unperturbed.py~

import numpy as np
import pdb
import matplotlib.pyplot as plt
import oscillatorLib as ol
import experimentLib
import matplotlib
import matplotlib.patches as patches
from matplotlib.ticker import FormatStrFormatter



######################################
######################################
######  SIMULATION PARAMETERS   ######
######################################
######################################

#####################################
### SYSTEM PARAMETERS:
dt = 0.0001
maxTime = 45


#####################################
### CELL PARAMETERS:
staticRate = 1/1.78  # Computed as 1/((1/.429) - 0.55), where .429 is the frequency of cells from 20160516
leakRate = 0#0.2

# Note: std of unstretched contractile events was 0.055 (averaged over three trials)
# random Std was chosen to generate a similar value:
randomStd = .0245
peakEpsilon = 1
epsilon_floor = 0.8  # Provides nonlinearity...
actionPotentialLength = 0.5  # measured from contractions on 20160516
contractionDelay = 0.005  # pretty random i suppose
peakForce = 1
peakCouplingRate = 10
c0 = 0
sensitivityWinType = 1
sensitivityMean = 0.6
sensitivityStd = 0.1
cellTitle = "cardiacOscillator_1"


####################################
### SUBSTRATE PARAMETERS:

funcType = 'sinusoidal'
minStrain = 0
maxStrain = 1
phi0 = 1.5*np.pi


omega0 = 2*np.pi / (actionPotentialLength + 1/staticRate)  # Note, this is natural contractile rate of cell
omega1 = 1.14 * omega0


####################################
####################################
####################################

sensitivityWinParam = {'sensitivityWinType' : sensitivityWinType, 'sensitivityMean' : sensitivityMean, 'sensitivityStd' : sensitivityStd}

strainFunctionParameters = {'funcType' : funcType, 'minStrain' : minStrain, 'maxStrain' : maxStrain, 'phi0' : phi0}

cell = ol.cardiac(dt, maxTime, staticRate, leakRate, randomStd, peakEpsilon, epsilon_floor, actionPotentialLength, contractionDelay, peakForce, c0, peakCouplingRate, sensitivityWinParam, cellTitle)

sub1 = ol.substrate(dt, maxTime, strainFunctionParameters, omega1)

uncoupled0 = ol.ap(cell, 0)
print("step")
#coupled1 = ol.ap(cell, sub1.epsilon)
#print("step")


#####################################
#####################################
#####################################

if 0:
    plt.plot(uncoupled0.t, uncoupled0.c, coupled3.t, coupled3.c)
    plt.show()



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##############################################################
########  POSTPROCESS DATA USING EXPERIMENTAL LIBS   #########
##############################################################
##############################################################
##############################################################
##############################################################
##############################################################

experimentTitle = '20160516_model1'


maxStrain = .13

cellNaturalFreq = 1/np.mean(np.diff(uncoupled0.ix))

#######################################
# Optional:  Use nominal substrate frequency (no phase data!)

useAvailableSubstrateEvents = 1  # Set to unity to use *data* for substrate, as opposed to measured frequency



cellEvents = [uncoupled0.ix]#, coupled1.ix]
subEvents = [[]]#, sub1.ix]
title = ['uncoup0']#, 'coup1']

voltage = np.zeros(len(cellEvents))
startTime = np.arange(len(cellEvents))
nominalSubFreq = np.zeros(len(cellEvents))
reactionTime = 0
subEventTimeShift = np.zeros(len(cellEvents))



params = {'cellEvents':cellEvents, 'subEvents':subEvents, 'voltage':voltage, 'startTime':startTime, 'dt':dt, 'useAvailableSubstrateEvents':useAvailableSubstrateEvents, 'nominalSubFreq':nominalSubFreq, 'reactionTime':reactionTime, 'subEventTimeShift':subEventTimeShift, 'maxStrain':maxStrain, 'cellNaturalFreq':cellNaturalFreq, 'title':title, 'experimentTitle':experimentTitle}



s1 = experimentLib.experiment(params)

u0 = s1.genUnstretchedMeasurement(0)
#m1 = s1.genStretchedMeasurement(1)





if 0:
    ol.animateCoupledUncoupled(sub3.epsilon, coupled3.c, uncoupled0.c, DF=500)

#sub1.epsilon

print("cellFreq(u0) =", u0.cellFreq)
print()
#print("subFreq(m3) =", m1.subFreq)
#print("cellFreq(m3) =", m1.cellFreq)
#print()

print("u0 std", np.std(np.diff(u0.cellEvents)))
print("u0 mean", np.mean(np.diff(u0.cellEvents)))
#print("m3 std", np.std(np.diff(m3.cellEvents)))
#print("m3 mean", np.mean(np.diff(m3.cellEvents)))

#plt.plot(m1.t2, m1.dTheta, m2.t2, m2.dTheta, m3.t2, m3.dTheta, m4.t2, m4.dTheta, m5.t2, m5.dTheta)
#plt.show()


###########################################################

if 0:
    ####################################################
    # Plot histograms of substrate phase:
    measurementList = [m3, m4, m5, m6, m7, m8]
    
    
    nRows = 2
    nColumns = 3
    figsize = (14,6)
    top=0.93
    bottom=0.12
    left=0.07
    right=0.92
    hspace=0.32   # vertical spacing between rows
    wspace=0.22
    hist_maxProbability = 1
    
    s1.plotSubstratePhaseHistograms(measurementList, nRows, nColumns, figsize, top, bottom, left, right, hspace, wspace, hist_maxProbability)
    
    
    
    ####################################################
    # Plot histogram of stretched taus:
    measurementList = [m3, m4, m5, m6, m7, m8]
    
    nRows = 2
    nColumns = 3
    figsize = (14,6)
    top=0.93
    bottom=0.12
    left=0.07
    right=0.92
    hspace=0.32   # vertical spacing between rows
    wspace=0.22
    
    hist_maxProbability = 1.1
    nBins = 16
    
    s1.stretchedTauHistogram(measurementList, nRows, nColumns, figsize, top, bottom, left, right, hspace, wspace, hist_maxProbability, nBins)
    
    
    #####################################################
    # Plot histogram of unstretched taus:
    
    unstretchedList = [u0, u1, u2]
    
    nRows = 1
    nColumns = 3
    figsize = (14, 3)
    
    top = 0.87
    bottom = 0.19
    left=0.1
    right=0.92
    hspace=0.32
    wspace=0.22
    nBins = 16
    hist_maxProbability = 1.1
    
    if 0:
        # Vertical array!
        nRows = 3
        nColumns = 1
        figsize = (4,10)
        top = .96
        bottom = 0.12
        left = 0.2
        right = 0.9
    
    s1.unstretchedTauHistogram(unstretchedList, nRows, nColumns, figsize, top, bottom, left, right, hspace, wspace, hist_maxProbability, nBins)
    
    
    ########################################################
    # Frequency plot:
    
    figsize = (4.5,4.5)
    top = 0.95
    left = 0.18
    right = 0.95
    bottom = 0.1
    
    
    s1.plotFrequencyErrorbars(figsize, top, bottom, left, right, hspace, wspace)
    
    #########################################################
    # Plot relative phase:
    

    m3.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)
    m4.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)
    m5.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)
    m6.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)
    m7.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)
    m8.plotRelativePhase(figsize, top=0.9, bottom=0.11, left=0.15, right=0.95)