Coverage for larch/xafs/__init__.py: 100%
24 statements
« prev ^ index » next coverage.py v7.6.0, created at 2024-10-16 21:04 +0000
« prev ^ index » next coverage.py v7.6.0, created at 2024-10-16 21:04 +0000
1__DOC__ = '''
2XAFS Functions for Larch, essentially Ifeffit 2
4The functions here include (but are not limited to):
6function description
7------------ ------------------------------
8pre_edge pre_edge subtraction, normalization
9autobk XAFS background subtraction (mu(E) to chi(k))
10xftf forward XAFS Fourier transform (k -> R)
11xftr backward XAFS Fourier transform, Filter (R -> q)
12ftwindow create XAFS Fourier transform window
14feffpath create a Feff Path from a feffNNNN.dat file
15path2chi convert a single Feff Path to chi(k)
16ff2chi sum a set of Feff Paths to chi(k)
18feffit_dataset create a Dataset for Feffit
19feffit_transform create a Feffit transform group
20feffit fit a set of Feff Paths to Feffit Datasets
21feffit_report create a report from feffit() results
22'''
25from .xafsutils import KTOE, ETOK, set_xafsGroup, etok, ktoe, guess_energy_units
26from .xafsft import xftf, xftr, xftf_fast, xftr_fast, ftwindow, xftf_prep
27from .pre_edge import pre_edge, preedge, find_e0, energy_align, find_energy_step
28from .prepeaks import prepeaks_setup, pre_edge_baseline, prepeaks_fit
29from .feffdat import FeffDatFile, FeffPathGroup, feffpath, path2chi, ff2chi, use_feffpath
30from .feffit import (FeffitDataSet, TransformGroup, feffit,
31 feffit_dataset, feffit_transform, feffit_report,
32 feffit_conf_map)
34from .autobk import autobk, autobk_lmfit, autobk_delta_chi
35from .mback import mback, mback_norm
36from .diffkk import diffkk, diffKKGroup
37from .fluo import fluo_corr
39## from .cif2feff import cif_sites, cif2feff6l
41from .feffrunner import FeffRunner, feffrunner, feff6l, feff8l, find_exe
42from .feff8lpath import feff8_xafs
43from .feffutils import get_feff_pathinfo
45from .cauchy_wavelet import cauchy_wavelet
46from .deconvolve import xas_convolve, xas_deconvolve
47from .estimate_noise import estimate_noise
48from .rebin_xafs import rebin_xafs, sort_xafs
49from .sigma2_models import sigma2_eins, sigma2_debye, sigma2_correldebye, gnxas
52def _larch_init(_larch):
53 """initialize xafs"""
54 # initialize _xafs._feff_executable
55 _larch.symtable.set_symbol('_xafs._feff_executable', find_exe('feff6l'))
56 _larch.symtable.set_symbol('_xafs._feff8_executable', find_exe('feff8l'))
59_larch_groups = (diffKKGroup, FeffRunner, FeffDatFile, FeffPathGroup,
60 TransformGroup, FeffitDataSet)
62_larch_builtins = {'_xafs': dict(autobk=autobk, autobk_lmfit=autobk_lmfit,
63 autobk_delta_chi=autobk_delta_chi,
64 etok=etok, ktoe=ktoe,
65 guess_energy_units=guess_energy_units,
66 diffkk=diffkk, xftf=xftf, xftr=xftr,
67 xftf_prep=xftf_prep, xftf_fast=xftf_fast,
68 xftr_fast=xftr_fast, ftwindow=ftwindow,
69 find_e0=find_e0, pre_edge=pre_edge,
70 find_energy_step=find_energy_step,
71 energy_align=energy_align,
72 prepeaks_setup=prepeaks_setup,
73 prepeaks_fit=prepeaks_fit,
74 pre_edge_baseline=pre_edge_baseline,
75 mback=mback, mback_norm=mback_norm,
76 cauchy_wavelet=cauchy_wavelet,
77 xas_deconvolve=xas_deconvolve,
78 xas_convolve=xas_convolve,
79 fluo_corr=fluo_corr,
80 estimate_noise=estimate_noise,
81 rebin_xafs=rebin_xafs,
82 sort_xafs=sort_xafs,
83 gnxas=gnxas,
84 sigma2_eins=sigma2_eins,
85 sigma2_debye=sigma2_debye, feffit=feffit,
86 feffit_dataset=feffit_dataset,
87 feffit_transform=feffit_transform,
88 feffit_report=feffit_report,
89 feffit_conf_map=feffit_conf_map,
90 feffrunner=feffrunner, feff6l=feff6l,
91 feff8l=feff8l,
92 feffpath= feffpath,
93 use_feffpath= use_feffpath,
94 path2chi=path2chi, ff2chi=ff2chi,
95 feff8_xafs=feff8_xafs,
96 get_feff_pathinfo=get_feff_pathinfo)}