def xrayFluo(atom,density,energy=7.,length=30.,I0=1e10,\
det_radius=1.,det_dist=10.,det_material="Si",det_thick=300,verbose=True):
""" compound: anything periodictable would understand
density: in mM
length: sample length in um
energy: in keV, could be array
"""
import periodictable
from periodictable import xsf
wavelength = 12.398/energy
atom = periodictable.__dict__[atom]
# 1e3 -> from mM to M
# 1e3 -> from L to cm3
# so 1 mM = 1e-3M/L = 1e-6 M/cm3
density_g_cm3 = density*1e-6*atom.mass
n = xsf.index_of_refraction(atom,density=density_g_cm3,wavelength=wavelength)
attenuation_length = xrayAttLenght( atom,density=density_g_cm3,energy=energy )
# um-> m: 1e-6
fraction_absorbed = 1.-np.exp(-length*1e-6/attenuation_length)
if verbose:
print("Fraction of x-ray photons absorbed by the sample:",fraction_absorbed)
## detector ##
det_area = np.pi*det_radius**2
det_solid_angle = det_area/(4*np.pi*det_dist**2)
if verbose:
print("Detector fraction of solid angle:",det_solid_angle)
det_att_len = xrayAttLenght(det_material,wavelength=atom.K_alpha)
det_abs = 1-np.exp(-det_thick*1e-6/det_att_len)
if verbose:
print("Detector efficiency (assuming E fluo = E_K_alpha):",det_abs)
eff = fraction_absorbed*det_solid_angle*det_abs
if verbose:
print("Overall intensity (as ratio to incoming one):",eff)
return eff
def xrayAttLenght(*args,**kw):
from periodictable import xsf
n = xsf.index_of_refraction(*args,**kw)
if not "wavelength" in kw:
wavelength = 12.398/np.asarray(kw["energy"])
else:
wavelength = np.asarray(kw["wavelength"])
attenuation_length = np.abs( (wavelength*1e-10)/ (4*np.pi*np.imag(n)) )
return attenuation_length
def refractive_index(element, eV, mass_density=None):
"""Refractive index using periodictable package.
Imaginary part is positive i.e. optics rather than x-ray convention.
Args:
mass_density (float or None): in kg/m^3. If not given, then :func:`physdata.periodic_table.mass_density`
is used.
"""
if mass_density is None:
mass_density = periodic_table.mass_density(element)
# xsf function accepts keV and g/cm^3
n = xsf.index_of_refraction(compound=element, energy=eV / 1e3, density=mass_density / 1e3).conj()
return n
def attenuation_length(compound,
density=None,
natural_density=None,
energy=None,
wavelength=None):
"""
Calculates the attenuation length for a compound
Transmisison if then exp(-thickness/attenuation_length)
:Parameters:
*compound* : Formula initializer
Chemical formula.
*density* : float | |g/cm^3|
Mass density of the compound, or None for default.
*natural_density* : float | |g/cm^3|
Mass density of the compound at naturally occurring isotope abundance.
*wavelength* : float or vector | |Ang|
Wavelength of the X-ray.
*energy* : float or vector | keV
Energy of the X-ray, if *wavelength* is not specified.
:Returns:
*attenuation_length* : vector | |m|
as function of (energy)
:Notes:
against http://henke.lbl.gov/optical_constants/
"""
if energy is not None: wavelength = xray_wavelength(energy)
assert wavelength is not None, "scattering calculation needs energy or wavelength"
if (numpy.isscalar(wavelength)): wavelength = numpy.array([wavelength])
n = index_of_refraction(compound=compound,
density=density,
natural_density=natural_density,
wavelength=wavelength)
attenuation_length = (wavelength * 1e-10) / (4 * numpy.pi * numpy.imag(n))
return numpy.abs(attenuation_length)
E = 12 # Energy in keV
M = 'Be' # Material
R = 50 # CRL radius of curvature
N = 40 # number of refractive lens
M = getattr(pt, '%s'%M) # I dont know how, but 'eval' - not good idea!)
name = getattr(pt.elements, '%s'%M).name # name of element
density = M.density # density
mass = M.mass # mass of element
lyamda = ptx.xray_energy(E)
n = ptx.index_of_refraction(M, energy=E) # index of refraction
delta = 1-n.real # Delta
beta = -n.imag # Beta
u = 4*np.pi*beta/(lyamda*1e-10) # Linear attenuation coefficient
Lpi = 1e-10*lyamda/(2*delta)
F = (R*1e-6)/(2*N*delta) # CRL focus distance (thin lens)
e1 = (2*np.log(2)/np.pi)**.5 # V.Kohn coefficient
Aeff = e1*(F*lyamda*1e-10*delta/beta)**.5 # CRL effective aperture (V.Kohn)
Aeff_1m = e1*(1*lyamda*1e-10*delta/beta)**.5 # CRL effective aperture @ 1m focus distance
print ('Material %s (%s)'%(M, name))
print ('Density %s g/cm^3'%density)
print ('\nEnergy %s keV'%E)
def getDelta(E, material="Be", density=None):
""" returns 1-real(index_of-refraction) for a given material at a given energy"""
delta = 1 - real(
xsf.index_of_refraction(material, density=density, energy=E))
return delta
def get_delta(self, E, material="Be", density=None):
delta = 1-np.real(xsf.index_of_refraction(material, density=density,
energy=E))
return delta