def restore(fname, top_level=True, _larch=None):
"""restore data from a json Larch save file
Arguments
---------
top_level bool whether to restore to _main [True]
Returns
-------
None with `top_level=True` or group with `top_level=False`
Notes
-----
1. With top_level=False, a new group containing the
recovered data will be returned.
"""
grouplist = _larch.symtable._sys.saverestore_groups
datalines = open(fname, 'r').readlines()
line1 = datalines.pop(0)
if not line1.startswith("#Larch Save File:"):
raise ValueError("%s is not a valid Larch save file" % fname)
version_string = line1.split(':')[1].strip()
version_info = [s for s in version_string.split('.')]
ivar = 0
header = {'version': version_info}
varnames = []
gname = fix_varname('restore_%s' % fname)
out = Group(name=gname)
for line in datalines:
line = line[:-1]
if line.startswith('#save.'):
key, value = line[6:].split(':', 1)
value = value.strip()
if key == 'nitems': value = int(value)
header[key] = value
elif line.startswith('#=>'):
name = fix_varname(line[4:].strip())
ivar += 1
if name in (None, 'None', '__unknown__') or name in varnames:
name = 'var_%5.5i' % (ivar)
varnames.append(name)
else:
val = decode4js(json.loads(line), grouplist)
setattr(out, varnames[-1], val)
setattr(out, '_restore_metadata_', header)
if top_level:
_main = _larch.symtable
for objname in dir(out):
setattr(_main, objname, getattr(out, objname))
return
return out
def restore(fname, top_level=True, _larch=None):
"""restore data from a json Larch save file
Arguments
---------
top_level bool whether to restore to _main [True]
Returns
-------
None with `top_level=True` or group with `top_level=False`
Notes
-----
1. With top_level=False, a new group containing the
recovered data will be returned.
"""
grouplist = _larch.symtable._sys.saverestore_groups
datalines = open(fname, 'r').readlines()
line1 = datalines.pop(0)
if not line1.startswith("#Larch Save File:"):
raise ValueError("%s is not a valid Larch save file" % fname)
version_string = line1.split(':')[1].strip()
version_info = [s for s in version_string.split('.')]
ivar = 0
header = {'version': version_info}
varnames = []
gname = fix_varname('restore_%s' % fname)
out = Group(name=gname)
for line in datalines:
line = line[:-1]
if line.startswith('#save.'):
key, value = line[6:].split(':', 1)
value = value.strip()
if key == 'nitems': value = int(value)
header[key] = value
elif line.startswith('#=>'):
name = fix_varname(line[4:].strip())
ivar += 1
if name in (None, 'None', '__unknown__') or name in varnames:
name = 'var_%5.5i' % (ivar)
varnames.append(name)
else:
val = decode4js(json.loads(line), grouplist)
setattr(out, varnames[-1], val)
setattr(out, '_restore_metadata_', header)
if top_level:
_main = _larch.symtable
for objname in dir(out):
setattr(_main, objname, getattr(out, objname))
return
return out
def onRead(self, path):
if path in self.controller.file_groups:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
filedir, filename = os.path.split(path)
pref = fix_varname(filename.replace('.', '_'))
if len(pref) > 15:
pref = pref[:15]
groupname = pref
count, maxcount = 0, 999
while hasattr(self.larch.symtable, groupname) and count < maxcount:
count += 1
groupname = '%s_%2.2i' % (pref, count)
if self.config['chdir_on_fileopen']:
os.chdir(filedir)
kwargs = dict(filename=path,
_larch=self.larch_buffer.larchshell,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onRead_OK)
# check for athena projects
if is_athena_project(path):
self.show_subframe('athena_import', AthenaImporter, **kwargs)
