t < timeSpan:
- r[i].integrate(r[i].t+dtime)
- recording[i].append(r[i].y[2] - r[i].y[4])
-
- # Show results of simulations
- for i in range(len(parameter)):
- pylab.subplot( len(parameter), 1, i+1)
- if i==0:
- pylab.title("Simulations based on Fig. 3 from Jansen and Rit 1995")
- pylab.ylabel( "C = " + str(parameter[i]) )
- pylab.plot(recording[i][firstPointToDisplay:])
- pylab.show()
-
- def menuButtonQuit(self, control):
- self.Exit()
-
-if __name__ == '__main__':
- app = PyBrainSimGUI(0)
- app.MainLoop()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rg...@us...> - 2009-09-13 23:39:38
|
Revision: 131
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=131&view=rev
Author: rgoj
Date: 2009-09-13 23:39:27 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* Removing the old text based PyBrainSim.py script to make room for PyBrainSimGUI.
Removed Paths:
-------------
trunk/src/PyBrainSim.py
Deleted: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py 2009-09-13 23:37:32 UTC (rev 130)
+++ trunk/src/PyBrainSim.py 2009-09-13 23:39:27 UTC (rev 131)
@@ -1,265 +0,0 @@
-# PyBrainSim
-# Copyright 2009 Roman Goj
-#
-# This file is part of PyBrainSim.
-#
-# PyBrainSim is free software: you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-#
-# PyBrainSim is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along with
-# PyBrainSim. If not, see <http://www.gnu.org/licenses/>.
-
-"""
-PyBrainSim is an interactive tool for the simulation and visualization of the
-electromagnetic activity of the brain, currently under development.
-
-This script can be executed to run an example simulation, using the Head and
-GeneratorDummy classes. Currently it only generates a list of integer
-numbers... but work is under way to make it simulate the brain... Have fun!
-
-pybrainsim.sourceforge.net
-"""
-
-import numpy
-from random import random
-from scipy.integrate import ode
-
-from Head import Head
-from HeadModel import HeadModel
-from HeadModelHalfSphere import HeadModelHalfSphere
-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
-
-welcomeMessage = "\n\
-Welcome to this early version of PyBrainSim\n\n\
-Choose the type of simulation you would like to perform:\n\
- 1. Example dummy simulation\n\
- 2. Incrementing numbers, one generator and a stimulus\n\
- 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\
- 6. A single sinusoidal generator but with two registration sites\n\
- 7. A presentation of the 3d head model\n\
- 8. A model of a cortical area, based on Jansen and Rit 1995."
-
-print(welcomeMessage)
-userChoice = input("Your choice: ")
-print("\n")
-
-if userChoice == 1:
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleStimulus = StimulusDummy('Stim', exampleHead)
- exampleGenerator = GeneratorDummy('Gen', exampleHead)
- exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print(exampleExperiment.getRecording())
-elif userChoice == 2:
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleStimulus = Stimulus('Stim', exampleHead)
- exampleStimulus.setStimulusTimes([0.3, 0.6])
- exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
- exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
-elif userChoice == 3:
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(10)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
- exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
-
- exampleStimulus1 = Stimulus('Stim1', exampleHead)
- exampleStimulus2 = Stimulus('Stim2', exampleHead)
- 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.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
- print("\nSimulations resulted in the following recording:")
- print exampleExperiment.getRecording()
-elif userChoice == 4:
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- exampleHead.setSamplingFrequency(128)
- exampleHead.addRegistrationSite([0, 0, 0])
-
- 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()
-elif userChoice == 5:
- exampleHead = Head()
- exampleHeadModel = HeadModel(exampleHead)
- 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):
- 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]))
-
- 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, 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]])
-
- exampleStimulus = Stimulus('Stim', exampleHead)
- exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
- 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()))
- exampleExperiment.plotRecording()
-elif userChoice == 7:
- exampleHead = Head()
- exampleHead.displayHead()
-elif userChoice == 8:
- # This class will produce noise that will be fed into the modelled
- # cortical area as input.
