Python Group.energy方法代码示例

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import energy [as 别名]
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()
#.........这里部分代码省略.........

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import energy [as 别名]
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)
#.........这里部分代码省略.........

# 需要导入模块: from larch import Group [as 别名]
# 或者: from larch.Group import energy [as 别名]
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: