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Magnetoscope.pyw
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Magnetoscope.pyw
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# -*- coding: utf-8 -*-
"""
Created on Fri Mar 15 03:11:55 2013
@author: Ali
"""
from ConfigFileReader import ConfigFileReader
import datetime
import sys
import matplotlib
import matplotlib.pylab as py
from matplotlib import pyplot as plt
from matplotlib.widgets import Button
from matplotlib.text import Text
from PyQt4 import QtGui
from PyQt4 import QtCore
from matplotlib.ticker import FuncFormatter
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
import numpy as np
import myfilters
import math
import serial
import time
import os
global otimestamp
global tstamp
global fcoeffs
global N
global Area
global axfreq
otimestamp=0
tstamp=0
class LivePlot(FigureCanvas):
"""
Matplotlib widget to plot the raw data
"""
def __init__(self,parent,updatefunc):
myf = "Probe.conf"
mycfg = ConfigFileReader(myf)
self.lockInnF = mycfg.getRotFreq()
self.fsamp = mycfg.SamplingFreq()
self.slope = mycfg.getCalibration()
com = mycfg.getComPort()
self.Dbug = mycfg.getDebugMode()
self.newdataplotlimit = mycfg.NewDataPlotLimit()
self.updatefunc = updatefunc
self.xmax = mycfg.GetPlotWindowLength()
self.MyFile = mycfg.getDebugFile()
self.measurement = mycfg.GetNoOfMeas()
self.newdata = 0
self.oVphase=-999999
self.wrapper=0
self.wrapper1 = 0
self.oCphase = -999999
self.lastzeromark=0
self.thiszeromark=0
self.frequencyvalid=False
self.frequencyvalid=True
self.oldV=0
self.linelength=44
self.filtfreq = 0
self.f = 0
self.NB = 0
self.a11=0
self.a12=0
self.a22=0
self.b1=0
self.b2=0
self.a=0
self.b=0
self.d=0
self.meanB = 0
self.reset_mean = True
self.cofs=myfilters.gbutter(0.5,self.fsamp,6)
self.myfilter0 = myfilters.gIIR(self.cofs)
self.myfilter1 = myfilters.gIIR(self.cofs)
self.myfilter2 = myfilters.gIIR(self.cofs)
self.myfilter3 = myfilters.gIIR(self.cofs)
# Phase determined cap filter
self.myfilter4 = myfilters.gIIR(self.cofs)
self.myfilter5 = myfilters.gIIR(self.cofs)
self.cofs2=myfilters.gbutter(self.lockInnF/5,self.lockInnF,8)
self.myfilter6 = myfilters.gIIR(self.cofs2)
mylabels = ['V (mV)','Vc (V)','Cap-amp (mV)',\
'Vamp (mV)','d (in)','f (Hz)',\
'Vphi','Cphi','B (mT)']
# Define the color scheme for the subplots
mycolor = ['b-','r-','k-',
'b-','r-','k-',
'b-','r-','k-']
mycolor2 =['b-','r-','k-',
'b-','r-','k-',
'b-','r-','k-']
# For annotation of mean and std deviation of plot
self.myann=[]
self.ax=[]
self.lines=[]
self.lines2=[]
self.fig = Figure()
self.fig.subplots_adjust(left=0.085, right =0.95, wspace=0.5, hspace =0.3)
y_formatter = matplotlib.ticker.ScalarFormatter(useOffset=False)
self.canvas = FigureCanvas.__init__(self,self.fig)
self.setParent(parent)
self.main_frame = QtGui.QWidget()
self.mainlayout = QtGui.QVBoxLayout()
self.mainlayout.addWidget(self.canvas)
self.button = QtGui.QPushButton('Update Frequency (f)')
self.mainlayout.addWidget(self.button)
self.button.setMaximumSize(200, 200)
self.mainlayout.addStretch()
self.button.setShortcut(0x46)
self.button.clicked.connect(self.change_freq)
self.button1 = QtGui.QPushButton('Capture Data and Reset Mean (D)')
self.mainlayout.addWidget(self.button1)
self.button1.setMaximumSize(200, 200)
self.mainlayout.addSpacing(1000)
self.button1.setShortcut(0x44)
self.button1.clicked.connect(self.BMean)
self.buttonq = QtGui.QPushButton('Quit (q)')
self.mainlayout.addWidget(self.buttonq)
self.buttonq.setMaximumSize(100, 100)
self.buttonq.setShortcut(0x51)
self.buttonq.clicked.connect(self.Quit)
self.setLayout(self.mainlayout)
