old_contents: import numpy as np
  
  class Fluorophore:
      """A single fluorophore is specified by its 3D position, (unit) absorption
      dipole moment (theta, phi), and (unit) emission dipole moment (theta, phi).
      """
      def __init__(self, position=np.array([0, 0, 0]),
                   mu_abs=np.array([0, 0]),
                   mu_em=np.array([0, 0])):
          self.position = position
          self.mu_abs = mu_abs        
          self.mu_em = mu_em
          self.mu_ind = 0
  
new_contents: import numpy as np
  
  class Fluorophore:
      """A fluorophore is specified by its orientation (in theta and phi spherical
      coordinates), it distribution (using a kappa watson distribution), and a
      constant (c) proportional to the fluorohphore's brightness.
      """
      def __init__(self, theta=np.pi/2, phi=0, kappa=None, c=1.0):
          self.theta = theta
          self.phi = phi
          self.kappa = kappa
          self.c = c        
  
subject: Modify Fluorophore for more convenient coordinates.