def get_x_ray_CoFe():
xdb = XrayDB()
lines_Fe = xdb.xray_lines('Fe', excitation_energy=20e3)
lines_Co = xdb.xray_lines('Co', excitation_energy=20e3)
intensity_Ka1 = (lines_Fe['Ka1'].intensity + lines_Fe['Ka2'].intensity +
lines_Fe['Ka3'].intensity)
return lines_Fe, lines_Co, intensity_Ka1
def test_xray_line_strengths():
xdb = XrayDB()
assert len(xdb.xray_line_strengths('Hg', excitation_energy=2800)) == 2
assert len(xdb.xray_line_strengths('Hg', excitation_energy=12000)) == 3
assert len(xdb.xray_line_strengths('Hg', excitation_energy=12500)) == 9
assert len(xdb.xray_line_strengths('Hg', excitation_energy=14300)) == 13
assert len(xdb.xray_line_strengths('Hg', excitation_energy=16000)) == 17
def initUI(self):
"""
initialize the GUI components
"""
self.sampleFileName = self.sampleFileNameLineEdit.text()
self.doubleValidator = QDoubleValidator()
self.integerValidator = QIntValidator()
if self.sampleFileName == '':
self.sampleFileName = None
self.sampleNumsChanged()
self.bkgNumChanged()
self.stdNumChanged()
#self.sampleThicknessLineEdit.setValidator(self.doubleValidator)
self.bkgThicknessLineEdit.setValidator(self.doubleValidator)
self.stdThicknessLineEdit.setValidator(self.doubleValidator)
self.sampleThickness = float(self.sampleThicknessLineEdit.text())
self.bkgThickness = float(self.bkgThicknessLineEdit.text())
self.energyNpts = self.energyNptsSpinBox.value()
self.repeatNpts = self.repeatSpinBox.value()
self.normStd = self.normStdSampleComboBox.currentText()
self.stdThickness = float(self.stdThicknessLineEdit.text())
self.xMinMaxText = self.xMinMaxLineEdit.text()
self.xMin, self.xMax = list(map(float, self.xMinMaxText.split(':')))
self.interpType = self.interpComboBox.currentText()
self.progressBar.setMinimum(0)
self.progressBar.setValue(0)
self.xdb = XrayDB()
def __init__(self, parent=None):
"""
"""
QWidget.__init__(self, parent)
loadUi('UI_Forms/XAnoS_EnergySteps.ui', self)
self.xrdb = XrayDB()
self.initialize_UI()
self.init_signals()
def test_xraydb_version():
xdb = XrayDB()
version = xdb.get_version()
assert 'XrayDB Version: 4.0, Python' in version
hist = xdb.get_version(with_history=True)
assert len(hist) > 350
hist = hist.split('\n')
assert len(hist) > 4
def __init__(self, formula=None):
self.formula = formula
self.xdb = XrayDB()
cols = ['symbol', 'covalent_radius_cordero']
ptable = get_table('elements')
x = ptable[cols]
self.covalent_radius = x.set_index('symbol').T.to_dict(
'index')['covalent_radius_cordero']
if formula is not None:
self.parse(self.formula)
def plotTransmission(symbol, edge="K", thickness=0.001, energies=None):
""" Plots absorption in a given material as function of wavelength.
:param symbol: The chemical symbol of the material.
:type symbol: str
:param edge: The requested absorption edge (K, L1, L2, M1, M2, ...)
:type edge: str
:param thickness: The material thickness in centimeters."
:type thickness: float
:param energies: For which energies to plot the transmission.
:type energies: ndarray
"""
# Instantiate the database.
xdb = XrayDB()
# Get info on requested edge.
edge_data = xdb.xray_edge(symbol, edge)
edge_position = edge_data[0]
edge_fyield = edge_data[1]
edge_jump = edge_data[2]
# Mass density (ambient).
rho = xdb.density(symbol)
# Fix energy range.
min_energy = 0.7 * edge_position
max_energy = 1.3 * edge_position
# Setup arrays
if energies is None:
energies = numpy.linspace(min_energy, max_energy, 1024)
mu = xdb.mu_chantler(symbol, energy=energies)
# Convert to iterable if needed.
if not hasattr(thickness, "__iter__"):
thickness = [thickness]
absorption = [numpy.exp(-mu * rho * th) for th in thickness]
for i, abso in enumerate(absorption):
pyplot.plot(energies,
abso,
lw=2,
label=r"%3.1f $\mu$m" % (thickness[i] * 1e4))
pyplot.xlabel('Energy (eV)')
pyplot.ylabel('Transmission')
pyplot.legend()
pyplot.title("%s %s-edge" % (symbol, edge))
pyplot.show()
def signoise(filels, inter, edge):
jj = inter
data = EData(filels[jj])
df = data.reader(data.datain)
edgelib = XrayDB()
edgenom = edgelib.xray_edge(edge, 'K')[0]
if len(df[df['e'] > 100 + edgenom]) < 20:
edgenom = edgelib.xray_edge(edge, 'L3')[0]
dftrim = df[df['e'] > 100 + edgenom]
xfsmean = dftrim[dftrim.columns[1]].mean()
xfsstd = dftrim[dftrim.columns[1]].std()
return xfsmean, xfsstd
def __init__(self):
self.E = None
self.I = None
self.sI = None
self.min_E = 0
self.max_E = np.inf
self.xdb = XrayDB()
self.lines_Fe = self.xdb.xray_lines('Fe', excitation_energy=20e3)
self.lines_Co = self.xdb.xray_lines('Co', excitation_energy=20e3)
self.intensity_Ka1 = (self.lines_Fe['Ka1'].intensity +
self.lines_Fe['Ka2'].intensity +
self.lines_Fe['Ka3'].intensity)
def test_ionization_potentials():
xdb = XrayDB()
assert xdb.ionization_potential('air') == 33.8
assert xdb.ionization_potential('helium') == 41.3
assert xdb.ionization_potential('He') == 41.3
assert xdb.ionization_potential('Si') == 3.68
with pytest.raises(ValueError):
xdb.ionization_potential('p10')
def test_density():
xdb = XrayDB()
assert_allclose(xdb.density('Ne'), 0.00090, rtol=0.01)
assert_allclose(xdb.density('Ti'), 4.506, rtol=0.01)
assert_allclose(xdb.density('Kr'), 0.00375, rtol=0.01)
assert_allclose(xdb.density('Mo'), 10.28, rtol=0.01)
assert_allclose(xdb.density('Pd'), 12.03, rtol=0.01)
assert_allclose(xdb.density('Au'), 19.3, rtol=0.01)
with pytest.raises(ValueError):
xdb.density('Mx')
def __init__(self,
x=0,
rmin=0.0,
rmax=30.0,
Nr=31,
Rc=10.0,
strho=1.0,
tst=2.0,
lrho=0.5,
lexp=10.0,
rhosol=0.0,
norm=1.0,
bkg=0.0,
mpar={}):
"""
Documentation
x : independent variable in the form of a scalar or an array
Rc : Radial distance in Angstroms after which the solvent contribution starts
strho : Concentration of the ions of interest in the stern layer in Molar
tst : Thickness of stern layer in Angstroms
lrho : The maximum concentration of the diffuse layer in Molars
lexp : The decay length of the diffuse layer assuming exponential decay
rhosol : The surrounding bulk density
norm : Density of particles in Moles/Liter
bkg : Constant background
"""
if type(x) == list:
self.x = np.array(x)
else:
self.x = x
self.rmin = rmin
self.rmax = rmax
self.Nr = Nr
self.Rc = Rc
self.strho = strho
self.tst = tst
self.lrho = lrho
self.lexp = lexp
self.rhosol = rhosol
self.norm = norm
self.bkg = bkg
self.__mpar__ = mpar #If there is any multivalued parameter
self.choices = {
