diff --git a/doc/reference/material.rst b/doc/reference/material.rst index 1df8d98c0..ac6057149 100644 --- a/doc/reference/material.rst +++ b/doc/reference/material.rst @@ -18,7 +18,9 @@ .. autoattribute:: exspy.material.elements :annotation: -Database of element properties. The following properties are included: +Database of element properties. + +The following properties are included: .. code:: @@ -32,32 +34,50 @@ Database of element properties. The following properties are included: └── Physical_properties └── density_gcm3 -Examples: +The X-ray lines energies are taken from Chantler et al. [1]_. -.. code:: +The line weight, more precisely the approximate line weight for K, L, M +shells are taken from the Electron Probe Quantification (EPQ) library [2]_. + +The field ``threshold`` and ``edge`` are taken from the Gatan EELS atlas +https://eels.info/atlas, as retrieved in June 2020. + +Examples + +>>> exspy.material.elements.Fe.General_properties +├── Z = 26 +├── atomic_weight = 55.845 +└── name = iron +>>> exspy.material.elements.Fe.Physical_properties +└── density (g/cm^3) = 7.874 +>>> exspy.material.elements.Fe.Atomic_properties.Xray_lines +├── Ka +│ ├── energy (keV) = 6.404 +│ └── weight = 1.0 +├── Kb +│ ├── energy (keV) = 7.0568 +│ └── weight = 0.1272 +├── La +│ ├── energy (keV) = 0.705 +│ └── weight = 1.0 +├── Lb3 +│ ├── energy (keV) = 0.792 +│ └── weight = 0.02448 +├── Ll +│ ├── energy (keV) = 0.615 +│ └── weight = 0.3086 +└── Ln + ├── energy (keV) = 0.62799 + └── weight = 0.12525 + + +References + +.. [1] Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., + Kotochigova, S.A., and Zucker, D.S. (2005), X-Ray Form Factor, + Attenuation and Scattering Tables (version 2.1). + https://dx.doi.org/10.18434/T4HS32 - >>> exspy.material.elements.Fe.General_properties - ├── Z = 26 - ├── atomic_weight = 55.845 - └── name = iron - >>> exspy.material.elements.Fe.Physical_properties - └── density (g/cm^3) = 7.874 - >>> exspy.material.elements.Fe.Atomic_properties.Xray_lines - ├── Ka - │ ├── energy (keV) = 6.404 - │ └── weight = 1.0 - ├── Kb - │ ├── energy (keV) = 7.0568 - │ └── weight = 0.1272 - ├── La - │ ├── energy (keV) = 0.705 - │ └── weight = 1.0 - ├── Lb3 - │ ├── energy (keV) = 0.792 - │ └── weight = 0.02448 - ├── Ll - │ ├── energy (keV) = 0.615 - │ └── weight = 0.3086 - └── Ln - ├── energy (keV) = 0.62799 - └── weight = 0.12525 +.. [2] Ritchie, N. EPQ is the Electron Probe Quantification library + - the basis for DTSA-II. + https://github.com/usnistgov/EPQ diff --git a/doc/user_guide/bibliography.rst b/doc/user_guide/bibliography.rst index 20aefe95d..e405efbe8 100644 --- a/doc/user_guide/bibliography.rst +++ b/doc/user_guide/bibliography.rst @@ -17,12 +17,9 @@ Bibliography .. _Chantler2005: :ref:`[Chantler2005] ` - C. Chantler, K. Olsen, R. Dragoset, - J. Chang, A. Kishore, S. Kotochigova, and D. Zucker, "Detailed Tabulation - of Atomic Form Factors, Photoelectric Absorption and Scattering Cross - Section, and Mass Attenuation Coefficients for Z = 1-92 from E = 1-10 eV - to E = 0.4-1.0 MeV" *NIST Standard Reference Data* - [``_]. + Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, + S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and + Scattering Tables (version 2.1). https://dx.doi.org/10.18434/T4HS32. .. _Egerton2011: diff --git a/exspy/_misc/elements.py b/exspy/_misc/elements.py index ba7153143..35cb37bb4 100644 --- a/exspy/_misc/elements.py +++ b/exspy/_misc/elements.py @@ -4996,6 +4996,14 @@ └── Physical_properties └── density_gcm3 +The X-ray lines energies are taken from Chantler et al. [1]_. + +The line weight, more precisely the approximate line weight for K, L, M +shells are taken from the Electron Probe Quantification (EPQ) library [2]_. + +The field ``threshold`` and ``edge`` are taken from the Gatan EELS atlas +https://eels.info/atlas, as retrieved in June 2020. + Examples -------- >>> exspy.material.elements.Fe.General_properties @@ -5023,6 +5031,18 @@ └── Ln ├── energy (keV) = 