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.. _python_api:
Using XrayDB from Python
=========================
The `python` directory contains the source code for a Python module for
XrayDB. This module gives a user-friendly wrapping of the XrayDB, and
automates the the conversion of data from sqlite database into Python and
numpy arrays. The module requires the `numpy`, `scipy` and `sqlalchemy`
modules, all of which are readily available and can be installed with::
pip install xraydb
The current version of the Python module is |release|, corresponding to
version 6 of `xraydb.sqlite`.
The Python xraydb module
----------------------------------
.. module:: xraydb
To use the XrayDB from Python, you can import the `xraydb` module and start
using it:
>>> import xraydb
>>> xraydb.atomic_number('Ag')
47
#
# X-ray elastic (Thomson) scattering factors:
>>> import numpy as np
>>> q =np.linspace(0, 5, 11)
>>> xraydb.f0('Fe', q)
array([25.994603 , 11.50848469, 6.55945765, 4.71039413, 3.21048827,
2.20939146, 1.65112769, 1.36705887, 1.21133507, 1.10155689,
1.0035555 ])
#
# X-ray emission lines:
>>> for name, line in xraydb.xray_lines('Zn', 'K').items():
... print(name, ' = ', line)
...
Ka3 = XrayLine(energy=8462.8, intensity=0.000316256, initial_level='K', final_level='L1')
Ka2 = XrayLine(energy=8614.1, intensity=0.294353, initial_level='K', final_level='L2')
Ka1 = XrayLine(energy=8637.2, intensity=0.576058, initial_level='K', final_level='L3')
Kb3 = XrayLine(energy=9567.6, intensity=0.0438347, initial_level='K', final_level='M2')
Kb1 = XrayLine(energy=9570.4, intensity=0.0846229, initial_level='K', final_level='M3')
Kb5 = XrayLine(energy=9648.8, intensity=0.000815698, initial_level='K', final_level='M4,5')
#
# X-ray absorption edges:
>>> xraydb.xray_edge('As', 'K')
XrayEdge(energy=11867.0, fyield=0.548989, jump_ratio=7.314)
#
# X-ray attenuation factors:
>>> as_kedge = xraydb.xray_edge('As', 'K').energy
>>> energies = np.linspace(-50, 50, 5) + as_kedge
>>> muvals = xraydb.mu_elam('As', energies)
>>> for en, mu in zip(energies, muvals):
... print("{:.0f} {:8.2f}".format(en, mu))
...
11817 26.07
11842 25.92
11867 25.77
11892 178.32
11917 177.38
.. index:: xraydb Python module
.. _xraydb-function_table:
**Table of XrayDB function for Atomic and X-ray data for the elements**
Most of these function return some element-specific property from the
element symbol or atomic number. Some of the data extends to Z=98 (Cf),
but some data may not be available for Z > 92 (U). Except where noted,
the data comes from :cite:`Elam_Ravel_Sieber`.
======================================= =======================================================================
xraydb functions description
======================================= =======================================================================
:func:`atomic_number` atomic number from symbol
:func:`atomic_symbol` atomic symbol from number
:func:`atomic_mass` atomic mass
:func:`atomic_name` atomic name (English)
:func:`atomic_density` density of pure element
:func:`f0` elastic scattering factor (:cite:`Waasmaier_Kirfel`)
:func:`f0_ions` list of valid "ions" for :func:`f0` (:cite:`Waasmaier_Kirfel`)
:func:`xray_edge` xray edge data for a particular element and edge
:func:`xray_edges` dictionary of all X-ray edges data for an element
:func:`xray_lines` dictionary of all X-ray emission line data for an element
:func:`fluor_yield` fluorescent yield for an X-ray emission line
:func:`ck_probability` Coster-Kronig transition probability between two atomic levels
:func:`mu_elam` absorption cross-section, photo-electric or total for an element
:func:`coherent_cross_section_elam` coherent scattering cross-section for an element
:func:`incoherent_cross_section_elam` incoherent scattering cross-section for an element
:func:`chantler_energies` energies of tabulation for Chantler data (:cite:`Chantler`)
:func:`f1_chantler` :math:`f'(E)` anomalous scattering factor (:cite:`Chantler`)
:func:`f2_chantler` :math:`f"(E)` anomalous scattering factor (:cite:`Chantler`)
:func:`mu_chantler` absorption cross-section (:cite:`Chantler`)
:func:`guess_edge` guess element and edge from energy of absorption edge
:func:`chemparse` parse a chemical formula to atomic abundances
:func:`validate_formula` test whether a chemical formula can be parsed.
:func:`get_materials` get a dictionary of known materials {name:(formula, density)}
:func:`get_material` get a (formula, density) tuple for a material in the materials database
:func:`find_material` get a material instance for a material in the materials database
:func:`add_material` add a material to local materials database
:func:`material_mu` absorption cross-section for a material at X-ray energies
:func:`material_mu_components` dictionary of elemental components of `mu` for material
:func:`xray_delta_beta` anomalous index of refraction for material and energy
:func:`darwin_width` Darwin widths for monochromator crystals
:func:`mirror_reflectivity` X-ray reflectivities for mirror materials (thick slab limit)
:func:`ionization_potential` effective ionization potential for a gas, as for ion chambers
:func:`ionchamber_fluxes` calculate fluxes from ion chamber voltages, gases, and sensitivities
======================================= =======================================================================
.. autofunction:: get_xraydb
Atomic Properties
----------------------
.. autofunction:: atomic_number
.. autofunction:: atomic_symbol
.. autofunction:: atomic_mass
.. autofunction:: atomic_name
.. autofunction:: atomic_density
Elastic Scattering Factors
---------------------------------
.. autofunction:: f0
.. autofunction:: f0_ions
X-ray Edges
-----------------------
.. autofunction:: xray_edge
.. autofunction:: xray_edges
.. autofunction:: core_width
.. autofunction:: guess_edge
X-ray Emission Lines
-----------------------
.. autofunction:: xray_lines
.. autofunction:: fluor_yield
.. autofunction:: ck_probability
Absorption and Scattering Cross-sections
--------------------------------------------
.. autofunction:: mu_elam
.. autofunction:: coherent_cross_section_elam
.. autofunction:: incoherent_cross_section_elam
.. autofunction:: chantler_energies
.. autofunction:: f1_chantler
.. autofunction:: f2_chantler
.. autofunction:: mu_chantler
Chemical and Materials database
----------------------------------------
.. autofunction:: chemparse
.. autofunction:: validate_formula
.. autofunction:: get_materials
.. autofunction:: find_material
.. autofunction:: get_material
.. autofunction:: add_material
X-ray properties of materials
------------------------------------
For some further examples, see :ref:`example_calcs`.
.. autofunction:: material_mu
.. autofunction:: material_mu_components
.. autofunction:: xray_delta_beta
.. autofunction:: darwin_width
.. autofunction:: mirror_reflectivity
.. autofunction:: ionization_potential
.. autofunction:: ionchamber_fluxes
|
