Addition of 3 more databases

pyxray/parser/chantler2005.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+"""
+Parser for the NIST FFAST database compiled by Chantler C. T., et.al.
+"""
+
+# Standard library modules.
+import logging
+import os
+import pkgutil
+
+# Third party modules.
+
+
+# Local modules.
+import pyxray.parser.base as base
+from pyxray.descriptor import Reference, Element
+from pyxray.property import (
+    ElementAtomicWeight,
+    ElementMassDensity,
+    AtomicSubshellBindingEnergy,
+)
+
+# Globals and constants variables.
+logger = logging.getLogger(__name__)
+
+CHANTLER2005 = Reference(
+    "chantler2005",
+    author="Chantler, C.T. and Olsen, K. and Dragoset, R.A. and Chang, J. and Kishore, A.R. and Kotochigova, S.A. and "
+           "Zucker, D.S.",
+    year="2005",
+    title="X-Ray Form Factor, Attenuation, and Scattering Tables (version 2.1)",
+    publisher="National Institute of Standards and Technology, Gaithersburg, MD, USA",
+    doi="10.18434/T4HS32",
+    howpublished="Online",
+    url="http://physics.nist.gov/ffast",
+)
+
+_SUBSHELLS = [
+    base.K,
+    base.L1,
+    base.L2,
+    base.L3,
+    base.M1,
+    base.M2,
+    base.M3,
+    base.M4,
+    base.M5,
+    base.N1,
+    base.N2,
+    base.N3,
+    base.N4,
+    base.N5,
+    base.N6,
+    base.N7,
+    base.O1,
+    base.O2,
+    base.O3,
+    base.O4,
+    base.O5,
+    base.P1,
+    base.P2,
+    base.P3,
+]
+
+_NUM_SUBSHELLS = 24
+_MAX_Z = 92
+
+
+class Chantler2005Parser(base._Parser):
+
+    def __iter__(self):
+        relpath = os.path.join("..", "data", "shelldata.csv")
+        content = pkgutil.get_data(__name__, relpath).decode("utf8")
+
+        rows = content.splitlines()
+
+        for z in range(1, len(rows)):
+            row = [item.strip() for item in rows[z].split(',')]
+            element = Element(z)
+
+            prop = ElementAtomicWeight(CHANTLER2005, element, float(row[0]))
+            logger.debug("Parsed: {0}".format(prop))
+            yield prop
+
+            prop = ElementMassDensity(CHANTLER2005, element, float(row[2])*1e3)
+            logger.debug("Parsed: {0}".format(prop))
+            yield prop
+
+            for i in range(_NUM_SUBSHELLS):
+                value = row[i+7]
+                if value:
+                    prop = AtomicSubshellBindingEnergy(CHANTLER2005, element, _SUBSHELLS[i], float(value))
+                    logger.debug("Parsed: {0}".format(prop))
+                    yield prop
+
+            self.update(int(z / _MAX_Z * 100))

pyxray/parser/deslattes2005.py

@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+"""
+Parser for Elam 2002
+"""
+
+# Standard library modules.
+import logging
+
+# Third party modules.
+import requests
+
+
+# Local modules.
+import pyxray.parser.base as base
+from pyxray.descriptor import Reference, Element, XrayTransition
+from pyxray.property import (
+    AtomicSubshellBindingEnergy,
+    XrayTransitionEnergy,
+)
+
+# Globals and constants variables.
+logger = logging.getLogger(__name__)
+
+DESLATTES2005THEORY = Reference(
+    "deslattes2005_theory",
+    author="Deslattes, R.D. and Kessler Jr., E.G. and Indelicato, P. and Billy, L. de and Lindroth, E. and Anton, J. "
+           "and Coursey, J.S. and Schwab, D.J. and Chang, C. and Sukumar, R. and Olsen, K. and Dragoset, R.A.",
+    year="2005",
+    title="X-ray Transition Energies (version 1.2)",
+    publisher="National Institute of Standards and Technology, Gaithersburg, MD, USA",
+    doi="10.18434/T4859Z",
+    howpublished="Online",
+    url="http://physics.nist.gov/XrayTrans",
+)
+
+DESLATTES2005DIRECT = Reference(
+    "deslattes2005_direct",
+    author="Deslattes, R.D. and Kessler Jr., E.G. and Indelicato, P. and Billy, L. de and Lindroth, E. and Anton, J. "
+           "and Coursey, J.S. and Schwab, D.J. and Chang, C. and Sukumar, R. and Olsen, K. and Dragoset, R.A.",
+    year="2005",
+    title="X-ray Transition Energies (version 1.2)",
+    publisher="National Institute of Standards and Technology, Gaithersburg, MD, USA",
+    doi="10.18434/T4859Z",
+    howpublished="Online",
+    url="http://physics.nist.gov/XrayTrans",
+)
+
+DESLATTES2005COMBINED = Reference(
+    "deslattes2005_combined",
+    author="Deslattes, R.D. and Kessler Jr., E.G. and Indelicato, P. and Billy, L. de and Lindroth, E. and Anton, J. "
+           "and Coursey, J.S. and Schwab, D.J. and Chang, C. and Sukumar, R. and Olsen, K. and Dragoset, R.A.",
+    year="2005",
+    title="X-ray Transition Energies (version 1.2)",
+    publisher="National Institute of Standards and Technology, Gaithersburg, MD, USA",
+    doi="10.18434/T4859Z",
+    howpublished="Online",
+    url="http://physics.nist.gov/XrayTrans",
+)
+
+DESLATTES2005VAPOR = Reference(
+    "deslattes2005_vapor",
+    author="Deslattes, R.D. and Kessler Jr., E.G. and Indelicato, P. and Billy, L. de and Lindroth, E. and Anton, J. "
+           "and Coursey, J.S. and Schwab, D.J. and Chang, C. and Sukumar, R. and Olsen, K. and Dragoset, R.A.",
+    year="2005",
+    title="X-ray Transition Energies (version 1.2)",
+    publisher="National Institute of Standards and Technology, Gaithersburg, MD, USA",
+    doi="10.18434/T4859Z",
+    howpublished="Online",
+    url="http://physics.nist.gov/XrayTrans",
+)
+
+_ELEMENT_LOOKUP = {
+    "Ne": Element(10), "Na": Element(11), "Mg": Element(12), "Al": Element(13), "Si": Element(14), "P": Element(15),
+    "S": Element(16), "Cl": Element(17), "Ar": Element(18), "K": Element(19), "Ca": Element(20), "Sc": Element(21),
+    "Ti": Element(22), "V": Element(23), "Cr": Element(24), "Mn": Element(25), "Fe": Element(26), "Co": Element(27),
+    "Ni": Element(28), "Cu": Element(29), "Zn": Element(30), "Ga": Element(31), "Ge": Element(32), "As": Element(33),
+    "Se": Element(34), "Br": Element(35), "Kr": Element(36), "Rb": Element(37), "Sr": Element(38), "Y": Element(39),
+    "Zr": Element(40), "Nb": Element(41), "Mo": Element(42), "Tc": Element(43), "Ru": Element(44), "Rh": Element(45),
+    "Pd": Element(46), "Ag": Element(47), "Cd": Element(48), "In": Element(49), "Sn": Element(50), "Sb": Element(51),
+    "Te": Element(52), "I": Element(53), "Xe": Element(54), "Cs": Element(55), "Ba": Element(56), "La": Element(57),
+    "Ce": Element(58), "Pr": Element(59), "Nd": Element(60), "Pm": Element(61), "Sm": Element(62), "Eu": Element(63),
+    "Gd": Element(64), "Tb": Element(65), "Dy": Element(66), "Ho": Element(67), "Er": Element(68), "Tm": Element(69),
+    "Yb": Element(70), "Lu": Element(71), "Hf": Element(72), "Ta": Element(73), "W": Element(74), "Re": Element(75),
+    "Os": Element(76), "Ir": Element(77), "Pt": Element(78), "Au": Element(79), "Hg": Element(80), "Tl": Element(81),
+    "Pb": Element(82), "Bi": Element(83), "Po": Element(84), "At": Element(85), "Rn": Element(86), "Fr": Element(87),
+    "Ra": Element(88), "Ac": Element(89), "Th": Element(90), "Pa": Element(91), "U": Element(92), "Np": Element(93),
+    "Pu": Element(94), "Am": Element(95), "Cm": Element(96), "Bk": Element(97), "Cf": Element(98), "Es": Element(99),
+    "Fm": Element(100),
+}
+
+_SUBSHELL_LOOKUP = {
+    "K": base.K,
+    "L1": base.L1,
+    "L2": base.L2,
+    "L3": base.L3,
+    "M1": base.M1,
+    "M2": base.M2,
+    "M3": base.M3,
