def findbeamasa(asa,beampos=None,oriidx=None):
"""Finds the beam position of an ASA measurement.
Inputs:
asa: ASA dictionary (with the fields 'pixels' and 'position') or a list of them.
beampos: if None (default): a figure is presented for user interaction.
Otherwise it should be a floating point value, the beam position.
oriidx: if *asa* is not a list, this is ignored. Otherwise this is the
index in the list according to which the primary beam position is to
be determined. Special values are None (determine beam position
one-by-one), or 'avg' (to determine the beam position one-by-one and
average them).
"""
if type(asa)!=type([]) and type(asa)!=type(tuple()):
asa=[asa]
oriidx=None
if beampos is not None: #we already have a beam position, set oriidx to None to skip beam finding.
oriidx=None
if type(oriidx)==type(1): #find the peak position acccording to the oriidx-th measurement
pylab.clf()
beampos=guitools.findpeak(asa[oriidx]['pixels'],asa[oriidx]['position'],
prompt='Select the beam area and press ENTER or an empty area to cancel.')
elif oriidx=='avg': # find all beam positions and average
bps=np.zeros(len(asa))
for i in range(len(asa)):
pylab.clf()
bps[i]=guitools.findpeak(asa[i]['pixel'],asa[i]['position'],
prompt='Select the beam area and press ENTER or an empty area to cancel.')
beampos=bps.mean()
for a in asa:
# If we are here, two cases are possible:
# 1) we already have a beampos value
# 2) beampos is None and oriidx is None.
if beampos is not None: #1
beampos1=beampos
else: #2
pylab.clf()
beampos1=guitools.findpeak(a['pixels'],a['position'],
prompt='Select the beam area and press ENTER or an empty area to cancel.')
a['params']['BeamPos']=beampos1
return
def agstcalib(xdata,ydata,peaks,peakmode='Lorentz',wavelength=1.54,d=48.68,returnq=True):
"""Find q-range from AgSt (or AgBeh) measurements.
Inputs:
xdata: vector of abscissa values (typically pixel numbers)
ydata: vector of scattering data (counts)
peaks: list of the orders of peaks (ie. [1,2,3])
peakmode: what type of function should be fitted on the peak. Possible
values: 'Lorentz' and 'Gauss'
wavelength: wavelength of the X-ray radiation. Default is Cu Kalpha,
1.54 Angstroems
d: the periodicity of the sample (default: 48.68 A for silver
stearate)
returnq: returns only the q-range if True. If False, returns the
pixelsize/dist and beamcenter values
Output:
If returnq is true then the q-scale in a vector which is of the
same size as xdata.
If returnq is false, then a,b,aerr,berr where a is pixelsize/dist,
b is the beam center coordinate in pixels and aerr and berr
are their errors, respectively
Notes:
A graphical window will be popped up len(peaks)-times, each prompting
the user to zoom on the n-th peak. After the last peak was
selected, the function returns.
"""
pcoord=[]
for p in peaks:
tmp=guitools.findpeak(xdata,ydata,('Zoom to peak %d and press ENTER' % p),peakmode,scaling='log')
pcoord.append(tmp)
pcoord=np.array(pcoord)
n=np.array(peaks)
a=(n*wavelength)/(2*d)
x=2*a*np.sqrt(1-a**2)/(1-2*a**2)
LperH,xcent,LperHerr,xcenterr=fitting.linfit(x,pcoord)
print 'pixelsize/dist:',1/LperH,'+/-',LperHerr/LperH**2
print 'beam position:',xcent,'+/-',xcenterr
if returnq:
return calcqrangefrom1D(xdata,xcent,LperH,1,wavelength)
else:
return 1/LperH,xcent,LperHerr/LperH**2,xcenterr
def tripcalib(xdata,ydata,peakmode='Lorentz',wavelength=1.54,qvals=2*np.pi*np.array([0.21739,0.25641,0.27027]),returnq=True):
"""Find q-range from Tripalmitine measurements.
Inputs:
xdata: vector of abscissa values (typically pixel numbers)
ydata: vector of scattering data (counts)
peakmode: what type of function should be fitted on the peak. Possible
values: 'Lorentz' and 'Gauss'
wavelength: wavelength of the X-ray radiation. Default is Cu Kalpha,
1.54 Angstroems
qvals: a list of q-values corresponding to peaks. The default values
are for Tripalmitine
returnq: True if the q-range is to be returned. False if the fit
parameters are requested instead of the q-range
Output:
The q-scale in a vector which is of the same size as xdata, if
returnq was True.
Otherwise a,b,aerr,berr where q=a*x+b and x is the pixel number
Notes:
A graphical window will be popped up len(qvals)-times, each prompting
the user to zoom on the n-th peak. After the last peak was
selected, the q-range will be returned.
"""
pcoord=[]
peaks=range(len(qvals))
for p in peaks:
tmp=guitools.findpeak(xdata,ydata,
('Zoom to peak %d (q = %f) and press ENTER' % (p,qvals[p])),
peakmode,scaling='lin')
pcoord.append(tmp)
pcoord=np.array(pcoord)
a,b,aerr,berr=fitting.linfit(pcoord,qvals)
if returnq:
return a*xdata+b
else:
return a,b,aerr,berr
