def separateData(rawFileName, indexFileName, prefix):
rawFile = open(rawFileName,'r')
'''raw stuff'''
# read header, rip into dictionary
rawHeaderDict = getHeader(rawFile)
# grab data
# convert according to rx.cantilever and sign conventions
data = rx.readDataFileArray(rawFile)
# need to get cantilever values, micron conversion, and polarity stuff
cantileverDict = rx.getCantileverData(rawHeaderDict['cantilever'])
data = convertData(data,cantileverDict)
'''index stuff'''
# open index file
indexFile = open(indexFileName,'r')
# use matrix open from roxanne
# create dictionary from index entries
indexDict = rx.readDataFileArray(indexFile)
# converting string to float facilitates later formatting
indexDict['pulloffAngle'] = map(float,indexDict['pulloffAngle'])
#print dict to stdout
#print indexDict
# todo:check if file name exists (to deal with multiple trials)
for i in range(len(indexDict['pulloffAngle'])):
# construct file name
fileOutName = prefix
fileOutName += 'a%02d.data' % indexDict['pulloffAngle'][i]
print fileOutName,
print 'opening',
fileOut = open(fileOutName,'w')
print 'writing',
outputDictAsText(rawHeaderDict, fileOut)
outputDictAsTextByIndex(indexDict, i, fileOut)
fileOut.write('<data>\n')
# output header
# output data list
startIndex = int(indexDict['startIndex'][i])
endIndex = int(indexDict['endIndex'][i])
keys = data.keys()
keys.sort()
colWidth = max(map(len, keys)) + 1
for key in keys:
fileOut.write(key.ljust(colWidth))
fileOut.write('\n')
# get starting time
startTime = data['time'][startIndex]
for j in range(startIndex, endIndex + 1):
for key in keys:
if key == 'time':
fileOut.write(str(data[key][j]-startTime).ljust(colWidth))
else:
fileOut.write(str(data[key][j]).ljust(colWidth))
fileOut.write('\n')
print 'finishing'
def main():
import sys
sys.path.append('../roxanne')
sys.path.append('../../roxanne')
import roxanne
import glob
import os.path
import numpy
parseFileIn = open('testOut.dat','r')
parseDict = roxanne.readDataFileArray(parseFileIn)
print parseDict.keys()
fOut = open('analyzed.data','w')
fileNameList = glob.glob('a*.0.data')
outputList = ['fileName',
'anglePitch',
'forceMaxAdhesion',
'forceMaxShear']
# removed angle pulloff from output list
sep = '\t'
headerString = sep.join(outputList)
fOut.write(headerString)
fOut.write('\n')
for fileName in fileNameList:
print 'processing file : ' + fileName
# TODO - pulloff angle from trajectory file name
fileIn = open(fileName)
headerDict = roxanne.readDataFileHeader(fileIn)
dataDict = roxanne.readDataFileArray(fileIn)
voltageLateral = map(float,dataDict['voltageForceLateral'])
voltageNormal = map(float,dataDict['voltageForceNormal'])
positionNormalMicron = map(float,dataDict['voltagePositionX']) * 10
positionLateralMicron = map(float,dataDict['voltagePositionY']) * 10
voltageLateral = -numpy.array(voltageLateral)
voltageNormal = numpy.array(voltageNormal)
positionNormalMicron = numpy.array(positionNormalMicron) * 10
positionLateralMicron = numpy.array(positionLateralMicron) * 10
cantileverDict = roxanne.getCantileverData(headerDict['cantilever'])
normalStiffness = cantileverDict['normalStiffness']
lateralStiffness = cantileverDict['lateralStiffness']
normalDisplacement = cantileverDict['normalDisplacement']
lateralDisplacement = cantileverDict['lateralDisplacement']
lateralAmplification = float(headerDict['latAmp'])
normalAmplification = float(headerDict['norAmp'])
rollAngle = float(headerDict['rollAngle'])
pitchAngle = float(headerDict['pitchAngle'])
# anglePulloff = float(headerDict['anglePulloff'])
defaultAmplification = 100
lateralDisplacement = (lateralDisplacement * lateralAmplification /
defaultAmplification)
normalDisplacement = (normalDisplacement * normalAmplification /
defaultAmplification)
