def plotTime(fileIn):
rx.readDataFileHeader(fileIn)
data = rx.readDataFileArray(fileIn)
timeStrings = data['time']
timeSeconds = [float(ts[0:2])*3600+float(ts[3:5])*60+float(ts[6:]) for ts in timeStrings]
import numpy as np
timeSeconds = np.array(timeSeconds)
timeSeconds = timeSeconds - timeSeconds[0]
#print timeSeconds
plt.plot(timeSeconds,'o')
def __init__(self, fileName, fOut):
super(plotBox, self).__init__()
self.isAccepted = True
self.fOut = fOut
self.message = "Analysis Acceptable?"
self.vPlot = VPlotContainer(padding=10)
self.vPlot.stack_order = "top_to_bottom"
topPlot = OverlayPlotContainer(padding=10)
self.vPlot.add(topPlot)
bottomPlot = OverlayPlotContainer(padding=10)
self.vPlot.add(bottomPlot)
# def parseFileName():
self.fileName = fileName
# get complete path of data file
fullFileName = os.path.abspath(fileName)
self.fileName = os.path.split(fullFileName)[1]
self.shortFileName = os.path.splitext(self.fileName)[1]
self.plotTitle = self.shortFileName
# def readData():
fileIn = open(fileName, "r")
hD = rx.readDataFileHeader(fileIn)
dD = rx.readDataFileArray(fileIn)
self.normal = numpy.array(map(float, dD["voltageForceNormal"]))
self.shear = numpy.array(map(float, dD["voltageForceLateral"]))
self.index = numpy.arange(len(self.normal))
# index dictionary
iD = rx.parseForceTrace(hD, dD)
self.pointX[0] = iD["indexContact"]
self.pointY[0] = self.normal[iD["indexContact"]]
self.pointX[1] = iD["indexMaxPreload"]
self.pointY[1] = self.normal[iD["indexMaxPreload"]]
self.pointX[2] = iD["indexMaxAdhesion"]
self.pointY[2] = self.normal[iD["indexMaxAdhesion"]]
# def constructPlots():
self.plotdata = ArrayPlotData(
index=self.index, normal=self.normal, shear=self.shear, pointX=self.pointX, pointY=self.pointY
)
self.normalPlot = Plot(self.plotdata)
self.normalPlot.plot(("index", "normal"), type="line", color="blue")
self.normalPlot.plot(
("pointX", "pointY"),
type="scatter",
marker="diamond",
marker_size=5,
color=(0.0, 0.0, 1.0, 0.5),
outline_color="none",
)
# set range of plot
self.normalPlot.value_range.set_bounds(-1.5, 1.5)
self.shearPlot = Plot(self.plotdata)
self.shearPlot.plot(("index", "shear"), type="line", color="green")
self.normalPlot.overlays.append(
customTool(
plotBox=self,
component=self.normalPlot,
axis="index_x",
inspect_mode="indexed",
write_metadata=True,
color="black",
is_listener=False,
)
)
self.normalPlot.tools.append(rx.SimpleZoom(self.normalPlot))
self.normalPlot.tools.append(PanTool(self.normalPlot, drag_button="right"))
self.normalPlot.title = "Normal Force Trace"
self.shearPlot.title = "Shear Force Trace"
topPlot.add(self.shearPlot)
bottomPlot.add(self.normalPlot)
self.shearPlot.index_range = self.normalPlot.index_range
def __init__(self, fileName, fOut):
super(plotBox, self).__init__()
self.isAccepted = True
self.fOut = fOut
self.message = 'Analysis Acceptable?'
self.vPlot = VPlotContainer(padding = 10)
self.vPlot.stack_order = 'top_to_bottom'
topPlot = OverlayPlotContainer(padding = 10)
self.vPlot.add(topPlot)
bottomPlot = OverlayPlotContainer(padding = 10)
self.vPlot.add(bottomPlot)
# def parseFileName():
self.fileName = fileName
# get complete path of data file
fullFileName = os.path.abspath(fileName)
self.fileName = os.path.split(fullFileName)[1]
self.shortFileName = os.path.splitext(self.fileName)[1]
self.plotTitle = self.shortFileName
# def readData():
fileIn = open(fileName,'r')
hD = rx.readDataFileHeader(fileIn)
dD = rx.readDataFileArray(fileIn)
self.normal = numpy.array(map(float,dD['voltageForceNormal']))
self.shear = numpy.array(map(float,dD['voltageForceLateral']))
self.index = numpy.arange(len(self.normal))
# index dictionary
iD = rx.parseForceTrace(hD,dD)
self.pointX[0] = iD['indexContact']
self.pointY[0] = self.normal[iD['indexContact']]
self.pointX[1] = iD['indexMaxPreload']
self.pointY[1] = self.normal[iD['indexMaxPreload']]
self.pointX[2] = iD['indexMaxAdhesion']
self.pointY[2] = self.normal[iD['indexMaxAdhesion']]
# def constructPlots():
self.plotdata = ArrayPlotData(index = self.index,
normal = self.normal,
shear = self.shear,
pointX = self.pointX,
pointY = self.pointY)
self.normalPlot = Plot(self.plotdata)
self.normalPlot.plot(('index','normal'), type = 'line',
color = 'blue')
self.normalPlot.plot(('pointX','pointY'), type = 'scatter',
marker = 'diamond',
marker_size = 5,
color = (0.0,0.0,1.0,0.5),
outline_color = 'none')
self.normalPlot.value_range.set_bounds(-1,1)
self.shearPlot = Plot(self.plotdata)
self.shearPlot.plot(('index','shear'),type='line',color='green')
self.normalPlot.overlays.append(customTool(plotBox = self,
component = self.normalPlot,
axis = 'index_x',
inspect_mode = 'indexed',
write_metadata = True,
color = 'black',
is_listener = False))
self.normalPlot.tools.append(rx.SimpleZoom(self.normalPlot))
self.normalPlot.tools.append(PanTool(self.normalPlot,drag_button = 'right'))
self.normalPlot.title = 'Normal Force Trace'
self.shearPlot.title = 'Shear Force Trace'
topPlot.add(self.shearPlot)
bottomPlot.add(self.normalPlot)
self.shearPlot.index_range = self.normalPlot.index_range
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
#!/usr/bin/env python
import sys
sys.path.append('/Users/dsoto/current/swDataFlat/roxanne')
import roxanne as rx
import numpy as np
fileNames = ['front','back']
for thisFileName in fileNames:
fileName = thisFileName + '.data'
fileIn = open(fileName, 'r')
headDict = rx.readDataFileHeader(fileIn)
dataDict = rx.readDataFileArray(fileIn)
#print dataDict.keys()
timeStrings = dataDict['time']
timeSeconds = [float(ts[0:2])*3600+float(ts[3:5])*60+float(ts[6:])
for ts in timeStrings]
import numpy as np
timeSeconds = np.array(timeSeconds)
timeSeconds = timeSeconds - timeSeconds[0]
dataDict['time'] = map(str,timeSeconds)
dataDict['time'] = timeSeconds
voltageLateral = map(float,dataDict['voltageForceLateral'])
voltageNormal = map(float,dataDict['voltageForceNormal'])
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()