0.62799 └── weight = 0.12525 + + +References +---------- +.. [1] Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., + Kotochigova, S.A., and Zucker, D.S. (2005), X-Ray Form Factor, + Attenuation and Scattering Tables (version 2.1). + https://dx.doi.org/10.18434/T4HS32 + +.. [2] Ritchie, N. EPQ is the Electron Probe Quantification library + - the basis for DTSA-II. + https://github.com/usnistgov/EPQ """ # read dictionary of atomic numbers from eXSpy, and add the elements that diff --git a/exspy/_misc/material.py b/exspy/_misc/material.py index 08f6c034d..3fe2be39a 100644 --- a/exspy/_misc/material.py +++ b/exspy/_misc/material.py @@ -314,7 +314,7 @@ def mass_absorption_coefficient(element, energies): Mass absorption coefficient (mu/rho) of a X-ray absorbed in a pure material. - The mass absorption is retrieved from the database of Chantler2005 + The mass absorption is retrieved from the database of Chantler et al. [*]_. Parameters ---------- @@ -339,12 +339,11 @@ def mass_absorption_coefficient(element, energies): -------- exspy.material.mass_absorption_mixture - Note - ---- - See https://dx.doi.org/10.18434/T4HS32 - Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, - S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and - Scattering Tables (version 2.1). + References + ---------- + .. [*] Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, + S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and + Scattering Tables (version 2.1). https://dx.doi.org/10.18434/T4HS32 """ energies_db = np.array(ffast_mac[element].energies_keV) macs = np.array(ffast_mac[element].mass_absorption_coefficient_cm2g) @@ -372,7 +371,7 @@ def _mass_absorption_mixture(weight_percent, elements, energies): mixture of elements. The mass absorption coefficient is calculated as a weighted mean of the - weight percent and is retrieved from the database of Chantler2005. + weight percent and is retrieved from the database of Chantler et al. [*]_. Parameters ---------- @@ -400,12 +399,11 @@ def _mass_absorption_mixture(weight_percent, elements, energies): -------- exspy.material.mass_absorption - Note - ---- - See https://dx.doi.org/10.18434/T4HS32 - Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, - S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and - Scattering Tables (version 2.1). + References + ---------- + .. [*] Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, + S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and + Scattering Tables (version 2.1). https://dx.doi.org/10.18434/T4HS32 """ if len(elements) != len(weight_percent): raise ValueError("Elements and weight_fraction should have the same length") @@ -430,7 +428,7 @@ def mass_absorption_mixture(weight_percent, elements="auto", energies="auto"): mixture of elements. The mass absorption coefficient is calculated as a weighted mean of the - weight percent and is retrieved from the database of Chantler2005. + weight percent and is retrieved from the database of Chantler et al. [*]_. Parameters ---------- @@ -461,13 +459,11 @@ def mass_absorption_mixture(weight_percent, elements="auto", energies="auto"): -------- exspy.material.mass_absorption_coefficient - Note - ---- - See https://dx.doi.org/10.18434/T4HS32 - Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, - S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and - Scattering Tables (version 2.1). - + References + ---------- + .. [*] Chantler, C.T., Olsen, K., Dragoset, R.A., Kishore, A.R., Kotochigova, + S.A., and Zucker, D.S. (2005), X-Ray Form Factor, Attenuation and + Scattering Tables (version 2.1). https://dx.doi.org/10.18434/T4HS32 """ from hyperspy.signals import BaseSignal diff --git a/upcoming_changes/87.enhancements.rst b/upcoming_changes/87.enhancements.rst new file mode 100644 index 000000000..60d63144c --- /dev/null +++ b/upcoming_changes/87.enhancements.rst @@ -0,0 +1 @@ +Mention source of :attr:`~exspy.material.elements` database in docstring \ No newline at end of file