} #If there are choices available for any fixed parameters
self.__xrdb__ = XrayDB()
self.init_params()
self.output_params = {'scaler_parameters': {}}
def __init__(
self,
x=0,
E=12.0,
fname1='W:/Tianbo_Collab/Mo132.xyz',
eta1=1.0,
fname2='/media/sf_Mrinal_Bera/Documents/MA-Collab/XTal_data/P2W12.xyz',
eta2=0.0,
rmin=0.0,
rmax=10.0,
Nr=100,
qoff=0.0,
sol=18.0,
sig=0.0,
norm=1,
bkg=0.0,
mpar={}):
"""
Calculates the form factor for two different kinds of molecules in cm^-1 for which the XYZ coordinates of the all the atoms composing the molecules are known
x scalar or array of reciprocal wave vectors
E Energy of the X-rays at which the scattering pattern is measured
fname1 Name with path of the .xyz file containing X, Y, Z coordinates of all the atoms of the molecule of type 1
eta1 Fraction of molecule type 1
fname2 Name with path of the .xyz file containing X, Y, Z coordinates of all the atoms of the moleucule of type 2
eta2 Fraction of molecule type 2
rmin Minimum radial distance for calculating electron density
rmax Maximum radial distance for calculating electron density
Nr Number of points at which electron density will be calculated
qoff Q-offset may be required due to uncertainity in Q-calibration
sol No of electrons in solvent molecule (Ex: H2O has 18 electrons)
sig Debye-waller factor
norm Normalization constant which can be the molar concentration of the particles
bkg Background
"""
if type(x) == list:
self.x = np.array(x)
else:
self.x = np.array([x])
if os.path.exists(fname1):
self.fname1 = fname1
else:
self.fname1 = None
self.eta1 = eta1
if os.path.exists(fname2):
self.fname2 = fname2
else:
self.fname2 = None
self.eta2 = eta2
self.rmin = rmin
self.__rmin__ = rmin
self.rmax = rmax
self.__rmax__ = rmax
self.Nr = Nr
self.__Nr__ = Nr
self.norm = norm
self.bkg = bkg
self.E = E
self.sol = sol
self.qoff = qoff
self.sig = sig
self.__mpar__ = mpar #If there is any multivalued parameter
self.choices = {
} #If there are choices available for any fixed parameters
self.__fnames__ = [self.fname1, self.fname2]
self.__E__ = E
self.__xdb__ = XrayDB()
#if self.fname1 is not None:
# self.__Natoms1__,self.__pos1__,self.__f11__=self.readXYZ(self.fname1)
#if self.fname2 is not None:
# self.__Natoms2__,self.__pos2__,self.__f12__=self.readXYZ(self.fname2)
self.__x__ = self.x
self.__qoff__ = self.qoff
self.output_params = {'scaler_parameters': {}}
class Formol: #Please put the class name same as the function name
re = 2.818e-5 #Classical electron radius in Angstroms
No = 6.023e23 #Avagadro's number
def __init__(
self,
x=0,
E=12.0,
fname1='W:/Tianbo_Collab/Mo132.xyz',
eta1=1.0,
fname2='/media/sf_Mrinal_Bera/Documents/MA-Collab/XTal_data/P2W12.xyz',
eta2=0.0,
rmin=0.0,
rmax=10.0,
Nr=100,
qoff=0.0,
sol=18.0,
sig=0.0,
norm=1,
bkg=0.0,
mpar={}):
"""
Calculates the form factor for two different kinds of molecules in cm^-1 for which the XYZ coordinates of the all the atoms composing the molecules are known
x scalar or array of reciprocal wave vectors
E Energy of the X-rays at which the scattering pattern is measured
fname1 Name with path of the .xyz file containing X, Y, Z coordinates of all the atoms of the molecule of type 1
eta1 Fraction of molecule type 1
fname2 Name with path of the .xyz file containing X, Y, Z coordinates of all the atoms of the moleucule of type 2
eta2 Fraction of molecule type 2
rmin Minimum radial distance for calculating electron density
rmax Maximum radial distance for calculating electron density
Nr Number of points at which electron density will be calculated
qoff Q-offset may be required due to uncertainity in Q-calibration
sol No of electrons in solvent molecule (Ex: H2O has 18 electrons)
sig Debye-waller factor
norm Normalization constant which can be the molar concentration of the particles
bkg Background
"""
if type(x) == list:
self.x = np.array(x)
else:
self.x = np.array([x])
if os.path.exists(fname1):
self.fname1 = fname1
else:
self.fname1 = None
self.eta1 = eta1
if os.path.exists(fname2):
self.fname2 = fname2
else:
self.fname2 = None
self.eta2 = eta2
self.rmin = rmin
self.__rmin__ = rmin
self.rmax = rmax
self.__rmax__ = rmax
self.Nr = Nr
self.__Nr__ = Nr
self.norm = norm
self.bkg = bkg
self.E = E
self.sol = sol
self.qoff = qoff
self.sig = sig
self.__mpar__ = mpar #If there is any multivalued parameter
self.choices = {
} #If there are choices available for any fixed parameters
self.__fnames__ = [self.fname1, self.fname2]
self.__E__ = E
self.__xdb__ = XrayDB()
#if self.fname1 is not None:
# self.__Natoms1__,self.__pos1__,self.__f11__=self.readXYZ(self.fname1)
#if self.fname2 is not None:
# self.__Natoms2__,self.__pos2__,self.__f12__=self.readXYZ(self.fname2)
self.__x__ = self.x
self.__qoff__ = self.qoff
self.output_params = {'scaler_parameters': {}}
def init_params(self):
"""
Define all the fitting parameters like
self.param.add('sig',value=0,vary=0)
"""
self.params = Parameters()
self.params.add('eta1',
value=self.eta1,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
self.params.add('eta2',
value=self.eta2,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
self.params.add('qoff',
value=self.qoff,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
self.params.add('norm',
value=self.norm,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
self.params.add('bkg',
value=self.bkg,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
self.params.add('sig',
value=self.sig,
vary=0,
min=-np.inf,
max=np.inf,
expr=None,
brute_step=0.1)
def readXYZ(self, fname):
"""
Reads the xyz file to read the atomic positions and put it in dictionary
"""
fh = open(fname, 'r')
lines = fh.readlines()
Natoms = eval(lines[0])
atoms = {'Natoms': Natoms}
cen = np.zeros(3)
atoms['elements'] = []
for i in range(Natoms):
line = lines[i + 2].split()
pos = np.array(list((map(eval, line[1:]))))
if line[0] not in atoms['elements']:
atoms['elements'].append(line[0])
atoms[i] = {'element': line[0], 'pos': pos}
cen = cen + pos
cen = cen / Natoms
for i in range(Natoms):
atoms[i]['pos'] = atoms[i]['pos'] - cen
atoms[i]['distance'] = np.sqrt(np.sum(atoms[i]['pos']**2))
return atoms
def calc_xtal_rho(self, fname, rmin=0, rmax=10, Nr=81, energy=None):
"""
Calculates radially averaged complex electron density in el/Angs^3 of a molecule from the co-ordinates obtained from X-ray crystallography.
