def Writer(self, TreeName, filename=None):
#print filename
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
Parms = self.Histograms[TreeName]['Instrument Parameters'][0]
for parm in Parms:
if parm in [
'Type',
'Source',
]:
line = '"Instparm: %s","%s"' % (parm, Parms[parm][0])
elif parm in [
'Lam',
'Zero',
]:
line = '"Instparm: %s",%10.6f' % (parm, Parms[parm][1])
else:
line = '"Instparm: %s",%10.2f' % (parm, Parms[parm][1])
self.Write(line)
Samp = self.Histograms[TreeName]['Sample Parameters']
for samp in Samp:
if samp in ['InstrName', 'Type']:
line = '"Samparm: %s",%s' % (samp, Samp[samp])
elif samp in [
'Azimuth', 'Chi', 'Gonio. radius', 'Omega', 'Phi',
'Pressure', 'Temperature', 'Time'
]:
line = '"Samparm: %s",%10.2f' % (samp, Samp[samp])
elif samp in [
'DisplaceX', 'DisplaceY', 'Scale', 'Shift', 'SurfRoughA',
'SurfRoughB', 'Transparency'
]:
line = '"Samparm: %s",%10.2f' % (samp, Samp[samp][0])
else:
continue
self.Write(line)
WriteList(self, ("x", "y_obs", "weight", "y_calc", "y_bkg", "Q"))
digitList = 2 * ((13, 3), ) + ((13, 5), ) + 3 * ((13, 3), )
for vallist in zip(
histblk['Data'][0],
histblk['Data'][1],
histblk['Data'][2],
histblk['Data'][3],
histblk['Data'][4],
#histblk['Data'][5],
2 * np.pi / G2lat.Pos2dsp(Parms, histblk['Data'][0])):
line = ""
for val, digits in zip(vallist, digitList):
if line: line += ','
line += G2py3.FormatValue(val, digits)
self.Write(line)
self.CloseFile()
def Writer(self, TreeName, filename=None):
import GSASIIlattice as G2lat
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
inst = histblk['Instrument Parameters'][0]
self.Write(str(TreeName)[5:]) # drop 'PWDR '
if 'Lam1' in inst:
print(
'Do you really want to write a multi-wavelength pattern in Q?')
lam = 0.
else:
lam = inst['Lam'][1]
self.Write("Q{:>20.6f}".format(lam))
self.Write("Intensity")
self.Write(" " + str(len(histblk['Data'][0])))
for X, Y in zip(histblk['Data'][0], histblk['Data'][1]):
line = " %5.7e" % (2. * np.pi / G2lat.Pos2dsp(inst, X))
line += " %5.7e" % Y
self.Write(line)
self.CloseFile()
def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]):
'''Write PDF-related data (G(r), S(Q),...) into files, as
selected.
:param str PDFentry: name of the PDF entry in the tree. This is
used for comments in the file specifying where it came from;
it can be arbitrary
:param str fileroot: name of file(s) to be written. The extension
will be ignored.
:param list PDFsaves: flags that determine what type of file will be
written:
PDFsaves[0], if True writes a I(Q) file with a .iq extension
PDFsaves[1], if True writes a S(Q) file with a .sq extension
PDFsaves[2], if True writes a F(Q) file with a .fq extension
PDFsaves[3], if True writes a G(r) file with a .gr extension
PDFsaves[4], if True writes G(r) in a pdfGUI input file with
a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are
both True, the pdfGUI overwrites the G(r) file.
PDFsaves[5], if True writes F(Q) & g(R) with .fq & .gr extensions
overwrites these if selected by option 2, 3 or 4
:param dict PDFControls: The PDF parameters and computed results
:param dict Inst: Instrument parameters from the PDWR entry used
to compute the PDF. Needed only when PDFsaves[4] is True.
:param list Limits: Computation limits from the PDWR entry used
to compute the PDF. Needed only when PDFsaves[4] is True.
