Coverage for /Users/Newville/Codes/xraylarch/larch/xafs/__init__.py: 100%
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« prev ^ index » next coverage.py v7.3.2, created at 2023-11-09 10:08 -0600
« prev ^ index » next coverage.py v7.3.2, created at 2023-11-09 10:08 -0600
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)
33from .autobk import autobk
34from .mback import mback, mback_norm
35from .diffkk import diffkk, diffKKGroup
36from .fluo import fluo_corr
38## from .cif2feff import cif_sites, cif2feff6l
40from .feffrunner import FeffRunner, feffrunner, feff6l, feff8l, find_exe
41from .feff8lpath import feff8_xafs
42from .feffutils import get_feff_pathinfo
44from .cauchy_wavelet import cauchy_wavelet
45from .deconvolve import xas_convolve, xas_deconvolve
46from .estimate_noise import estimate_noise
47from .rebin_xafs import rebin_xafs, sort_xafs
48from .sigma2_models import sigma2_eins, sigma2_debye, sigma2_correldebye, gnxas
51def _larch_init(_larch):
52 """initialize xafs"""
53 # initialize _xafs._feff_executable
54 _larch.symtable.set_symbol('_xafs._feff_executable', find_exe('feff6l'))
55 _larch.symtable.set_symbol('_xafs._feff8_executable', find_exe('feff8l'))
58_larch_groups = (diffKKGroup, FeffRunner, FeffDatFile, FeffPathGroup,
59 TransformGroup, FeffitDataSet)
61_larch_builtins = {'_xafs': dict(autobk=autobk, etok=etok, ktoe=ktoe,
62 guess_energy_units=guess_energy_units,
63 diffkk=diffkk, xftf=xftf, xftr=xftr,
64 xftf_prep=xftf_prep, xftf_fast=xftf_fast,
65 xftr_fast=xftr_fast, ftwindow=ftwindow,
66 find_e0=find_e0, pre_edge=pre_edge,
67 find_energy_step=find_energy_step,
68 energy_align=energy_align,
69 prepeaks_setup=prepeaks_setup,
70 prepeaks_fit=prepeaks_fit,
71 pre_edge_baseline=pre_edge_baseline,
72 mback=mback, mback_norm=mback_norm,
73 cauchy_wavelet=cauchy_wavelet,
74 xas_deconvolve=xas_deconvolve,
75 xas_convolve=xas_convolve,
76 fluo_corr=fluo_corr,
77 estimate_noise=estimate_noise,
78 rebin_xafs=rebin_xafs,
79 sort_xafs=sort_xafs,
80 gnxas=gnxas,
81 sigma2_eins=sigma2_eins,
82 sigma2_debye=sigma2_debye, feffit=feffit,
83 feffit_dataset=feffit_dataset,
84 feffit_transform=feffit_transform,
85 feffit_report=feffit_report,
86 feffrunner=feffrunner, feff6l=feff6l,
87 feff8l=feff8l,
88 feffpath= feffpath,
89 use_feffpath= use_feffpath,
90 path2chi=path2chi, ff2chi=ff2chi,
91 feff8_xafs=feff8_xafs,
92 get_feff_pathinfo=get_feff_pathinfo)}