def import_xdi(name): if name[-3:] == 'txt': data_raw = np.loadtxt(name) data = Group() data.energy = data_raw[:,2] data.mu = data_raw[:,8]/data_raw[:,5] else: data_raw = np.loadtxt(name) data = Group() data.energy = data_raw[:,0] data.mu = data_raw[:,1] data.i0 = data_raw[:,2] return data
def gsexdi_deadtime_correct(fname, channelname, subdir='DT_Corrected',
bad=None, _larch=None):
"""convert GSE XDI fluorescence XAFS scans to dead time corrected files"""
if not is_GSEXDI(fname):
print("'%s' is not a GSE XDI scan file\n" % fname)
return
out = Group()
out.orig_filename = fname
try:
xdi = read_gsexdi(fname, bad=bad, _larch=_larch)
except:
print('Could not read XDI file ', fname)
return
for attr in ('energy', 'i0', 'i1', 'i2', 'tscaler',
'counttime', 'scan_start_time', 'scan_end_time'):
if hasattr(xdi, attr):
setattr(out, attr, getattr(xdi, attr))
# some scans may not record separate counttime, but TSCALER
# is clock ticks for a 50MHz clock
if not hasattr(out, 'counttime'):
out.counttime = xdi.tscaler * 2.e-8
if hasattr(xdi, 'energy_readback'):
out.energy = xdi.energy_readback
arrname = None
channelname = channelname.lower().replace(' ', '_')
for arr in xdi.array_labels:
if arr.lower().startswith(channelname):
arrname = arr
break
if arrname is None:
print('Cannot find Channel %s in file %s '% (channelname, fname))
return
out.ifluor = getattr(xdi, arrname)
out.ifluor_raw = getattr(xdi, arrname)
arrname_raw = arrname + '_nodtc'
if arrname_raw in xdi.array_labels:
out.ifluor_raw = getattr(xdi, arrname_raw)
out.mufluor = out.ifluor / out.i0
if hasattr(out, 'i1') or hasattr(out, 'itrans'):
i1 = getattr(out, 'i1', None)
if i1 is None:
i1 = getattr(out, 'itrans', None)
if i1 is not None:
i1 = i1 / out.i0
i1[np.where(i1<2.0e-20)] = 2.0e-20
out.mutrans = -np.log(i1)
npts = len(out.energy)
buff = ['# XDI/1.0 GSE/1.0']
header = OrderedDict()
hgroups = ['beamline', 'facility', 'mono', 'undulator', 'detectors',
'scaler', 'detectorstage', 'samplestage', 'scan', 'scanparameters']
hskip = ['scanparameters.end', 'scanparameters.start']
for agroup in hgroups:
attrs = xdi._xdi.attrs.get(agroup, {})
if agroup == 'mono': agroup = 'monochromator'
header[agroup] = OrderedDict()
for sname in sorted(attrs.keys()):
if "%s.%s" %( agroup, sname) not in hskip:
header[agroup][sname] = attrs[sname]
header['facility']['name'] = 'APS'
header['facility']['xray_source'] = '3.6 cm undulator'
header['beamline']['name'] = '13-ID-E, GSECARS'
header['detectors']['i0'] = '20cm ion chamber, He'
header['detectors']['ifluor'] = 'Si SDD Vortex ME-4, 4 elements'
header['detectors']['ifluor_electronics'] = 'Quantum Xspress3 3.1.10'
mono_cut = 'Si(111)'
if xdi.mono_dspacing < 2:
mono_cut = 'Si(311)'
header['monochromator']['name'] = "%s, LN2 cooled" % mono_cut
out_arrays = OrderedDict()
out_arrays['energy'] = ('energy', 'eV')
out_arrays['mufluor'] = ('mufluor', None)
if hasattr(out, 'i1'):
out_arrays['mutrans'] = ('mutrans', None)
out_arrays['ifluor'] = ('ifluor', '# deadtime-corrected')
out_arrays['ifluor_raw'] = ('ifluor_raw', '# not deadtime-corrected')
out_arrays['i0'] = ('i0', None)
if hasattr(out, 'i1'):
out_arrays['itrans'] = ('i1', None)
if hasattr(out, 'i2'):
out_arrays['irefer'] = ('i2', None)
if hasattr(out, 'counttime'):
out_arrays['counttime'] = ('counttime', 'sec')
arrlabel = []
for iarr, aname in enumerate(out_arrays):
lab = "%12s " % aname
if iarr == 0: lab = "%11s " % aname
arrlabel.append(lab)
extra = out_arrays[aname][1]
if extra is None: extra = ''
buff.append("# Column.%i: %s %s" % (iarr+1, aname, extra))
arrlabel = '#%s' % (' '.join(arrlabel))
ncol = len(out_arrays)
for family, fval in header.items():
for attr, val in fval.items():
buff.append("# %s.%s: %s" % (family.title(), attr, val))
buff.append("# ///")
for comment in xdi._xdi.comments.split('\n'):
c = comment.strip()
if len(c) > 0:
buff.append('# %s' % c)
buff.extend(["# summed %s fluorescence data from %s" % (channelname, fname),
"# Dead-time correction applied",
"#"+ "-"*78, arrlabel])
efmt = "%11.4f"
ffmt = "%13.7f"
gfmt = "%13.7g"
for i in range(npts):
dline = ["", efmt % out.energy[i], ffmt % out.mufluor[i]]
if hasattr(out, 'i1'):
dline.append(ffmt % out.mutrans[i])
dline.extend([gfmt % out.ifluor[i],
gfmt % out.ifluor_raw[i],
gfmt % out.i0[i]])
if hasattr(out, 'i1'):
dline.append(gfmt % out.i1[i])
if hasattr(out, 'i2'):
