def run(self,nToDo='all', width=50, plotFileName=None):
if plotFileName:
pdf = PdfPages(plotFileName)
else:
pdf = None
if nToDo == 'all': nToDo = self.n
for iToDo in range(nToDo):
ind = self.res[iToDo,1]
print "begin iToDo=",iToDo,' nToDo',nToDo,' centered at ind=',ind,' x=',self.wsf.x[ind]
indStart = max(0,self.res[iToDo,1]-width)
indEnd = min(len(self.wsf.x), self.res[iToDo,1]+width+1-10)
f = self.wsf.x[indStart:indEnd]
I = self.wsf.I[indStart:indEnd]
Ierr = self.wsf.Ierr[indStart:indEnd]
Q = self.wsf.Q[indStart:indEnd]
Qerr = self.wsf.Qerr[indStart:indEnd]
res = Resonator(f,I,Ierr,Q,Qerr)
rf = res.resfit()
line = "%4i %17.6f %17.2f %17.2f %17.2f %17.2f\n"%(iToDo,rf['f0'],rf['Q'],rf['Qi'],rf['Qc'],rf['chi2Mazin'])
self.logFile.write(line)
self.logFile.flush()
print line
res.plot(rf,pdf)
if pdf:
pdf.close()
self.logFile.close()
def run(self, nToDo='all', width=50, plotFileName=None):
if plotFileName:
pdf = PdfPages(plotFileName)
else:
pdf = None
if nToDo == 'all': nToDo = self.n
print nToDo
for iToDo in range(nToDo):
ind = self.res[iToDo, 1]
print "begin iToDo=", iToDo, ' nToDo', nToDo, ' centered at ind=', ind, ' x=', self.wsf.x[
ind]
indStart = max(0, self.res[iToDo, 1] - width)
indEnd = min(len(self.wsf.x), self.res[iToDo, 1] + width + 1 - 10)
f = self.wsf.x[indStart:indEnd]
I = self.wsf.I[indStart:indEnd]
Ierr = self.wsf.Ierr[indStart:indEnd]
# Ierr = self.wsf.Ierr
Q = self.wsf.Q[indStart:indEnd]
Qerr = self.wsf.Qerr[indStart:indEnd]
# Qerr = self.wsf.Qerr
res = Resonator(f, I, Ierr, Q, Qerr)
rf = res.resfit()
line = "%4i %17.6f %17.2f %17.2f %17.2f %17.2f\n" % (
self.res[iToDo, 0], rf['f0'], rf['Q'], rf['Qi'], rf['Qc'],
rf['chi2Mazin'])
self.logFile.write(line)
self.logFile.flush()
print line
res.plot(rf, pdf)
if pdf:
pdf.close()
self.logFile.close()
def testMagModel(self):
f = np.loadtxt("resonatorTestQIMA.txt", usecols=(1,))
I = np.loadtxt("resonatorTestQIMA.txt", usecols=(2,))
Ierr = 0.001*np.ones(len(I))
Q = np.loadtxt("resonatorTestQIMA.txt", usecols=(3,))
Qerr = 0.001*np.ones(len(Q))
res = Resonator(f,I,Ierr,Q,Qerr)
qfp = res.quickFitPrep()
x = qfp['functkw']['x']
p = qfp['p0']
yModel = Resonator.magModel(x,p)
yData = qfp['functkw']['y']
err = qfp['functkw']['err']
mdl = Resonator.magDiffLin(p, fjac=None, x=x, y=yData, err=err)
chi2 = np.power(mdl[1],2).sum()
print "chi2=",chi2
parinfo = qfp['parinfo']
functkw = qfp['functkw']
m = mpfit(Resonator.magDiffLin, p, parinfo=parinfo, functkw=functkw, quiet=1)
print "m=",m
pFit = m.params
yFit = Resonator.magModel(x,pFit)
plt.clf()
plt.plot(x,yData,label="data")
plt.plot(x,yModel,label="first guess model")
plt.plot(x,yFit,label="fit model")
plt.legend(loc='lower right')
title="Q=%.1f f0=%.5f carrier=%.3f depth=%.2f \n slope=%.1f curve=%.1f w=%.1f"%tuple(pFit.tolist())
plt.title(title)
plt.savefig("testMagModel.png")
def testQuickFit(self):
f = np.loadtxt("resonatorTestQIMA.txt", usecols=(1,))
I = np.loadtxt("resonatorTestQIMA.txt", usecols=(2,))
Ierr = 0.001*np.ones(len(I))
Q = np.loadtxt("resonatorTestQIMA.txt", usecols=(3,))
Qerr = 0.001*np.ones(len(Q))
res = Resonator(f,I,Ierr, Q, Qerr)
