def processasa(filenames,dist,distminus,pixelsize,beamprofile_or_mat,wavelength=1.54,dirs='.'):
if type(filenames)==type(''):
filenames=[filenames]
asas=B1io.readasa(filenames,dirs)
setdistanceasa(asas,dist,distminus)
for a in asas:
a['params']['wavelength']=wavelength
findbeamasa(asas)
setpixelsizeasa(asas,pixelsize)
for a in asas:
a['Intensity']=a['position']
a['Error']=a['poserror']
if beamprofile_or_mat is None:
continue
Idesm,Edesm,mat=desmearflat(a['pixels']-a['params']['BeamPos'],
a['position'],a['poserror'],
beamprofile_or_mat,1,a['params']['Dist'],
a['params']['PixelSize'],
a['params']['Title'],NMC=1000)
a['Idesm']=Idesm
a['Edesm']=Edesm
a['smearingmatrix']=mat
return asas
def asaxsseqeval(data,param,asaxsenergies,chemshift,fprimefile,samples=None,seqname=None,element=0):
"""Evaluate an ASAXS sequence, derive the basic functions
Inputs:
data: list of data structures as read by eg. readintnorm
param: list of parameter structures as read by eg. readintnorm
asaxsenergies: the UNCALIBRATED (aka. "apparent") energy values for
the ASAXS evaluation. At least 3 should be supplied.
chemshift: chemical shift. The difference of the calibrated edge energy
measured on the sample (E_s) and the theoretical edge energy for an
isolated atom (E_t). If E_s>E_t then chemshift is positive.
fprimefile: file name (can include path) for the f' data, as created
by Hephaestus. The file should have three columns:
enegy<whitespace>fprime<whitespace>fdoubleprime<newline>.
Lines beginning with # are ignored.
samples [optional]: a string or a list of strings of samplenames to be
treated. If omitted, all samples are evaluated.
seqname [optional]: if given, the following files will be created:
seqname_samplename_ie.txt : summarized intensities and errors
seqname_samplename_basicfun.txt: the asaxs basic functions with
their errors
seqname_samplename_separation.txt: I_0, (I_1-I_2)/(f1_1-f1_2),
(I_2-I_3)/(f1_2-f1_3) and the pure resonant term, with their
errors
seqname_f1f2.eps: f' and f'' diagram
seqname_samplename_basicfun.eps: basic functions displayed
seqname_samplename_separation.eps: separated curves, I_0 and pure
resonant displayed
seqname.log: logging
element [optional]: if nonzero, this is the atomic number of the
resonant element. If zero (default), the evaluation is carried out
according to Stuhrmann. Nonzero yields the PSFs.
"""
if samples is None:
samples=utils.unique([param[i]['Title'] for i in range(0,len(data))]);
print "Found samples: ", samples
if type(samples)!=types.ListType:
samples=[samples];
if seqname is not None:
logfile=open('%s.log' % seqname,'wt')
logfile.write('ASAXS sequence name: %s\n' % seqname)
logfile.write('Time: %s' % time.asctime())
asaxsecalib=[];
#asaxsenergies=np.array(utils.unique(asaxsenergies,lambda a,b:(abs(a-b)<2)))
asaxsenergies=np.array(asaxsenergies);
for j in range(0,len(asaxsenergies)):
asaxsecalib.append([param[i]['EnergyCalibrated']
for i in range(0,len(data))
if abs(param[i]['Energy']-asaxsenergies[j])<2][0]);
asaxsecalib=np.array(asaxsecalib);
print "Calibrated ASAXS energies:", asaxsecalib
fprimes=B1io.readf1f2(fprimefile);
pylab.plot(fprimes[:,0],fprimes[:,1],'b-');
pylab.plot(fprimes[:,0],fprimes[:,2],'r-');
asaxsf1=np.interp(asaxsecalib-chemshift,fprimes[:,0],fprimes[:,1]);
asaxsf2=np.interp(asaxsecalib-chemshift,fprimes[:,0],fprimes[:,2]);
print "f' values", asaxsf1
print "f'' values", asaxsf2
if seqname is not None:
logfile.write('Calibrated ASAXS energies:\n')
for i in range(len(asaxsenergies)):
logfile.write("%f -> %f\tf1=%f\tf2=%f\n" % (asaxsenergies[i],asaxsecalib[i],asaxsf1[i],asaxsf2[i]))
logfile.write('Chemical shift (eV): %f\n' % chemshift)
logfile.write('Atomic number supplied by the user: %d\n' % element)
logfile.write('fprime file: %s\n' % fprimefile)
pylab.plot(asaxsecalib-chemshift,asaxsf1,'b.',markersize=10);
pylab.plot(asaxsecalib-chemshift,asaxsf2,'r.',markersize=10);
pylab.legend(['f1','f2'],loc='upper left');
pylab.xlabel('Photon energy (eV)');
pylab.ylabel('Anomalous corrections (e.u.)');
pylab.title('Anomalous correction factors')
if seqname is not None:
pylab.savefig('%s_f1f2.eps' % seqname,dpi=300,transparent='True',format='eps')
if len(asaxsenergies)<3:
print "At least 3 energies should be given!"
return
for s in samples:
print "Evaluating sample %s" % s
if seqname is not None:
logfile.write('Sample: %s\n' % s)
q=None;
counter=None;
fsns=None
for k in range(0,len(data)): #collect the intensities energy-wise.