- class NeuralNoise:
- def __init__(self, timeSpan, dtime):
- self.noise = []
- self.dtime = dtime
- self.timePoints = range( int(timeSpan//dtime+1) )
- # Random noise distributed evenly between 120 and 320
- for i in self.timePoints:
- self.noise.append( 120+200*random() )
- def getNoise(self, time):
- # Searching for the appropriate time point
- for i in self.timePoints:
- if time < self.timePoints[i]*self.dtime:
- # Interpolating between the randomly generated values
- return self.noise[i] + \
- (self.noise[i+1]-self.noise[i]) \
- * ((self.timePoints[i]*self.dtime-time)/self.dtime)
-
- # The sigmoid function
- def sigmoidFunction(v):
- """Constants taken from Jansen and Rit 1995, p. 360"""
- cEzero = 2.5
- cR = 0.56
- cVzero = 6
-
- """Sigmoid function taken from Jansen and Rit 1995, p. 360"""
- return 2*cEzero / ( 1 + numpy.exp( cR*( cVzero - v ) ) )
-
- # Defining the equations
- def f(t, y, noiseObject, cC):
- cA=3.25
- ca=100.0
- cB=22.0
- cb=50.0
- cC1=cC
- cC2=0.8*cC1
- cC3=0.25*cC1
- cC4=0.25*cC1
- noise = noiseObject.getNoise(t)
- #print("Time: " + str(t) + " Noise: " + str(noise))
- return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
- ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
- 2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
- ) - 2*cb*y[5] - cb**2*y[4]]
-
- # How many seconds should be modelled and how accurately
- timeSpan = 3
- dtime = 0.001
- firstPointToDisplay = 1000
-
- # A noise object that will be used as input into the equations
- someNoise = NeuralNoise(timeSpan+1, dtime*10)
-
- # Initial conditions
- y0, t0 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 0
-
- # Preparing for simulations
- r = []
- recording = [ [], [], [], [], [], [] ]
- parameter = [ 68, 128, 135, 270, 675, 1350 ]
-
- # Differential equation integration
- for i in range(len(parameter)):
- # Preparing the integration
- r.append(ode(f).set_integrator('vode', method='bdf'))
- r[i].set_initial_value(y0, t0)
- r[i].set_f_params( someNoise, parameter[i] )
- # Integrating
- print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
- while r[i].successful() and r[i].t < timeSpan:
- r[i].integrate(r[i].t+dtime)
- recording[i].append(r[i].y[2] - r[i].y[4])
-
- # Show results of simulations
- from pylab import *
- for i in range(len(parameter)):
- subplot( len(parameter), 1, i+1)
- if i==0:
- title("Simulations based on Fig. 3 from Jansen and Rit 1995")
- ylabel( "C = " + str(parameter[i]) )
- plot(recording[i][firstPointToDisplay:])
- show()
-else:
- print("No such option unfortunately...")
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|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-09-13 23:38:39
|
#108: Implement the main window allowing the user to graphically choose example
simulations.
-----------------------+----------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Simple graphical user interface
Component: Interface | Resolution: fixed
Keywords: |
-----------------------+----------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/108#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...> - 2009-09-13 23:37:51
|
Revision: 130
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=130&view=rev
Author: rgoj
Date: 2009-09-13 23:37:32 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* Added all the content from the PyBrainSim script, preparing PyBrainSimGUI one to be the main executable.
* Removed all the left over code from wxPython tutorials.
Modified Paths:
--------------
trunk/src/PyBrainSimGUI.pyw
Modified: trunk/src/PyBrainSimGUI.pyw
===================================================================
--- trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:11:44 UTC (rev 129)
+++ trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:37:32 UTC (rev 130)
@@ -30,92 +30,252 @@
import wx
from wx import xrc
+import numpy
+import pylab
+from random import random
+from scipy.integrate import ode
+
+from Head import Head
+from HeadModel import HeadModel
+from HeadModelHalfSphere import HeadModelHalfSphere
+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
+
class PyBrainSimGUI(wx.App):
def OnInit(self):
self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
- #self.InitFrame()
- #self.InitMenu()
- #self.InitEverythingElse()
self.frame = self.res.LoadFrame(None, "menuFrame")
self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton2, id=xrc.XRCID("menuButton2"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton3, id=xrc.XRCID("menuButton3"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton4, id=xrc.XRCID("menuButton4"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton5, id=xrc.XRCID("menuButton5"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton6, id=xrc.XRCID("menuButton6"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton7, id=xrc.XRCID("menuButton7"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton8, id=xrc.XRCID("menuButton8"))
self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
- #self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
- #self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
- #self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
- #self.result = xrc.XRCCTRL(self.panel, "Result")
- #self.first_arg.SetValue("Hi")
- #self.second_arg.SetValue("You")
- #self.result.SetValue("man")
- #self.menuBar = self.res.LoadMenuBar("MenuBar")
- #self.frame.SetMenuBar(self.menuBar)
- #sizer = self.panel.GetSizer()
- #sizer.Fit(self.frame)
- #sizer.SetSizeHints(self.frame)
self.frame.Show()
return True
def menuButton1(self, control):
- print "Hullo World!"