# Define plot parameters.
for i in range(9):
# 3 rows 3 column ith plot
self.ax.append(self.fig.add_subplot(3,3,i+1))
# show the last 20s(VoltageSamples_03-07-13_153318xmax defines the length of window for plot)
self.ax[-1].set_xlim(0,self.xmax)
# Enable autoscale for both axis
self.ax[-1].autoscale(enable=True, axis='both', tight=False)
# Format the yaxis data such that the data appears on lhs
self.ax[-1].yaxis.set_major_formatter(y_formatter)
# Set the y-axis labels
self.ax[-1].set_ylabel(mylabels[i])
# Set the x-axis labels
self.ax[-1].set_xlabel('time(s)')
# Annotate top center, the mean and the dev of the plots
an = self.ax[-1].annotate('Hi Fish',xy=(0.3,1.0),xycoords='axes fraction')
self.myann.append(an)
newline, = self.ax[-1].plot([],[],mycolor[i],label=mylabels[i])
self.lines.append(newline)
newline, = self.ax[-1].plot([],[],mycolor2[i])
self.lines2.append(newline)
self.time=[] # Collect the sampling time data from COM port
self.Vdata=[] # Collect EMF voltage data from COM port
self.Cdata=[] # Collect Cap-voltage data from COM port
self.Rdata=[] # Collect rotation data from zero crossings of Voltage data
self.VAMP=[] # EMF filtered amplitude
self.VPHS=[] # EMF filtered phase
self.CAMP=[] # Cap voltage filtered amplitude
self.CPHS=[] # Cap voltage filtered phase
self.BAMP=[] # B-field average amplitude
self.CAMP1=[] # Average Cap amplitude derived by using initial phase from voltage data
self.freq=[] # Get frequency of rotationfrom PyQt4 import QtCore
self.Inphase=[]
self.Inquad=[]
self.sampling=[]
if (self.Dbug == True):
print "Magnetoscope is in DEBUG Mode..."
self.myfile = open (self.MyFile,'r')
self.filedata=[]
for lines in self.myfile:
self.filedata.append(lines)
self.myfile.close()
self.recordNo=0
self.timer = self.startTimer(1)
else:
print "Starting Magnetoscope..."
self.ser=serial.Serial(port=com,
baudrate=115200,
bytesize=serial.EIGHTBITS,
parity=serial.PARITY_NONE,
stopbits=serial.STOPBITS_ONE)
self.ser.timeout = 3
self.timer = self.startTimer(100)
self.fig.canvas.draw()
self.timerEvent(None)
def getdata(self):
global otimestamp # old timestamp
global tstamp # new timestamp
if (self.Dbug == True):
#for fileline in self.myfile:
i= self.filedata[self.recordNo].split()
#print i
self.recordNo+=1
else:
samples = self.ser.readline()
i = samples.split()
if (len(i)==3):
tstamp = otimestamp +float(i[0])*0.001
otimestamp = tstamp
# Error Check for Corrupted Data
try:
v_data =float(i[1]) # get voltage data
except ValueError:
print 'Corrupted Data'
exit()
try:
c_data = float(i[2]) # get cap voltage data
except ValueError:
print 'Corrupted Data'
exit()
samp_data =float(i[0]) # sampling data
return tstamp,v_data,c_data,samp_data
# if the sample lengself.posbox.textC- Positionhanged.connect(self.CurrPos)th is not 3 then return 0's from PyQt4 import QtCore
return 0,0,0,0
def analysis(self,Volt,Time):
ip = float(Volt)*math.cos(Time*self.lockInnF*2*np.pi)
iq = float(Volt)*math.sin(Time*self.lockInnF*2*np.pi)
return (ip, iq)
def analysisC(self, CV,Time,vph):
# Cap amplitude is calculated from the initial phase data of EMF plot
# cap voltage leads emf by 90
voffs=-0.087
iq = float(CV)*math.sin(Time*self.lockInnF*2*np.pi + vph+voffs + math.pi/2)
