| Dear Larch developers (Matt), I believe I found an error in the mback function where I get a NameError saying the name ‘f1_chantler’ is not defined. I found that simply adding f1_chantler to the larch_plugins.xray import section in mback.py fixes the problem. I have included the modified mback.py code, my input data (SigScan226827.txt), project code (mback_test.py), and the error I received (mback_error.txt). I am running python 2.7 with anaconda as my manager, macOS Sierra v10.12, on a mid-2015 15” MacBook pro. I hope this report is correct and helpful. Regards, Sean Sean Fackler, PhD
Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734 |
import pandas as pd import matplotlib.pylab as plt from larch import * from larch_plugins.xafs import pre_edge from larch_plugins.xafs import mback
scandata_f = []
#Working for SigScans
def rdin(filename):
scandata_f = pd.read_csv(filename, sep='\t', skiprows=15)
if not ("Counter 0" in scandata_f.columns):
scandata_f = pd.read_csv(filename, sep='\t', skiprows=14)
print scandata_f.columns
if not ("Counter 0" in scandata_f.columns):
print ("Problem with header. skipping 12 or 10 lines did not make it. Check input file.")
return None
return scandata_f
scandata_f = rdin("/Users/SeanFackler/data/ALS092016/160923/SigScan26827.txt")
# print scandata_f.Energy
def prepare_scan(scandata_f, datacounter="TEY_up", reference_counter='Izero'):
# Preparing Scan (normalization)
if 'Counter 4' in scandata_f.columns:
clockname = 'Counter 4'
elif 'Counter 6' in scandata_f.columns:
clockname = 'Counter 6'
else:
print("No counter for clock found (looked for 'Counter 4' and 'Counter 6'). Defaulting to 'Counter 0'.")
clockname = 'Counter 0'
scandata_f["I_Norm0"] = scandata_f[datacounter].astype(float) / scandata_f[reference_counter].astype(float)
scandata_f["I_Normt"] = scandata_f[datacounter].astype(float) / scandata_f[clockname].astype(float)
scandata_f["Energy"] = scandata_f["Energy"].round(1)
# scandata_f["Z"] = scandata_f["Z"].round(2)
return (scandata_f)
prepare_scan(scandata_f)
mylarch = Interpreter()
scandata_f.e = scandata_f.Energy#
scandata_f.mu = scandata_f.I_Norm0#
mback(scandata_f.e, scandata_f.mu, group=scandata_f, z=8, edge='K', order=1, whiteline=6, fit_erfc=True,
_larch=mylarch)
print scandata_f.mback_params.e0
plt.plot(scandata_f.e, scandata_f.f2)
plt.plot(scandata_f.e, scandata_f.fpp)
plt.plot(scandata_f.e, 5*scandata_f.mu)
plt.show()
from larch import Group, Parameter, isgroup, Minimizer, parse_group_args
from larch_plugins.math import index_of
from larch_plugins.xray import xray_edge, xray_line, f1_chantler, f2_chantler, f1f2
from larch_plugins.xafs import set_xafsGroup, find_e0
import numpy as np
from scipy.special import erfc
MAXORDER = 6
def match_f2(p):
"""
Objective function for matching mu(E) data to tabulated f''(E) using the MBACK
algorithm and, optionally, the Lee & Xiang extension.
"""
s = p.s.value
a = p.a.value
em = p.em.value
xi = p.xi.value
c0 = p.c0.value
eoff = p.en - p.e0.value
norm = a*erfc((p.en-em)/xi) + c0 # erfc function + constant term of polynomial
for i in range(MAXORDER): # successive orders of polynomial
j = i+1
attr = 'c%d' % j
if hasattr(p, attr):
norm = norm + getattr(getattr(p, attr), 'value') * eoff**j
func = (p.f2 + norm - s*p.mu) * p.theta / p.weight
if p.leexiang:
func = func / s*p.mu
return func
def mback(energy, mu, group=None, order=3, z=None, edge='K', e0=None, emin=None, emax=None,
whiteline=None, leexiang=False, tables='chantler', fit_erfc=False, return_f1=False,
_larch=None):
"""
Match mu(E) data for tabulated f''(E) using the MBACK algorithm and,
optionally, the Lee & Xiang extension
Arguments:
energy, mu: arrays of energy and mu(E)
order: order of polynomial [3]
group: output group (and input group for e0)
z: Z number of absorber
edge: absorption edge (K, L3)
e0: edge energy
emin: beginning energy for fit
emax: ending energy for fit
whiteline: exclusion zone around white lines
leexiang: flag to use the Lee & Xiang extension
tables: 'chantler' (default) or 'cl'
fit_erfc: True to float parameters of error function
return_f1: True to put the f1 array in the group
Returns:
group.f2: tabulated f2(E)
group.f1: tabulated f1(E) (if return_f1 is True)
group.fpp: matched data
group.mback_params: Group of parameters for the minimization
References:
* MBACK (Weng, Waldo, Penner-Hahn): http://dx.doi.org/10.1086/303711
* Lee and Xiang: http://dx.doi.org/10.1088/0004-637X/702/2/970
* Cromer-Liberman: http://dx.doi.org/10.1063/1.1674266
* Chantler: http://dx.doi.org/10.1063/1.555974
"""
