roentgen - read the docs · ii. roentgen, release 1.1.dev6+gcd4d4e1 this is a python package for...

roentgenRelease 1.1.dev6+gcd4d4e1

Sep 08, 2020

CONTENTS

1 Guide 3

2 Reference 19

3 Examples 27

4 Contributing 35

5 Authors 37

6 License 39

7 Changelog 43

8 Indices and tables 45

Python Module Index 47

Index 49

i

roentgen, Release 1.1.dev6+gcd4d4e1

This is a Python package for the quantitative analysis of the interaction of energetic x-rays with matter. This package isnamed after one of the discoverers of X-rays, Wilhelm Roentgen. He was awarded the very first Nobel Prize in Physics“in recognition of the extraordinary services he has rendered by the discovery of the remarkable rays subsequentlynamed after him”. X-rays were originally referred to as Roentgen rays.

CONTENTS 1

https://en.wikipedia.org/wiki/Wilhelm_R�ntgen


2 CONTENTS

CHAPTER

ONE

GUIDE

This is a Python package for the quantitative analysis of the interaction of energetic x-rays with matter. This package isnamed after one of the discoverers of X-rays, Wilhelm Roentgen. He was awarded the very first Nobel Prize in Physics“in recognition of the extraordinary services he has rendered by the discovery of the remarkable rays subsequentlynamed after him”. X-rays were originally referred to as Roentgen rays.

The scope of this package is evolving but it currently includes the penetration or absorption of x-rays in materials.These materials may be metals, gases, biological, or detector materials. It also includes the generation of x-rays fromemission lines.

1.1 Theory of Transmission and Absorption

1.1.1 Mass Attenuation Coefficient

If a narrow beam of monoenergetic photons with intensity, 𝐼0, are impinged on a material of thickness 𝑥,the intensityis attenuated exponentially,

𝐼(𝑥) = 𝐼0 exp(−𝜇𝑥)

The parameter 𝜇 is called the linear attenuation coefficient and measures the absorptivity of the material. It hasunits of 𝑐𝑚−1. This value captures the sum of the probabilities of individual processes which might remove anindividual photon from the impinging beam. Those interactions most relevant to the x-ray and gamma-ray range arethe photoelectric interaction and Compton scattering. In a photoelectric interaction, the entire incident energy of theinteracting photon is absorbed by the material while in Compton scattering, only a portion of the incident energy isabsorbed. These interactions are energy dependent which means that the linear attenuation coefficient is also. Anotherway to represent the linear attenuation coefficient is through the mass attenuation coefficient or

𝜇𝑚 =𝜇

𝜌

where 𝜌 is the density of the medium. It has units of 𝑐𝑚2𝑔−1. This is the measure used by this module.

This equation can be re-written in the following form

𝜇

𝜌=

1

𝑥ln

(︂𝐼0𝐼

)︂which suggests a method for measuring the mass attenuation coefficient.

3

https://en.wikipedia.org/wiki/Wilhelm_R�ntgen


1.1.2 Transmission and Absorption

As described above the probability of transmission through a material is given by

𝐼𝑡𝑟𝑎𝑛𝑠 = 𝐼0 exp

(︂−𝜇

𝜌𝑥

)︂therefore the absorption is given by

𝐼𝑡𝑟𝑎𝑛𝑠 = 𝐼0

(︂1− exp

(︂−𝜇

𝜌𝑥

)︂)︂

1.1.3 Multiple Materials

Since we are dealing with probabilities of interactions if there are multiple materials present the probabilities must bemultiplied. For example, if we are interested in the amount of flux which passes through two materials, a and b, bothwith thickness x, it is given by the following equation


(︂−𝜇𝑎

𝜌𝑎𝑥

)︂exp

(︂−𝜇𝑏

𝜌𝑏𝑥

)︂which can be simplified to


(︂−(︂𝜇𝑎

𝜌𝑎+

𝜇𝑏

𝜌𝑏

)︂𝑥

)︂If we are interested in the amount of flux deposited in a detector of thickness, t made of material b after travelingthrough material a with thickness T

𝐹 = 𝐼0 exp

(︂−𝜇𝑎

𝜌𝑎𝑇

)︂(︂1− exp

(︂−𝜇𝑏

𝜌𝑏𝑡

)︂)︂

1.1.4 Reference

• Mass attenuation coefficient Wikipedia

1.2 Transmission and Absorption of X-rays in matter

The purpose of this guide is to present an overview of the roentgen.absorption module which provides for thecalculation of the transmission and absorption of X-rays through and by various materials.