# use cantilever values to convert voltages to forces
lateralForceMuN = (voltageLateral *
lateralStiffness / lateralDisplacement)
normalForceMuN = (voltageNormal * normalStiffness /
normalDisplacement)
# get location of filename in parseDict
# and pull data from same index in the other arrays
#fileName = os.path.splitext(fileName)
#fileName = fileName[0]
fileNames = parseDict['dataFileName']
indexFileName = fileNames.index(fileName)
indexContact = parseDict['indexContact'][indexFileName]
indexPreload = parseDict['indexMaxPreload'][indexFileName]
indexMaxAdhesion = parseDict['indexMaxAdhesion'][indexFileName]
indexContact = int(indexContact)
indexPreload = int(indexPreload)
indexMaxAdhesion = int(indexMaxAdhesion)
# get forces at contact, preload, pulloff
normalForceContactMuN = normalForceMuN[indexContact]
normalForcePreloadMuN = normalForceMuN[indexPreload]
normalForcePulloffMuN = normalForceMuN[indexMaxAdhesion]
shearForceContactMuN = lateralForceMuN[indexContact]
shearForcePreloadMuN = lateralForceMuN[indexPreload]
shearForcePulloffMuN = lateralForceMuN[indexMaxAdhesion]
normalCantileverVoltageContact = voltageNormal[indexContact]
normalCantileverVoltagePreload = voltageNormal[indexPreload]
normalCantileverVoltageMaxAdhesion = voltageNormal[indexMaxAdhesion]
normalStagePositionContact = positionNormalMicron[indexContact]
normalStagePositionPreload = positionNormalMicron[indexPreload]
normalStagePositionMaxAdhesion = positionNormalMicron[indexMaxAdhesion]
# calculate effective stage preload
normalStagePreload = (normalStagePositionMaxAdhesion -
normalStagePositionContact)
# calculate effective cantilever deflection
normalCantileverDeflection = ((normalCantileverVoltageContact -
normalCantileverVoltageMaxAdhesion)/
normalDisplacement)
# calculate effective microwedge deflection (effective preload)
effectivePreload = normalCantileverDeflection + normalStagePreload
# adhesion force = maxAdhesion - force at contact
maxAdhesionMuN = (normalForcePulloffMuN -
normalForceContactMuN)
# shear force = maxShear - force at contact
maxShearMuN = (shearForcePulloffMuN -
shearForceContactMuN)
# calculate effective stiffness of structure
# force at preload - force at contact = force of preload
forcePreload = normalForcePreloadMuN - normalForceContactMuN
stageMovement = normalStagePositionPreload - normalStagePositionContact
normalCantileverDeflection = ((normalCantileverVoltageContact -
normalCantileverVoltagePreload)/
normalDisplacement)
# stage movement between contact and preload - cantilever deflection
effectiveStiffness = forcePreload/(stageMovement-normalCantileverDeflection)
# print indexContact
# input()
fOut.write(fileName + '\t')
fOut.write('% 5.1f\t' % pitchAngle )
# fOut.write('% 5.3f\t' % effectivePreload)
fOut.write('% 5.3f\t' % maxAdhesionMuN)
fOut.write('% 5.3f\t' % maxShearMuN)
# fOut.write('% 5.3f\t' % normalStagePositionPreload)
# fOut.write('% 5.3f\t' % normalStagePositionContact)
# fOut.write('% 5.3f\t' % forcePreload)
# fOut.write('% 5.3f\t' % stageMovement)
# fOut.write('% 5.3f\t' % effectiveStiffness)
fOut.write('\n')
fOut.close()
def main():
#dataDirectory = '../031-20100111-sws16-ls/data/separated/'
dataDirectory = '../033-20100302-sws17-ls/data/separated/'
parsedFileName = dataDirectory + '033-analyzedAngle.data'
parsedFileName = dataDirectory + '033-parsed.dat'
parseFileIn = open(parsedFileName)
parseDict = rx.readDataFileArray(parseFileIn)
angle = convertToFloatArray(parseDict['angle'])
fileNameList = parseDict['dataFileName']
for i,fileName in enumerate(fileNameList):
fullFileName = dataDirectory + fileName
print('processing file : ', fullFileName)
fileIn = open(fullFileName)
headerDict = rx.readDataFileHeader(fileIn)
dataD = rx.readDataFileArray(fileIn)
# convert lists to arrays of floats
voltageLateral = convertToFloatArray(dataD['voltageForceLateral'])
voltageNormal = convertToFloatArray(dataD['voltageForceNormal'])
positionNormalMicron = convertToFloatArray(dataD['voltagePositionX'])
positionLateralMicron = convertToFloatArray(dataD['voltagePositionY'])
# make conversions
voltageLateral = -voltageLateral
voltageNormal = voltageNormal
positionLateralMicron = positionLateralMicron * 10.0
positionNormalMicron = positionNormalMicron * 10.0
cantileverDict = rx.getCantileverData(headerDict['cantilever'])
normalStiffness = cantileverDict['normalStiffness']
lateralStiffness = cantileverDict['lateralStiffness']
normalDisplacement = cantileverDict['normalDisplacement']
lateralDisplacement = cantileverDict['lateralDisplacement']
lateralAmplification = float(headerDict['latAmp'])
normalAmplification = float(headerDict['norAmp'])
defaultAmplification = 100
lateralDisplacement = (lateralDisplacement * lateralAmplification /
defaultAmplification)
normalDisplacement = (normalDisplacement * normalAmplification /
defaultAmplification)
# use cantilever values to convert voltages to forces
lateralForceMuN = (voltageLateral *
lateralStiffness / lateralDisplacement)
normalForceMuN = (voltageNormal * normalStiffness /
normalDisplacement)
# get location of filename in parseDict
# and pull data from same index in the other arrays
#fileName = os.path.splitext(fileName)
#fileName = fileName[0]
#fileNames = parseDict['dataFileName']
#fileNameNoPath = os.path.split(fileName)[1]
#indexFileName = fileNames.index(fileNameNoPath)
# get indices for events in force trace
indexContact = parseDict['indexContact'][i]
indexPreload = parseDict['indexMaxPreload'][i]
indexMaxAdhesion = parseDict['indexMaxAdhesion'][i]
indexContact = int(indexContact)
indexPreload = int(indexPreload)
indexMaxAdhesion = int(indexMaxAdhesion)
# get forces at contact, preload, pulloff
normalForceContactMuN = normalForceMuN[indexContact]
normalForcePreloadMuN = normalForceMuN[indexPreload]
normalForcePulloffMuN = normalForceMuN[indexMaxAdhesion]
shearForceContactMuN = lateralForceMuN[indexContact]
shearForcePreloadMuN = lateralForceMuN[indexPreload]
shearForcePulloffMuN = lateralForceMuN[indexMaxAdhesion]
lateralForceMuN = lateralForceMuN[0:indexMaxAdhesion]
normalForceMuN = normalForceMuN[0:indexMaxAdhesion]
# subtract off forces at contact?
# slice forces [0:indexMaxAdhesion]
lateralForceMuN -= shearForceContactMuN
normalForceMuN -= normalForceContactMuN
x = angle[i]/90.0
myColor = (x,0,1-x)
#print(myColor)
plt.grid()
plt.plot(lateralForceMuN, normalForceMuN,
color = mpl.cm.get_cmap('jet')(x),
label = str(i),
linewidth = 0.1,
alpha = 0.5)
plt.title('force space')
# plot forces on plot thang
#plt.legend()
#plt.colorbar()
#plt.show()
plt.savefig(dataDirectory+'forceSpace.pdf')
return
def main():
import sys
sys.path.append('../roxanne')
import roxanne
import glob
import os.path
import numpy
parseFileIn = open('parsed.data','r')
parseDict = roxanne.readDataFileArray(parseFileIn)
print parseDict.keys()
print parseDict
fOut = open('analyzed.data','w')
fileNameList = glob.glob('./data/*sws*.data')
outputList = ['fileName',
'cantileverDeflection',
'stagePreload',
'maxPreload',
'microwedgeDeflection',
'lateralSpringConstant']
sep = '\t'
headerString = sep.join(outputList)
fOut.write(headerString)
for fileName in fileNameList:
print 'processing file : ' + fileName
fileIn = open(fileName)
headerDict = roxanne.readDataFileHeader(fileIn)
dataDict = roxanne.readDataFileArray(fileIn)
fullFileName = os.path.abspath(fileName)
shortFileName = os.path.split(fullFileName)[1]
#shortFileName = os.path.splitext(shortFileName)[0]
voltageLateral = map(float,dataDict['voltageForceLateral'])