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = StimulusDummy('Stim', exampleHead)
+ exampleGenerator = GeneratorDummy('Gen', exampleHead)
+ exampleConnection = ConnectionDummy('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print(exampleExperiment.getRecording())
+ def menuButton2(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes([0.3, 0.6])
+ exampleGenerator = GeneratorNumberIncrementing('Gen', exampleHead)
+ exampleConnection = Connection('Con', exampleHead, exampleStimulus, exampleGenerator)
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0, exampleHead.runSimulation( 1.0 ))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton3(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(10)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ exampleExperiment = Experiment(exampleHead.getSamplingFrequency(), 1.0)
+ exampleExperiment.setStimulusTimes([[0.3, 0.6], [0.5]])
+
+ exampleStimulus1 = Stimulus('Stim1', exampleHead)
+ exampleStimulus2 = Stimulus('Stim2', exampleHead)
+ 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.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ print("\nSimulations resulted in the following recording:")
+ print exampleExperiment.getRecording()
+
+ def menuButton4(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ exampleHead.addRegistrationSite([0, 0, 0])
+
+ 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()
+
+ def menuButton5(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModel(exampleHead)
+ 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):
+ 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]))
+
+ exampleExperiment.setRecording(exampleHead.runSimulation(exampleExperiment.getDuration()))
+ exampleExperiment.plotRecording()
+
+ def menuButton6(self, control):
+ exampleHead = Head()
+ exampleHeadModel = HeadModelHalfSphere(exampleHead)
+ exampleHead.setSamplingFrequency(128)
+ 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]])
+
+ exampleStimulus = Stimulus('Stim', exampleHead)
+ exampleStimulus.setStimulusTimes(exampleExperiment.getStimulusTimes()[0])
+ 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()))
+ exampleExperiment.plotRecording()
+
+ def menuButton7(self, control):
+ exampleHead = Head()
+ exampleHead.displayHead()
+
+ def menuButton8(self, control):
+ # This class will produce noise that will be fed into the modelled
+ # cortical area as input.
+ class NeuralNoise:
+ def __init__(self, timeSpan, dtime):
+ self.noise = []
+ self.dtime = dtime
+ self.timePoints = range( int(timeSpan//dtime+1) )
+ # Random noise distributed evenly between 120 and 320
+ for i in self.timePoints:
+ self.noise.append( 120+200*random() )
+ def getNoise(self, time):
+ # Searching for the appropriate time point
+ for i in self.timePoints:
+ if time < self.timePoints[i]*self.dtime:
+ # Interpolating between the randomly generated values
+ return self.noise[i] + \
+ (self.noise[i+1]-self.noise[i]) \
+ * ((self.timePoints[i]*self.dtime-time)/self.dtime)
+
+ # The sigmoid function
+ def sigmoidFunction(v):
+ """Constants taken from Jansen and Rit 1995, p. 360"""
+ cEzero = 2.5
+ cR = 0.56
+ cVzero = 6
+
+ """Sigmoid function taken from Jansen and Rit 1995, p. 360"""
+ return 2*cEzero / ( 1 + numpy.exp( cR*( cVzero - v ) ) )
+
+ # Defining the equations
+ def f(t, y, noiseObject, cC):
+ cA=3.25
+ ca=100.0
+ cB=22.0
+ cb=50.0
+ cC1=cC
+ cC2=0.8*cC1
+ cC3=0.25*cC1
+ cC4=0.25*cC1
+ noise = noiseObject.getNoise(t)
+ #print("Time: " + str(t) + " Noise: " + str(noise))
+ return [y[1], cA*ca*( sigmoidFunction(y[2] - y[4]) ) - 2*ca*y[1] -
+ ca**2*y[0], y[3], cA*ca*( noise + cC2*sigmoidFunction(cC1*y[0]) ) -
+ 2*ca*y[3] - ca**2*y[2], y[5], cB*cb*( cC4*sigmoidFunction(cC3*y[0])
+ ) - 2*cb*y[5] - cb**2*y[4]]
+
+ # How many seconds should be modelled and how accurately
+ timeSpan = 3
+ dtime = 0.001
+ firstPointToDisplay = 1000
+
+ # A noise object that will be used as input into the equations
+ someNoise = NeuralNoise(timeSpan+1, dtime*10)