if param[k]['Title']!=s:
continue
if q is None:
q=np.array(data[k]['q']);
NQ=len(q);
Intensity=np.zeros((len(q),len(asaxsenergies)))
Errors=np.zeros((len(q),len(asaxsenergies)))
counter=np.zeros((1,len(asaxsenergies)))
fsns=[[] for l in range(len(asaxsenergies))]
if np.sum(q-np.array(data[k]['q']))>0:
print "Check the datasets once again: different q-scales!"
continue;
energyindex=np.absolute(asaxsenergies-param[k]['Energy'])<2
Intensity[:,energyindex]=Intensity[:,energyindex]+np.array(data[k]['Intensity']).reshape(NQ,1);
Errors[:,energyindex]=Intensity[:,energyindex]+(np.array(data[k]['Error']).reshape(NQ,1))**2;
counter[0,energyindex]=counter[0,energyindex]+1;
if pylab.find(len(energyindex))>0:
print pylab.find(energyindex)[0]
fsns[pylab.find(energyindex)[0]].append(param[k]['FSN']);
Errors=np.sqrt(Errors)
Intensity=Intensity/np.kron(np.ones((NQ,1)),counter)
if seqname is not None:
for i in range(0,len(asaxsenergies)):
logfile.write('FSNs for energy #%d:' % i)
for j in fsns[i]:
logfile.write('%d' % j)
logfile.write('\n')
datatosave=np.zeros((len(q),2*len(asaxsenergies)+1))
datatosave[:,0]=q;
for i in range(len(asaxsenergies)):
datatosave[:,2*i+1]=Intensity[:,i]
datatosave[:,2*i+2]=Errors[:,i]
np.savetxt('%s_%s_ie.txt' % (seqname, s),datatosave,delimiter='\t')
# now we have the Intensity and Error matrices fit to feed to asaxsbasicfunctions()
N,M,R,DN,DM,DR=asaxsbasicfunctions(Intensity,Errors,asaxsf1,asaxsf2,element=element);
sep12,dsep12,sep23,dsep23,R1,dR1=asaxspureresonant(Intensity[:,0],Intensity[:,1],Intensity[:,2],
Errors[:,0],Errors[:,1],Errors[:,2],
asaxsf1[0],asaxsf1[1],asaxsf1[2],
asaxsf2[0],asaxsf2[1],asaxsf2[2])
Ireconst=N+M*2*asaxsf1[0]+R*(asaxsf1[0]**2+asaxsf2[0]**2)
if seqname is not None:
datatosave=np.zeros((len(q),7))
datatosave[:,0]=q;
datatosave[:,1]=N.flatten(); datatosave[:,2]=DN.flatten();
datatosave[:,3]=M.flatten(); datatosave[:,4]=DM.flatten();
datatosave[:,5]=R.flatten(); datatosave[:,6]=DR.flatten();
np.savetxt('%s_%s_basicfun.txt' % (seqname, s),datatosave,delimiter='\t')
datatosave[:,1]=sep12.flatten(); datatosave[:,2]=dsep12.flatten();
datatosave[:,3]=sep23.flatten(); datatosave[:,4]=dsep23.flatten();
datatosave[:,5]=R1.flatten(); datatosave[:,6]=dR1.flatten();
np.savetxt('%s_%s_separation.txt' % (seqname, s),datatosave,delimiter='\t')
pylab.figure()
#pylab.errorbar(q,Intensity[:,0],Errors[:,0],label='I_0',marker='.')
#pylab.errorbar(q,N.flatten(),DN.flatten(),label='Nonresonant',marker='.')
#pylab.errorbar(q,M.flatten(),DM.flatten(),label='Mixed',marker='.')
#pylab.errorbar(q,R.flatten(),DR.flatten(),label='Resonant',marker='o')
pylab.plot(q,Intensity[:,0],label='I_0',marker='.')
pylab.plot(q,N.flatten(),label='Nonresonant',marker='.')
pylab.plot(q,M.flatten(),label='Mixed',marker='.')
pylab.plot(q,R.flatten(),label='Resonant',marker='o')
pylab.plot(q,Ireconst.flatten(),label='I_0_reconstructed',marker='.')
pylab.title("ASAXS basic functions for sample %s" % s)
pylab.xlabel(u"q (1/%c)" % 197)
pylab.ylabel("Scattering cross-section (1/cm)")
pylab.gca().set_xscale('log');
pylab.gca().set_yscale('log');
pylab.legend();
pylab.savefig('%s_%s_basicfun.eps'%(seqname,s),dpi=300,format='eps',transparent=True)
pylab.figure()
#pylab.errorbar(q,Intensity[:,0],Errors[:,0],label='I_0',marker='.')
#pylab.errorbar(q,sep12,dsep12,label='(I_0-I_1)/(f1_0-f1_1)',marker='.')
#pylab.errorbar(q,sep23,dsep23,label='(I_1-I_2)/(f1_1-f1_2)',marker='.')
#pylab.errorbar(q,R1.flatten(),dR1.flatten(),label='Pure resonant',marker='.')
pylab.plot(q,Intensity[:,0],label='I_0',marker='.')
pylab.plot(q,sep12,label='(I_0-I_1)/(f1_0-f1_1)',marker='.')
pylab.plot(q,sep23,label='(I_1-I_2)/(f1_1-f1_2)',marker='.')
pylab.plot(q,R1.flatten(),label='Pure resonant',marker='.')
pylab.title("ASAXS separated and pure resonant terms for sample %s" % s)
pylab.xlabel(u"q (1/%c)" % 197)
pylab.ylabel("Scattering cross-section (1/cm)")
pylab.gca().set_xscale('log');
pylab.gca().set_yscale('log');
pylab.legend();
pylab.savefig('%s_%s_separation.eps'%(seqname,s),dpi=300,format='eps',transparent=True)
logfile.close()
pylab.show()