return iq
# Now update the frequency...
def update_freq(self,Time,Rot):
if Rot==0:
self.thiszeromark = Time
# Calculate the new rotation frequency
frequen = 1.0/(-self.lastzeromark+self.thiszeromark)
for count in range(1000):
x= self.myfilter6.filtered(frequen)
self.f = x
self.lastzeromark=self.thiszeromark
return self.f
def change_freq(self):
self.lockInnF = self.f
print self.lockInnF
def nonzero(self,*arg):
for i in arg:
if i!=0: return True
return False
# DC average after filtering
def Amp_Phase(self,fp,fq):
Vaf =2.0*( np.sqrt(fp**2 +fq**2))
# Calculate phase
Vpf = np.arctan2(fp, fq)
return Vaf,Vpf
def Mag_Amp(self,V,f):
global N,Area
N = 59
Area = 1.0*1.125*2.54e-2*2.54e-2
# V = N*A*B*2*pi*f
BField1 = V/(N*Area*2*np.pi*f)
return(BField1)
def BMean(self):
self.reset_mean = True
def Quit(self):
reply = QtGui.QMessageBox.question(self, 'Message',
"Are you sure?", QtGui.QMessageBox.Yes |
QtGui.QMessageBox.No, QtGui.QMessageBox.No)
if reply == QtGui.QMessageBox.Yes:
print "Quitting Application..."
if (self.Dbug == True):
app.quit()
sys.exit(app.exec_())
else:
self.ser.flush()
self.ser.close()
app.quit()
sys.exit(app.exec_())
def timerEvent(self,evt):
"""
This code will be called, whenever the timer triggers,
don't rename this method
"""
# Get the data every time the timer triggers
#newdata=0
if self.Dbug==True:
haveData=True
else:
haveData=False
while haveData==True or \
(( self.Dbug==False) and (self.ser.inWaiting()>self.linelength)):
t,V,C,s=self.getdata()
haveData=False
if np.sign(V)<np.sign(self.oldV):
r=0
else:
r=1
self.oldV=V
if self.nonzero(t,V,C):
IP,IQ = self.analysis(V,t)
IPC,IQC = self.analysis(C,t)
Vamp,Vphase = self.Amp_Phase(self.myfilter0.filtered(IP),\
self.myfilter1.filtered(IQ))
Bfield = self.Mag_Amp(Vamp,self.lockInnF)
Camp,Cphase = self.Amp_Phase(self.myfilter2.filtered(IPC),
self.myfilter3.filtered(IQC))
Vphase = Vphase + self.wrapper*2*math.pi
Vphase_uw = Vphase
if self.oVphase==-999999: self.oVphase=Vphase
if Vphase-self.oVphase>math.pi:
Vphase=Vphase-2*math.pi
self.wrapper = self.wrapper -1
elif self.oVphase-Vphase>math.pi:
Vphase=Vphase+2*math.pi
self.wrapper = self.wrapper +1
self.oVphase=Vphase
Cphase = Cphase + self.wrapper1*2*math.pi
if self.oCphase==-999999: self.oCphase=Cphase
if Cphase-self.oCphase>math.pi:
Cphase=Cphase-2*math.pi
self.wrapper1 = self.wrapper1 -1
elif self.oCphase-Cphase>math.pi:
Cphase=Cphase+2*math.pi
self.wrapper1 = self.wrapper1 +1
self.oCphase=Cphase
IA = self.analysisC(C,t,Vphase_uw)
Camp1=2.0*self.myfilter4.filtered(IA)
dist = Camp1/self.slope
self.Vdata.append(V)
self.Cdata.append(C)
self.time.append(t)
self.Inphase.append(IP)
self.Inquad.append(IQ)
self.Rdata.append(r)
self.VAMP.append(Vamp)
self.VPHS.append(Vphase)
self.CAMP.append(dist)
self.CPHS.append(Cphase)
self.BAMP.append(Bfield)
self.CAMP1.append(Camp1*1000)
self.sampling.append(s)
self.freq.append(self.f)
self.newdata+=1
# Clear the buffer
if len(self.Vdata)>(self.xmax*100):
self.Vdata.pop(0)
self.time.pop(0)
self.Cdata.pop(0)
self.Rdata.pop(0)
self.VAMP.pop(0)
self.VPHS.pop(0)
self.CAMP.pop(0)
self.CPHS.pop(0)
self.freq.pop(0)
self.BAMP.pop(0)
self.CAMP1.pop(0)
self.sampling.pop(0)
if self.reset_mean==True:
if self.NB>0 :
self.updatefunc(self.tB,self.t2B,self.NB\
,self.tC,self.t2C,self.NC,True)
self.tB = 0
self.t2B = 0
self.NB = 0
self.tC = 0
self.t2C = 0
self.NC = 0
self.FB=[]
self.CA=[]
self.reset_mean=False
self.FB.append(Bfield)
self.CA.append(Camp1*1000)
self.NB = self.NB + 1
self.tB = self.tB + Bfield
self.t2B = self.t2B + Bfield*Bfield
self.NC = self.NC + 1
self.tC =self.tC + Camp1*1000
self.t2C =self.t2C + Camp1*Camp1*1e6
while self.NB>self.measurement:
self.tB = self.tB - self.FB[0]
self.t2B = self.t2B - self.FB[0]*self.FB[0]
self.NB = self.NB - 1
self.FB.pop(0)
#self.NB = len(self.FB)
while self.NC>1000:
self.tC = self.tC - self.CA[0]
self.t2C = self.t2C - self.CA[0]*self.CA[0]
self.NC = self.NC-1
self.CA.pop(0)
self.a11=0
self.a12=0
self.a22=0
self.b1=0
self.b2=0
a=0
b=0
t0=self.time[0]
for tn,Vphase in zip(self.time,self.VPHS):
t=tn-t0
self.a11+=t*t
self.a12+=1*t
self.a22+=1
self.b1+=t*Vphase
self.b2+=1*Vphase
det = self.a11*self.a22-self.a12*self.a12
if det!=0:
b = 1.0/det * (self.a22*self.b1-self.a12*self.b2)
a = 1.0/det * (-self.b1*self.a12+self.b2*self.a11)
vphasefit=[]
for t,phase in zip(self.time,self.VPHS):
vphasefit.append(a+b*(t-t0))
self.f=self.myfilter6.filtered(self.lockInnF+b/(2*math.pi))
Data=zip(*zip(self.Vdata,self.Cdata,self.CAMP1,\
self.VAMP,self.CAMP,self.freq,self.VPHS,self.CPHS,self.BAMP))
mymeans=[]
mystds=[]
if self.newdata>self.newdataplotlimit:
self.updatefunc(self.tB,self.t2B,self.NB,self.tC,self.t2C,self.NC,False)
self.newdata=0
for i in range(len(Data)):
self.ax[i].set_xlim(self.time[0],self.time[0]+self.xmax)
if len(Data[i])>2:
mymin = min(Data[i])
mymax = max(Data[i])
mymeans.append(np.mean(Data[i]))
mystds.append(np.std(Data[i]))
if mymax>mymin:
self.ax[i].set_ylim(mymin,mymax)
#if (i==0):self.mlayout.setFocus()
ll =len(self.time)
tets=range(10)
self.lines[i].set_data(tets,tets)
self.lines[i].set_data(self.time[0:ll],Data[i][0:ll])
if i==6:
self.lines2[i].set_data(self.time[0:ll],vphasefit[0:ll]) #this is not the problem
mystr="slope: {0:8.5f}".format(b)
else:
self.lines2[i].set_data([self.time[0],self.time[0]+self.xmax],[mymeans[i], mymeans[i]])
mystr="{0:8.5f} ({1:6.5f})".format(mymeans[i],mystds[i])
self.myann[i].set_text(mystr)
self.fig.canvas.draw()
class StatusInfo(QtGui.QWidget):
def __init__(self,parent):
super(StatusInfo,self).__init__(parent)
self.canvas = QtGui.QWidget()
self.value=0
#self.setMaximumSize(400,400)
self.setMaximumWidth(300)
self.setMinimumWidth(300)
self.sw =QtGui.QLabel("MAGNETOSCOPE V.1.0\nCreators:\nDr. Stephan Schlamminger\
\nDr.Frank Seifert\nAlireza Panna\nLeon Chao")
self.mainlayout = QtGui.QVBoxLayout()
self.mainlayout.addWidget(self.sw)
names = ["00/00/00","00:00:00","No of Measurements",\
"0","Mean B (mT)",\
"0.00","Std B (mT)", "0.00", \
"Cap-Amp (mV)", "0.00","Cap-Std (mV)",\
"0.00"]
ss=20
ls=48
fontsizes=[ls,ls,ss,ls,ss,ls,ss,ls,ss,ls,ss,ls]
self.labels=[]
self.mainlayout.addStretch()
for na,fs in zip(names,fontsizes):
self.labels.append( QtGui.QLabel(na))
# if fs==ls:
self.labels[-1].setMinimumSize(280,int(fs*1.5))
self.labels[-1].setMaximumSize(280,int(fs*1.5))
myFont=QtGui.QFont("Times",fs)
self.labels[-1].setFont(myFont)
self.mainlayout.addWidget(self.labels[-1])