fname :: .xyz file having all the X, Y, Z coordinates of atoms of the molecule in Angstroms
rmin :: Minimum radial distance in Angstroms (If rmin=0 then calculaiton will be done with rmin=1e-3 to avoid r=0 in the density calculation)
rmax :: Maximum radial distance in Angstroms
Nr :: (Use odd numbers only) No. of points between rmin and rmax at which the electron density has to be calculated
energy :: Energy in keV at which the electron density will be calculated
"""
atoms = self.readXYZ(fname)
if rmin < 1e-6:
rmin = 1e-3
r = np.linspace(rmin, rmax, Nr)
dr = r[1] - r[0]
rho = np.zeros(Nr) * (1.0 + 0.0j)
for ele in atoms['elements']:
distances = [
atoms[i]['distance'] for i in range(atoms['Natoms'])
if atoms[i]['element'] == ele
]
Nrho, _ = np.histogram(distances,
bins=Nr,
range=(rmin - dr / 2, rmax + dr / 2))
if energy is None:
rho = rho + Nrho * (
self.__xdb__.f0(ele, 0.0)
) #+xrdb.f1_chantler(element=ele,energy=energy*1e3,smoothing=0))
else:
f1 = self.__xdb__.f1_chantler(element=ele,
energy=energy * 1e3,
smoothing=0)
f2 = self.__xdb__.f2_chantler(element=ele,
energy=energy * 1e3,
smoothing=0)
rho = rho + Nrho * (self.__xdb__.f0(ele, 0.0) + f1 + 1.0j * f2)
#print(r[:-1]+(),rho)
return r, rho / 4 / np.pi / r**2 / dr #+self.sol*np.where(rho<1e-6,1.0,0.0)
def calc_form(self, q, r, rho):
"""
Calculates the isotropic form factor in cm^-1 using the isotropic electron density as a funciton of radial distance
q :: scaler or array of reciprocal reciprocal wave vector in inv. Angstroms at which the form factor needs to be calculated in
r :: array of radial distances at which he electron density in known in Angstroms
rho :: array of electron densities as a funciton of radial distance in el/Angstroms^3. Note: The electron density should decay to zero at the last radial distance
"""
dr = r[1] - r[0]
q = q + self.__qoff__
form = np.zeros_like(q)
for r1, rho1 in zip(r, rho):
form = form + 4 * np.pi * r1 * rho1 * np.sin(q * r1) / q
form = self.No * self.re**2 * np.absolute(
form)**2 * dr**2 * 1e-16 / 1e3 # in cm^-1/moles
return form
def y(self):
"""
Define the function in terms of x to return some value
"""
self.__qoff__ = self.params['qoff']
#if self.__fnames__!=[None,None]:
#Contribution from first molecule
if self.fname1 is not None:
if self.__fnames__[0] != self.fname1 or self.__E__ != self.E or len(
self.__x__
) != len(self.x) or self.__x__[-1] != self.x[
-1] or self.__qoff__ != self.qoff or self.__Nr__ != self.Nr or self.__rmin__ != self.rmin or self.__rmax__ != self.rmax:
self.__r1__, self.__rho1__ = self.calc_xtal_rho(self.fname1,
rmin=self.rmin,
rmax=self.rmax,
Nr=self.Nr,
energy=self.E)
form1 = self.calc_form(self.x, self.__r1__, self.__rho1__)
self.output_params['rho_1'] = {
'x': self.__r1__,
'y': np.real(self.__rho1__)
}
#Contribution from second molecule
if self.fname2 is not None:
if self.__fnames__[1] != self.fname2 or self.__E__ != self.E or len(
self.__x__
) != len(self.x) or self.__x__[-1] != self.x[
-1] or self.__qoff__ != self.qoff or self.__Nr__ != self.Nr or self.__rmin__ != self.rmin or self.__rmax__ != self.rmax:
self.__r2__, self.__rho2__ = self.calc_xtal_rho(self.fname2,
rmin=self.rmin,
rmax=self.rmax,
Nr=self.Nr,
energy=self.E)
form2 = self.calc_form(self.x, self.__r2__, self.__rho2__)
self.output_params['rho_2'] = {
'x': self.__r2__,
'y': np.real(self.__rho2__)
}
self.__fnames__ = [self.fname1, self.fname2]
self.__E__ = self.E
self.__x__ = self.x
self.__rmin__ = self.rmin
self.__rmax__ = self.rmax
self.__Nr__ = self.Nr
if self.__fnames__[0] is not None and self.__fnames__[1] is not None:
self.output_params[os.path.basename(self.fname1) + '_1'] = {
'x': self.x,
'y': self.norm * self.eta1 * form1
}
self.output_params[os.path.basename(self.fname2) + '_1'] = {
'x': self.x,
'y': self.norm * self.eta2 * form2
}
self.output_params['bkg'] = {
'x': self.x,
'y': self.bkg * np.ones_like(self.x)
}
return (self.eta1 * form1 + self.eta2 * form2
) * self.norm * np.exp(-self.x**2 * self.sig**2) + self.bkg
elif self.__fnames__[0] is not None and self.__fnames__[1] is None:
self.output_params[os.path.basename(self.fname1) + '_1'] = {
'x': self.x,
'y': self.norm * self.eta1 * form1
}
self.output_params['bkg'] = {
'x': self.x,
'y': self.bkg * np.ones_like(self.x)
}
return self.eta1 * form1 * self.norm * np.exp(
-self.x**2 * self.sig**2) + self.bkg
elif self.__fnames__[0] is None and self.__fnames__[1] is not None:
self.output_params[os.path.basename(self.fname2) + '_1'] = {
'x': self.x,
'y': self.norm * self.eta2 * form2
}
self.output_params['bkg'] = {
'x': self.x,
'y': self.bkg * np.ones_like(self.x)
}
return self.eta2 * form2 * self.norm * np.exp(
-self.x**2 * self.sig**2) + self.bkg
else:
return np.ones_like(self.x)
from xraydb import XrayDB
import matplotlib.pyplot as plt
import operator
import numpy
import scipy.optimize as optimization
import scipy
xray = XrayDB()
Energy_Value = [i for i in range(12000, 26010, 10)]
dn_count = 1
#real Xray source data
source_xray = numpy.loadtxt('/ufs/piao/Desktop/data_xray.txt')
source_xray = source_xray.transpose()
source_xray[0] = source_xray[0] * 0.01165211 - 0.147653
print source_xray
#detector efficiency data
detector_efficiency = numpy.loadtxt('/ufs/piao/Downloads/Default Dataset.csv', delimiter=',')
detector_efficiency = detector_efficiency.transpose()
detector_efficiency[1] = detector_efficiency[1] / 100
print detector_efficiency
def counting_on_threshold_source_real(threshold_kev):
i = 0
for element in source_xray[0]:
if element > threshold_kev:
from xraydb import XrayDB
db = XrayDB()
def extract(dat, key):
val = dat.get(key, [' '])[0]
if isinstance(val, float) and val > 1:
val = int(round(val))
return str(val)
elnames = ('', 'hydrogen', 'helium', 'lithium', 'beryllium', 'boron', 'carbon',
'nitrogen', 'oxygen', 'fluorine', 'neon', 'sodium', 'magnesium',
'aluminum', 'silicon', 'phosphorus', 'sulfur', 'chlorine', 'argon',
'potassium', 'calcium', 'scandium', 'titanium', 'vanadium',
'chromium', 'manganese', 'iron', 'cobalt', 'nickel', 'copper',
'zinc', 'gallium', 'germanium', 'arsenic', 'selenium', 'bromine',
