def __init__(self, parent): QDialog.__init__(self, parent) self.parent_window=parent parent.initiateReflectivityPlot.connect(self.update_fr) self.ui=Ui_Dialog() self.ui.setupUi(self) self.setWindowTitle(u'QuickNXS - Polarization') self._WLitems=[] self._FMitems=[] self._Xitems=[] self.update_fr()
class PolarizationDialog(QDialog):
Icurrent={}
_auto_change_active=False
polarization_parameters=None
def __init__(self, parent):
QDialog.__init__(self, parent)
self.parent_window=parent
parent.initiateReflectivityPlot.connect(self.update_fr)
self.ui=Ui_Dialog()
self.ui.setupUi(self)
self.setWindowTitle(u'QuickNXS - Polarization')
self._WLitems=[]
self._FMitems=[]
self._Xitems=[]
self.update_fr()
def update_fr(self):
'''
Plot the different flipping ratios of the current dataset.
'''
if self._auto_change_active:
return
parent=self.parent_window
if parent.active_data is None or parent.refl is None:
return
opts=parent.refl.options
data=parent.active_data
channels=data.keys()
self.ui.flippingRatios.clear()
self.ui.wavelengthPol.clear()
self.drawFRs()
if not (('++' in channels and '+-' in channels) or
('++' in channels and '-+' in channels)):
self.ui.flippingRatios.draw()
return
FR1=0;FR2=0
I={}
nos=[item[0] for item in self._WLitems]
if opts['number'] in nos:
this_index=nos.index(opts['number'])
lmin=float(self.ui.wlTable.item(this_index, 1).text())
lmax=float(self.ui.wlTable.item(this_index, 2).text())
else:
lmin=0.; lmax=15.
if '++' in channels and '-+' in channels:
p=Reflectivity(data['++'], **opts)
m=Reflectivity(data['-+'], **opts)
I['++']=p;I['-+']=m
reg=where((p.Rraw>0)&(m.Rraw>0)&(p.lamda>=lmin)&(p.lamda<=lmax))
fr, dfr=self.calc_fr(p, m)
FR1=fr[reg].mean()
self.ui.flippingRatios.errorbar(p.lamda[reg], fr[reg], yerr=dfr[reg], fmt='-r', label=u'SF$_1$')
if '++' in channels and '+-' in channels:
p=Reflectivity(data['++'], **opts)
m=Reflectivity(data['+-'], **opts)
I['++']=p;I['+-']=m
reg=where((p.Rraw>0)&(m.Rraw>0)&(p.lamda>=lmin)&(p.lamda<=lmax))
fr, dfr=self.calc_fr(p, m)
FR2=fr[reg].mean()
self.ui.flippingRatios.errorbar(p.lamda[reg], fr[reg], yerr=dfr[reg], fmt='-b', label=u'SF$_2$')
if len(channels)==4:
I['--']=Reflectivity(data['--'], **opts)
reg=where((I['++'].Rraw>0)&(I['+-'].Rraw>0)&(I['-+'].Rraw>0)&
(I['--'].Rraw>0)&(p.lamda>=lmin)&(p.lamda<=lmax))
phi, _dphi, Fp, _dFp, Fa, _dFa=self.calc_pols(I)
self.ui.PolLabel.setText(u'φ=%.3f F1=%.3f F2=%.3f'%(phi[reg].mean(), Fp[reg].mean(),
Fa[reg].mean()))
#self.ui.wavelengthPol.errorbar(p.lamda[reg], phi[reg], yerr=dphi[reg], fmt='-b', label=u'$\\phi$')
#self.ui.wavelengthPol.errorbar(p.lamda[reg], Fp[reg], yerr=dFp[reg], fmt='-r', label=u'F$_1$')
#self.ui.wavelengthPol.errorbar(p.lamda[reg], Fa[reg], yerr=dFa[reg], fmt='-g', label=u'F$_2$')
else:
self.ui.PolLabel.setText('')
#self.ui.wavelengthPol.legend()
self.ui.wavelengthPol.set_xlabel(u'$\\lambda$ [Å]')
self.ui.wavelengthPol.set_ylabel(u'Efficiency')
self.ui.wavelengthPol.canvas.ax.axhline(1., color='black')
self.ui.wavelengthPol.draw()
self.ui.flippingRatios.legend()
self.ui.flippingRatios.set_xlabel(u'$\\lambda$ [Å]')
self.ui.flippingRatios.set_ylabel(u'Flipping Ratio')
self.ui.flippingRatios.draw()
self.ui.FR1.setText("%.1f"%FR1)
self.ui.FR2.setText("%.1f"%FR2)
self.Icurrent=(opts['number'], I, opts['x_pos'])
def calc_fr(self, p, m):
fr=p.Rraw/m.Rraw
dfr=sqrt((p.dRraw/m.Rraw)**2+(m.dRraw*p.Rraw/m.Rraw**2)**2)
return fr, dfr
def calc_pols(self, I):
'''
Calculate efficiency parameters from intensities using the
formulas (11) given in [ARWildes2007]_.
'''
I00=I['++'].Rraw;I01=I['+-'].Rraw;I10=I['-+'].Rraw;I11=I['--'].Rraw
ddI00=I['++'].dRraw**2;ddI01=I['+-'].dRraw**2;ddI10=I['-+'].dRraw**2;ddI11=I['--'].dRraw**2
# combined polarizer/analyzer efficiency
phi1=(I00-I01)*(I00-I10)
phi2=(I00*I11-I01*I10)
phi=phi1/phi2
# error propagation
ddphi1=((ddI00+ddI01)*(I00-I10)**2)+((ddI00+ddI10)*(I00-I01)**2)
ddphi2=(ddI00*I11**2+ddI11*I00**2)+(ddI01*I10**2+ddI10*I01**2)
dphi=sqrt(ddphi1/phi2**2+ddphi2*phi1**2/phi2**4)
# flipper 1 efficiency
Fp1=(I00-I01-I10+I11)
Fp2=2.*(I00-I01)
Fp=Fp1/Fp2
ddFp1=(ddI00+ddI01+ddI10+ddI11)
ddFp2=4.*(ddI00+ddI01)
dFp=sqrt(ddFp1/Fp2**2+ddFp2*Fp1**2/Fp2**4)
# flipper 2 efficiency
Fa1=Fp1
Fa2=2.*(I00-I10)
Fa=Fa1/Fa2
ddFa1=ddFp1
ddFa2=4.*(ddI00+ddI10)
dFa=sqrt(ddFa1/Fa2**2+ddFa2*Fa1**2/Fa2**4)
return phi, dphi, Fp, dFp, Fa, dFa
def calc_fullpols(self, I, FM):
'''
Calculate all 4 polariation parameter from a direct beam measurement and a magnetic
materials measurement.
'''
phi, dphi, Fp, dFp, Fa, dFa=self.calc_pols(I)
F00=FM['++'].Rraw;F01=FM['+-'].Rraw;F10=FM['-+'].Rraw;F11=FM['--'].Rraw
#ddF00=FM['++'].dRraw**2;ddF01=FM['+-'].dRraw**2;ddF10=FM['-+'].dRraw**2;ddF11=FM['--'].dRraw**2
p1=(1-2*Fa)*F00+(2*Fa-1)*F10-F01+F11
p2=(1-2*Fa)*F00+(2*Fa-1)*F01-F10+F11
p=0.5*(sqrt(phi*p1/p2)+1)
dp=dphi
# ddp1=0.
# ddp2=0.
# ddp12=ddp1/p2**2+ddp2*p1**2/p2**4
# ddphi=dphi**2
# ddphip12=ddphi*(p1/p2)**2+ddp12*phi**2
a=(phi/(2*p-1)+1)/2.