voltageNormal = map(float,dataDict['voltageForceNormal'])
positionNormalMicron = map(float,dataDict['voltagePositionX']) * 10
positionLateralMicron = map(float,dataDict['voltagePositionY']) * 10
voltageLateral = -numpy.array(voltageLateral)
voltageNormal = numpy.array(voltageNormal)
positionNormalMicron = numpy.array(positionNormalMicron) * 10
positionLateralMicron = numpy.array(positionLateralMicron) * 10
cantileverDict = roxanne.getCantileverData(headerDict['cantilever'])
normalStiffness = cantileverDict['normalStiffness']
lateralStiffness = cantileverDict['lateralStiffness']
normalDisplacement = cantileverDict['normalDisplacement']
lateralDisplacement = cantileverDict['lateralDisplacement']
lateralAmplification = float(headerDict['latAmp'])
normalAmplification = float(headerDict['norAmp'])
rollAngle = float(headerDict['rollAngle'])
pitchAngle = float(headerDict['pitchAngle'])
defaultAmplification = 100
lateralDisplacement = (lateralDisplacement * lateralAmplification /
defaultAmplification)
normalDisplacement = (normalDisplacement * normalAmplification /
defaultAmplification)
# use cantilever values to convert voltages to forces
lateralForceMuN = (voltageLateral *
lateralStiffness / lateralDisplacement)
normalForceMuN = (voltageNormal * normalStiffness /
normalDisplacement)
# get location of filename in parseDict
# and pull data from same index in the other arrays
fileName = os.path.splitext(fileName)
fileName = fileName[0]
fileNames = parseDict['dataFileName']
indexFileName = fileNames.index(shortFileName)
indexContact = parseDict['indexContact'][indexFileName]
indexPreload = parseDict['indexMaxPreload'][indexFileName]
indexMaxAdhesion = parseDict['indexMaxAdhesion'][indexFileName]
indexContact = int(indexContact)
indexPreload = int(indexPreload)
indexMaxAdhesion = int(indexMaxAdhesion)
# get forces at contact, preload, pulloff
normalForceContactMuN = normalForceMuN[indexContact]
normalForcePreloadMuN = normalForceMuN[indexPreload]
normalForcePulloffMuN = normalForceMuN[indexMaxAdhesion]
shearForceContactMuN = lateralForceMuN[indexContact]
shearForcePreloadMuN = lateralForceMuN[indexPreload]
shearForcePulloffMuN = lateralForceMuN[indexMaxAdhesion]
normalCantileverVoltageContact = voltageNormal[indexContact]
normalCantileverVoltagePreload = voltageNormal[indexPreload]
normalCantileverVoltageMaxAdhesion = voltageNormal[indexMaxAdhesion]
shearCantileverVoltageContact = voltageLateral[indexContact]
shearCantileverVoltagePreload = voltageLateral[indexPreload]
shearCantileverVoltageMaxAdhesion = voltageLateral[indexMaxAdhesion]
normalStagePositionContact = positionNormalMicron[indexContact]
normalStagePositionPreload = positionNormalMicron[indexPreload]
normalStagePositionMaxAdhesion = positionNormalMicron[indexMaxAdhesion]
shearStagePositionContact = positionLateralMicron[indexContact]
shearStagePositionPreload = positionLateralMicron[indexPreload]
shearStagePositionMaxAdhesion = positionLateralMicron[indexMaxAdhesion]
# calculate preload
# in the shear bending test, this is from the shear trace
stagePreload = shearStagePositionPreload - shearStagePositionContact
# calculate deflection
cantileverDeflection = ((shearCantileverVoltagePreload -
shearCantileverVoltageContact) /
lateralDisplacement)
# calculate effective microwedge deflection (effective preload)
microwedgeDeflection = stagePreload + cantileverDeflection
# preload force
maxPreload = (normalForcePreloadMuN - normalForceContactMuN)
fOut.write(fileName + '\t')
fOut.write('% 5.1f\t' % cantileverDeflection)
fOut.write('% 5.3f\t' % stagePreload)
fOut.write('% 5.3f\t' % maxPreload)
fOut.write('% 5.3f\t' % microwedgeDeflection)
fOut.write('% 5.3f\t' % lateralSpringConstant)
fOut.write('\n')
fOut.close()