pyxray

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pyxray is a Python library that defines basic object to specify atomic subshells and X-ray transitions. The objects also provide critical information as the energy, existence and different notations of the X-ray transitions.

pyxray supports 3.6+ (no Python 2.x support).

Installation

Easiest way to install using pip::

pip install pyxray

For development installation from the git repository::

git clone git@github.com/openmicroanalysis/pyxray.git
cd pyxray
pip install -e .
pre-commit install

See development section below

Methods

All methods below are accessed by importing pyxray:

.. code:: python

import pyxray

Variables of the methods are defined as follows

• element: either

  • Element <http://github.com/openmicroanalysis/pyxray/blob/master/pyxray/descriptor.py>_ object
  • atomic number
  • symbol (case insensitive)
  • name (in any language, case insensitive)
  • object with attribute atomic_number or z

• atomic_shell: either

  • AtomicShell <http://github.com/openmicroanalysis/pyxray/blob/master/pyxray/descriptor.py>_ object
  • principal quantum number
  • any notation (case insensitive)

• atomic_subshell: either

  • AtomicSubshell <http://github.com/openmicroanalysis/pyxray/blob/master/pyxray/descriptor.py>_ object
  • a tuple of principal quantum number, azimuthal quantum number and total angular momentum nominator (e.g. (1, 0, 1) for the atomic subshell 1s^{0.5}
  • any notation (case insensitive)

• xray_transition: either

  • XrayTransition <http://github.com/openmicroanalysis/pyxray/blob/master/pyxray/descriptor.py>_ object
  • a tuple of source and destination subshells
  • any notation (case insensitive)

• language: language code (e.g. en, fr, de)

• notation: name of a notation (case insensitive), iupac, siegbahn and orbital are usually supported

• encoding: type of encoding, either ascii, utf16, html or latex

• reference: reference to use to retrieve this value, either

  • Reference <http://github.com/openmicroanalysis/pyxray/blob/master/pyxray/descriptor.py>_ object
  • BibTeX key of a reference
  • None, the newest reference will be returned

Element properties

Properties associated with an element, defined as the ground state of an atom where the number of protons equal the number of electrons.

• pyxray.element(element) Returns element descriptor.

• pyxray.element_atomic_number(element) Returns atomic number of an element.

  Examples:

  .. code:: python

  pyxray.element_atomic_number('fe') #=> 26
  pyxray.element_atomic_number('Fe') #=> 26
  pyxray.element_atomic_number('iron') #=> 26
  pyxray.element_atomic_number('eisen') #=> 26

• pyxray.element_symbol(element, reference=None) Returns symbol of an element.

• pyxray.element_name(element, language='en', reference=None) Returns full name of an element, in the language specified.

• pyxray.element_atomic_weight(element, reference=None) Returns atomic weight of an element. The atomic weight is defined by the CIAAW as it is the ratio of the average atomic mass of an element over 1/12 of the mass of the carbon-12 atom.

• pyxray.element_mass_density_kg_per_m3(element, reference=None) Returns mass density (in kg/m3) of an element.

• pyxray.element_mass_density_g_per_cm3(element, reference=None) Returns mass density (in g/cm3) of an element.

• pyxray.element_xray_transition(element, reference=None) Returns X-ray transition descriptor if x-ray transition has a probability greater than 0 for that element.

• pyxray.element_xray_transitions(element, xray_transition_set=None, reference=None) Returns all X-ray transitions which have a probability greater than 0 for that element. If xray_transition_set is not None, returns all x-ray transitions for this x-ray transition set.

Atomic shell properties

Properties associated with an atomic shell <https://en.wikipedia.org/wiki/Electron_shell>_, defined by its principal quantum number.

• pyxray.atomic_shell(atomic_shell) Returns atomic shell descriptor.

• pyxray.atomic_shell_notation(atomic_shell, notation, encoding='utf16', reference=None) Returns notation of an atomic shell.

Atomic subshell properties

Properties associated with an atomic subshell <https://en.wikipedia.org/wiki/Electron_shell#Subshells>_, a subdivision of atomic shells.

• pyxray.atomic_subshell(atomic_subshell) Returns atomic subshell descriptor.

• pyxray.atomic_subshell_notation(atomic_subshell, notation, encoding='utf16', reference=None) Returns notation of an atomic subshell.

  Examples:

  .. code:: python

  pyxray.atomic_subshell_notation('L3', 'iupac', 'latex') #=> 'L$_{3}$'
  pyxray.atomic_subshell_notation('L3', 'orbital') #-> '2p3/2'

• pyxray.atomic_subshell_binding_energy_eV(element, atomic_subshell, reference=None) Returns binding energy of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_radiative_width_eV(element, atomic_subshell, reference=None) Returns radiative width of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_nonradiative_width_eV(element, atomic_subshell, reference=None) Returns nonradiative width of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_occupancy(element, atomic_subshell, reference=None) Returns occupancy of an element and atomic subshell.

X-ray transition properties

Properties associated with an electron transition, relaxation process of an electron between quantum states leading to X-rays emission.

• pyxray.xray_transition(xray_transition) Returns X-ray transition descriptor.

• pyxray.xray_transition_notation(xray_transition, notation, encoding='utf16', reference=None) Returns notation of an X-ray transition.

  Examples:

  .. code:: python

  pyxray.transition_notation('Ka1', 'iupac') #=> 'K-L3'
  pyxray.transition_notation('Ka', 'iupac') #=> 'K-L2,3'
  pyxray.transition_notation('L3-M1', 'siegbahn', 'ascii') #=> 'Ll'

• pyxray.xray_transition_energy_eV(element, xray_transition, reference=None) Returns energy of an element and X-ray transition (in eV).

  Examples:

  .. code:: python

  pyxray.xray_transition_energy_eV(14, 'Ka1') #=> 1740.0263764535946
  pyxray.xray_transition_energy_eV(14, 'Ma1') #=> NotFound exception

• pyxray.xray_transition_probability(element, xray_transition, reference=None) Returns probability of an element and X-ray transition.

• pyxray.xray_transition_relative_weight(element, xray_transition, reference=None) Returns relative weight of an element and X-ray transition.

X-ray line

Object to represent an x-ray transition and its properties.

• pyxray.xray_line(element, xray_transition, reference=None) Returns X-ray line descriptor.

.. code:: python

xrayline = pyxray.xray_line(14, 'Ka1') xrayline.atomic_number #=> 14 xrayline.transition #=> XrayTransition(2, 1, 3, 1, 0, 1) xrayline.iupac #=> Si K–L3 xrayline.siegbahn #=> Si Kα1 xrayline.energy_eV #=> 1740.0 xrayline.probability #=> 0.031705199999999996 xrayline.relative_weight #=> 1.0

As any other descriptors, X-ray line objects are immutable and hashable so they can be used as keys of a dictionary.

.. code:: python

xrayline1 = pyxray.xray_line(13, 'Ka1') xrayline2 = pyxray.xray_line('Al', 'Ka1') xrayline1 == xrayline2 #=> True pyxray.xray_line(13, 'Ka1') == pyxray.xray_line(13, 'Ka') #=> False

To sort X-ray lines, use one of their properties:

.. code:: python

from operator import attrgetter lines = [pyxray.xray_line(14, 'Ka1'), pyxray.xray_line(13, 'Ka1'), pyxray.xray_line(14, 'Ll')] sorted(lines, key=attrgetter('energy_eV')) #=> [XrayLine(Si L3–M1), XrayLine(Al K–L3), XrayLine(Si K–L3)]

Composition

Defines a composition of a compound.

To create a composition, use the class methods:

• Composition.from_pure(z)
• Composition.from_formula(formula)
• Composition.from_mass_fractions(mass_fractions, formula=None)
• Composition.from_atomic_fractions(atomic_fractions, formula=None)

Use the following attributes to access the composition values:

• mass_fractions: dict where the keys are atomic numbers and the values weight fractions.
• atomic_fractions: dict where the keys are atomic numbers and the values atomic fractions.
• formula: chemical formula

The composition object is immutable, i.e. it cannot be modified once created. Equality can be checked. It is hashable. It can be pickled or copied.

Release notes

1.7

• #19 <https://github.com/openmicroanalysis/pyxray/pull/19>_ Get transitions for light elements when no probability are available
• #20 <https://github.com/openmicroanalysis/pyxray/pull/20>_ Use GitHub Actions for continuous integration. Add pre-commit hooks and black formatting.

1.6.1

• Fix deprecation warning with new setuptools
• Fix problem with requests caching

1.6

• Add ordering of Element, AtomicShell, AtomicSubshell
• Use sqlalchemy <https://sqlalchemy.org>_ to create and interact with database
• Add probability and relative weight properties to XrayLine
• Add possibility to define preferred references

1.5

• Add composition object

1.4

• #13 <https://github.com/openmicroanalysis/pyxray/pull/13>_ Add DTSA X-ray subshell and line data
• #14 <https://github.com/openmicroanalysis/pyxray/pull/14>_ Use dataclasses for descriptors and properties

1.3.4

• Fix descriptors can be copied and pickled.

1.3.3

• Fix method element_xray_transitions not to return duplicates.

1.3.2

• Add energy to XrayLine.
• Fix missing energy property for x-ray transition sets from JEOL database.
• Clean up of unit tests.

1.3.1

• Make XrayLine a descriptor and add method to create it from database.

1.2.1

• Fix in build process.

1.2.0

• Add XrayLine class.

Contributors

• @drix00 <https://github.com/drix00>_

Development

pyxray stores all data for the above functions in a SQLite database. The database is constructed during the build process of the Python package (i.e. python setup.py build) using registered parsers. The provided parsers are located in the package pyxray.parser, but external parsers can be provided by registering to the entry point pyxray.parser. In short, the database is not provide in the source code, only in the distributed version. It is therefore necessary to build the SQLite database when running pyxray in development mode. Building the database will take several minutes. In short, in the pyxray folder, run

.. code:: shell

pip install -e .[develop] python3 setup.py build

Build the documentation:

.. code-block:: console

$ cd docs
$ make html

Add or modify the API documentation:

.. code-block:: console

$ cd docs
$ sphinx-apidoc -o source/api -e -f -P ../pyxray
$ make html

License

The library is provided under the MIT license.

pyxray was partially developed as part of the doctorate thesis project of Philippe T. Pinard at RWTH Aachen University (Aachen, Germany) under the supervision of Dr. Silvia Richter.

Copyright (c) 2015-2016/06 Philippe Pinard and Silvia Richter

Copyright (c) 2016/06-2020 Philippe Pinard