da=dp
return p, dp, a, da, Fp, dFp, Fa, dFa
def addWL(self):
self._WLitems.append(self.Icurrent)
self._FMitems.append(None)
row=self.ui.wlTable.rowCount()
reg=True
for value in self.Icurrent[1].values():
reg=reg&(value.Rraw>0)
lmin=value.lamda[reg][0]
lmax=value.lamda[reg][-1]
self._auto_change_active=True
self.ui.wlTable.insertRow(row)
self.ui.wlTable.setItem(row, 0, QTableWidgetItem(self.Icurrent[0]))
self.ui.wlTable.setItem(row, 1, QTableWidgetItem(str(lmin)))
self.ui.wlTable.setItem(row, 2, QTableWidgetItem(str(lmax)))
self._auto_change_active=False
self.ui.wlTable.setItem(row, 3, QTableWidgetItem('None'))
def clearWL(self):
self._WLitems=[]
self._FMitems=[]
self.polarization_parameters=None
self.ui.exportButton.setEnabled(False)
self.ui.wlTable.setRowCount(0)
self.ui.wavelengthPol.clear()
self.ui.flippingRatios.clear()
self.ui.wavelengthPol.draw()
self.ui.flippingRatios.draw()
self.ui.exportButton.setEnabled(False)
def assignFM(self):
tbl=self.ui.wlTable
selection=tbl.selectedItems()
if len(selection)==0:
return
row=tbl.row(selection[0])
if not (self._WLitems[row][1].values()[0].lamda==self.Icurrent[1].values()[0].lamda).all():
return
self._FMitems[row]=self.Icurrent
tbl.setItem(row, 3, QTableWidgetItem(self.Icurrent[0]))
def drawFRs(self, active_number=None):
errbars=self.ui.polErrorbars.isChecked()
use_FM=(len(self._FMitems)>0) and (not any([item is None for item in self._FMitems]))
if use_FM:
lamda_all=[]
p_all=[]
a_all=[]
Fa_all=[]
Fp_all=[]
for i, (no, I, ignore) in enumerate(self._WLitems):
lamda=I.values()[0].lamda
reg=((lamda>=float(self.ui.wlTable.item(i, 1).text()))&
(lamda<=float(self.ui.wlTable.item(i, 2).text())))
if len(I)==4:
if not use_FM:
phi, dphi, Fp, dFp, Fa, dFa=self.calc_pols(I)
if not errbars:
dphi=None;dFp=None;dFa=None
else:
dphi=dphi[reg];dFp=dFp[reg];dFa=dFa[reg]
self.ui.wavelengthPol.errorbar(lamda[reg], phi[reg], yerr=dphi,
ls='-', color='#008888', label=u'$\\phi$')
self.ui.wavelengthPol.errorbar(lamda[reg], Fp[reg], yerr=dFp,
ls='-', color='red', label=u'F$_1$')
self.ui.wavelengthPol.errorbar(lamda[reg], Fa[reg], yerr=dFa,
ls='-', color='orange', label=u'F$_2$')
else:
p, dp, a, da, Fp, dFp, Fa, dFa=self.calc_fullpols(I, self._FMitems[i][1])
if not errbars:
dp=None;da=None;dFp=None;dFa=None
else:
dp=dp[reg];da=da[reg];dFp=dFp[reg];dFa=dFa[reg]
lamda_all.append(lamda[reg])
p_all.append(p[reg]);a_all.append(a[reg])
Fp_all.append(Fp[reg]);Fa_all.append(Fa[reg])
self.ui.wavelengthPol.errorbar(lamda[reg], p[reg], yerr=dp,
ls='-', color='green', label=u'p')
self.ui.wavelengthPol.errorbar(lamda[reg], a[reg], yerr=da,
ls='-', color='blue', label=u'a')
self.ui.wavelengthPol.errorbar(lamda[reg], Fp[reg], yerr=dFp,
ls='-', color='red', label=u'F$_p$')
self.ui.wavelengthPol.errorbar(lamda[reg], Fa[reg], yerr=dFa,
ls='-', color='orange', label=u'F$_a$')
if i==0:
self.ui.wavelengthPol.legend()
if no==active_number:
continue
if '++' in I and '+-' in I:
fr, dfr=self.calc_fr(I['++'], I['+-'])
self.ui.flippingRatios.errorbar(lamda[reg], fr[reg], yerr=dfr[reg], fmt='-b', label=None)
if '++' in I and '-+' in I:
fr, dfr=self.calc_fr(I['++'], I['-+'])
self.ui.flippingRatios.errorbar(lamda[reg], fr[reg], yerr=dfr[reg], fmt='-r', label=None)
if use_FM:
self.refinePolarizationParameters(lamda_all, p_all, a_all, Fa_all, Fp_all)