mag = np.loadtxt("resonatorTestQIMA.txt", usecols=(4,))
phase = np.loadtxt("resonatorTestQIMA.txt", usecols=(5,))
for j in range(len(I)):
self.assertAlmostEqual(I[j],res.I[j])
self.assertAlmostEqual(Q[j],res.Q[j])
self.assertAlmostEqual(mag[j],res.mag[j],places=5)
self.assertAlmostEqual(phase[j],res.phase[j],places=6)
dist1 = np.loadtxt("resonatorTestDist1.txt", usecols=(1,))
for j in range(len(res.dist1)):
self.assertAlmostEqual(res.dist1[j],dist1[j], places=6)
self.assertEquals(len(res.dist1),len(dist1))
self.assertEquals(50, res.residx)
self.assertAlmostEquals(-0.35312287, res.xrc1)
self.assertAlmostEquals(5.9134903, res.yrc1, places=6)
m = res.quickFit()
print m.params
# The values from the idl version are similar, but not too close
idl = [34093.219, 2.8350927, 0.11120927, 0.76291197,
3993.5131, 0.0000000, 0.0000000]
self.assertAlmostEqual(m.params[0]/idl[0],0.7965, places=4)
self.assertAlmostEqual(m.params[1]/idl[1],1, places=5)
self.assertAlmostEqual(m.params[2]/idl[2],1.239136, places=5)
self.assertAlmostEqual(m.params[3]/idl[3],1.035355, places=5)
self.assertAlmostEqual(m.params[4]/idl[4],0.202167, places=5)
def testResfit(self):
pdfPages = PdfPages("testResfit.pdf")
f = np.loadtxt("resonatorTestQIMA.txt", usecols=(1,))
I = np.loadtxt("resonatorTestQIMA.txt", usecols=(2,))
Ierr = 0.001*np.ones(len(I))
Q = np.loadtxt("resonatorTestQIMA.txt", usecols=(3,))
Qerr = 0.001*np.ones(len(Q))
res = Resonator(f,I,Ierr,Q,Qerr)
rf = res.resfit()
res.plot(rf,pdfPages)
pdfPages.close()
def testResModel(self):
f = np.loadtxt("resonatorTestQIMA.txt", usecols=(1,))
I = np.loadtxt("resonatorTestQIMA.txt", usecols=(2,))
Ierr = 0.001*np.ones(len(I))
Q = np.loadtxt("resonatorTestQIMA.txt", usecols=(3,))
Qerr = 0.001*np.ones(len(Q))
res = Resonator(f,I,Ierr,Q,Qerr)
rfp = res.resFitPrep()
x = rfp['functkw']['x']
p = rfp['p0']
yModel = Resonator.resModel(x,p)
yData = rfp['functkw']['y']
err = rfp['functkw']['err']
rdl = Resonator.resDiffLin(p, fjac=None, x=x, y=yData, err=err)
chi2 = np.power(rdl[1],2).sum()
print "chi2=",chi2
parinfo = rfp['parinfo']
functkw = rfp['functkw']
m = mpfit(Resonator.resDiffLin, p, parinfo=parinfo, functkw=functkw, quiet=1)
pFit = m.params
rdlFit = Resonator.resDiffLin(pFit, fjac=None, x=x, y=yData, err=err)
chi2Fit = np.power(rdlFit[1],2).sum()
print "chi2Fit=",chi2Fit
yFit = Resonator.resModel(x,pFit)
plt.clf()
print "xrc1,yrc1=",res.xrc1,res.yrc1
plt.plot(yData.real,yData.imag,"o",mfc='none',label="data")
#plt.plot(yData.real[0],yData.imag[0],"+",label="first data")
#plt.plot(yModel.real,yModel.imag,label="model")
#plt.plot(yModel.real[0],yModel.imag[0],"o",label="first model")
plt.plot(yFit.real,yFit.imag,label="fit")
#plt.plot(yFit.real[0],yFit.imag[0],"o",label="first fit")
#plt.legend(loc='center')
#title="Q=%.1f f0=%.5f carrier=%.3f depth=%.2f \n slope=%.1f curve=%.1f w=%.1f"%tuple(pFit.tolist())
#plt.title(title)
plt.axvline(linewidth=1,color='b',x=res.xrc1,linestyle=":")
plt.axhline(linewidth=1,color='b',y=res.yrc1,linestyle=":")
plt.axes().set_aspect('equal')
plt.savefig("testResModel.png")