order=int(order)
if order < 1: order = 1 # set order of polynomial
if order > MAXORDER: order = MAXORDER
### implement the First Argument Group convention
energy, mu, group = parse_group_args(energy, members=('energy', 'mu'),
defaults=(mu,), group=group,
fcn_name='mback')
if len(energy.shape) > 1:
energy = energy.squeeze()
if len(mu.shape) > 1:
mu = mu.squeeze()
group = set_xafsGroup(group, _larch=_larch)
if e0 is None: # need to run find_e0:
e0 = xray_edge(z, edge, _larch=_larch)[0]
if e0 is None:
e0 = group.e0
if e0 is None:
find_e0(energy, mu, group=group)
### theta is an array used to exclude the regions <emin, >emax, and
### around white lines, theta=0.0 in excluded regions, theta=1.0 elsewhere
(i1, i2) = (0, len(energy)-1)
if emin is not None: i1 = index_of(energy, emin)
if emax is not None: i2 = index_of(energy, emax)
theta = np.ones(len(energy)) # default: 1 throughout
theta[0:i1] = 0
theta[i2:-1] = 0
if whiteline:
pre = 1.0*(energy<e0)
post = 1.0*(energy>e0+float(whiteline))
theta = theta * (pre + post)
if edge.lower().startswith('l'):
l2 = xray_edge(z, 'L2', _larch=_larch)[0]
l2_pre = 1.0*(energy<l2)
l2_post = 1.0*(energy>l2+float(whiteline))
theta = theta * (l2_pre + l2_post)
## this is used to weight the pre- and post-edge differently as
## defined in the MBACK paper
weight1 = 1*(energy<e0)
weight2 = 1*(energy>e0)
weight = np.sqrt(sum(weight1))*weight1 + np.sqrt(sum(weight2))*weight2
## get the f'' function from CL or Chantler
if tables.lower() == 'chantler':
f1 = f1_chantler(z, energy, _larch=_larch)
f2 = f2_chantler(z, energy, _larch=_larch)
else:
(f1, f2) = f1f2(z, energy, edge=edge, _larch=_larch)
group.f2=f2
if return_f1: group.f1=f1
n = edge
if edge.lower().startswith('l'): n = 'L'
params = Group(s = Parameter(1, vary=True, _larch=_larch), # scale of data
xi = Parameter(50, vary=fit_erfc, min=0, _larch=_larch), # width of erfc
em = Parameter(xray_line(z, n, _larch=_larch)[0], vary=False, _larch=_larch), # erfc centroid
e0 = Parameter(e0, vary=False, _larch=_larch), # abs. edge energy
## various arrays need by the objective function
en = energy,
mu = mu,
f2 = group.f2,
weight = weight,
theta = theta,
leexiang = leexiang,
_larch = _larch)
if fit_erfc:
params.a = Parameter(1, vary=True, _larch=_larch) # amplitude of erfc
else:
params.a = Parameter(0, vary=False, _larch=_larch) # amplitude of erfc
for i in range(order): # polynomial coefficients
setattr(params, 'c%d' % i, Parameter(0, vary=True, _larch=_larch))
fit = Minimizer(match_f2, params, _larch=_larch, toler=1.e-5)
fit.leastsq()
eoff = energy - params.e0.value
normalization_function = params.a.value*erfc((energy-params.em.value)/params.xi.value) + params.c0.value
for i in range(MAXORDER):
j = i+1
attr = 'c%d' % j
if hasattr(params, attr):
normalization_function = normalization_function + getattr(getattr(params, attr), 'value') * eoff**j
group.fpp = params.s*mu - normalization_function
group.mback_params = params
def registerLarchPlugin(): # must have a function with this name!
return ('_xafs', { 'mback': mback })
Date: 9/23/2016 Start, Stop, Increment Energy Start: 510.00000000 Stop: 600.00000000 Increment: 1.00000000 Delay After Move (s): 0.00000000 Count Time (s): 0.50000000 Scan Number: 1 Bi-directional: No Stay at End: 1 Description Length: 0 Time of Day Time (s) Energy Channeltron Counter 0 Counter 2 Counter 3 Counter 4 Counter 5 Counter 6 Izero TEY_up TEY_dn Analog 2 Analog 3 Energy Beam Current Main Chamber Pressure Flow Cell Pressure Temp A Temp B Temp C Temp D Gate 15:12:23 1352.71500000 509.99969665 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 12982.00000000 37195.21092979 -1368.93399063 -0.01070992 0.01628112 509.99969435 500.10353699 0.00000000 0.00000364 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15:12:27 4.51600000 511.00063267 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13061.00000000 37358.78805411 -1296.60815766 -0.01134910 0.01569551 511.00061182 500.01541748 0.00000000 0.00000365 0.00000000 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/Users/SeanFackler/anaconda/bin/python
/Users/SeanFackler/PycharmProjects/msp_sean/mback_test.py
Traceback (most recent call last):
File "/Users/SeanFackler/PycharmProjects/msp_sean/mback_test.py", line 53, in
<module>
_larch=mylarch)
File "/Users/SeanFackler/anaconda/share/larch/plugins/xafs/mback.py", line
122, in mback
f1 = f1_chantler(z, energy, _larch=_larch)
NameError: global name 'f1_chantler' is not defined
Process finished with exit code 1
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