def refinePolarizationParameters(self, lamda_all, p_all, a_all, Fa_all, Fp_all):
# fit polarization parameters
# for polarizer and analyzer efficiency use Pn function
# and for flippers linear regression
lamda=hstack(lamda_all).astype(float64)
p=hstack(p_all).astype(float64)
a=hstack(a_all).astype(float64)
Fa=hstack(Fa_all).astype(float64)
Fp=hstack(Fp_all).astype(float64)
order=argsort(lamda)
lamda=lamda[order]
p=p[order]
a=a[order]
Fa=Fa[order]
Fp=Fp[order]
res=mpfit(Pn_residuals, [0.995, 1.55, 0.15], functkw=dict(lamda=lamda, Pdata=a), nprint=0)
a_params=res.params
res=mpfit(Pn_residuals, [0.995, 4.5, 0.15], functkw=dict(lamda=lamda, Pdata=p), nprint=0)
p_params=res.params
res=mpfit(lin_residuals, [0., 1.], functkw=dict(lamda=lamda, data=Fa), nprint=0)
Fa_params=res.params
res=mpfit(lin_residuals, [0., 1.], functkw=dict(lamda=lamda, data=Fp), nprint=0)
Fp_params=res.params # store polarization parameters and data columns
self.polarization_parameters=([lamda, p, Pn(lamda, *p_params)],
[lamda, a, Pn(lamda, *a_params)],
[lamda, Fp, lamda*Fp_params[0]+Fp_params[1]],
[lamda, Fa, lamda*Fa_params[0]+Fa_params[1]],
p_params, a_params, Fp_params, Fa_params)
self.ui.wavelengthPol.plot(lamda, Pn(lamda, *p_params), color='green')
self.ui.wavelengthPol.plot(lamda, Pn(lamda, *a_params), color='blue')
self.ui.wavelengthPol.plot(lamda, lamda*Fp_params[0]+Fp_params[1], color='red')
self.ui.wavelengthPol.plot(lamda, lamda*Fa_params[0]+Fa_params[1], color='orange')
self.ui.exportButton.setEnabled(True)
def exportPolarizationParameters(self):
name=QFileDialog.getSaveFileName(parent=self, caption=u'Select export file prefix',
filter='ASCII files (*.dat);;All files (*.*)')
if name!='':
name=unicode(name)
if name.endswith('.dat'):
prefix=name[:-4]
else:
prefix=name
# export parameters
f=open(prefix+'_parameters.dat', 'w')
f.write('## Polarizer:\n# Pmax, lamda_0, s\n%g, %g, %g\n'%
tuple(self.polarization_parameters[4]))
f.write('## Analyzer:\n# Pmax, lamda_0, s\n%g, %g, %g\n'%
tuple(self.polarization_parameters[5]))
f.write('## Flipper1:\n# a, b\n%g, %g\n'%
tuple(self.polarization_parameters[6]))
f.write('## Flipper2:\n# a, b\n%g, %g\n'%
tuple(self.polarization_parameters[7]))
f.close()
for name, (x, y, fy) in zip(['p', 'a', 'Fp', 'Fa'], self.polarization_parameters[:4]):
f=open(prefix+'_%s.dat'%name, 'w')
f.write('## Wavelength dependence of polarization parameter\n# lambda, data, fit\n')
savetxt(f, array([x, y, fy]).T)
f.close()
def exportFR(self):
name=QFileDialog.getSaveFileName(parent=self, caption=u'Select export file name',
filter='ASCII files (*.dat);;All files (*.*)')
if name!='':
name=unicode(name)
if not name.endswith('.dat'):
name+=u'.dat'
lamdas=[]
FR1s=[]
dFR1s=[]
FR2s=[]
dFR2s=[]
for i, (ignore, I, ignore) in enumerate(self._WLitems):
lamda=I.values()[0].lamda
reg=((lamda>=float(self.ui.wlTable.item(i, 1).text()))&
(lamda<=float(self.ui.wlTable.item(i, 2).text())))
lamdas.append(lamda[reg])
if '++' in I and '+-' in I:
fr, dfr=self.calc_fr(I['++'], I['+-'])
FR2s.append(fr[reg])
dFR2s.append(dfr[reg])
if '++' in I and '-+' in I:
fr, dfr=self.calc_fr(I['++'], I['-+'])
FR1s.append(fr[reg])
dFR1s.append(dfr[reg])
if len(FR1s)!=len(lamdas):
FR1s=hstack(lamdas)*0.;dFR1s=hstack(lamdas)*0.
