text:  
  # this is the cheap way to edit parameters without entering variables in the main python code.
  # made to be imported in the main.py 
  
  ############################################
  #
  #       File parameters
  #
  #############################################
  
  # put data in a directory
  # the directory name can be relative or absolute path somewhere on Your computer
  # This directory must exist before starting the absorption.py
  datadir= "../../data"
  
  
  # following variables are used to construct the name for the data files, so we can find and analyze them later:
  appname="abs_09"
  
  
  # some data can be reused, especially the transmission of the different fluorescence lines through the sample_thickness
  # since this takes long, we can reuse it by referencing the previous calculation here:
  simappname="abs_08"
  
  #############################################
  #
  # Calculation parameters
  #
  #############################################
  
  # V is for Voxel
  # Vsize=2E-7               #  m - I'd like 10nm, but no computer is going ot make it
  
  # Only for the test: 
  #to test the code in a fast run, use larger voxel size, but take care that it is not larger than the box
  Vsize=2E-6
  
  # these describe the dimensions of the calculated volume
  # it makes sense that the box size is larger than the beam diameter
  sample_thickness=3.0E-4    # 0.3 mm
  beam_dia = 3.2E-5 # 20 mu
  # this is actually setting the half of the size of the box: the actual box is from -box_Y_size to box_Y_size:
  box_Y_size = 30.0E-6 # 50 mu
  box_Z_size = 17.0E-6 # 35 mu
  
  # Intensity of the primary beam is used to get the dose values in a realistic order of magnitudes.
  # the funny numer here is taken from the experimental data
  I0=20334375 # photon/s - flux, beam intensity
  
  # the list of primary beam energies to perform the calculation for. 
  # one can run multiple energies or make a different parameter file for each
  # E_beam=[5000,8000,12000,18000,25000, 30000,35000]
  E_beam=[8000]
  
  
  #############################################
  #
  #       Material parameters
  #
  #############################################
  
  elements=["Ca", "P", "O", "N", "C"]
  
  
  # TODO should use the database for this!
  # TODO use xraylib for this and for atomic scattering factors!
  #      but then I would have several fluorescence lines for each edge and all the proportionality factors...
  #      here I just assume that there is no K-beta, everything goes into one channel. Makes the liee easier...
  
  fluorescence_E={
      "C":277,
      "N":392,
      "O":524,
      "P":2010,
      "Ca":3690
  }
  
  fluorescence_yield_K={
      "C":2.570e-03,
      "N":4.350e-03,
      "O":6.91E-3,
      "P":6.42E-2,
      "Ca":0.1687
  }
  
  # TODO: use all available lines in the cascade
  # fluorescence Yield for Ca for L1 and L3 lines is:
  # Shell  Yield     
  # K   1.687e-01 
  # L1  1.963e-04 
  # L3  2.850e-04 
  #
  # Energy of the L-lines is 0.3-0.4 keV
  #
  