1.2.1 Mass Attenuation Coefficient

The primary component that mediates the x-ray attenuation through a material is its mass attenuation coefficient.These tabulated values can be inspected using roentgen.absorption.MassAttenuationCoefficient.To create one:

from roentgen.absorption import MassAttenuationCoefficientsi_matten = MassAttenuationCoefficient('Si')

Tabulated values for all elements are provided as well as additional specialized materials. Elements can be specificiedby their symbol name or by their full name (e.g. Si, Silicon). A list of all of the elements is provided by:

4 Chapter 1. Guide

https://en.wikipedia.org/wiki/Mass_attenuation_coefficient


roentgen.elements

Specialized materials, referred to as compounds, are also available. A complete list is provided by:

roentgen.compounds

Here is the mass attenuation coefficient for Silicon.

import astropy.units as uimport matplotlib.pyplot as pltfrom roentgen.absorption import MassAttenuationCoefficient

si_matten = MassAttenuationCoefficient('Si')plt.plot(si_matten.energy, si_matten.data)plt.yscale('log')plt.xscale('log')plt.xlabel('Energy [' + str(si_matten.energy[0].unit) + ']')plt.ylabel('Mass Attenuation Coefficient [' + str(si_matten.data[0].unit) + ']')plt.title(si_matten.name)

100 101 102 103 104

Energy [keV]

10 1

100

101

102

103

Mas

s Atte

nuat

ion

Coef

ficie

nt [c

m2

/ g]

Silicon

1.2. Transmission and Absorption of X-rays in matter 5


1.2.2 Material

In order to determine the x-ray attenuation through a material the roentgen.absorption.Material object isprovided. This object can be created by providing the thickness of the material through which the x-rays are interacting.The thickness must be given by a Quantity. For example, a 500 micron thick layer of Aluminum can be createdlike so:

al = Material('Al', 500 * u.micron)

An optional density can also be provided. A default density is assumed if none is provided. Default values can befound in elements.csv for elements or in compounds_mixtures.csv for compounds. To inspect the density:

al.density

Using this object it is possible to get the absorption and transmission as a function of energy:

energy = u.Quantity(np.arange(1,30), 'keV')al.transmission(energy)al.absoprtion(energy)

Here is a plot of the transmission of x-rays through 500 micron of Aluminum, a standard thickness for electronicsboxes. The transmission and absorption is given on a scale from 0 (no absorption or no transmission) to 1 (completeabsorption or complete transmission).

import numpy as npimport matplotlib.pyplot as pltimport astropy.units as u

from roentgen.absorption import Material

al = Material('Al', 500 * u.micron)energy = u.Quantity(np.arange(1, 30, 0.2), 'keV')

plt.plot(energy, al.transmission(energy))plt.ylabel('Transmission')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.title(al.name)

From the above plot, one can see that the this thickness of Aluminum blocks almost all x-rays below about 7 keV.The relationship between transmission and absorption can be seen in the following plot for 500 microns of Silicon, astandard thickness for a soft x-ray detector.



si = Material('Si', 500 * u.micron)energy = u.Quantity(np.arange(1, 50), 'keV')

plt.plot(energy, si.absorption(energy), label='Absorption')plt.plot(energy, si.transmission(energy), label='Transmission')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.title(si.name)plt.legend(loc='lower left')

6 Chapter 1. Guide

https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity


0 5 10 15 20 25 30Energy [keV]

0.0

0.2

0.4

0.6

0.8

Tran

smiss

ion

Aluminum



0 10 20 30 40 50Energy [keV]

0.0

0.2

0.4

0.6

0.8

1.0

Silicon

AbsorptionTransmission

8 Chapter 1. Guide


Besides elements, a number of compounds and mixtures are also available. As a simple example, here is the transmis-sion of x-rays through 10 meters of air.



thickness = 10 * u.mair = Material('air', thickness)energy = u.Quantity(np.arange(1, 30, 0.2), 'keV')

plt.plot(energy, air.transmission(energy))plt.ylabel('Transmission')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.title("{0} {1}".format(str(thickness), air.name))

0 5 10 15 20 25 30Energy [keV]

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Tran

smiss

ion

10.0 m Air (dry)

This plot shows that air, though not a dense material, does block low energy x-rays over long distances. For conve-nience, the function density_ideal_gas is provided which can calculate the density of a gas given a pressureand temperature.



1.2.3 Compounds

Materials can be added together to form more complex optical paths. If two or more materials are added together theyform a roentgen.absorption.Compound. A simple example is the transmission through air and then througha thermal blanket composed of a thin layer of mylar and Aluminum:

optical_path = Material('air', 2 * u.m) + Material('mylar', 5 * u.micron) + Material(→˓'Al', 5 * u.micron)

This new object also provides transmission and absorption of the combination of these materials. Here is a plot of thattransmission over energy



optical_path = Material('air', 2 * u.m) + Material('mylar', 5 * u.micron) + Material(→˓'Al', 5 * u.micron)energy = u.Quantity(np.arange(1, 30, 0.2), 'keV')

plt.plot(energy, optical_path.transmission(energy), label='Transmission')plt.ylabel('Efficiency')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.legend(loc='upper left')

Frequently, it is useful to consider the response function of a particular detector which includes absorption throughmaterials in front of a detector. This can be calculated by multiplying the transmission of the materials before thedetector with the absorption of the detector material.

To simplify this process, the roentgen.absorption.Response class is provided. The following example usesthe same optical path as defined above and assumes a Silicon detector.

import astropy.units as uimport matplotlib.pyplot as pltfrom roentgen.absorption import Material, Responseimport numpy as np

optical_path = [Material('air', 2 * u.m), Material('mylar', 5 * u.micron), Material(→˓'Al', 5 * u.micron)]detector = Material('Si', 500 * u.micron)resp = Response(optical_path=optical_path, detector=detector)energy = u.Quantity(np.arange(1, 30, 0.2), 'keV')

plt.plot(energy, resp.response(energy))plt.xlabel('Energy [' + str(energy.unit) + ']')plt.ylabel('Response')

This plot shows that the peak efficiency for this detector system is less than 50% and lies around 15 keV.

10 Chapter 1. Guide


0 5 10 15 20 25 30Energy [keV]

0.0

0.2

0.4

0.6

0.8

Effic

ienc

y

Transmission



0 5 10 15 20 25 30Energy [keV]

0.0

0.1

0.2

0.3

0.4

Resp

onse

12 Chapter 1. Guide


1.3 Comparison with CXRO

The Center for X-ray Optics (CXRO) at LBL provides an online tool to calculate the X-ray transmission throughmaterials called the X-ray Interactions with Matter. This section compares the results of this package with those ofCXRO. The primary difference between results from this package and those from CXRO are that we make use of theNIST-provided Mass Attenuation coefficients while the CXRO makes use of optical constants from the following

• B.L. Henke, E.M. Gullikson, and J.C. Davis. X-ray interactions: photoabsorption, scattering, transmission, andreflection at E=50-30000 eV, Z=1-92, Atomic Data and Nuclear Data Tables Vol. 54 (no.2), 181-342 (July 1993)

These data only extend up to 30 keV while the NIST-provided data extend to 20 MeV. For more information on datasources see the README in the data directory. The comparison here shows that the results generally agree with eachother.

import osimport matplotlib.pyplot as plt

import numpy as npfrom astropy.io import asciifrom astropy.table import Tableimport astropy.units as ufrom astropy.constants import atm

import roentgenfrom roentgen.absorption import Materialfrom roentgen.util import density_ideal_gas

cxro_filenames = ('be_100micron.dat', 'al_1mm.dat', 'si_500micron.dat','water_1000micron.dat', 'ge_500micron.dat','air_1m_1atm_295kelvin.dat')

cxro_files = [os.path.join(roentgen._data_directory, 'cxro', f) for f incxro_filenames]

material_list = ['Be', 'Al', 'Si', 'water', 'ge', 'air']thick_list = [100 * u.micron, 1 * u.mm, 500 * u.micron, 1000 * u.micron, 500 * u.→˓micron, 1 * u.m]

def trans_plot(ax, x, a, b):ax.plot(x, a, label='cxro', linewidth=5)ax.plot(x, b, label='roentgen')

ax.grid(which='major', alpha=0.7)ax.grid(which='minor', alpha=0.2)ax.set_yscale('log')ax.set_ylim(1e-7, 1)ax.legend()

fig, axis = plt.subplots(len(material_list), figsize=(10, 20))

for ax, this_material, this_thickness, this_file in zip(axis, material_list, thick_→˓list, cxro_files):

cxro_data = Table(ascii.read(this_file, data_start=2, delimiter=' ', names=[→˓'energy', 'transmission']))

if this_material == 'air':density = density_ideal_gas(atm, 295 * u.Kelvin)

(continues on next page)

1.3. Comparison with CXRO 13

http://www.cxro.lbl.gov/

http://henke.lbl.gov/optical_constants/

https://www.nist.gov/pml/x-ray-mass-attenuation-coefficients

https://ned.ipac.caltech.edu/level5/Sept16/Henke/Henke.pdf

https://ned.ipac.caltech.edu/level5/Sept16/Henke/Henke.pdf


(continued from previous page)

mat = Material(this_material, thickness=this_thickness, density=density)else:

mat = Material(this_material, thickness=this_thickness)transmission = mat.transmission(u.Quantity(cxro_data['energy'], 'eV'))print(f'{this_material} {mat.density}')trans_plot(ax, cxro_data['energy']/1000, cxro_data['transmission'], transmission)ax.set_title(f'{this_material} {this_thickness}')ax.set_ylabel('Transmission')

plt.show()

1.4 Graphical User Interface

This package provides a simple graphical user interface to enable quick calculations of x-ray transmission and absorp-tion through materials. This GUI makes use of bokeh.

To run it locally use the following command:

bokeh serve --show <roengten_directory>/gui

A working version of the GUI can be found installed on heroku at the following url https://roentgen-gui.herokuapp.com/gui.

1.5 Emission Lines

Characteristic radiation come from interactions between a high-energy particle, such as an electron, and an orbitalelectron in an atom. These interactions or collisions can, if the energy of the incoming electron is greater than thebinding energy of the orbital electron, kick out the electron and leave a vacancy. An electron from a high energy levelcan move down to fill the vacancy. In the process, it gives up energy which is emitted in the form of a photon. Forinner orbitals vacancies, these photons are generally in the x-ray regime. This process is schematically shown in thediagram below.

There are two notations used to refer to these transitions. Siegbahn notation has historically been used in the areaof X-ray spectroscopy. Though still widely used, it has been replaced by a newer nomenclature recommended bythe International Union of Pure and Applied Chemistry (IUPAC). It is referred to here as IUPAC notation. Thecorrespondence between these two nomenclatures is shown in the table below.

14 Chapter 1. Guide

https://bokeh.pydata.org

https://roentgen-gui.herokuapp.com/gui

https://roentgen-gui.herokuapp.com/gui


0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

Be 100.0 microncxroroentgen

0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

Al 1.0 mmcxroroentgen

0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

Si 500.0 microncxroroentgen

0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

water 1000.0 microncxroroentgen

0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

ge 500.0 microncxroroentgen

0 5 10 15 20 25 3010 7

10 5

10 3

10 1

Tran

smiss

ion

air 1.0 mcxroroentgen

1.5. Emission Lines 15


Table 1: Emission line translationsiegbahn iupacK1 K-L3K2 K-L2K1 K-M3K3 K-M2L1 L3-M5L2 L3-M4L1 L2-M4L2 L3-N5L3 L1-M3L4 L1-M2L5 L3-O4,5L6 L3-N1L7 L1-O1L9 L1-M5Ll L3-M1M1 M5-N7

For a more full listing see Table VIII.2 in IUPAC Report.

The energies of the x-rays from these transitions are unique to each element and are provided by a number of sources.This package makes use of those provided by the X-ray Data Booklet (October 2009). It provides energies in Table1-3 as well as relative intensities. More precise transition energies can be found at the NIST X-ray transition energiesdatabase.

The full table of energies is provided in:

from roentgen import emission_lines

It is possible to search for all known characteristic lines in an energy range with:

>>> import astropy.units as u>>> from roentgen.lines import get_lines>>> lines = get_lines(5 * u.keV, 5.2 * u.keV)>>> print(lines)energy z transition intensity

eV------ --- ---------- ---------5013.5 59 L2 115033.7 59 L1 1005034.0 54 L1 85042.1 57 L1 605156.5 56 L2,15 205177.2 63 Ll 4

If you are only interested in lines from a particular element, the search can be limited with:

>>> import astropy.units as u>>> from roentgen.lines import get_lines>>> ni_lines = get_lines(5 * u.keV, 10 * u.keV, element='Ni')>>> print(ni_lines)energy z transition intensity

eV------ --- ---------- ---------


16 Chapter 1. Guide

http://old.iupac.org/reports/V/spectro/partVIII.pdf

https://xdb.lbl.gov

https://xdb.lbl.gov/Section1/Table_1-3.pdf

https://xdb.lbl.gov/Section1/Table_1-3.pdf

https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html

https://physics.nist.gov/PhysRefData/XrayTrans/Html/search.html



7460.9 28 K2 518264.7 28 K1,3 177478.2 28 K1 100

1.5. Emission Lines 17


18 Chapter 1. Guide

CHAPTER

TWO

REFERENCE

2.1 Material

2.1.1 roentgen.absorption Package

Classes

Compound(materials) An object which enables the calculation of the x-raytransmission and absorption of a compound material(i.e.

MassAttenuationCoefficient(material) The mass attenuation coefficient.Material(**func_kwargs) An object which enables the calculation of the x-ray

transmission and absorption of a material (e.g.Response(optical_path, detector) An object to handle the response of a detector material

which includes an optical path or filter through whichx-rays must first traverse before reaching the detector.

Compound

class roentgen.absorption.Compound(materials)Bases: object

An object which enables the calculation of the x-ray transmission and absorption of a compound material (i.e.many materials). This object is usually created automatically when Material objects are added together.

Parameters materials (list) – A list of Material objects

Examples

>>> from roentgen.absorption.material import Material, Compound>>> import astropy.units as u>>> detector = Compound([Material('Pt', 5 * u.um), Material('cdte', 500 * u.um)])

19

https://docs.python.org/3/library/functions.html#object

https://docs.python.org/3/library/stdtypes.html#list


Methods Summary

absorption(energy) Provides the absorption fraction (0 to 1).transmission(energy) Provide the transmission fraction (0 to 1).

Methods Documentation

absorption(energy)Provides the absorption fraction (0 to 1).

Parameters energy (astropy.units.Quantity) – An array of energies in keV.

transmission(energy)Provide the transmission fraction (0 to 1).

Parameters energy (astropy.units.Quantity) – An array of energies in keV

MassAttenuationCoefficient

class roentgen.absorption.MassAttenuationCoefficient(material)Bases: object

The mass attenuation coefficient.

Parameters material_str (str) – A string representation of the material which includes anelement symbol (e.g. Si), an element name (e.g. Silicon), or the name of a compound (e.g. cdte,mylar).

dataThe mass attenuation data values.

Type astropy.units.Quantity array

energyThe energy values of the mass attenuation values.

Type astropy.units.Quantity

symbolThe material symbol

Type str

nameThe material name

Type str

funcA function which returns the interpolated mass attenuation value at any given energy. Energies must begiven by an astropy.units.Quantity.

Type lambda func

20 Chapter 2. Reference




https://docs.python.org/3/library/stdtypes.html#str







Material

class roentgen.absorption.Material(**func_kwargs)Bases: object

An object which enables the calculation of the x-ray transmission and absorption of a material (e.g. an elementor a compound/mixture).

Parameters

• material_str (str) – A string representation of the material which includes an ele-ment symbol (e.g. Si), an element name (e.g. Silicon), or the name of a compound (e.g.cdte, mylar). For all supported elements see elements.csv and for compounds seecompounds_mixtures.csv.

• thickness (astropy.units.Quantity) – The thickness of the material

• density (astropy.units.Quantity) – The density of the material. If not pro-vided uses default values which can be found in elements.csv for elements or incompounds_mixtures.csv for compounds.

symbolThe material symbol

Type str

nameThe material name

Type str

mass_attenuation_coefficientThe mass attenuation coefficient for the material.

Type MassAttenuationCoefficient

Examples

>>> from roentgen.absorption.material import Material>>> import astropy.units as u>>> detector = Material('cdte', 500 * u.um)>>> thermal_blankets = Material('mylar', 0.5 * u.mm)

Methods Summary

absorption(energy) Provides the absorption fraction (0 to 1).transmission(energy) Provide the transmission fraction (0 to 1).

2.1. Material 21









absorption(energy)Provides the absorption fraction (0 to 1).


transmission(energy)Provide the transmission fraction (0 to 1).

Parameters energy (astropy.units.Quantity) – An array of energies in keV

Response

class roentgen.absorption.Response(optical_path, detector)Bases: object

An object to handle the response of a detector material which includes an optical path or filter through whichx-rays must first traverse before reaching the detector.

Parameters

• optical_path (list) – A list of Material objects which make up the optical path.

• detector (Material or None) – A Material which represents the detector materialwhere the x-rays are absorbed. If provided with None, than assume a perfectly absorbingdetector material.

Examples

>>> from roentgen.absorption.material import Material, Response>>> import astropy.units as u>>> optical_path = [Material('air', 1 * u.m), Material('Al', 500 * u.mm)]>>> resp = Response(optical_path, detector=Material('cdte', 500 * u.um))

Methods Summary

response(energy) Returns the response as a function of energy whichcorresponds to the transmission through the opticalpath multiplied by the absorption in the detector.


response(energy)Returns the response as a function of energy which corresponds to the transmission through the opticalpath multiplied by the absorption in the detector.






https://docs.python.org/3/library/stdtypes.html#list

https://docs.python.org/3/library/constants.html#None



Class Inheritance Diagram

Compound

MassAttenuationCoefficient

Material

Response

2.2 Emmision Lines

2.2.1 roentgen.lines Package

Functions

get_lines(energy_low, energy_high[, element]) Retrieve all emission lines in an energy range.

get_lines

roentgen.lines.get_lines(energy_low, energy_high, element=None)Retrieve all emission lines in an energy range.

Parameters

• energy_low (astropy.units.Quantity) – The low end of the energy range

• energy_high (astropy.units.Quantity) – The high end of the energy range

• element (str, optional) – Select only lines from a specific element

Returns line_list

Return type astropy.table.QTable

2.2. Emmision Lines 23




https://docs.astropy.org/en/stable/api/astropy.table.QTable.html#astropy.table.QTable


2.3 Utilities

2.3.1 roentgen.util Package

Functions

density_ideal_gas(pressure, temperature) Given pressure and temperature of a dry gas, return thedensity using the ideal gas law

get_atomic_number(element_str) Return the atomic number of the elementget_compound_index(compound_str) Return the index of the compound in the compound ta-

bleget_density(material_str) Given a material name return the default densityget_element_symbol(element_str) Return the element abbreviationis_an_element(element_str) Returns True if the string represents an elementis_in_known_compounds(compound_str) Returns True is the compound is in the list of known

compounds

density_ideal_gas

roentgen.util.density_ideal_gas(pressure, temperature)Given pressure and temperature of a dry gas, return the density using the ideal gas law

get_atomic_number

roentgen.util.get_atomic_number(element_str)Return the atomic number of the element

get_compound_index

roentgen.util.get_compound_index(compound_str)Return the index of the compound in the compound table

get_density

roentgen.util.get_density(material_str)Given a material name return the default density

get_element_symbol

roentgen.util.get_element_symbol(element_str)Return the element abbreviation



is_an_element

roentgen.util.is_an_element(element_str)Returns True if the string represents an element

is_in_known_compounds

roentgen.util.is_in_known_compounds(compound_str)Returns True is the compound is in the list of known compounds

2.3. Utilities 25

CHAPTER

THREE

EXAMPLES

3.1 Getting and plotting the Mass Attenuation Coefficient

import numpy as npimport matplotlib.pyplot as plt

import astropy.units as ufrom astropy.visualization import quantity_supportquantity_support()from roentgen.absorption import MassAttenuationCoefficient

cdte_atten = MassAttenuationCoefficient('cdte')

energy = u.Quantity(np.arange(1, 1000), 'keV')atten = cdte_atten.func(energy)

plt.plot(energy, atten)plt.plot(cdte_atten.energy, cdte_atten.data, 'o')plt.yscale('log')plt.xscale('log')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.ylabel('Mass attenuation Coefficient [' + str(atten.unit) + ']')plt.title(cdte_atten.name)plt.show()

3.2 Finding the x-ray absorption of different detector materials


import astropy.units as ufrom astropy.visualization import quantity_supportquantity_support()


thickness = 500 * u.micron

material_list = ['cdte', 'Si', 'Ge']energy = u.Quantity(np.arange(1, 100, 0.1), 'keV')


27


100 101 102 103 104

Energy [keV]

10 1

100

101

102

103

104

Mas

s atte

nuat

ion

Coef

ficie

nt [c

m2

/ g]

Cadmium Telluride

28 Chapter 3. Examples



for material in material_list:mat = Material(material, thickness)plt.plot(energy, mat.absorption(energy), label=mat.name)

plt.xlabel('Energy [' + str(energy.unit) + ']')plt.ylabel('Absorption')plt.legend(loc='lower left')plt.show()

0 20 40 60 80 100Energy [keV]

0.0

0.2

0.4

0.6

0.8

1.0

Abso

rptio

n

Cadmium TellurideSiliconGermanium

3.3 Plotting the x-ray spectrum from a particular element


from astropy.visualization import quantity_supportimport astropy.units as ufrom astropy.modeling.models import Lorentz1Dquantity_support()

from roentgen.lines import get_lines


3.3. Plotting the x-ray spectrum from a particular element 29



element = 'Ni'energy_range = u.Quantity([7000, 9000], 'eV')

lines = get_lines(energy_range[0], energy_range[1], element=element)spectrum = Lorentz1D(0, x_0=0)for row in lines:

spectrum += Lorentz1D(amplitude=row['intensity'], x_0=row['energy'].value,fwhm=100)

plt.title(element)for row in lines:

plt.vlines([row['energy'].value], [0], row['intensity'],label=f'{row["energy"]} eV {row["transition"]}')

energy_axis = np.linspace(energy_range[0].value, energy_range[1].value, 1000)plt.plot(energy_axis, spectrum(energy_axis))

plt.xlim(energy_range[0].value, energy_range[1].value)plt.ylim(0)plt.ylabel('intensity')plt.xlabel('eV')plt.legend(loc='upper right')plt.show()

7000 7250 7500 7750 8000 8250 8500 8750 9000eV

0

20

40

60

80

100

120

140

inte

nsity

Ni8264.7 eV eV K 1,37478.2 eV eV K 17460.9 eV eV K 2



3.4 Finding all x-ray lines in an energy range

import matplotlib.pyplot as plt


from roentgen.lines import get_lines

energy_range = [4, 4.2] * u.keVlines = get_lines(energy_range[0], energy_range[1])

for row in lines:plt.vlines([row['energy']], [0], row['intensity'], label=f'{row["z"]} {row[

→˓"transition"]}')

plt.ylabel('intensity')plt.legend(loc='upper left')plt.show()

4020 4040 4060 4080 4100 4120

0

20

40

60

80

100

inte

nsity

20 K 1,352 L 121 K 221 K 154 L 251 L 2,1554 L 157 Ll50 L 1

3.4. Finding all x-ray lines in an energy range 31


3.5 Finding the response of an x-ray detector



from roentgen.absorption import Material, Response

optical_path = [Material('air', 2 * u.m), Material('mylar', 5 * u.micron), Material(→˓'Al', 5 * u.micron)]detector = Material('Si', 500 * u.micron)

resp = Response(optical_path=optical_path, detector=detector)energy = u.Quantity(np.linspace(1, 100, 300), 'keV')

plt.plot(energy, resp.response(energy), label='detector with optical path')plt.plot(energy, detector.absorption(energy), label='detector without optical path')plt.xlabel('Energy [' + str(energy.unit) + ']')plt.ylabel('Response')plt.ylim(0, 1)plt.legend()plt.show()

0 20 40 60 80 100Energy [keV]

0.0

0.2

0.4

0.6

0.8

1.0

Resp

onse

detector with optical pathdetector without optical path



3.6 Finding the x-ray transmission through different materials




thickness = 5 * u.mm

material_list = ['air', 'Al', 'Pb']energy = u.Quantity(np.arange(1, 100, 0.1), 'keV')

for material in material_list:mat = Material(material, thickness)plt.plot(energy, mat.transmission(energy), label=mat.name)

plt.title(f"Thickness = {thickness}")plt.ylabel('Transmission')plt.legend(loc='lower right')plt.show()

0 20 40 60 80 100keV

0.0

0.2

0.4

0.6

0.8

1.0

Tran

smiss

ion

Thickness = 5.0 mm

Air (dry)AluminumLead

3.6. Finding the x-ray transmission through different materials 33


3.7 Checking on edges in the Mass Attenuation Coefficient


import astropy.units as ufrom astropy.visualization import quantity_supportquantity_support()from roentgen.absorption import MassAttenuationCoefficient

e = np.linspace(1e-3, 1e-2, 1000)*u.MeVte = MassAttenuationCoefficient('Te')plt.plot(e, te.func(e), 'x', label='Interpolated')plt.plot(te.energy, te.data, color='black', label='Data')plt.loglog()plt.xlim(4e-3, 6e-3)plt.ylim(1e2, 1e3)plt.xlabel('Photon Energy (MeV)')plt.ylabel(r'$\mu / \rho$ (cm$^{2}$ g$^{-1}$)')plt.title('Te')plt.legend()plt.show()

4 × 10 3 5 × 10 3 6 × 10 3

Photon Energy (MeV)

102

103

2 × 102

3 × 102

4 × 102

6 × 102

/ (c

m2 g

1 )

Te

InterpolatedData


CHAPTER

FOUR

CONTRIBUTING

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.Have a look at the great guide from the sunpy project which provides advice for new contributors.

35

https://github.com/sunpy/sunpy/blob/master/CONTRIBUTING.rst

https://sunpy.org


36 Chapter 4. Contributing

CHAPTER

FIVE

AUTHORS

• Steven D. Christe https://github.com/ehsteve

37

https://github.com/ehsteve


38 Chapter 5. Authors

CHAPTER

SIX

LICENSE

Copyright 2019, Steven D. Christe

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance withthe License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an“AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See theLicense for the specific language governing permissions and limitations under the License.

—

Apache License Version 2.0, January 2004 http://www.apache.org/licenses/

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

“License” shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through9 of this document.

“Licensor” shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.

“Legal Entity” shall mean the union of the acting entity and all other entities that control, are controlled by, or areunder common control with that entity. For the purposes of this definition, “control” means (i) the power, direct orindirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership offifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.

“You” (or “Your”) shall mean an individual or Legal Entity exercising permissions granted by this License.

“Source” form shall mean the preferred form for making modifications, including but not limited to software sourcecode, documentation source, and configuration files.

“Object” form shall mean any form resulting from mechanical transformation or translation of a Source form, includingbut not limited to compiled object code, generated documentation, and conversions to other media types.

“Work” shall mean the work of authorship, whether in Source or Object form, made available under the License, asindicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendixbelow).

“Derivative Works” shall mean any work, whether in Source or Object form, that is based on (or derived from) theWork and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, anoriginal work of authorship. For the purposes of this License, Derivative Works shall not include works that remainseparable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof.

“Contribution” shall mean any work of authorship, including the original version of the Work and any modifications oradditions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Workby the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For

39

http://www.apache.org/licenses/LICENSE-2.0

http://www.apache.org/licenses/


the purposes of this definition, “submitted” means any form of electronic, verbal, or written communication sent tothe Licensor or its representatives, including but not limited to communication on electronic mailing lists, source codecontrol systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of dis-cussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designatedin writing by the copyright owner as “Not a Contribution.”

“Contributor” shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has beenreceived by Licensor and subsequently incorporated within the Work.

2. Grant of Copyright License.

Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publiclydisplay, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.

3. Grant of Patent License.

Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide,non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made,use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claimslicensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of theirContribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation againstany entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporatedwithin the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You underthis License for that Work shall terminate as of the date such litigation is filed.

4. Redistribution.

You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or withoutmodifications, and in Source or Object form, provided that You meet the following conditions:

You must give any other recipients of the Work or Derivative Works a copy of this License; and Youmust cause any modified files to carry prominent notices stating that You changed the files; and You mustretain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark,and attribution notices from the Source form of the Work, excluding those notices that do not pertain to anypart of the Derivative Works; and If the Work includes a “NOTICE” text file as part of its distribution, thenany Derivative Works that You distribute must include a readable copy of the attribution notices containedwithin such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works,in at least one of the following places: within a NOTICE text file distributed as part of the DerivativeWorks; within the Source form or documentation, if provided along with the Derivative Works; or, withina display generated by the Derivative Works, if and wherever such third-party notices normally appear.The contents of the NOTICE file are for informational purposes only and do not modify the License. Youmay add Your own attribution notices within Derivative Works that You distribute, alongside or as anaddendum to the NOTICE text from the Work, provided that such additional attribution notices cannot beconstrued as modifying the License.

You may add Your own copyright statement to Your modifications and may provide additional or different licenseterms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works asa whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions statedin this License.

5. Submission of Contributions.

Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You tothe Licensor shall be under the terms and conditions of this License, without any additional terms or conditions.Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement youmay have executed with Licensor regarding such Contributions.

6. Trademarks.

40 Chapter 6. License


This License does not grant permission to use the trade names, trademarks, service marks, or product names of theLicensor, except as required for reasonable and customary use in describing the origin of the Work and reproducingthe content of the NOTICE file.

7. Disclaimer of Warranty.

Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor providesits Contributions) on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, eitherexpress or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT,MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determin-ing the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise ofpermissions under this License.

8. Limitation of Liability.

In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required byapplicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable toYou for damages, including any direct, indirect, special, incidental, or consequential damages of any character arisingas a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss ofgoodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), evenif such Contributor has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability.

While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptanceof support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, inaccepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of anyother Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liabilityincurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additionalliability.

END OF TERMS AND CONDITIONS

41


42 Chapter 6. License

CHAPTER

SEVEN

CHANGELOG

7.1 0.1.0 (2017-03-24)

• First release

7.2 1.0.0 (2020-04-23)

• First stable release

• Added gui, deployed to heroku

• added data and support for emission lines

• Added Response class

• Major update to documentation and moved to sunpy doc theme

43


44 Chapter 7. Changelog

CHAPTER

EIGHT

INDICES AND TABLES

• genindex

• modindex

• search

45


46 Chapter 8. Indices and tables

PYTHON MODULE INDEX

rroentgen.absorption, 19roentgen.lines, 23roentgen.util, 24

47


48 Python Module Index

INDEX

Aabsorption() (roentgen.absorption.Compound

method), 20absorption() (roentgen.absorption.Material

method), 22

CCompound (class in roentgen.absorption), 19

Ddata (roentgen.absorption.MassAttenuationCoefficient

attribute), 20density_ideal_gas() (in module roentgen.util), 24

Eenergy (roentgen.absorption.MassAttenuationCoefficient

attribute), 20

Ffunc (roentgen.absorption.MassAttenuationCoefficient

attribute), 20

Gget_atomic_number() (in module roentgen.util), 24get_compound_index() (in module roentgen.util),

24get_density() (in module roentgen.util), 24get_element_symbol() (in module roentgen.util),

24get_lines() (in module roentgen.lines), 23

Iis_an_element() (in module roentgen.util), 25is_in_known_compounds() (in module roent-

gen.util), 25

Mmass_attenuation_coefficient (roent-

gen.absorption.Material attribute), 21MassAttenuationCoefficient (class in roent-

gen.absorption), 20

Material (class in roentgen.absorption), 21module

roentgen.absorption, 19roentgen.lines, 23roentgen.util, 24

Nname (roentgen.absorption.MassAttenuationCoefficient

attribute), 20name (roentgen.absorption.Material attribute), 21

RResponse (class in roentgen.absorption), 22response() (roentgen.absorption.Response method),

22roentgen.absorption

module, 19roentgen.lines

module, 23roentgen.util

module, 24

Ssymbol (roentgen.absorption.MassAttenuationCoefficient

attribute), 20symbol (roentgen.absorption.Material attribute), 21

Ttransmission() (roentgen.absorption.Compound

method), 20transmission() (roentgen.absorption.Material

method), 22

49

roentgen - read the docs · ii. roentgen, release 1.1.dev6+gcd4d4e1 this is a python package for...

Documents