else:
self.show_subframe('readfile', ColumnDataFileFrame, **kwargs)
def merge_groups(self, grouplist, master=None, yarray='mu', outgroup=None):
"""merge groups"""
cmd = """%s = merge_groups(%s, master=%s,
xarray='energy', yarray='%s', kind='cubic', trim=True)"""
glist = "[%s]" % (', '.join(grouplist))
outgroup = fix_varname(outgroup.lower())
if outgroup is None:
outgroup = 'merged'
outgroup = unique_name(outgroup, self.file_groups, max=1000)
cmd = cmd % (outgroup, glist, master, yarray)
self.larch.eval(cmd)
if master is None:
master = grouplist[0]
this = self.get_group(outgroup)
master = self.get_group(master)
if not hasattr(this, 'xasnorm_config'):
this.xasnorm_config = {}
this.xasnorm_config.update(master.xasnorm_config)
this.datatype = master.datatype
this.xdat = 1.0*this.energy
this.ydat = 1.0*getattr(this, yarray)
this.yerr = getattr(this, 'd' + yarray, 1.0)
if yarray != 'mu':
this.mu = this.ydat
this.plot_xlabel = 'energy'
this.plot_ylabel = yarray
return outgroup
def merge_groups(self, grouplist, master=None, yarray='mu', outgroup=None):
"""merge groups"""
cmd = """%s = merge_groups(%s, master=%s,
xarray='energy', yarray='%s', kind='cubic', trim=True)"""
glist = "[%s]" % (', '.join(grouplist))
outgroup = fix_varname(outgroup.lower())
if outgroup is None:
outgroup = 'merged'
outgroup = unique_name(outgroup, self.file_groups, max=1000)
cmd = cmd % (outgroup, glist, master, yarray)
self.larch.eval(cmd)
if master is None:
master = grouplist[0]
this = self.get_group(outgroup)
master = self.get_group(master)
if not hasattr(this, 'xasnorm_config'):
this.xasnorm_config = {}
this.xasnorm_config.update(master.xasnorm_config)
this.datatype = master.datatype
this.xdat = 1.0 * this.energy
this.ydat = 1.0 * getattr(this, yarray)
this.plot_xlabel = 'energy'
this.plot_ylabel = yarray
return outgroup
def assign_gsescan_groups(group):
labels = group.array_labels
labels = []
for i, name in enumerate(group.pos_desc):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.pos[i, :])
for i, name in enumerate(group.sums_names):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.sums_corr[i, :])
for i, name in enumerate(group.det_desc):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.det_corr[i, :])
group.array_labels = labels
def assign_gsescan_groups(group):
labels = group.array_labels
labels = []
for i, name in enumerate(group.pos_desc):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.pos[i, :])
for i, name in enumerate(group.sums_names):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.sums_corr[i, :])
for i, name in enumerate(group.det_desc):
name = fix_varname(name.lower())
labels.append(name)
setattr(group, name, group.det_corr[i, :])
group.array_labels = labels
def onReadScan(self, evt=None):
dlg = wx.FileDialog(self,
message="Load Column Data File",
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
path = path.replace('\\', '/')
if path in self.file_groups:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
filedir, filename = os.path.split(path)
pref = fix_varname((filename + '____')[:7]).replace('.', '_')
count, maxcount = 1, 9999
groupname = "%s%3.3i" % (pref, count)
while hasattr(self.larch.symtable, groupname) and count < maxcount:
count += 1
groupname = '%s%3.3i' % (pref, count)
if self.config['chdir_on_fileopen']:
os.chdir(filedir)
fh = open(path, 'r')
line1 = fh.readline().lower()
fh.close()
reader = read_ascii
if 'epics stepscan file' in line1:
reader = read_gsexdi
elif 'epics scan' in line1:
reader = gsescan_group