'''
import scipy.interpolate as scintp
fileroot = os.path.splitext(fileroot)[0]
if PDFsaves[0]: #I(Q)
iqfilename = fileroot+'.iq'
iqdata = PDFControls['I(Q)'][1]
iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
iqfile = open(iqfilename,'w')
iqfile.write('#T I(Q) %s\n'%(PDFentry))
iqfile.write('#L Q I(Q)\n')
qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
iqnew = zip(qnew,iqfxn(qnew))
for q,iq in iqnew:
iqfile.write("%15.6g %15.6g\n" % (q,iq))
iqfile.close()
G2Print (' I(Q) saved to: '+iqfilename)
if PDFsaves[1]: #S(Q)
sqfilename = fileroot+'.sq'
sqdata = PDFControls['S(Q)'][1]
sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
sqfile = open(sqfilename,'w')
sqfile.write('#T S(Q) %s\n'%(PDFentry))
sqfile.write('#L Q S(Q)\n')
qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
sqnew = zip(qnew,sqfxn(qnew))
for q,sq in sqnew:
sqfile.write("%15.6g %15.6g\n" % (q,sq))
sqfile.close()
G2Print (' S(Q) saved to: '+sqfilename)
if PDFsaves[2]: #F(Q)
fqfilename = fileroot+'.fq'
fqdata = PDFControls['F(Q)'][1]
fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
fqfile = open(fqfilename,'w')
fqfile.write('#T F(Q) %s\n'%(PDFentry))
fqfile.write('#L Q F(Q)\n')
qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
fqnew = zip(qnew,fqfxn(qnew))
for q,fq in fqnew:
fqfile.write("%15.6g %15.6g\n" % (q,fq))
fqfile.close()
G2Print (' F(Q) saved to: '+fqfilename)
if PDFsaves[3]: #G(R)
grfilename = fileroot+'.gr'
grdata = PDFControls['G(R)'][1]
grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
grfile = open(grfilename,'w')
grfile.write('#T G(R) %s\n'%(PDFentry))
grfile.write('#L R G(R)\n')
rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
grnew = zip(rnew,grfxn(rnew))
for r,gr in grnew:
grfile.write("%15.6g %15.6g\n" % (r,gr))
grfile.close()
G2Print (' G(R) saved to: '+grfilename)
if PDFsaves[4]: #pdfGUI file for G(R)
import GSASIImath as G2mth
import GSASIIlattice as G2lat
grfilename = fileroot+'.gr'
grdata = PDFControls['G(R)'][1]
qdata = PDFControls['I(Q)'][1][0]
grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
grfile = open(grfilename,'w')
rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
grnew = zip(rnew,grfxn(rnew))
grfile.write('[DEFAULT]\n')
grfile.write('\n')
grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
grfile.write('\n')
grfile.write('# input and output specifications\n')
grfile.write('dataformat = Qnm\n')
grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
grfile.write('outputtype = gr\n')
grfile.write('\n')
grfile.write('# PDF calculation setup\n')
if 'x' in Inst['Type']:
grfile.write('mode = %s\n'%('xray'))
elif 'N' in Inst['Type']:
grfile.write('mode = %s\n'%('neutron'))
wave = G2mth.getMeanWave(Inst)
grfile.write('wavelength = %.5f\n'%(wave))
formula = ''
for el in PDFControls['ElList']:
formula += el
num = PDFControls['ElList'][el]['FormulaNo']
if num == round(num):
formula += '%d'%(int(num))
else:
formula += '%.2f'%(num)
grfile.write('composition = %s\n'%(formula))
grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
grfile.write('qmaxinst = %.2f\n'%(highQ))
grfile.write('qmin = %.5f\n'%(qdata[0]))
grfile.write('qmax = %.4f\n'%(qdata[-1]))
grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
grfile.write('rstep = 0.01\n')
grfile.write('\n')
grfile.write('# End of config '+63*'-')
grfile.write('\n')
grfile.write('#### start data\n')
grfile.write('#S 1\n')
grfile.write('#L r($\\AA$) G($\\AA^{-2}$)\n')
for r,gr in grnew:
grfile.write("%15.2F %15.6F\n" % (r,gr))
grfile.close()
G2Print (' G(R) saved to: '+grfilename)
# DTG
if len(PDFsaves) > 5 and PDFsaves[5]: # RMCProfile files for F(Q) & g(r) overwrites any above
fqfilename = fileroot+'.fq'
fqdata = PDFControls['F(Q)'][1]
fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
fqfile = open(fqfilename,'w')
qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
nq = qnew.shape[0]
fqfile.write('%20d\n'%nq-1)
fqfile.write(fqfilename+'\n')
fqnew = zip(qnew,fqfxn(qnew))
for q,fq in fqnew[1:]:
fqfile.write("%15.6g %15.6g\n" % (q,fq))
fqfile.close()
G2Print (' F(Q) saved to: '+fqfilename)
grfilename = fileroot+'.gr'
grdata = PDFControls['g(r)'][1]
grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
grfile = open(grfilename,'w')
rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
nr = rnew.shape[0]
grfile.write('%20d\n'%nr-1)
grfile.write(grfilename+'\n')
grnew = zip(rnew,grfxn(rnew))
for r,gr in grnew[1:]:
grfile.write("%15.6g %15.6g\n" % (r,gr))
grfile.close()
G2Print (' G(R) saved to: '+grfilename)