self.lastr=""
self.myedit=QtGui.QLabel("Press 'D' to capture")
#self.myedit=QtGui.QText
self.myedit.setBaseSize(280,100)
#self.myedit.baseSize(QtCore.QSize(80,100))
self.myedit.setMaximumSize(280,100)
self.myedit.setMinimumSize(280,100)
self.myedit.adjustSize()
self.mainlayout.addWidget(self.myedit)
self.setMaximumWidth(300)
self.setMinimumWidth(300)
#self.mainlayout.addStretch()
self.setLayout(self.mainlayout)
def makestrings(self,L,mymean,mystd):
if L>3:
le = L
# mv = np.mean(myArray)
# st = np.std(myArself.mlayout.setFocus() ray)
di = int(math.ceil(-math.log10(mystd/math.sqrt(le)))+1)
mele = math.ceil(math.log10(abs(mymean)))
if mele<0:
mele=2
if di<0:
di=1
mele=int(mele+1+di)
if mele<di:
mele=int(di+1)
length_str = "{0:4d}".format(le)
try:
mean_str= "{0:{le}.{si}f}".format(mymean,le=mele,si=di)
except:
print "le=",mele," si=",di
mean_str="Error"
try:
sigma_str = "{0:{le}.{si}f}".format(mystd,le=di+2,si=di)
except:
print "le=",mele," si=",di
sigma_str="Error"
else:
length_str="No Data"
mean_str="No Data"
sigma_str="No Data"
return length_str,mean_str,sigma_str
def calc_mean_sig(self, S,S2,L):
m = S/L
V = 1.0/(L-1)*(S2-S*S/L)
try:
Sig= math.sqrt(V)
except:
print V,L,S2,S
return L,m,Sig
def updateMe(self,tB,t2B,NB,tC,t2C,NC,writeToFile):
if NC<3 :return
if NB<3 :return
L,M,S = self.calc_mean_sig(tB,t2B,NB)
s2,s4,s6 = self.makestrings(L,M,S)
L,M,S = self.calc_mean_sig(tC,t2C,NC)
du,s8,s10 = self.makestrings(L,M,S)
now = datetime.datetime.now()
dastr = now.strftime("%m/%d/%y")
tistr = now.strftime("%H:%M:%S")
self.labels[0].setText(dastr)
self.labels[1].setText(tistr)
self.labels[3].setText(s2)
self.labels[5].setText(s4)
self.labels[7].setText(s6)
self.labels[9].setText(s8)
self.labels[11].setText(s10)
if writeToFile==True:
dastr2 = now.strftime("%m%d%y")
fn = "MP_{0}.dat".format(dastr2)
if os.path.isfile(fn)==False:
myfile = open(fn,'w')
header="#Date Time Length B[mT] sigma[mT] Cap[mV] sigma[mV]\n"
myfile.write(header)
myfile = open(fn,'a')
mystr="{0}\t{1}\t\t{2}\t\t{3}\t\t{4}\t\t{5}\t\t{6}\n".format(
dastr,tistr,s2,\
s4,s6,s8, \
s10)
myfile.write(mystr)
myfile.close()
mystr="{0} {1} mT {2} mV \n".format(
tistr,\
s4, s8)
self.lastr = self.lastr+mystr
mylines =self.lastr.split("\n")
test = [i for i in mylines[-5:]]
testr = "\n".join(test)
self.myedit.setText(testr)
def updateText(self,value):
s=str(value)
self.label1.setText(s)
def add_one(self):
self.value+=1
self.updateText(self.value)
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.main_widget = QtGui.QWidget(self)
self.main_widget.setAutoFillBackground(True)
self.main_widget.setPalette(QtGui.QPalette(QtGui.QColor(255,255,255)))
self.main_widget.setFont(QtGui.QFont("Helvetica", 9.5))
hbl = QtGui.QHBoxLayout(self.main_widget)
inf = StatusInfo(self.main_widget)
qmc = LivePlot(self.main_widget,inf.updateMe)
hbl.addWidget(qmc)
hbl.addWidget(inf)
# set the focus on the main widget
self.main_widget.setFocus()
# set the central widget of MainWindow to main_widget
self.setCentralWidget(self.main_widget)
app = QtGui.QApplication(sys.argv)
aw = ApplicationWindow()
aw.show()
#aw.showFullScreen()
sys.exit(app.exec_())
#time.sleep(1)
#ser.flush()
#ser.close()