'krypton', 'rubidium', 'strontium', 'yttrium', 'zirconium',
'niobium', 'molybdenum', 'technetium', 'ruthenium', 'rhodium',
'palladium', 'silver', 'cadmium', 'indium', 'tin', 'antimony',
'tellurium', 'iodine', 'xenon', 'cesium', 'barium', 'lanthanum',
'cerium', 'praseodymium', 'neodymium', 'promethium', 'samarium',
'europium', 'gadolinium', 'terbium', 'dysprosium', 'holmium',
'erbium', 'thulium', 'ytterbium', 'lutetium', 'hafnium', 'tantalum',
'tungsten', 'rhenium', 'osmium', 'iridium', 'platinum', 'gold',
'mercury', 'thallium', 'lead', 'bismuth', 'polonium', 'astatine',
'radon', 'francium', 'radium', 'actinium', 'thorium',
'protactinium', 'uranium', 'neptunium', 'plutonium', 'americium',
'curium', 'berkelium', 'californium')
chemstates = {
def _larch_init(_larch):
"""initialize xraydb"""
setsym = _larch.symtable.set_symbol
setsym('_xray._xraydb', XrayDB())
setsym('_xray._materials', _read_materials_db())
class XAnoS_Batch_Processor_2(QWidget):
"""
"""
def __init__(self, parent=None):
QWidget.__init__(self, parent=None)
loadUi('UI_Forms/ASAXS_Batch_Processor_2.ui', self)
self.initUI()
self.init_signals()
try:
self.open_settings()
except:
pass
self.stop = False
def initUI(self):
"""
initialize the GUI components
"""
self.sampleFileName = self.sampleFileNameLineEdit.text()
self.doubleValidator = QDoubleValidator()
self.integerValidator = QIntValidator()
if self.sampleFileName == '':
self.sampleFileName = None
self.sampleNumsChanged()
self.bkgNumChanged()
self.stdNumChanged()
#self.sampleThicknessLineEdit.setValidator(self.doubleValidator)
self.bkgThicknessLineEdit.setValidator(self.doubleValidator)
self.stdThicknessLineEdit.setValidator(self.doubleValidator)
self.sampleThickness = float(self.sampleThicknessLineEdit.text())
self.bkgThickness = float(self.bkgThicknessLineEdit.text())
self.energyNpts = self.energyNptsSpinBox.value()
self.repeatNpts = self.repeatSpinBox.value()
self.normStd = self.normStdSampleComboBox.currentText()
self.stdThickness = float(self.stdThicknessLineEdit.text())
self.xMinMaxText = self.xMinMaxLineEdit.text()
self.xMin, self.xMax = list(map(float, self.xMinMaxText.split(':')))
self.interpType = self.interpComboBox.currentText()
self.progressBar.setMinimum(0)
self.progressBar.setValue(0)
self.xdb = XrayDB()
def init_signals(self):
"""
Initialize signals
:return:
"""
self.selectFileNamePushButton.clicked.connect(self.openSampleFname)
self.firstSampleNumsLineEdit.returnPressed.connect(
self.sampleNumsChanged)
#self.firstSampleNumsLineEdit.textEdited.connect(self.sampleNumsChanged)
self.bkgSpinBox.valueChanged.connect(self.bkgNumChanged)
self.stdSpinBox.valueChanged.connect(self.stdNumChanged)
self.mtSpinBox.valueChanged.connect(self.mtNumChanged)
self.airSpinBox.valueChanged.connect(self.airNumChanged)
self.sampleThicknessLineEdit.returnPressed.connect(
self.sampleThicknessChanged)
#self.sampleThicknessLineEdit.textEdited.connect(self.sampleThicknessChanged)
self.stdThicknessLineEdit.returnPressed.connect(
self.stdThicknessChanged)
#self.stdThicknessLineEdit.textEdited.connect(self.stdThicknessChanged)
self.bkgThicknessLineEdit.returnPressed.connect(
self.bkgThicknessChanged)
#self.bkgThicknessLineEdit.textEdited.connect(self.bkgThicknessChanged)
self.sampleSetSpinBox.valueChanged.connect(self.sampleSetChanged)
self.energyNptsSpinBox.valueChanged.connect(self.energyNptsChanged)
self.repeatSpinBox.valueChanged.connect(self.repeatNptsChanged)
self.normStdSampleComboBox.currentIndexChanged.connect(
self.normStdChanged)
self.xMinMaxLineEdit.returnPressed.connect(self.xMinMaxChanged)
self.interpComboBox.currentIndexChanged.connect(self.interpTypeChanged)
self.processPushButton.clicked.connect(self.process)
self.stopPushButton.clicked.connect(self.stopProcess)
def stopProcess(self):
self.stop = True
def process(self):
if self.spikeFilterCheckBox.isChecked():
do_avg = True
else:
do_avg = False
if not self.duplicateNums():
self.infoTextEdit.clear()
if self.sampleFileName is not None:
bg_num = self.bkgNum
gc_num = self.stdNum
air_num = self.airNum
mt_num = self.mtNum
fdir = os.path.dirname(self.sampleFileName)
mean_dir = os.path.join(fdir, 'Mean')
ctimes = self.sampleSet * self.repeatNpts
data = {}
bsub_data = {}
if not os.path.exists(mean_dir):
os.makedirs(os.path.join(fdir, 'Mean'))
snames = {}
bnames = {}
gnames = {}
self.progressBar.setMaximum(self.energyNpts - 1)
self.progressBar.setMinimum(0)
self.progressBar.setValue(0)
outputNames = []
self.outputFnames = []
for j in range(0, self.energyNpts):
if self.stop:
self.stop = False
self.progressBar.setValue(0)
return
# Calculating mean of air scattering if the airNum is other than 0
if air_num != 0:
fnum = []
for i in range(air_num + ctimes * j,
air_num + ctimes * j + self.repeatNpts):
fnum.append(i)
bnames[i] = self.sampleFileName + '%04d.txt' % i
data, oaname = average1DSAXS(
self.sampleFileName,
num=fnum,
delete_prev=False,
data=data,
extra_key=fnum[0],
textEdit=self.infoTextEdit,
spike_filter=do_avg)
# Calculating mean of MT capillary if the mtNum is other than 0
if mt_num != 0:
fnum = []
for i in range(mt_num + ctimes * j,
mt_num + ctimes * j + self.repeatNpts):
fnum.append(i)
bnames[i] = self.sampleFileName + '%04d.txt' % i
data, omname = average1DSAXS(
self.sampleFileName,
num=fnum,
delete_prev=False,
data=data,
extra_key=fnum[0],
textEdit=self.infoTextEdit,
spike_filter=do_avg)
if air_num != 0:
obsmfname = os.path.basename(self.sampleFileName +
'_%04d_bsub.txt' %
fnum[0])
data, bsmfname = bkgSub1DSAXS(
data,
omname,
data,
oaname,
obsmfname,
thickness=0.02,
cf=1.0,
bg_factor=1.0,
norm=1.0,
data=data,
textEdit=self.infoTextEdit)
#calculating mean of background
fnum = []
for i in range(bg_num + ctimes * j,
bg_num + ctimes * j + self.repeatNpts):
fnum.append(i)
bnames[i] = self.sampleFileName + '%04d.txt' % i
data, obname = average1DSAXS(self.sampleFileName,
num=fnum,
delete_prev=False,
data=data,
extra_key=fnum[0],
textEdit=self.infoTextEdit,
spike_filter=do_avg)
if mt_num != 0:
obsbfname = os.path.basename(self.sampleFileName +
'_%04d_bsub.txt' %
fnum[0])
data, bsbfname = bkgSub1DSAXS(