else:
FR1s=hstack(FR1s);dFR1s=hstack(dFR1s)
if len(FR2s)!=len(lamdas):
FR2s=hstack(lamdas)*0.;dFR2s=hstack(lamdas)*0.
else:
FR2s=hstack(FR2s);dFR2s=hstack(dFR2s)
lamdas=hstack(lamdas)
f=open(name, 'w')
f.write('## Wavelength dependence of flipping ratio\n')
f.write('# lambda, FR1, dFR1, FR2, dFR2, P1, P2\n')
savetxt(f, array([lamdas, FR1s, dFR1s, FR2s, dFR2s,
sqrt((FR1s-1.)/(FR1s+1.)), sqrt((FR2s-1.)/(FR2s+1.))]).T)
f.close()
def exportFRDetector(self):
'''
Save the x,lamda vs. FR data to ASCII file.
'''
name=QFileDialog.getSaveFileName(parent=self, caption=u'Select export file name',
filter='ASCII files (*.dat);;All files (*.*)')
if name!='':
name=unicode(name)
else:
return
f=open(name, 'w')
f.write('## Pixel dependence of flipping ratio\n# lambda, X, FR1, dFR1\n')
for ignore, I, xpos in self._Xitems:
lamda=I.values()[0].lamda
fr, dfr=self.calc_fr(I['++'], I['+-'])
reg=I['++'].Rraw>0
savetxt(f, array([ones_like(fr[reg])*xpos, lamda[reg], fr[reg], dfr[reg]]).T)
f.write('\n')
f.close()
def addX(self):
self._Xitems.append(self.Icurrent)
row=self.ui.xTable.rowCount()
self._auto_change_active=True
self.ui.xTable.insertRow(row)
self.ui.xTable.setItem(row, 0, QTableWidgetItem(self.Icurrent[0]))
self.ui.xTable.setItem(row, 1, QTableWidgetItem(str(self.Icurrent[2])))
self._auto_change_active=False
if len(self._Xitems)>2:
self.drawXFR()
self.ui.exportDetButton.setEnabled(True)
def addXMultiple(self):
'''
Convenience function to add multiple subsequent datasets for different detector angles.
'''
items, OK=QInputDialog.getInt(self, u'Add multiple datasets',
u'Enter the number of subsequent datasets to be added:',
value=1, min=0, max=304, step=1)
if not OK or items==0:
return
self.addX()
if items==1:
return
self._x_items_to_go=items-1
self.parent_window.initiateReflectivityPlot.connect(self._addXMultiple)
self.parent_window.nextFile()
def _addXMultiple(self):
self._x_items_to_go-=1
self.addX()
if self._x_items_to_go==0:
self._x_items_to_go=None
self.parent_window.initiateReflectivityPlot.disconnect(self._addXMultiple)
return
self.parent_window.nextFile()
def drawXFR(self):
plot=self.ui.detectorPol
plot.clear_fig()
lamdas=[]
Xs=[]
FRs=[]
for ignore, I, xpos in self._Xitems:
lamda=I.values()[0].lamda
lamdas.append(lamda)
FRs.append(I['++'].Rraw/I['+-'].Rraw)
Xs.append(ones_like(lamda)*xpos)
plot.pcolormesh(array(Xs), array(lamdas), array(FRs), cmap=self.parent_window.color)
plot.cplot.set_clim(30, 150)
plot.set_xlabel(u'X [pix]')
plot.set_ylabel(u'$\\lambda$ [Å]')
plot.canvas.fig.colorbar(plot.cplot)
plot.draw()
def clearX(self):
self._Xitems=[]
self.ui.xTable.setRowCount(0)
self.ui.detectorPol.clear()
self.ui.detectorPol.draw()
self.ui.exportDetButton.setEnabled(False)
def closeEvent(self, *args, **kwargs):
# disconnect when closed as object is not actually destroyed and will slow down plots
self.parent_window.initiateReflectivityPlot.disconnect(self.update_fr)
self.close()
