def parse_jsonathena(text, filename):
"""parse a JSON-style athena file"""
jsdict = json.loads(text)
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
header = []
athena_names = []
for key, val in jsdict.items():
if key.startswith('_____head'):
header.append(val)
elif key.startswith('_____journ'):
journal = val
elif key.startswith('_____order'):
athena_names = val
out.journal = journal
out.header = '\n'.join(header)
out.group_names = []
for name in athena_names:
label = name
dat = jsdict[name]
x = np.array(dat['x'], dtype='float64')
y = np.array(dat['y'], dtype='float64')
this = Group(athena_id=name,
energy=x,
mu=y,
bkg_params=Group(),
fft_params=Group(),
athena_params=Group())
if 'i0' in dat:
this.i0 = np.array(dat['i0'], dtype='float64')
if 'signal' in dat:
this.signal = np.array(dat['signal'], dtype='float64')
if 'stddev' in dat:
this.stddev = np.array(dat['stddev'], dtype='float64')
if 'args' in dat:
for key, val in dat['args'].items():
if key.startswith('bkg_'):
setattr(this.bkg_params, key[4:], asfloat(val))
elif key.startswith('fft_'):
setattr(this.fft_params, key[4:], asfloat(val))
elif key == 'label':
label = this.label = val
else:
setattr(this.athena_params, key, asfloat(val))
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, name)
name = fix_varname(label)
if name.startswith('_'):
name = 'd' + name
setattr(out, name, this)
out.group_names.append(name)
return out
def parse_jsonathena(text, filename):
"""parse a JSON-style athena file"""
jsdict = json.loads(text)
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
header = []
athena_names = []
for key, val in jsdict.items():
if key.startswith('_____head'):
header.append(val)
elif key.startswith('_____journ'):
journal = val
elif key.startswith('_____order'):
athena_names = val
out.journal = journal
out.header = '\n'.join(header)
out.group_names = []
for name in athena_names:
label = name
dat = jsdict[name]
x = np.array(dat['x'], dtype='float64')
y = np.array(dat['y'], dtype='float64')
this = Group(athena_id=name, energy=x, mu=y,
bkg_params=Group(), fft_params=Group(),
athena_params=Group())
if 'i0' in dat:
this.i0 = np.array(dat['i0'], dtype='float64')
if 'signal' in dat:
this.signal = np.array(dat['signal'], dtype='float64')
if 'stddev' in dat:
this.stddev = np.array(dat['stddev'], dtype='float64')
if 'args' in dat:
for key, val in dat['args'].items():
if key.startswith('bkg_'):
setattr(this.bkg_params, key[4:], asfloat(val))
elif key.startswith('fft_'):
setattr(this.fft_params, key[4:], asfloat(val))
elif key == 'label':
label = this.label = val
else:
setattr(this.athena_params, key, asfloat(val))
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, name)
name = fix_varname(label)
if name.startswith('_'):
name = 'd' + name
setattr(out, name, this)
out.group_names.append(name)
return out
def parse_perlathena(text, filename):
"""
parse old athena file format to Group of Groups
"""
lines = text.split('\n')
athenagroups = []
raw = {'name':''}
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))
header = [vline]
journal = {}
is_header = True
for t in lines:
if t.startswith('#') or len(t) < 2 or 'undef' in t:
if is_header:
header.append(t)
continue
is_header = False
key = t.split(' ')[0].strip()
key = key.replace('$', '').replace('@', '')
if key == 'old_group':
raw['name'] = plarray2json(t)
elif key == '[record]':
athenagroups.append(raw)
raw = {'name':''}
elif key == 'journal':
journal = plarray2json(t)
elif key == 'args':
raw['args'] = plarray2json(t)
elif key == 'xdi':
raw['xdi'] = t
elif key in ('x', 'y', 'i0', 'signal', 'stddev'):
raw[key] = np.array([float(x) for x in plarray2json(t)])
elif key == '1;': # end of list
pass
else:
print(" do not know what to do with key ", key, raw['name'])
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
out.journal = journal
out.group_names = []
out.header = '\n'.join(header)
for dat in athenagroups:
label = dat.get('name', 'unknown')
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 'signal' in dat:
this.signal = dat['signal']
if 'stddev' in dat:
this.stddev = dat['stddev']
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:], asfloat(val))
elif key.startswith('fft_'):
setattr(this.fft_params, key[4:], asfloat(val))
elif key == 'label':
label = this.label = val
elif key in ('valence', 'lasso_yvalue',
'epsk', 'epsr', 'importance'):
setattr(this, key, asfloat(val))
elif key in ('atsym', 'edge', 'provenance'):
setattr(this, key, val)
else:
setattr(this.athena_params, key, asfloat(val))
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, dat['name'])
name = fix_varname(label)
if name.startswith('_'):
name = 'd' + name
setattr(out, name, this)
out.group_names.append(name)
return out
def parse_perlathena(text, filename):
"""
parse old athena file format to Group of Groups
"""
lines = text.split('\n')
athenagroups = []
raw = {'name':''}
vline = lines.pop(0)
if "Athena project file -- " not in vline:
raise ValueError("%s '%s': invalid Athena File" % (ERR_MSG, filename))
major, minor, fix = '0', '0', '0'
if 'Demeter' in vline:
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))
else:
try:
vs = vline.split("Athena project file -- Athena version")[1]
major, minor, fix = vs.split('.')
except:
raise ValueError("%s '%s': cannot read version" % (ERR_MSG, filename))
header = [vline]
journal = ['']
is_header = True
for t in lines:
if t.startswith('#') or len(t) < 2 or 'undef' in t:
if is_header:
header.append(t)
continue
is_header = False
key = t.split(' ')[0].strip()
key = key.replace('$', '').replace('@', '').replace('%', '').strip()
if key == 'old_group':
raw['name'] = plarray2json(t)
elif key == '[record]':
athenagroups.append(raw)
raw = {'name':''}
elif key == 'journal':
journal = parse_arglist(t)
elif key == 'args':
raw['args'] = parse_arglist(t)
elif key == 'xdi':
raw['xdi'] = t
elif key in ('x', 'y', 'i0', 'signal', 'stddev'):
raw[key] = np.array([float(x) for x in plarray2json(t)])
elif key in ('1;', 'indicator', 'lcf_data', 'plot_features'):
pass
else:
print(" do not know what to do with key '%s' at '%s'" % (key, raw['name']))
out = Group()
out.__doc__ = """XAFS Data from Athena Project File %s""" % (filename)
out.journal = '\n'.join(journal)
out.group_names = []
out.header = '\n'.join(header)
for dat in athenagroups:
label = dat.get('name', 'unknown')
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 'signal' in dat:
this.signal = dat['signal']
if 'stddev' in dat:
this.stddev = dat['stddev']
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:], asfloat(val))
elif key.startswith('fft_'):
setattr(this.fft_params, key[4:], asfloat(val))
elif key == 'label':
label = this.label = val
elif key in ('valence', 'lasso_yvalue',
'epsk', 'epsr', 'importance'):
setattr(this, key, asfloat(val))
elif key in ('atsym', 'edge', 'provenance'):
setattr(this, key, val)
else:
setattr(this.athena_params, key, asfloat(val))
this.__doc__ = """Athena Group Name %s (key='%s')""" % (label, dat['name'])
name = fix_varname(label)
if name.startswith('_'):
name = 'd' + name
setattr(out, name, this)
out.group_names.append(name)
return out