def GetOStretchByIndices(sep,force,idxStart,idxEnd):
mParams = []
mPredictedX = []
mPredictedY = []
# make (linear fits for each)
for realIdxInit,realIdxFinal in zip(idxStart,idxEnd):
toFitX = sep[realIdxInit:realIdxFinal]
toFitY = force[realIdxInit:realIdxFinal]
# get the parameters
params,_,predictedOStretch = pGenUtil.GenFit(toFitX,toFitY)
# add the values we need...
mParams.append(params)
mPredictedX.append(toFitX)
mPredictedY.append(predictedOStretch)
# POST: all parameters calculared
# need to get the start of the delta L0
L0Init = pGenUtil.lineIntersectParam(mParams[0],mParams[1])
# get the end of the final
L0Final = pGenUtil.lineIntersectParam(mParams[1],mParams[2])
approxDelL0 = L0Final-L0Init
# get the midpoint, to find the overstretching force
midPoint = L0Init + 0.5 * approxDelL0
# get the index of the midpoint
idxBetween = np.argmin(np.abs(sep-midPoint))
# if for some reason the data is very noisy, just
# use the mean index of the transition (index 2)
# to get the indices...
indexOStretch = 1
if (idxBetween < idxStart[indexOStretch]):
startTx = idxStart[indexOStretch]
endTx = idxEnd[indexOStretch]
idxBetween = np.mean([startTx,endTx])
whereOStretch = sep[idxBetween]
oStretchForce = np.polyval(mParams[1],whereOStretch)
return mParams,mPredictedX,mPredictedY,whereOStretch,oStretchForce
def getTouchoffCalibration(timeAppr,forceAppr,mDerivApproach,isApproach):
idxStart,idxEnd = getCrossIdxFromApproach(mDerivApproach)
# fit lines to the force
# start and end *always demarcate the start and end (ish) of the invols
# if we are approach, we take everything *before* as constant
# if we are touchoff, we take everything *after* as constant
if (isApproach):
constantSlice = np.s_[0:idxStart]
touchoffSlice = np.s_[idxStart:idxEnd]
else:
constantSlice = np.s_[idxEnd:]
touchoffSlice = np.s_[idxStart:idxEnd]
timeApprLow = timeAppr[constantSlice]
timeTouch = timeAppr[touchoffSlice]
paramsFirst,stdFirst,predFirst= pGenUtil.GenFit(timeApprLow,
forceAppr[constantSlice])
paramsSecond,stdSecond,predSecond = \
pGenUtil.GenFit(timeTouch,forceAppr[touchoffSlice])
# XXX get error estimate using standard deviations?
timeSurface = pGenUtil.lineIntersectParam(paramsFirst,
paramsSecond)
idxSurface = np.argmin(np.abs(timeAppr-timeSurface))
# set the variables we care about
calibObj = CalibrateObject(idxStart,idxEnd,
constantSlice,touchoffSlice,
paramsFirst,stdFirst,predFirst,
paramsSecond,stdSecond,predSecond,
timeSurface,idxSurface)
return calibObj