elif 'xdi' in line1:
reader = read_xdi
dgroup = reader(str(path), _larch=self.larch)
if reader == gsescan_group:
assign_gsescan_groups(dgroup)
dgroup._path = path
dgroup._filename = filename
dgroup._groupname = groupname
self.show_subframe('coledit',
EditColumnFrame,
group=dgroup,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onReadScan_Success)
dlg.Destroy()
def onRead(self, path):
if path in self.controller.file_groups:
if wx.ID_YES != popup(self, "Re-read file '%s'?" % path,
'Re-read file?'):
return
filedir, filename = os.path.split(path)
pref= fix_varname(filename.replace('.', '_'))
if len(pref) > 15:
pref = pref[:15]
groupname = pref
count, maxcount = 0, 999
while hasattr(self.larch.symtable, groupname) and count < maxcount:
count += 1
groupname = '%s_%2.2i' % (pref, count)
if self.config['chdir_on_fileopen']:
os.chdir(filedir)
# check for athena projects
if is_athena_project(path):
self.show_subframe('athena_import', AthenaImporter,
filename=path, _larch=self.larch,
read_ok_cb=partial(self.onRead_OK,
overwrite=False))
return
## not athena, plain ASCII:
fh = open(path, 'r')
line1 = fh.readline().lower()
fh.close()
reader = read_ascii
if 'epics stepscan file' in line1:
reader = read_gsexdi
elif 'epics scan' in line1:
reader = gsescan_group
elif 'xdi' in line1:
reader = read_xdi
dgroup = reader(str(path), _larch=self.larch)
if reader == gsescan_group:
assign_gsescan_groups(dgroup)
dgroup.path = path
dgroup.filename = filename
dgroup.groupname = groupname
self.show_subframe('coledit', EditColumnFrame, group=dgroup,
last_array_sel=self.last_array_sel,
_larch=self.larch,
read_ok_cb=partial(self.onRead_OK,
overwrite=False))
def onReadData(self, event=None):
wildcard = 'Data file (*.dat)|*.dat|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Open Data File',
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
path = None
if dlg.ShowModal() == wx.ID_OK:
path = os.path.abspath(dlg.GetPath()).replace('\\', '/')
dlg.Destroy()
if path is None:
return
if is_athena_project(path):
self.show_subframe(name='athena_import', filename=path,
creator=AthenaImporter,
read_ok_cb=self.onReadAthenaProject_OK)
else:
filedir, filename = os.path.split(path)
pref = fix_varname((filename + '_'*8)[:8]).replace('.', '_').lower()
count, maxcount = 1, 9999
groupname = "%s%3.3i" % (pref, count)
while hasattr(self.larchshell.symtable, groupname) and count < maxcount:
count += 1
groupname = '%s%3.3i' % (pref, count)
fh = open(path, 'r')
line1 = fh.readline().lower()
fh.close()
reader = read_ascii
if 'epics stepscan file' in line1:
reader = read_gsexdi
elif 'epics scan' in line1:
reader = gsescan_group
elif 'xdi' in line1:
reader = read_xdi
dgroup = reader(str(path), _larch=self.larchshell._larch)
dgroup._path = path
dgroup._filename = filename
dgroup._groupname = groupname
self.show_subframe(name='coledit', event=None,
creator=ColumnDataFileFrame,
filename=path,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onReadScan_Success)
def onOK(self, event=None):
""" build arrays according to selection """
if not hasattr(self.dgroup, '_xdat'):
self.onColumnChoice()
if self.wid_groupname is not None:
self.dgroup._groupname = fix_varname(self.wid_groupname.GetValue())
if self.plotframe is not None:
try:
self.plotframe.Destroy()
except:
pass
if self.read_ok_cb is not None:
self.read_ok_cb(self.dgroup, self.array_sel)
self.Destroy()
def onOK(self, event=None):
""" build arrays according to selection """
if self.wid_groupname is not None:
self.outgroup.groupname = fix_varname(self.wid_groupname.GetValue())
yerr_op = self.yerr_op.GetStringSelection().lower()
if yerr_op.startswith('const'):
self.outgroup.yerr = self.yerr_const.GetValue()
elif yerr_op.startswith('array'):
yerr = self.yerr_arr.GetStringSelection().strip()
self.outgroup.yerr = get_data(rawgroup, yerr)
elif yerr_op.startswith('sqrt'):
self.outgroup.yerr = np.sqrt(outgroup.ydat)
if self.read_ok_cb is not None:
self.read_ok_cb(self.outgroup, array_sel=self.array_sel)
self.Destroy()
def onReadData(self, event=None):
wildcard = 'Data file (*.dat)|*.dat|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Open Data File',
defaultDir=os.getcwd(),
wildcard=FILE_WILDCARDS,
style=wx.FD_OPEN | wx.FD_CHANGE_DIR)
dgroup = None
if dlg.ShowModal() == wx.ID_OK:
path = os.path.abspath(dlg.GetPath()).replace('\\', '/')
filedir, filename = os.path.split(path)
pref = fix_varname((filename + '_' * 8)[:8]).replace('.',
'_').lower()
count, maxcount = 1, 9999
groupname = "%s%3.3i" % (pref, count)
while hasattr(self.larchshell.symtable,
groupname) and count < maxcount:
count += 1
groupname = '%s%3.3i' % (pref, count)
fh = open(path, 'r')
line1 = fh.readline().lower()
fh.close()
reader = read_ascii
if 'epics stepscan file' in line1:
reader = read_gsexdi
elif 'epics scan' in line1:
reader = gsescan_group
elif 'xdi' in line1:
reader = read_xdi
dgroup = reader(str(path), _larch=self.larchshell.larch)
dgroup._path = path
dgroup._filename = filename
dgroup._groupname = groupname
dlg.Destroy()
if dgroup is not None:
self.show_subframe(name='coledit',
event=None,
creator=EditColumnFrame,
group=dgroup,
last_array_sel=self.last_array_sel,
read_ok_cb=self.onReadScan_Success)
def onMergeData(self, event=None):
groups = []
for checked in self.controller.filelist.GetCheckedStrings():
groups.append(self.controller.file_groups[str(checked)])
if len(groups) < 1:
return
outgroup = unique_name('merge', self.controller.file_groups)
dlg = MergeDialog(self, groups, outgroup=outgroup)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
fname = res.group
gname = fix_varname(res.group.lower())
yname = 'norm' if res.ynorm else 'mu'
self.controller.merge_groups(groups, master=res.master,
yarray=yname, outgroup=gname)
self.install_group(gname, fname, overwrite=False)
self.controller.filelist.SetStringSelection(fname)
def onOK(self, event=None):
""" import groups """
for name in self.grouplist.GetCheckedStrings():
rawgroup = getattr(self.all, name)
npts = len(rawgroup.energy)
outgroup = Group(datatype='xas',
path="%s::%s" %(self.filename, name),
filename=name,
groupname = fix_varname(name),
raw=rawgroup,
xdat=rawgroup.energy,
ydat=rawgroup.mu,
y=rawgroup.mu,
yerr=1.0,
npts=npts, _index=1.0*np.arange(npts),
plot_xlabel='Energy (eV)',
plot_ylabel='mu')
self.read_ok_cb(outgroup, array_sel=None, overwrite=True)
self.Destroy()
def onOK(self, event=None):
""" import groups """
for name in self.grouplist.GetCheckedStrings():
rawgroup = getattr(self.all, name)
npts = len(rawgroup.energy)
outgroup = Group(datatype='xas',
path="%s::%s" % (self.filename, name),
filename=name,
groupname=fix_varname(name),
raw=rawgroup,
xdat=rawgroup.energy,
ydat=rawgroup.mu,
y=rawgroup.mu,
yerr=1.0,
npts=npts,
_index=1.0 * np.arange(npts),
plot_xlabel='Energy (eV)',
plot_ylabel='mu')
if self.read_ok_cb is not None:
self.read_ok_cb(outgroup, array_sel=None, overwrite=True)
self.Destroy()
def onMergeData(self, event=None):
groups = OrderedDict()
for checked in self.controller.filelist.GetCheckedStrings():
cname = str(checked)
groups[cname] = self.controller.file_groups[cname]