+
+ # Initial conditions
+ y0, t0 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], 0
+
+ # Preparing for simulations
+ r = []
+ recording = [ [], [], [], [], [], [] ]
+ parameter = [ 68, 128, 135, 270, 675, 1350 ]
+
+ # Differential equation integration
+ for i in range(len(parameter)):
+ # Preparing the integration
+ r.append(ode(f).set_integrator('vode', method='bdf'))
+ r[i].set_initial_value(y0, t0)
+ r[i].set_f_params( someNoise, parameter[i] )
+ # Integrating
+ print("Performing simulation " + str(i+1) + "/" + str(len(parameter)))
+ while r[i].successful() and r[i].t < timeSpan:
+ r[i].integrate(r[i].t+dtime)
+ recording[i].append(r[i].y[2] - r[i].y[4])
+
+ # Show results of simulations
+ for i in range(len(parameter)):
+ pylab.subplot( len(parameter), 1, i+1)
+ if i==0:
+ pylab.title("Simulations based on Fig. 3 from Jansen and Rit 1995")
+ pylab.ylabel( "C = " + str(parameter[i]) )
+ pylab.plot(recording[i][firstPointToDisplay:])
+ pylab.show()
+
def menuButtonQuit(self, control):
self.Exit()
- #def InitFrame(self):
- # self.frame = self.res.LoadFrame(None, "MainFrame")
- # self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
- # self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
- # self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
- # self.result = xrc.XRCCTRL(self.panel, "Result")
- # self.first_arg.SetValue("Hi")
- # self.second_arg.SetValue("You")
- # self.result.SetValue("man")
- #def InitMenu(self):
- # self.menuBar = self.res.LoadMenuBar("MenuBar")
- # self.frame.Bind(wx.EVT_MENU, self.Add, id=xrc.XRCID("AddMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Subtract, id=xrc.XRCID("SubtractMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Multiply, id=xrc.XRCID("MultiplyMenuItem"))
- # self.frame.Bind(wx.EVT_MENU, self.Divide, id=xrc.XRCID("DivideMenuItem"))
- # self.frame.SetMenuBar(self.menuBar)
- #def InitEverythingElse(self):
- # sizer = self.panel.GetSizer()
- # sizer.Fit(self.frame)
- # sizer.SetSizeHints(self.frame)
- # self.frame.Show()
- #def InitArgs(self):
- # try:
- # self.first = float(self.first_arg.GetValue())
- # except ValueError:
- # return self.BadFloatValue(self.first_arg)
- # try:
- # self.second = float(self.second_arg.GetValue())
- # except ValueError:
- # return self.BadFloatValue(self.second_arg)
- # return True
- #def BadFloatValue(self, control):
- # dlg = wx.MessageDialog(self.frame, "I can't convert this to float.",
- # 'Conversion error', wx.OK | wx.ICON_ERROR)
- # dlg.ShowModal()
- # dlg.Destroy()
- # control.SetFocus()
- # control.SetSelection(-1, -1)
- # return False
- #def Add(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first + self.second))
- #def Subtract(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first - self.second))
- #def Multiply(self, evt):
- # if self.InitArgs():
- # self.result.SetValue(str(self.first * self.second))
- #def Divide(self, evt):
- # if self.InitArgs():
- # if self.second != 0:
- # self.result.SetValue(str(self.first / self.second))
- # else:
- # self.result.SetValue("#ERROR")
-
if __name__ == '__main__':
app = PyBrainSimGUI(0)
app.MainLoop()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: PyBrainSim - T. i. <no...@so...> - 2009-09-13 23:29:10
|
#105: Write a simple test of the gui in a new source file
-----------------------+----------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Simple graphical user interface
Component: Interface | Resolution: fixed
Keywords: |
-----------------------+----------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/105#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...> - 2009-09-13 23:11:52
|
Revision: 129
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=129&view=rev
Author: rgoj
Date: 2009-09-13 23:11:44 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* Adding a file that runs the GUI menu, that for now does only that, but will soon become the main PyBrainSim script overriding the old one.
Added Paths:
-----------
trunk/src/PyBrainSimGUI.pyw
Added: trunk/src/PyBrainSimGUI.pyw
===================================================================
--- trunk/src/PyBrainSimGUI.pyw (rev 0)
+++ trunk/src/PyBrainSimGUI.pyw 2009-09-13 23:11:44 UTC (rev 129)
@@ -0,0 +1,121 @@
+#!/usr/bin/python
+
+# 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/>.
+
+"""
+PyBrainSim is an interactive tool for the simulation and visualization of the
+electromagnetic activity of the brain, currently under development.
+
+This script allows you to choose from a few example simulations, ranging from
+adding numbers to neural mass models.
+
+pybrainsim.sourceforge.net
+"""
+
+import wx
+from wx import xrc
+
+class PyBrainSimGUI(wx.App):
+ def OnInit(self):
+ self.res = xrc.XmlResource("PyBrainSimGUI.xrc")
+ #self.InitFrame()
+ #self.InitMenu()
+ #self.InitEverythingElse()
+
+ self.frame = self.res.LoadFrame(None, "menuFrame")
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButton1, id=xrc.XRCID("menuButton1"))
+ self.frame.Bind(wx.EVT_BUTTON, self.menuButtonQuit, id=xrc.XRCID("menuButtonQuit"))
+ #self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
+ #self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
+ #self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
+ #self.result = xrc.XRCCTRL(self.panel, "Result")
+ #self.first_arg.SetValue("Hi")
+ #self.second_arg.SetValue("You")
+ #self.result.SetValue("man")
+ #self.menuBar = self.res.LoadMenuBar("MenuBar")
+ #self.frame.SetMenuBar(self.menuBar)
+ #sizer = self.panel.GetSizer()
+ #sizer.Fit(self.frame)
+ #sizer.SetSizeHints(self.frame)
+ self.frame.Show()
+ return True
+
+ def menuButton1(self, control):
+ print "Hullo World!"
+
+ def menuButtonQuit(self, control):
+ self.Exit()
+
+ #def InitFrame(self):
+ # self.frame = self.res.LoadFrame(None, "MainFrame")
+ # self.panel = xrc.XRCCTRL(self.frame, "MainPanel")
+ # self.first_arg = xrc.XRCCTRL(self.panel, "FirstArg")
+ # self.second_arg = xrc.XRCCTRL(self.panel, "SecondArg")
+ # self.result = xrc.XRCCTRL(self.panel, "Result")
+ # self.first_arg.SetValue("Hi")
+ # self.second_arg.SetValue("You")
+ # self.result.SetValue("man")
+ #def InitMenu(self):
+ # self.menuBar = self.res.LoadMenuBar("MenuBar")
+ # self.frame.Bind(wx.EVT_MENU, self.Add, id=xrc.XRCID("AddMenuItem"))
+ # self.frame.Bind(wx.EVT_MENU, self.Subtract, id=xrc.XRCID("SubtractMenuItem"))
+ # self.frame.Bind(wx.EVT_MENU, self.Multiply, id=xrc.XRCID("MultiplyMenuItem"))
+ # self.frame.Bind(wx.EVT_MENU, self.Divide, id=xrc.XRCID("DivideMenuItem"))
+ # self.frame.SetMenuBar(self.menuBar)
+ #def InitEverythingElse(self):
+ # sizer = self.panel.GetSizer()
+ # sizer.Fit(self.frame)
+ # sizer.SetSizeHints(self.frame)
+ # self.frame.Show()
+ #def InitArgs(self):
+ # try:
+ # self.first = float(self.first_arg.GetValue())
+ # except ValueError:
+ # return self.BadFloatValue(self.first_arg)
+ # try:
+ # self.second = float(self.second_arg.GetValue())
+ # except ValueError:
+ # return self.BadFloatValue(self.second_arg)
+ # return True
+ #def BadFloatValue(self, control):
+ # dlg = wx.MessageDialog(self.frame, "I can't convert this to float.",
+ # 'Conversion error', wx.OK | wx.ICON_ERROR)
+ # dlg.ShowModal()
+ # dlg.Destroy()
+ # control.SetFocus()
+ # control.SetSelection(-1, -1)
+ # return False
+ #def Add(self, evt):
+ # if self.InitArgs():
+ # self.result.SetValue(str(self.first + self.second))
+ #def Subtract(self, evt):
+ # if self.InitArgs():
+ # self.result.SetValue(str(self.first - self.second))
+ #def Multiply(self, evt):
+ # if self.InitArgs():
+ # self.result.SetValue(str(self.first * self.second))
+ #def Divide(self, evt):
+ # if self.InitArgs():
+ # if self.second != 0:
+ # self.result.SetValue(str(self.first / self.second))
+ # else:
+ # self.result.SetValue("#ERROR")
+
+if __name__ == '__main__':
+ app = PyBrainSimGUI(0)
+ app.MainLoop()
Property changes on: trunk/src/PyBrainSimGUI.pyw
___________________________________________________________________
Added: svn:executable
+ *
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|
|
From: <rg...@us...> - 2009-09-13 23:09:36
|
Revision: 128
http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=128&view=rev
Author: rgoj
Date: 2009-09-13 23:09:30 +0000 (Sun, 13 Sep 2009)
Log Message:
-----------
* Adding a wxWidgets XML Resource file, that describes the main menu for the new graphical PyBrainSim.
