#!/usr/bin/env python

import os
import sys
import copy
import os
import time
import gc

import numpy as np
from .. import Group, ValidateLarchPlugin
from ..utils import OrderedDict
from ..utils.strutils import bytes2str

from . import XDIFile, XDIFileException

from .xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr

@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=128, bad=None, **kws):
    """Read GSE XDI Scan Data to larch group,
    summing ROI data for MCAs and apply deadtime corrections
    """

    MAX_MCAS = nmca
    group = _larch.symtable.create_group()
    group.__name__ ='GSE XDI Data file %s' % fname
    xdi = XDIFile(str(fname))

    group._xdi = xdi
    group.path = fname
    path, suffix = os.path.split(fname)
    group.filename = suffix
    group.npts = xdi.npts
    group.bad_channels = bad

    for family in ('scan', 'mono', 'facility'):
        for key, val in xdi.attrs.get(family, {}).items():
            if '||' in val:
                val, addr = val.split('||')
            try:
                val = float(val)
            except:
                pass
            setattr(group, "%s_%s" % (family, key), val)

    ocrs, icrs = [], []
    ctime = None
    for attrname in dir(xdi):
        if attrname.lower() == 'counttime':
            ctime = getattr(xdi, attrname)
    if ctime is None:
        try:
            ctime = xdi.TSCALER / 5.e7
        except AttributeError:
            ctime = 1.0

    is_xspress3 = any(['13QX4' in a[1] for a in xdi.attrs['column'].items()])
    group.with_xspress3 = is_xspress3
    dtc_taus = XSPRESS3_TAUS
    if _larch.symtable.has_symbol('_sys.gsecars.xspress3_taus'):
        dtc_taus = _larch.symtable._sys.gsecars.xspress3_taus

    dtc_mode = 'icr/ocr'
    for i in range(MAX_MCAS):
        mca = "mca%i" % (i+1)
        ocr    = getattr(xdi, 'OutputCounts_%s' % mca, None)
        clock  = getattr(xdi, 'Clock_%s'        % mca, None)
        icr    = getattr(xdi, 'InputCounts_%s'  % mca, None)
        dtfact = getattr(xdi, 'DTFactor_%s'     % mca, None)
        resets = getattr(xdi, 'ResetTicks_%s'   % mca, None)
        allevt = getattr(xdi, 'AllEvent_%s'     % mca, None)
        if (ocr is None and icr is None and clock is None and
            dtfact is None and resets is None):
            nmca = i
            break
        if ocr is None:
            ocr = ctime
        ocr = ocr/ctime
        if icr is not None:
            icr = icr/ctime

        # Get ICR from one of several alternatives:
        # 1. InputCounts_mca was given
        # 2. DTFactor_mca was given
        # 3. ResetTicks_mca and AllEvets_mca were given
        # 4. Use "known values" for tau
        if icr is None:
            if dtfact is not None:
                icr = ocr * dtfact
                dtc_mode = 'dtfactor'
            elif (clock is not None and
                  resets is not None and
                  allevt is not None):
                dtfact = clock/(clock - (6*allevt + resets))
                icr = ocr * dtfact
                dtc_mode = 'resets'
        # finally estimate from measured values of tau:
        if icr is None:
            icr = 1.0*ocr
            dtc_mode = 'none'
            if is_xspress3:
                tau = dtc_taus[i]
                icr = estimate_icr(ocr*1.00, tau, niter=7)
                dtc_mode = 'saved_taus'
        ocrs.append(ocr)
        icrs.append(icr)

    group.dtc_mode =  dtc_mode
    if dtc_mode == 'saved_taus':
        group.dtc_taus = dtc_taus

    labels = []
    sums = OrderedDict()
    for i, arrname in enumerate(xdi.array_labels):
        dat = getattr(xdi, arrname)
        if arrname.lower() == 'data':
            arrname = '_data'
        aname = sumname = rawname = arrname.lower()
        if ('_mca' in aname and
            'outputcounts' not in aname and
            'dtfactor' not in aname and
            'clock' not in aname):
            sumname, imca = sumname.split('_mca')
            imca = int(imca) - 1
            datraw = dat*1.0
            rawname = sumname + '_nodtc'
            dat   = dat * icrs[imca]/ ocrs[imca]
            if any(np.isnan(dat)):
                nan_pts = np.where(np.isnan(dat))[0]
                dat[nan_pts] = datraw[nan_pts]

        setattr(group, aname, dat)
        if sumname not in labels:
            labels.append(sumname)
            sums[sumname] = dat
            if rawname != sumname:
                sums[rawname] = datraw
                if rawname not in labels:
                    labels.append(rawname)

        else:
            sums[sumname] = sums[sumname] + dat
            if rawname != sumname:
                sums[rawname] = sums[rawname] + datraw

    for name, dat in sums.items():
        if not hasattr(group, name):
            setattr(group, name, dat)

    for arrname in xdi.array_labels:
        sname = arrname.lower()
        if sname not in labels:
            labels.append(sname)

    data = []
    for name in labels:
        data.append(getattr(group, name))
    group.data = np.array(data)
    for imca in range(nmca):
        setattr(group, 'ocr_mca%i' % (imca+1), ocrs[imca])
        setattr(group, 'icr_mca%i' % (imca+1), icrs[imca])
    group.array_labels = labels
    return group


DTC_header = '''# XDI/1.1  Epics StepScan File/2.0
# Beamline.name:  13-ID-E, GSECARS
# Monochromator.name:  %(mono_cut)s, LN2 Cooled
# Monochromator.dspacing:  %(mono_dspace)s
# Facility.name: APS
# Facility.xray_source: 3.6 cm undulator
# Detectors.i0:  20cm ion chamber, He
# Detectors.ifluor:  Si SDD Vortex ME-4, 4 elements
# Detectors.ifluor_electronics:  Quantum Xspress3 3.1.10'''

def is_GSEXDI(filename):
    """test if file is GSE XDI data file
    reads only the first line of file
    """
    line1 = open(filename, 'r').readline()
    return (line1.startswith('#XDI/1') and 'Epics StepScan File' in line1)

@ValidateLarchPlugin
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
    TINY  = 2.e-20
    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[np.isnan(i1)] = TINY
            i1 = i1 / out.i0
            i1[np.where(i1<TINY)] = TINY
            out.mutrans = -np.log(i1)


    npts   = len(out.i0)
    col0_name = xdi.array_labels[0].lower()
    col0_units = None
    col0_data  = xdi.data[0, :]
    if col0_name == 'energy':
        col0_data  = out.energy
        col0_units = 'eV'

    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[col0_name]  = (col0_name, col0_units)
    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 bytes2str(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 % col0_data[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

#!/usr/bin/env python

import os
import sys
import copy
import os
import time
import gc

import numpy as np
from .. import Group, ValidateLarchPlugin
from ..utils import OrderedDict
from ..utils.strutils import bytes2str

from . import XDIFile, XDIFileException

from .xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr

@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=128, bad=None, **kws):
    """Read GSE XDI Scan Data to larch group,
    summing ROI data for MCAs and apply deadtime corrections
    """

    MAX_MCAS = nmca
    group = _larch.symtable.create_group()
    group.__name__ ='GSE XDI Data file %s' % fname
    xdi = XDIFile(str(fname))

    group._xdi = xdi
    group.path = fname
    path, suffix = os.path.split(fname)
    group.filename = suffix
    group.npts = xdi.npts
    group.bad_channels = bad

    for family in ('scan', 'mono', 'facility'):
        for key, val in xdi.attrs.get(family, {}).items():
            if '||' in val:
                val, addr = val.split('||')
            try:
                val = float(val)
            except:
                pass
            setattr(group, "%s_%s" % (family, key), val)

    ocrs, icrs = [], []
    ctime = None
    for attrname in dir(xdi):
        if attrname.lower() == 'counttime':
            ctime = getattr(xdi, attrname)
    if ctime is None:
        try:
            ctime = xdi.TSCALER / 5.e7
        except AttributeError:
            ctime = 1.0

    is_xspress3 = any(['13QX4' in a[1] for a in xdi.attrs['column'].items()])
    group.with_xspress3 = is_xspress3
    dtc_taus = XSPRESS3_TAUS
    if _larch.symtable.has_symbol('_sys.gsecars.xspress3_taus'):
        dtc_taus = _larch.symtable._sys.gsecars.xspress3_taus

    dtc_mode = 'icr/ocr'
    for i in range(MAX_MCAS):
        mca = "mca%i" % (i+1)
        ocr    = getattr(xdi, 'OutputCounts_%s' % mca, None)
        clock  = getattr(xdi, 'Clock_%s'        % mca, None)
        icr    = getattr(xdi, 'InputCounts_%s'  % mca, None)
        dtfact = getattr(xdi, 'DTFactor_%s'     % mca, None)
        resets = getattr(xdi, 'ResetTicks_%s'   % mca, None)
        allevt = getattr(xdi, 'AllEvent_%s'     % mca, None)
        if (ocr is None and icr is None and clock is None and
            dtfact is None and resets is None):
            nmca = i
            break
        if ocr is None:
            ocr = ctime
        ocr = ocr/ctime
        if icr is not None:
            icr = icr/ctime