if len(groups) < 1:
return
outgroup = unique_name('merge', self.controller.file_groups)
dlg = MergeDialog(self, list(groups.keys()), outgroup=outgroup)
res = dlg.GetResponse()
dlg.Destroy()
if res.ok:
fname = res.group
gname = fix_varname(res.group.lower())
master = self.controller.file_groups[res.master]
yname = 'norm' if res.ynorm else 'mu'
self.controller.merge_groups(list(groups.values()),
master=master,
yarray=yname,
outgroup=gname)
self.install_group(gname, fname, overwrite=False)
self.controller.filelist.SetStringSelection(fname)
def add_data(self, group, name, data):
name = fix_varname(name)
if self.isgroup(data):
g = self.add_h5group(group, name,
attrs={'larchtype': 'group',
'class': data.__class__.__name__})
for comp in dir(data):
self.add_data(g, comp, getattr(data, comp))
elif isinstance(data, (list, tuple)):
dtype = 'list'
if isinstance(data, tuple): dtype = 'tuple'
g = self.add_h5group(group, name, attrs={'larchtype': dtype})
for ix, comp in enumerate(data):
iname = 'item%i' % ix
self.add_data(g, iname, comp)
elif isinstance(data, dict):
g = self.add_h5group(group, name, attrs={'larchtype': 'dict'})
for key, val in data.items():
self.add_data(g, key, val)
elif isParameter(data):
g = self.add_h5group(group, name, attrs={'larchtype': 'parameter'})
self.add_h5dataset(g, 'json', data.asjson())
else:
d = self.add_h5dataset(group, name, data)
def read_athena(filename, match=None, do_preedge=True, do_bkg=True, do_fft=True, use_hashkey=False, _larch=None):
"""read athena project file
returns a Group of Groups, one for each Athena Group in the project file
Arguments:
filename (string): name of Athena Project file
match (sring): pattern to use to limit imported groups (see Note 1)
do_preedge (bool): whether to do pre-edge subtraction [True]
do_bkg (bool): whether to do XAFS background subtraction [True]
do_fft (bool): whether to do XAFS Fast Fourier transform [True]
use_hashkey (bool): whether to use Athena's hash key as the
group name instead of the Athena label [False]
Returns:
group of groups each named according the label used by Athena.
Notes:
1. To limit the imported groups, use the pattern in `match`,
using '*' to match 'all' '?' to match any single character,
or [sequence] to match any of a sequence of letters. The match
will always be insensitive to case.
3. do_preedge, do_bkg, and do_fft will attempt to reproduce the
pre-edge, background subtraction, and FFT from Athena by using
the parameters saved in the project file.
2. use_hashkey=True will name groups from the internal 5 character
string used by Athena, instead of the group label.
Example:
1. read in all groups from a project file:
cr_data = read_athena('My Cr Project.prj')
2. read in only the "merged" data from a Project, and don't do FFT:
zn_data = read_athena('Zn on Stuff.prj', match='*merge*', do_fft=False)
"""
from larch_plugins.xafs import pre_edge, autobk, xftf
if not os.path.exists(filename):
raise IOError("%s '%s': cannot find file" % (ERR_MSG, filename))
try:
fh = GzipFile(filename)
lines = [bytes2str(t) for t in fh.readlines()]
fh.close()
except:
raise ValueError("%s '%s': invalid gzip file" % (ERR_MSG, filename))
athenagroups = []
dat = {"name": ""}
Athena_version = None
vline = lines.pop(0)
if "Athena project file -- Demeter version" not in vline:
raise ValueError("%s '%s': invalid Athena File" % (ERR_MSG, filename))
major, minor, fix = "0", "0", "0"
try:
vs = vline.split("Athena project file -- Demeter version")[1]
major, minor, fix = vs.split(".")