Added Paths:
-----------
trunk/src/PyBrainSimGUI.xrc
Added: trunk/src/PyBrainSimGUI.xrc
===================================================================
--- trunk/src/PyBrainSimGUI.xrc (rev 0)
+++ trunk/src/PyBrainSimGUI.xrc 2009-09-13 23:09:30 UTC (rev 128)
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<resource xmlns="http://www.wxwindows.org/wxxrc" version="2.3.0.1">
+ <object class="wxFrame" name="menuFrame">
+ <style>wxDEFAULT_FRAME_STYLE|wxTAB_TRAVERSAL</style>
+ <size>450,390</size>
+ <title>PyBrainSim: Choose example simulation</title>
+ <object class="wxPanel" name="menuPanel">
+ <style>wxTAB_TRAVERSAL</style>
+ <object class="wxBoxSizer">
+ <orient>wxVERTICAL</orient>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton1">
+ <label>Example dummy simulation</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALIGN_CENTER_HORIZONTAL|wxALL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton2">
+ <label>Number generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton3">
+ <label>Two number generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton4">
+ <label>Sine generator and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton5">
+ <label>Random sine generators and stimuli</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton6">
+ <label>Sine generator, stimuli and two recording sites</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton7">
+ <label>Dummy 3D head model</label>
+ <default>0</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL|wxEXPAND</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButton8">
+ <label>Neural mass model of a single cortical area</label>
+ <default>1</default>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxEXPAND | wxALL</flag>
+ <border>5</border>
+ <object class="wxStaticLine" name="m_staticline2">
+ <style>wxLI_HORIZONTAL</style>
+ </object>
+ </object>
+ <object class="sizeritem">
+ <option>0</option>
+ <flag>wxALL|wxALIGN_CENTER_HORIZONTAL</flag>
+ <border>5</border>
+ <object class="wxButton" name="menuButtonQuit">
+ <label>Quit</label>
+ <default>0</default>
+ </object>
+ </object>
+ </object>
+ </object>
+ </object>
+</resource>
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: PyBrainSim - T. i. <no...@so...> - 2009-09-13 23:04:39
|
#106: Design the main window for the graphical PyBrainSim interface
--------------------+-------------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Simple graphical user interface
Component: Design | Resolution: fixed
Keywords: |
--------------------+-------------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/106#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...> - 2009-09-13 23:03:22
|
#104: Choose the libraries and method of creating the GUI
--------------------+-------------------------------------------------------
Reporter: rgoj | Owner: rgoj
Type: task | Status: closed
Priority: major | Milestone: Simple graphical user interface
Component: Design | Resolution: fixed
Keywords: |
--------------------+-------------------------------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
Comment:
wxWidgets, wxPython, XML Resources prepared with wxFormBuilder
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/104#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...> - 2009-09-13 19:28:18
|
#78: Test the differential equations solving on simple equations implemented in
the Head class.
-------------------------------------------+--------------------------------
Reporter: rgoj | Type: task
Status: closed | Priority: major
Milestone: Neural mass model simulation | Component: Tests
Resolution: fixed | Keywords:
-------------------------------------------+--------------------------------
Changes (by rgoj):
* status: new => closed
* resolution: => fixed
--
Ticket URL: <http://sourceforge.net/apps/trac/pybrainsim/ticket/78#comment:4>
PyBrainSim <http://sourceforge.net/projects/pybrainsim/>
An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.
|