dline.append(gfmt % out.i2[i])
if hasattr(out, 'counttime'):
dline.append(gfmt % out.counttime[i])
buff.append(" ".join(dline))
ofile = fname[:]
if ofile.startswith('..'):
ofile = ofile[3:]
ofile = ofile.replace('.', '_') + '.dat'
ofile = os.path.join(subdir, ofile)
if not os.path.exists(subdir):
os.mkdir(subdir)
try:
fout = open(ofile, 'w')
fout.write("\n".join(buff))
fout.close()
print("wrote %s, npts=%i, channel='%s'" % (ofile, npts, channelname))
except:
print("could not open / write to output file %s" % ofile)
return out
def gsexdi_deadtime_correct(fname, channelname, subdir='DT_Corrected',
bad=None, _larch=None):
"""convert GSE XDI fluorescence XAFS scans to dead time corrected files"""
if not is_GSEXDI(fname):
print("'%s' is not a GSE XDI scan file\n" % fname)
return
out = Group()
out.orig_filename = fname
try:
xdi = read_gsexdi(fname, bad=bad, _larch=_larch)
except:
print('Could not read XDI file ', fname)
return
for attr in ('energy', 'i0', 'i1', 'i2', 'tscaler',
'counttime', 'scan_start_time', 'scan_end_time'):
if hasattr(xdi, attr):
setattr(out, attr, getattr(xdi, attr))
# some scans may not record separate counttime, but TSCALER
# is clock ticks for a 50MHz clock
if not hasattr(out, 'counttime'):
out.counttime = xdi.tscaler * 2.e-8
if hasattr(xdi, 'energy_readback'):
out.energy = xdi.energy_readback
mono_cut = 'Si(111)'
if xdi.mono_dspacing < 2:
mono_cut = 'Si(311)'
header_args = {'mono_dspace': xdi.mono_dspacing, 'mono_cut': mono_cut}
arrname = None
channelname = channelname.lower().replace(' ', '_')
for arr in xdi.array_labels:
if arr.lower().startswith(channelname):
arrname = arr
break
if arrname is None:
print('Cannot find Channel %s in file %s '% (channelname, fname))
return
out.fl_corr = getattr(xdi, arrname)
out.fl_raw = getattr(xdi, arrname)
arrname_raw = arrname + '_nodtc'
if arrname_raw in xdi.array_labels:
out.fl_raw = getattr(xdi, arrname_raw)
out.mufluor = out.fl_corr / out.i0
npts = len(out.energy)
ncol = 6
arrlabel = ['#', ' energy ', ' mufluor ', ' i0 ', ' fluor_dtc',
' fluor_raw', ' counttime']
header = DTC_header % header_args
buff = [l.strip() for l in header.split('\n')]
has_i1, has_i2 = False, False
if hasattr(out, 'i1'):
ncol += 1
buff.append('# Column.%i: itrans ' % ncol)
arrlabel.append(' itrans ')
has_i1 = True
if hasattr(out, 'i2'):
ncol += 1
buff.append('# Column.%i: irefer ' % ncol)
arrlabel.append(' irefer ')
has_i2 = True
arrlabel = ' '.join(arrlabel)
buff.extend(["# Scan.start_time: %s" % out.scan_start_time,
"# ///",
"# summed %s fluorescence data from %s" % (channelname, fname),
"# Dead-time correction applied",
"#---------------------------------",
arrlabel])
fmt = " %11.3f %15.8f %14.3f %16.5f %14.2f %14.3f"
for i in range(npts):
dline = fmt % (out.energy[i], out.mufluor[i], out.i0[i],
out.fl_corr[i], out.fl_raw[i], out.counttime[i])
if has_i1: dline = "%s %14.3f" % (dline, out.i1[i])
if has_i2: dline = "%s %14.3f" % (dline, out.i2[i])
buff.append(dline)
ofile = fname[:]
if ofile.startswith('..'):
ofile = ofile[3:]
ofile = ofile.replace('.', '_') + '.dat'
ofile = os.path.join(subdir, ofile)
if not os.path.exists(subdir):
os.mkdir(subdir)
try:
fout = open(ofile, 'w')
fout.write("\n".join(buff))
fout.close()
print("wrote %s, npts=%i, channel='%s'" % (ofile, npts, channelname))
except:
print("could not open / write to output file %s" % ofile)
return out
from larch import Interpreter, Group
# now import larch-specific Python code
from larch_plugins.xafs import autobk, xftf
# create a larch interpreter, passed to most functions
my_larch = Interpreter(with_plugins=False)
# create an empty Group
xafsdat = Group()
# read data (here using np.loadtxt), stick into Group
# using "expected names" for XAFS data
rawdata = np.loadtxt('../xafsdata/fe2o3_rt1.xmu')
xafsdat.energy = rawdata[:, 0]
xafsdat.mu = rawdata[:, 1]
xafsdat.i0 = rawdata[:, 1]
# run autobk on the xafsdat Group, including a larch Interpreter....
# note that this expects 'energy' and 'mu' to be in xafsdat, and will
# write data for 'k', 'chi', 'kwin', 'e0', ... into xafsdat
autobk(xafsdat, rbkg=1.0, kweight=2, _larch=my_larch)
# Fourier transform to R space, again passing in a Group (here,
# 'k' and 'chi' are expected, and writitng out 'r', 'chir_mag',
# and so on
xftf(xafsdat, kmin=2, kmax=15, dk=3, kweight=2, _larch=my_larch)
#
# plot grid of results:
