# analogStimTable.py ---
#
# Filename: analogStimTable.py
# Description:
# Author: Upi Bhalla
#
# This program 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, or
# (at your option) any later version.
#
# This program 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 this program; see the file COPYING. If not, write to
# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
# Floor, Boston, MA 02110-1301, USA.
#
import numpy as np
import pylab
import moose
from moose import utils
def analogStimTable():
simtime = 150
simdt = 0.1
model = moose.Neutral('/model')
data = moose.Neutral('/data')
# This is the stimulus generator
stimtable = moose.StimulusTable('/model/stim')
a = moose.BufPool( '/model/a' )
b = moose.Pool( '/model/b' )
reac = moose.Reac( '/model/reac' )
reac.Kf = 0.1
reac.Kb = 0.1
moose.connect( stimtable, 'output', a, 'setConcInit' )
moose.connect( reac, 'sub', a, 'reac' )
moose.connect( reac, 'prd', b, 'reac' )
aPlot = moose.Table('/data/aPlot')
moose.connect(aPlot, 'requestOut', a, 'getConc')
bPlot = moose.Table('/data/bPlot')
moose.connect(bPlot, 'requestOut', b, 'getConc')
moose.setClock( stimtable.tick, simdt )
moose.setClock( a.tick, simdt )
moose.setClock( aPlot.tick, simdt )
####################################################
# Here we set up the stimulus table. It is half a sine-wave.
stim = [ np.sin(0.01 * float(i) ) for i in range( 314 )]
stimtable.vector = stim
stimtable.stepSize = 0 # This forces use of current time as x value
# The table will interpolate its contents over the time start to stop:
# At values less than startTime, it emits the first value in table
stimtable.startTime = 5
# At values more than stopTime, it emits the last value in table
stimtable.stopTime = 60
stimtable.doLoop = 1 # Enable repeat playbacks.
stimtable.loopTime = 10 + simtime / 2.0 # Repeat playback over this time
moose.reinit()
moose.start(simtime)
t = [ x * simdt for x in range( len( aPlot.vector ) )]
pylab.plot( t, aPlot.vector, label='Stimulus waveform' )
pylab.plot( t, bPlot.vector, label='Reaction product b' )
pylab.legend()
pylab.show()
[docs]def main():
"""
Example of using a StimulusTable as an analog signal source in
a reaction system. It could be used similarly to give other
analog inputs to a model, such as a current or voltage clamp signal.
This demo creates a StimulusTable and assigns it half a sine wave.
Then we assign the start time and period over which to emit the wave.
The output of the StimTable is sent to a pool **a**, which participates
in a trivial reaction::
table ----> a <===> b
The output of **a** and **b** are recorded in a regular table
for plotting.
"""
analogStimTable()
if __name__ == '__main__':
main
#
# stimtable.py ends here