from __future__ import print_function,division
import numpy as np
import os

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 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