        # Get ICR from one of several alternatives:
        # 1. InputCounts_mca was given
        # 2. DTFactor_mca was given
        # 3. ResetTicks_mca and AllEvets_mca were given
        # 4. Use "known values" for tau
        if icr is None:
            if dtfact is not None:
                icr = ocr * dtfact
                dtc_mode = 'dtfactor'
            elif (clock is not None and
                  resets is not None and
                  allevt is not None):
                dtfact = clock/(clock - (6*allevt + resets))
                icr = ocr * dtfact
                dtc_mode = 'resets'
        # finally estimate from measured values of tau:
        if icr is None:
            icr = 1.0*ocr
            dtc_mode = 'none'
            if is_xspress3:
                tau = dtc_taus[i]
                icr = estimate_icr(ocr*1.00, tau, niter=7)
                dtc_mode = 'saved_taus'
        ocrs.append(ocr)
        icrs.append(icr)

    group.dtc_mode =  dtc_mode
    if dtc_mode == 'saved_taus':
        group.dtc_taus = dtc_taus

    labels = []
    sums = OrderedDict()
    for i, arrname in enumerate(xdi.array_labels):
        dat = getattr(xdi, arrname)
        if arrname.lower() == 'data':
            arrname = '_data'
        aname = sumname = rawname = arrname.lower()
        if ('_mca' in aname and
            'outputcounts' not in aname and
            'dtfactor' not in aname and
            'clock' not in aname):
            sumname, imca = sumname.split('_mca')
            imca = int(imca) - 1
            datraw = dat*1.0
            rawname = sumname + '_nodtc'
            dat   = dat * icrs[imca]/ ocrs[imca]
            if any(np.isnan(dat)):
                nan_pts = np.where(np.isnan(dat))[0]
                dat[nan_pts] = datraw[nan_pts]

        setattr(group, aname, dat)
        if sumname not in labels:
            labels.append(sumname)
            sums[sumname] = dat
            if rawname != sumname:
                sums[rawname] = datraw
                if rawname not in labels:
                    labels.append(rawname)

        else:
            sums[sumname] = sums[sumname] + dat
            if rawname != sumname:
                sums[rawname] = sums[rawname] + datraw

    for name, dat in sums.items():
        if not hasattr(group, name):
            setattr(group, name, dat)

    for arrname in xdi.array_labels:
        sname = arrname.lower()
        if sname not in labels:
            labels.append(sname)

    data = []
    for name in labels:
        data.append(getattr(group, name))
    group.data = np.array(data)
    for imca in range(nmca):
        setattr(group, 'ocr_mca%i' % (imca+1), ocrs[imca])
        setattr(group, 'icr_mca%i' % (imca+1), icrs[imca])
    group.array_labels = labels
    return group


DTC_header = '''# XDI/1.1  Epics StepScan File/2.0
# Beamline.name:  13-ID-E, GSECARS
# Monochromator.name:  %(mono_cut)s, LN2 Cooled
# Monochromator.dspacing:  %(mono_dspace)s
# Facility.name: APS
# Facility.xray_source: 3.6 cm undulator
# Detectors.i0:  20cm ion chamber, He
# Detectors.ifluor:  Si SDD Vortex ME-4, 4 elements
# Detectors.ifluor_electronics:  Quantum Xspress3 3.1.10'''

def is_GSEXDI(filename):
    """test if file is GSE XDI data file
    reads only the first line of file
    """
    line1 = open(filename, 'r').readline()
    return (line1.startswith('#XDI/1') and 'Epics StepScan File' in line1)

@ValidateLarchPlugin
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
    TINY  = 2.e-20
    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[np.isnan(i1)] = TINY
            i1 = i1 / out.i0
            i1[np.where(i1<TINY)] = TINY
            out.mutrans = -np.log(i1)


    npts   = len(out.i0)
    col0_name = xdi.array_labels[0].lower()
    col0_units = None
    col0_data  = xdi.data[0, :]
    if col0_name == 'energy':
        col0_data  = out.energy
        col0_units = 'eV'

    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[col0_name]  = (col0_name, col0_units)
    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 bytes2str(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 % col0_data[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

#!/usr/bin/env python Read GSE XDI Scan Data to larch group,     summing ROI data for MCAs and apply deadtime corrections # Get ICR from one of several alternatives: # 1. InputCounts_mca was given # 2. DTFactor_mca was given # 3. ResetTicks_mca and AllEvets_mca were given # 4. Use "known values" for tau # finally estimate from measured values of tau: # XDI/1.1  Epics StepScan File/2.0 # Beamline.name:  13-ID-E, GSECARS # Monochromator.name:  %(mono_cut)s, LN2 Cooled # Monochromator.dspacing:  %(mono_dspace)s # Facility.name: APS # Facility.xray_source: 3.6 cm undulator # Detectors.i0:  20cm ion chamber, He # Detectors.ifluor:  Si SDD Vortex ME-4, 4 elements # Detectors.ifluor_electronics:  Quantum Xspress3 3.1.10 test if file is GSE XDI data file     reads only the first line of file convert GSE XDI fluorescence XAFS scans to dead time corrected files # some scans may not record separate counttime, but TSCALER # is clock ticks for a 50MHz clock