data,
obname,
data,
omname,
obsbfname,
thickness=self.bkgThickness,
cf=1.0,
bg_factor=1.0,
norm=1.0,
data=data,
textEdit=self.infoTextEdit)
# Calculating mean of GC
fnum = []
for i in range(gc_num + ctimes * j,
gc_num + ctimes * j + self.repeatNpts):
fnum.append(i)
gnames[i] = self.sampleFileName + '%04d.txt' % i
data, ogname = average1DSAXS(self.sampleFileName,
num=fnum,
delete_prev=False,
data=data,
extra_key=fnum[0],
textEdit=self.infoTextEdit,
spike_filter=do_avg)
if air_num != 0:
obsgfname = os.path.basename(self.sampleFileName +
'_%04d_bsub.txt' %
fnum[0])
data, bsgfname = bkgSub1DSAXS(
data,
ogname,
data,
oaname,
obsgfname,
thickness=self.stdThickness,
cf=1.0,
bg_factor=1.0,
norm=1.0,
data=data,
textEdit=self.infoTextEdit)
ene, cf, a, b = calc_cf(
bsgfname,
standard=self.normStd,
thickness=self.stdThickness,
xmin=self.xMin,
xmax=self.xMax,
interpolation_type=self.interpType)
else:
ene, cf, a, b = calc_cf(
ogname,
standard=self.normStd,
thickness=self.stdThickness,
xmin=self.xMin,
xmax=self.xMax,
interpolation_type=self.interpType)
if self.normStd == 'GC':
f0 = self.xdb.f0('C', q=0.0)
f1 = self.xdb.f1_chantler('C',
energy=ene * 1e3,
smoothing=0)
cf = cf * (f0[0] / (f0[0] + f1))**2
if air_num != 0:
data[bsgfname]['CF'] = cf
bsub_data[bsgfname] = data[bsgfname]
if air_num != 0 and mt_num != 0:
data[bsmfname]['CF'] = cf
bsub_data[bsmfname] = data[bsmfname]
if mt_num != 0:
data[bsbfname]['CF'] = cf
bsub_data[bsbfname] = data[bsbfname]
# Calculating mean of samples
t = 0
for sam_num in self.samNums:
fnum = []
for i in range(sam_num + ctimes * j,
sam_num + ctimes * j + self.repeatNpts):
fnum.append(i)
snames[i] = self.sampleFileName + '%04d.txt' % i
data, ofname = average1DSAXS(
self.sampleFileName,
num=fnum,
delete_prev=False,
data=data,
extra_key=fnum[0],
textEdit=self.infoTextEdit,
spike_filter=do_avg)
# Performing background subtraction
obsname = os.path.basename(self.sampleFileName +
'_%04d_bsub.txt' % fnum[0])
bg_factor = self.sampleThickness[t] / self.bkgThickness
data, bsfname = bkgSub1DSAXS(
data,
ofname,
data,
obname,
obsname,
thickness=self.sampleThickness[t],
cf=cf,
bg_factor=bg_factor,
norm=1.0,
data=data,
textEdit=self.infoTextEdit)
self.plotWidget.add_data(x=data[bsfname]['x'],y=data[bsfname]['CF']*data[bsfname]['y']/data[bsfname]['Thickness'],\
yerr=data[bsfname]['CF']*data[bsfname]['yerr']/data[bsfname]['Thickness'],name=str(fnum[0])+'_bsub')
bsub_data[bsfname] = data[bsfname]
#self.plotWidget.Plot([str(fnum[0])+'_bsub'])
outputNames.append(str(fnum[0]) + '_bsub')
self.outputFnames.append(bsfname)
self.progressBar.setValue(j)
self.plotWidget.Plot(outputNames)
QApplication.processEvents()
t += 1
self.data = data
#fdir,fnames=write1DSAXS(bsub_data,textEdit=self.infoTextEdit)
self.save_settings()
self.infoTextEdit.append(
'Batch processing completed successfully!')
self.infoTextEdit.moveCursor(QTextCursor.End)
QApplication.processEvents()
datadir = os.path.dirname(self.outputFnames[0])
macrofile = QFileDialog.getSaveFileName(
self,
caption='Save Macro File as:',
filter='Macro Files (*.macro)',
directory=datadir)[0]
macrofile = os.path.splitext(macrofile)[0] + '.macro'
fh = open(os.path.join(datadir, macrofile), 'w')
for tfname in self.outputFnames:
fh.write(tfname + '\n')
fh.close()
reply = QMessageBox.question(
self, 'Component Splitting',
'Do you like to get component splitting from the files?',
QMessageBox.Yes | QMessageBox.No, QMessageBox.Yes)
if reply == QMessageBox.Yes:
curdir = os.getcwd()
QProcess.startDetached(
"python",
[os.path.join(curdir, "XAnoS_Components.py")] +
self.outputFnames)
# w=XAnoS_Components()
# resolution = QDesktopWidget().screenGeometry()
# w.setGeometry(0, 0, resolution.width() - 100, resolution.height() - 100)
# w.move(int(resolution.width() / 2) - int(w.frameSize().width() / 2),
# int(resolution.height() / 2) - int(w.frameSize().height() / 2))
# w.setWindowTitle('XAnoS_Components')
# w.import_data(dataFiles=self.outputFnames)
# w.show()
else:
QMessageBox.warning(self, 'File Error',
'Please select first sample file',
QMessageBox.Ok)
else:
QMessageBox.warning(
self, 'Error',
'It seems you are using same file number for two different category of samples. Please check!',
QMessageBox.Ok)
def openSampleFname(self):
fname = QFileDialog.getOpenFileName(caption='Select sample file name',
filter="Sample Files (*.txt)")[0]
self.sampleFileNameLineEdit.setText(fname[:-9])
self.sampleNameChanged()
def sampleNumsChanged(self):
txt = self.firstSampleNumsLineEdit.text().replace(" ", "")
samNums = list(map(int, txt.split(",")))
if np.all(isinstance(x, int) for x in samNums):
self.samNums = samNums
else:
QMessageBox.warning(
self,
'Please provide integer values and if multiple separate them by commas in between.',
QMessageBox.Ok)
self.samNums = [1]
self.firstSampleNumsLineEdit.setText('1')
self.sampleThicknessChanged()
# try:
# txt=self.firstSampleNumsLineEdit.text().replace(" ","")
# samNums=list(map(int, txt.split(",")))
# if all(isinstance(x, int) for x in samNums):
# self.samNums=samNums
# else:
# QMessageBox.warning(self,
# 'Please provide integer values and if multiple separate them by commas in between.',\
# QMessageBox.Ok)
# self.samNums=[1]
# self.firstSampleNumsLineEdit.setText('1')
# self.save_settings()
# except:
# pass
def bkgNumChanged(self):
self.bkgNum = self.bkgSpinBox.value()
# if bkgNum in self.samNums:
# response = QMessageBox.question(self, 'As this number also exists as sample number, are you sure this number\
# belongs to backgroud?', QMessageBox.Yes, QMessageBox.No)
# if response == QMessageBox.Yes:
# self.bkgNum = bkgNum
# else:
# self.bkgSpinBox.setValue(str(self.bkgNum))
# else:
# self.bkgNum = bkgNum
# self.save_settings()
def stdNumChanged(self):
self.stdNum = self.stdSpinBox.value()
# if stdNum in self.samNums or stdNum==self.bkgNum:
# response = QMessageBox.question(self, 'As this number also exists as First Sample Nums, are you sure this number\
# belongs to background?', QMessageBox.Yes, QMessageBox.No)
# if response == QMessageBox.Yes:
# self.stdNum = stdNum
# else:
# self.stdSpinBox.setValue(self.stdNum)
# elif stdNum == self.bkgNum:
# response = QMessageBox.question(self, 'As this number also exists as First Bkg Num, are you sure this number\
# belongs to Std Num?', QMessageBox.Yes, QMessageBox.No)
# if response == QMessageBox.Yes:
# self.stdNum = stdNum
# else:
# self.stdSpinBox.setValue(self.stdNum)
# else:
# self.stdNum = stdNum
# self.save_settings()
def sampleSetChanged(self):
self.sampleSet = self.sampleSetSpinBox.value()
def mtNumChanged(self):
self.mtNum = self.mtSpinBox.value()
def airNumChanged(self):
self.airNum = self.airSpinBox.value()
def duplicateNums(self):
txt = self.firstSampleNumsLineEdit.text().replace(" ", "")
Nums = list(map(int, txt.split(",")))
Nums = Nums + [self.bkgNum, self.mtNum, self.airNum]
if self.mtNum != 0 and self.airNum != 0:
if np.unique(Nums).size != len(Nums):
return True
else:
return False
else:
return False
def sampleNameChanged(self):
self.sampleFileName = self.sampleFileNameLineEdit.text()
if self.sampleFileName == '':
self.sampleFileName = None
def sampleThicknessChanged(self):
#self.sampleThickness= float(self.sampleThicknessLineEdit.text())
txt = self.sampleThicknessLineEdit.text().replace(" ", "")
self.sampleThickness = list(map(float, txt.split(",")))
if len(self.samNums) != len(self.sampleThickness):
QMessageBox.warning(
self, 'Sample Error',
'Please provide %d thicknesses' % len(self.samNums),
QMessageBox.Ok)
#self.save_settings()
def bkgThicknessChanged(self):
self.bkgThickness = float(self.bkgThicknessLineEdit.text())
#self.save_settings()
def stdThicknessChanged(self):
self.stdThickness = float(self.stdThicknessLineEdit.text())
#self.save_settings()
def energyNptsChanged(self):
self.energyNpts = self.energyNptsSpinBox.value()
#self.save_settings()
def repeatNptsChanged(self):
self.repeatNpts = self.repeatSpinBox.value()
#self.save_settings()
def normStdChanged(self):
self.normStd = self.normStdSampleComboBox.currentText()
#self.save_settings()
def xMinMaxChanged(self):
self.xMinMaxText = self.xMinMaxLineEdit.text()
try:
self.xMin, self.xMax = list(map(float,
self.xMinMaxText.split(':')))
except:
self.xMin, self.xMax = 0.0, 1.0
self.xMinMaxLineEdit.setText('%.1f:%.1f' % self.xMin, self.xMax)
#self.save_settings()
def interpTypeChanged(self):
self.interpType = self.interpTypeComboBox.currentText()
#self.save_settings()
def save_settings(self):
fh = open('./batch_settings.txt', 'w+')
fh.write('samNums=' + str(self.samNums) + '\n')
fh.write('bkgNum=' + str(self.bkgNum) + '\n')
fh.write('stdNum=' + str(self.stdNum) + '\n')
fh.write('mtNum=' + str(self.mtNum) + '\n')
fh.write('airNum=' + str(self.airNum) + '\n')
fh.write('sampleThickness=' + str(self.sampleThickness) + '\n')
fh.write('bkgThickness=' + str(self.bkgThickness) + '\n')
fh.write('stdThickness=' + str(self.stdThickness) + '\n')
fh.write('normStd=' + self.normStd + '\n')
fh.write('xMinMax=' + self.xMinMaxText + '\n')
fh.write('interpType=' + self.interpType + '\n')
fh.write('energyNpts=' + str(self.energyNpts) + '\n')
fh.write('repeatNpts=' + str(self.repeatNpts) + '\n')
fh.write('sampleSet=' + str(self.sampleSet))
fh.close()
def open_settings(self):
fh = open('./batch_settings.txt', 'r')
lines = fh.readlines()
fh.close()
self.samNums = eval(lines[0].strip().split('=')[1])
samNums = ''
for i in self.samNums:
samNums += str(i) + ','
self.firstSampleNumsLineEdit.setText(samNums[:-1])
self.bkgNum = int(lines[1].strip().split('=')[1])
self.bkgSpinBox.setValue(self.bkgNum)
self.stdNum = int(lines[2].strip().split('=')[1])
self.stdSpinBox.setValue(self.stdNum)
self.mtNum = int(lines[3].strip().split('=')[1])
self.mtSpinBox.setValue(self.mtNum)
self.airNum = int(lines[4].strip().split('=')[1])
self.airSpinBox.setValue(self.airNum)
self.sampleThickness = eval(lines[5].strip().split('=')[1])
sampleThickness = ''
for i in self.sampleThickness:
sampleThickness += str(i) + ','
self.sampleThicknessLineEdit.setText(str(sampleThickness[:-1]))
self.bkgThickness = float(lines[6].strip().split('=')[1])
self.bkgThicknessLineEdit.setText(str(self.bkgThickness))
self.stdThickness = float(lines[7].strip().split('=')[1])
self.stdThicknessLineEdit.setText(str(self.stdThickness))
self.normStd = lines[8].strip().split('=')[1]
self.normStdSampleComboBox.setCurrentIndex(
self.normStdSampleComboBox.findText(self.normStd))
self.xMinMaxText = lines[9].strip().split('=')[1]
self.xMinMaxLineEdit.setText(self.xMinMaxText)
self.xMin, self.xMax = list(map(float, self.xMinMaxText.split(':')))
self.interpType = lines[10].strip().split('=')[1]
self.interpComboBox.setCurrentIndex(
self.interpComboBox.findText(self.interpType))
self.energyNpts = int(lines[11].strip().split('=')[1])
self.energyNptsSpinBox.setValue(self.energyNpts)
self.repeatNpts = int(lines[12].strip().split('=')[1])
self.repeatSpinBox.setValue(self.repeatNpts)
self.sampleSet = int(lines[13].strip().split('=')[1])
self.sampleSetSpinBox.setValue(self.sampleSet)
def theoretical_spectrum(element, Energy_Value):
return XrayDB().mu_elam(element, Energy_Value)
from xraydb import XrayDB
db = XrayDB()
def extract(dat, key):
val = dat.get(key, [' '])[0]
if isinstance(val, float) and val > 1:
val = int(round(val))
return str(val)
elnames = ('', 'hydrogen' , 'helium', 'lithium' , 'beryllium', 'boron' ,
'carbon' ,'nitrogen' , 'oxygen', 'fluorine' , 'neon' ,'sodium',
'magnesium', 'aluminum' , 'silicon', 'phosphorus' , 'sulfur',
'chlorine' , 'argon', 'potassium' , 'calcium', 'scandium' ,
'titanium','vanadium' , 'chromium','manganese' , 'iron',
'cobalt' , 'nickel','copper' , 'zinc','gallium' ,
'germanium','arsenic' , 'selenium','bromine' , 'krypton',
'rubidium' , 'strontium','yttrium' , 'zirconium','niobium' ,
'molybdenum','technetium' , 'ruthenium','rhodium' ,
'palladium','silver' , 'cadmium','indium' , 'tin', 'antimony' ,
'tellurium','iodine' , 'xenon','cesium' , 'barium','lanthanum' ,
'cerium','praseodymium', 'neodymium', 'promethium' ,
'samarium','europium' , 'gadolinium', 'terbium' ,
'dysprosium','holmium' , 'erbium','thulium' ,
'ytterbium','lutetium' , 'hafnium','tantalum' , 'tungsten',
'rhenium' , 'osmium','iridium' , 'platinum','gold' ,
'mercury','thallium' , 'lead','bismuth' , 'polonium', 'astatine',
'radon','francium' , 'radium','actinium' ,
'thorium','protactinium', 'uranium','neptunium' , 'plutonium',
'americium', 'curium', 'berkelium', 'californium')
chemstates = {'':'',
class Chemical_Formula:
def __init__(self, formula=None):
self.formula = formula
self.xdb = XrayDB()
cols = ['symbol', 'covalent_radius_cordero']
ptable = get_table('elements')
x = ptable[cols]
self.covalent_radius = x.set_index('symbol').T.to_dict(
'index')['covalent_radius_cordero']
if formula is not None:
self.parse(self.formula)
def parse(self, formula):
parsed = re.findall(r'([A-Z][a-z]*)([-+]?\d*\.*\d*)', formula)
self.formula_dict = {}
for a, b in parsed:
if b != '':
self.formula_dict[a] = float(b)
else:
self.formula_dict[a] = 1.0
return self.formula_dict
def elements(self):
"""
Provides a list of all the elements in the formula
:return:
"""
return list(self.formula_dict.keys())
def element_mole_ratio(self):
"""
Provides a dictionary of mole ratio of all the elements in the formula
:return:
"""
return self.formula_dict
def molar_mass(self):
"""
Provides the total Molar-mass of the compound represented by the formula
:return:
"""
return np.sum([
self.xdb.molar_mass(ele) * num
for ele, num in self.formula_dict.items()
])
def molecular_weight(self):
"""
Provides the Molecular-Weight of the compound represented by the formula
:return:
"""
return self.molar_mass()
def molar_mass_ratio(self, element):
"""
Provides the molecular-mass-ratio of the element in the chemical formula
:param element: Symbol of the element
:return:
"""
if element in self.formula_dict.keys():
tot = self.molar_mass()
return self.xdb.molar_mass(
element) * self.formula_dict[element] / tot
else:
return 0.0
def molar_volume(self):
"""Returns molar volumes in cm^3 or ml"""
volume = 0.0
for ele, moles in self.formula_dict.items():
volume += moles * 4 * np.pi * self.covalent_radius[ele]**3 / 3
return 6.023e23 * volume * 1e-30
def edgenom(filels, inter):
jj = inter
data = EData(filels[jj])
df = data.reader(data.datain)
df['diff'] = df[df.columns[1]].diff()
edgelib = XrayDB()
edgeid = 'pre_unkn'
for z in np.linspace(15, 77, 63):
if abs(
edgelib.xray_edge(edgelib.symbol(int(z)), 'K')[0] -
df['e'][df['diff'].idxmax()]) < 15:
edgeid = edgelib.symbol(int(z))
print(
edgelib.xray_edge(edgelib.symbol(int(z)), 'K')[0] -
df['e'][df['diff'].idxmax()])
print(edgeid)
print('K')
print(jj)
elif abs(
edgelib.xray_edge(edgelib.symbol(int(z)), 'L3')[0] -
df['e'][df['diff'].idxmax()]) < 15:
edgeid = edgelib.symbol(int(z))
print(edgeid)
print('L3')
print(jj)
print(
edgelib.xray_edge(edgelib.symbol(int(z)), 'K')[0] -
df['e'][df['diff'].idxmax()])
return df, edgeid, filels[jj]
def test_molar_mass():
xdb = XrayDB()
assert_allclose(xdb.molar_mass('Co'), 58.932, rtol=0.001)
with pytest.raises(ValueError):
xdb.molar_mass('Mx')
class EDXFit():
def __init__(self):
self.E = None
self.I = None
self.sI = None
self.min_E = 0
self.max_E = np.inf
self.xdb = XrayDB()
self.lines_Fe = self.xdb.xray_lines('Fe', excitation_energy=20e3)
self.lines_Co = self.xdb.xray_lines('Co', excitation_energy=20e3)
self.intensity_Ka1 = (self.lines_Fe['Ka1'].intensity +
self.lines_Fe['Ka2'].intensity +
self.lines_Fe['Ka3'].intensity)
def load_txt_file(self, txtfile, E_min=None, E_max=None, delimiter=','):
data_array = np.genfromtxt(txtfile, delimiter=delimiter)
E = data_array[:, 0]
I = data_array[:, 1]
# sort in ascending order
E, I = zip(*sorted(zip(E, I)))
E = np.asarray(E)
I = np.asarray(I)
# cut off data points out of range
valid_values = np.ones(len(I), dtype=bool)
if E_min:
valid_values = np.logical_and(valid_values, E > E_min)
if E_max:
valid_values = np.logical_and(valid_values, E < E_max)
E = E[valid_values]
I = I[valid_values]
# Poisson Error
sI = np.sqrt(I)
# scale to max. value
intMax_I = max(I)
I /= intMax_I
sI /= intMax_I
self.E = E
self.I = I
self.sI = sI
return E, I, sI
def load_edx_htm(self, htmfile):
elements = []
weight_percent = []
atomic_percent = []
data_array = [elements, weight_percent, atomic_percent]
with open(htmfile, 'r', errors='ignore') as f:
soup = BeautifulSoup(f, "lxml")
table_rows = soup.select("table tr")
for row in table_rows:
columns = row.findAll('td')
for i, row in enumerate(columns):
if i > 2: continue
if row.contents:
el = row.contents[0]
data_array[i].append(el)
return data_array
def estimateBackground(self, min_E_bg, max_E_bg, subtract=True):
assert (self.E is not None)
bg_E_range = np.logical_and(self.E > min_E_bg, self.E < max_E_bg)
E_bg = self.E[bg_E_range]
I_bg = self.I[bg_E_range]
sI_bg = self.sI[bg_E_range]
self.bg = np.mean(I_bg)
self.sbg = np.std(I_bg, ddof=1)
print(f'Estimated Background to: {self.bg} +/- {self.sbg}')
self.I -= self.bg
self.sI = np.sqrt(self.sI**2 + self.sbg**2)
def gaussian(self, x, mu, sig):
return np.exp(-((x - mu) / sig)**2 / 2)
def residuum(self, p, E, I, sI, Imodel):
return (I - Imodel(p, E)) / sI
def CoFe_model(self, p, E):
bg = p['bg']
sigma = p['sigma']
r_Fe = p['r_Fe']
r_Co = p['r_Co']
model = np.zeros(len(E))
for line in self.lines_Fe:
energy = self.lines_Fe[line].energy / 1e3
if energy < self.min_E or energy > self.max_E:
continue
intensity = self.lines_Fe[line].intensity
model += r_Fe * intensity * self.gaussian(E, energy, sigma)
for line in self.lines_Co:
energy = self.lines_Co[line].energy / 1e3
if energy < self.min_E or energy > self.max_E:
continue
intensity = self.lines_Co[line].intensity
model += r_Co * intensity * self.gaussian(E, energy, sigma)
return model + bg
def init_params_CoFe(self):
p = lmfit.Parameters()
p.add('bg', 0.01, min=0, vary=True)
p.add('sigma', 0.06, vary=True)
p.add('r_Co', 1, vary=True)
p.add('r_Fe', 2, vary=True)
self.p = p
return p
def fit(self, p, Imodel):
fit_result = lmfit.minimize(self.residuum,
p,
args=(self.E, self.I, self.sI, Imodel))
print(lmfit.fit_report(fit_result))
self.p = fit_result.params
def test_density():
xdb = XrayDB()
assert_allclose(xdb.molar_mass('Pb'), 207.2, rtol=0.001)
with pytest.raises(ValueError):
xdb.density('Mx')
def test_atomic_number():
xdb = XrayDB()
assert xdb.atomic_number('Ne') == 10
with pytest.raises(ValueError):
xdb.atomic_number('Mx')
class XAnoS_EnergySteps(QWidget):
"""
This widget calculates the Energy values at which the f' values are equidistant below the absorption edge of a selected element
"""
def __init__(self, parent=None):
"""
"""
QWidget.__init__(self, parent)
loadUi('UI_Forms/XAnoS_EnergySteps.ui', self)
self.xrdb = XrayDB()
self.initialize_UI()
self.init_signals()
def initialize_UI(self):
self.doubleValidator=QDoubleValidator()
self.elements = self.xrdb.atomic_symbols
self.elementComboBox.addItems(
[str(self.xrdb.atomic_number(element)) + ': ' + element for element in self.elements])
self.element=self.elementComboBox.currentText().split(': ')[1]
edges = self.xrdb.xray_edges(self.element)
self.edgeComboBox.addItems([key + ': %.4f' % (edges[key].energy / 1000) for key in edges.keys()])
self.EOffsetLineEdit.setValidator(self.doubleValidator)
self.minEnergyLineEdit.setValidator(self.doubleValidator)
self.maxEnergyLineEdit.setValidator(self.doubleValidator)
self.edgeChanged(self.edgeComboBox.currentText())
self.NStepsChanged(20)
self.energyOffset=float(self.EOffsetLineEdit.text())
def init_signals(self):
self.elementComboBox.currentTextChanged.connect(self.elementChanged)
self.edgeComboBox.currentTextChanged.connect(self.edgeChanged)
self.EOffsetLineEdit.textChanged.connect(self.energyOffsetChanged)
self.minEnergyLineEdit.textChanged.connect(self.minEnergyChanged)
self.maxEnergyLineEdit.textChanged.connect(self.maxEnergyChanged)
self.NStepsSpinBox.valueChanged.connect(self.NStepsChanged)
self.calculatePushButton.clicked.connect(self.calculate)
self.savePushButton.clicked.connect(self.saveFile)
def elementChanged(self, txt):
self.element=txt.split(': ')[1]
self.edgeComboBox.currentTextChanged.disconnect()
self.edgeComboBox.clear()
edges = self.xrdb.xray_edges(self.element)
self.edgeComboBox.addItems([key + ': %.4f' % (edges[key].energy / 1000) for key in edges.keys()])
self.edgeComboBox.currentTextChanged.connect(self.edgeChanged)
self.edgeChanged(self.edgeComboBox.currentText())
def edgeChanged(self,txt):
self.maxEnergy=float(txt.split(': ')[1])
self.maxEnergyLineEdit.setText('%.4f'%self.maxEnergy)
self.minEnergyLineEdit.setText('%.4f'%(np.max(self.maxEnergy-1,0)))
def energyOffsetChanged(self, txt):
self.energyOffset=float(txt)
def NStepsChanged(self, N):
self.NEnergy=N
def minEnergyChanged(self,txt):
self.minEnergy=float(txt)
def maxEnergyChanged(self,txt):
self.maxEnergy=float(txt)
def calculate(self):
edge_energy=self.maxEnergy*1000
min_energy=self.minEnergy*1000
element=self.element
steps=self.NEnergy
eoff=self.energyOffset
self.resultTextEdit.clear()
evals = np.linspace(edge_energy, min_energy, steps)
efine = np.linspace(edge_energy, min_energy, 1001)
f1 = self.xrdb.f1_chantler(element=element, energy=efine, smoothing=0)
f1vals = np.linspace(f1[0], f1[-1], steps)
e1vals = np.interp(f1vals, f1, efine)
self.evaltxt = ''
etemp = np.linspace(min_energy, edge_energy + (edge_energy - min_energy), 2001)
f1temp = self.xrdb.f1_chantler(element=element, energy=etemp, smoothing=0)
self.resultTextEdit.append("%10s\t%10s\t%10s\t%10s\t%10s" % ("Step", "f_value", "Mono_E", "Und_E", "f_1"))
for i in range(steps):
# print("%.5f\t%.3f"%(f1vals[i],e1vals[i]/1e3))
self.evaltxt = self.evaltxt + '%.4f,' % (e1vals[i] / 1e3 + eoff)
self.resultTextEdit.append("%10d\t%10.7f\t%10.4f\t%10.4f\t%10.7f" % (
i, f1vals[i], e1vals[i] / 1e3 + eoff, e1vals[i] / 1e3 + 0.17 + eoff,
self.xrdb.f1_chantler(
element=element, energy=e1vals[i], smoothing=0)))
self.plotWidget.add_data(x=etemp/1e3,y=f1temp,fit=True,name='continuous')
self.plotWidget.add_data(x=e1vals/1e3,y=f1vals,name='discrete')
self.plotWidget.Plot(['continuous','discrete'])
txt = 'Energy [' + self.evaltxt[:-1] + '] absolute coupled'
self.resultTextEdit.append('\n')
self.resultTextEdit.append(txt)
def saveFile(self):
try:
txt = 'Energy [' + self.evaltxt[:-1] + '] absolute coupled'
except:
QMessageBox.warning(self,'Save Error','Please calculate before saving!',QMessageBox.Ok)
return
fname=QFileDialog.getSaveFileName(parent=self,caption='Save file as', filter="Text files (*.txt )")[0]
fh = open(fname, 'w')
fh.write(txt)
fh.close()
def test_symbol():
xdb = XrayDB()
assert xdb.symbol(40) == 'Zr'
from PyQt5.uic import loadUi
from PyQt5.QtWidgets import QWidget, QApplication, QMessageBox, QMainWindow, QFileDialog, QDialog, QInputDialog, QTableWidgetItem, QLineEdit
from PyQt5.QtCore import pyqtSignal, Qt, QRegExp
from PyQt5.QtGui import QIntValidator, QDoubleValidator, QFont, QRegExpValidator, QValidator
from PyQt5.QtTest import QTest
import sys
import os
import numpy as np
import re
import scipy.constants
from xraydb import XrayDB
xdb = XrayDB()
class DoubleValidator(QDoubleValidator):
def __init__(self, parent, bottom=0):
QDoubleValidator.__init__(self, parent, bottom=bottom)
self.bottom = bottom
def validate(self, text, pos):
try:
if float(text) >= self.bottom:
state = QDoubleValidator.Acceptable
else:
state = QDoubleValidator.Invalid
except:
state = QDoubleValidator.Invalid
return state, text, pos
class RegExpValidator(QRegExpValidator):
import pylab as pl
print(sys.argv)
if len(sys.argv) == 7:
element = sys.argv[1]
edge_energy = 1e3 * float(sys.argv[2])
min_energy = 1e3 * float(sys.argv[3])
steps = int(sys.argv[4])
eoff = float(sys.argv[5])
try:
fname = sys.argv[6]
except:
fname = '/tmp/positionerFile.txt'
xrdb = XrayDB()
evals = np.linspace(edge_energy, min_energy, steps)
efine = np.linspace(edge_energy, min_energy, 1001)
f1 = xrdb.f1_chantler(element=element, energy=efine, smoothing=0)
f1vals = np.linspace(f1[0], f1[-1], steps)
e1vals = np.interp(f1vals, f1, efine)
print(np.diff(f1vals))
print(np.diff(e1vals))
evaltxt = ''
pl.figure()
etemp = np.linspace(min_energy, edge_energy + (edge_energy - min_energy),
1001)
f1temp = xrdb.f1_chantler(element=element, energy=etemp, smoothing=0)
pl.plot(etemp, f1temp, 'r-', label=element + '-Energy Edge')
print("%10s\t%10s\t%10s\t%10s\t%10s" %
("Step", "f_value", "Mono_E", "Und_E", "f_1"))