+    "M4": base.M4,
+    "M5": base.M5,
+    "N1": base.N1,
+    "N2": base.N2,
+    "N3": base.N3,
+    "N4": base.N4,
+    "N5": base.N5,
+    "N6": base.N6,
+    "N7": base.N7,
+}
+
+_BLEND_LOOKUP = {
+    "KL2,3": base.Ka,
+    "KM": XrayTransition(3, None, None, base.K),
+    "KM2,3": base.Kb1_3,
+    "KM4,5": base.Kb5,
+    "KN2,3": base.Kb2,
+    "KN4,5": base.Kb4,
+    "L2,3M1": base.Ll_n,
+    "L3M4,5": base.La,
+    "L1M2,3": base.Lb3_4,
+    "L1N2,3": base.Lg2_3,
+    "L3N4,5": base.Lb2_15,
+    "L3N6,7": base.Lu,
+    "L2N6,7": XrayTransition(4, 3, None, base.L2),
+    "L1N4,5": XrayTransition(4, 2, None, base.L1),
+    "L1N6,7": XrayTransition(4, 3, None, base.L1),
+}
+
+_NUM_ELEMENTS = 91
+_URL = "https://physics.nist.gov/cgi-bin/XrayTrans/search.pl?download=tab&element=All&lower=10&upper=1000000&units=eV"
+
+# Column numbers in table
+_ELE = 0
+_TRANS = 2
+_THEORY = 3
+_DIRECT = 5
+_COMBINED = 7
+_VAPOR = 9
+_BLEND = 11
+
+
+class Deslattes2005Parser(base._Parser):
+
+    def __iter__(self):
+        r = requests.get(_URL, stream=True)
+
+        r_iter = r.iter_lines()
+        while True:
+            if next(r_iter).decode("ascii").startswith('Ele.'):
+                break
+
+        for line in r_iter:
+            row = line.decode("ascii").split('\t')
+            element = _ELEMENT_LOOKUP[row[_ELE]]
+
+            transition_str = row[_TRANS]
+            if "edge" in transition_str:
+                subshell_str = transition_str.split()[0]
+                subshell = _SUBSHELL_LOOKUP[subshell_str]
+
+                yield from Deslattes2005Parser._edge_energy_parser(DESLATTES2005THEORY, element, subshell, row[_THEORY])
+                yield from Deslattes2005Parser._edge_energy_parser(DESLATTES2005DIRECT, element, subshell, row[_DIRECT])
+                yield from Deslattes2005Parser._edge_energy_parser(DESLATTES2005COMBINED, element, subshell,
+                                                                   row[_COMBINED])
+                yield from Deslattes2005Parser._edge_energy_parser(DESLATTES2005VAPOR, element, subshell, row[_VAPOR])
+                if subshell_str == 'K':
+                    self.update(int((element.z - 9) / _NUM_ELEMENTS * 100))
+
+            else:
+                transition = Deslattes2005Parser._get_transition(row[_TRANS])
+
+                blend_str = row[_BLEND]
+                blend = _BLEND_LOOKUP[row[_BLEND]] if blend_str else False
+
+                yield from Deslattes2005Parser._transition_energy_parser(DESLATTES2005THEORY, element, transition,
+                                                                         row[_THEORY])
+
+                yield from Deslattes2005Parser._transition_energy_parser(DESLATTES2005DIRECT, element, transition,
+                                                                         row[_DIRECT])
+
+                # If blend is stipulated (Eg. KL2,3) add the direct measured value also to the blend, but only once
+                if blend and (transition_str in blend_str or (blend_str == "KM" and transition_str == "KM1") or
+                              (blend_str == 'L2,3M1' and transition_str == 'L2M1')):
+                    yield from Deslattes2005Parser._transition_energy_parser(DESLATTES2005DIRECT, element, blend,
+                                                                             row[_DIRECT])
+
+    @staticmethod
+    def _get_transition(transition_str):
+        if transition_str[0] == 'K':
+            return XrayTransition(_SUBSHELL_LOOKUP[transition_str[1:]], base.K)
+        return XrayTransition(_SUBSHELL_LOOKUP[transition_str[2:]], _SUBSHELL_LOOKUP[transition_str[:2]])
+
+    @staticmethod
+    def _transition_energy_parser(reference, element, transition, value_ev_str):
+        if value_ev_str:
+            prop = XrayTransitionEnergy(reference, element, transition, float(value_ev_str))
+            logger.debug("Parsed: {0}".format(prop))
+            yield prop
+
+    @staticmethod
+    def _edge_energy_parser(reference, element, subshell, value_ev_str):
+        if value_ev_str:
+            prop = AtomicSubshellBindingEnergy(reference, element, subshell, float(value_ev_str))
+            logger.debug("Parsed: {0}".format(prop))
+            yield prop