except:
raise ValueError("%s '%s': cannot read version" % (ERR_MSG, filename))
if int(minor) < 9 or int(fix[:2]) < 21:
raise ValueError("%s '%s': file is too old to read" % (ERR_MSG, filename))
for t in lines:
if t.startswith("#") or len(t) < 2:
continue
key = t.split(" ")[0].strip()
key = key.replace("$", "").replace("@", "")
if key == "old_group":
dat["name"] = perl2json(t)
elif key == "[record]":
athenagroups.append(dat)
dat = {"name": ""}
elif key == "args":
dat["args"] = perl2json(t)
elif key in ("x", "y", "i0"):
dat[key] = np.array([float(x) for x in perl2json(t)])
if match is not None:
match = match.lower()
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
for dat in athenagroups:
label = dat["name"]
this = Group(
athena_id=label, energy=dat["x"], mu=dat["y"], bkg_params=Group(), fft_params=Group(), athena_params=Group()
)
if "i0" in dat:
this.i0 = dat["i0"]
if "args" in dat:
for i in range(len(dat["args"]) // 2):
key = dat["args"][2 * i]
val = dat["args"][2 * i + 1]
if key.startswith("bkg_"):
setattr(this.bkg_params, key[4:], val)
elif key.startswith("fft_"):
setattr(this.fft_params, key[4:], val)
elif key == "label":
this.label = val
if not use_hashkey:
label = this.label
else:
setattr(this.athena_params, key, val)
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, dat["name"])
olabel = fix_varname(label)
if match is not None:
if not fnmatch(olabel.lower(), match):
continue
if do_preedge or do_bkg:
pars = this.bkg_params
pre_edge(
this,
_larch=_larch,
e0=float(pars.e0),
pre1=float(pars.pre1),
pre2=float(pars.pre2),
norm1=float(pars.nor1),
norm2=float(pars.nor2),
nnorm=float(pars.nnorm) - 1,
make_flat=bool(pars.flatten),
)
if do_bkg and hasattr(pars, "rbkg"):
autobk(
this,
_larch=_larch,
e0=float(pars.e0),
rbkg=float(pars.rbkg),
kmin=float(pars.spl1),
kmax=float(pars.spl2),
kweight=float(pars.kw),
dk=float(pars.dk),
clamp_lo=float(pars.clamp1),
clamp_hi=float(pars.clamp2),
)
if do_fft:
pars = this.fft_params
kweight = 2
if hasattr(pars, "kw"):
kweight = float(pars.kw)
xftf(
this,
_larch=_larch,
kmin=float(pars.kmin),
kmax=float(pars.kmax),
kweight=kweight,
window=pars.kwindow,
dk=float(pars.dk),
)
setattr(out, olabel, this)
return out
def read_athena(filename,
match=None,
do_preedge=True,
do_bkg=True,
do_fft=True,
use_hashkey=False,
_larch=None):
"""read athena project file
returns a Group of Groups, one for each Athena Group in the project file
Arguments:
filename (string): name of Athena Project file
match (sring): pattern to use to limit imported groups (see Note 1)
do_preedge (bool): whether to do pre-edge subtraction [True]
do_bkg (bool): whether to do XAFS background subtraction [True]
do_fft (bool): whether to do XAFS Fast Fourier transform [True]
use_hashkey (bool): whether to use Athena's hash key as the
group name instead of the Athena label [False]
Returns:
group of groups each named according the label used by Athena.
Notes:
1. To limit the imported groups, use the pattern in `match`,
using '*' to match 'all' '?' to match any single character,
or [sequence] to match any of a sequence of letters. The match
will always be insensitive to case.
3. do_preedge, do_bkg, and do_fft will attempt to reproduce the
pre-edge, background subtraction, and FFT from Athena by using
the parameters saved in the project file.
2. use_hashkey=True will name groups from the internal 5 character
string used by Athena, instead of the group label.
Example:
1. read in all groups from a project file:
cr_data = read_athena('My Cr Project.prj')
2. read in only the "merged" data from a Project, and don't do FFT:
zn_data = read_athena('Zn on Stuff.prj', match='*merge*', do_fft=False)
"""
from larch_plugins.xafs import pre_edge, autobk, xftf
if not os.path.exists(filename):
raise IOError("%s '%s': cannot find file" % (ERR_MSG, filename))
try:
fh = GzipFile(filename)
lines = [bytes2str(t) for t in fh.readlines()]
fh.close()
except:
raise ValueError("%s '%s': invalid gzip file" % (ERR_MSG, filename))
athenagroups = []
dat = {'name': ''}
Athena_version = None
vline = lines.pop(0)
if "Athena project file -- Demeter version" not in vline:
raise ValueError("%s '%s': invalid Athena File" % (ERR_MSG, filename))
major, minor, fix = '0', '0', '0'
try:
vs = vline.split("Athena project file -- Demeter version")[1]
major, minor, fix = vs.split('.')
except:
raise ValueError("%s '%s': cannot read version" % (ERR_MSG, filename))
if int(minor) < 9 or int(fix[:2]) < 21:
raise ValueError("%s '%s': file is too old to read" %
(ERR_MSG, filename))
for t in lines:
if t.startswith('#') or len(t) < 2:
continue
key = t.split(' ')[0].strip()
key = key.replace('$', '').replace('@', '')
if key == 'old_group':
dat['name'] = perl2json(t)
elif key == '[record]':
athenagroups.append(dat)
dat = {'name': ''}
elif key == 'args':
dat['args'] = perl2json(t)
elif key in ('x', 'y', 'i0'):
dat[key] = np.array([float(x) for x in perl2json(t)])
if match is not None:
match = match.lower()
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
for dat in athenagroups:
label = dat['name']
this = Group(athena_id=label,
energy=dat['x'],
mu=dat['y'],
bkg_params=Group(),
fft_params=Group(),
athena_params=Group())
if 'i0' in dat:
this.i0 = dat['i0']
if 'args' in dat:
for i in range(len(dat['args']) // 2):
key = dat['args'][2 * i]
val = dat['args'][2 * i + 1]
if key.startswith('bkg_'):
setattr(this.bkg_params, key[4:], val)
elif key.startswith('fft_'):
setattr(this.fft_params, key[4:], val)
elif key == 'label':
this.label = val
if not use_hashkey:
label = this.label
else:
setattr(this.athena_params, key, val)
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label,
dat['name'])
olabel = fix_varname(label)
if match is not None:
if not fnmatch(olabel.lower(), match):
continue
if do_preedge or do_bkg:
pars = this.bkg_params
pre_edge(this,
_larch=_larch,
e0=float(pars.e0),
pre1=float(pars.pre1),
pre2=float(pars.pre2),
norm1=float(pars.nor1),
norm2=float(pars.nor2),
nnorm=float(pars.nnorm) - 1,
make_flat=bool(pars.flatten))
if do_bkg and hasattr(pars, 'rbkg'):
autobk(this,
_larch=_larch,
e0=float(pars.e0),
rbkg=float(pars.rbkg),
kmin=float(pars.spl1),
kmax=float(pars.spl2),
kweight=float(pars.kw),
dk=float(pars.dk),
clamp_lo=float(pars.clamp1),
clamp_hi=float(pars.clamp2))
if do_fft:
pars = this.fft_params
kweight = 2
if hasattr(pars, 'kw'):
kweight = float(pars.kw)
xftf(this,
_larch=_larch,
kmin=float(pars.kmin),
kmax=float(pars.kmax),
kweight=kweight,
window=pars.kwindow,
dk=float(pars.dk))
setattr(out, olabel, this)
return out