<gh_stars>0
from __future__ import division
from cctbx.array_family import flex
from scitbx.matrix import sqr, col
from cctbx.crystal_orientation import crystal_orientation, basis_type
import math
import numpy as np

class partiality_handler(object):
  """
  mod_partiality:
  1. Calculate partiality for given
  miller indices, crystal orientation, unit cell, wavelength.
  2. Cacluate spot centroid delta distance
  """
  def __init__(self):
    """
    Intialitze parameters
    """

  def calc_full_refl(self, I_o_p_set, sin_theta_over_lambda_sq_set,
                   G, B, p_set, rs_set, flag_volume_correction=True):
    I_o_full_set = I_o_p_set/(G * flex.exp(-2*B*sin_theta_over_lambda_sq_set) * p_set)
    return I_o_full_set

  def calc_spot_radius(self, a_star_matrix, miller_indices, wavelength):
    #calculate spot_radius based on rms delta_S for all spots
    S0 = -1*col((0,0,1./wavelength))
    sd_array = a_star_matrix.elems * miller_indices.as_vec3_double() + S0.elems
    rh_set = sd_array.norms() - (1/wavelength)
    return rh_set.standard_deviation_of_the_sample()

  def voigt(self, x, sig, nu):
    if nu < 0:
      nu = 0
    elif nu > 1:
      nu = 1
    f1 = nu * math.sqrt(math.log(2)/math.pi) * flex.exp(-4*math.log(2)*((x/sig)**2)) * (1/abs(sig))
    f2 = (1-nu)/(math.pi*abs(sig)*(1+(4*((x/sig)**2))))
    f3 = ((nu * math.sqrt(math.log(2)/math.pi))/abs(sig)) + ((1-nu)/(math.pi*abs(sig)))
    svx = (f1 + f2)/f3
    return svx

  def lognpdf(self, x, FWHM, zero):
    #find sig from root of this function
    zero = np.abs(zero)
    sig_range = np.arange(50)/100
    t = sig_range * math.sqrt(math.log(4))
    sig_set = np.array([sig_range[np.argmin(np.abs(( fwhm - (zero * (np.exp(t) - np.exp(-1*t))) )))] for fwhm in FWHM])
    #calc x0
    x0 = math.log(zero) + sig_set**2
    g = 1/( sig_set * math.sqrt(2*math.pi) * np.exp(x0-((sig_set**2)/2)) )
    #calc lognpdf
    X = zero - x
    f1 = 1/( X * sig_set * math.sqrt(2*math.pi) )
    f2 = np.exp( -1 * (np.log(X)-x0)**2 / (2*(sig_set**2)) )
    svx = flex.double(f1 * f2 / g)
    return svx

  def calc_partiality_anisotropy_set(self, my_uc, rotx, roty, miller_indices,
      ry, rz, r0, re, nu,
      bragg_angle_set, alpha_angle_set, wavelength, crystal_init_orientation,
      spot_pred_x_mm_set, spot_pred_y_mm_set, detector_distance_mm,
      partiality_model, flag_beam_divergence):
    #use III.4 in Winkler et al 1979 (A35; P901) for set of miller indices
    O = sqr(my_uc.orthogonalization_matrix()).transpose()
    R = sqr(crystal_init_orientation.crystal_rotation_matrix()).transpose()
    CO = crystal_orientation(O*R, basis_type.direct)
    CO_rotate = CO.rotate_thru((1,0,0), rotx
                 ).rotate_thru((0,1,0), roty)
    A_star = sqr(CO_rotate.reciprocal_matrix())
    S0 = -1*col((0,0,1./wavelength))
    #caculate rs
    rs_set = r0 + (re * flex.tan(bragg_angle_set))
    if flag_beam_divergence:
      rs_set += ((ry * flex.cos(alpha_angle_set))**2 + (rz * flex.sin(alpha_angle_set))**2)**(1/2)
    #calculate rh
    x = A_star.elems * miller_indices.as_vec3_double()
    sd_array = x + S0.elems
    rh_set = sd_array.norms() - (1/wavelength)
    #calculate partiality
    if partiality_model == "Lorentzian":
      partiality_set = ((rs_set**2)/((2*(rh_set**2))+(rs_set**2)))
    elif partiality_model == "Voigt":
      partiality_set = self.voigt(rh_set, rs_set, nu)
    elif partiality_model == "Lognormal":
      partiality_set = self.lognpdf(rh_set, rs_set, nu)
    #calculate delta_xy
    if sum(spot_pred_y_mm_set) == 0:
      #hack for dials integration - spot_pred_x_mm_set is s1 * to be fixed *
      delta_xy_set = (spot_pred_x_mm_set - sd_array).norms()
    else:
      d_ratio = -detector_distance_mm/sd_array.parts()[2]
      calc_xy_array = flex.vec3_double(sd_array.parts()[0]*d_ratio, \
          sd_array.parts()[1]*d_ratio, flex.double([0]*len(d_ratio)))
      pred_xy_array = flex.vec3_double(spot_pred_x_mm_set, spot_pred_y_mm_set, flex.double([0]*len(d_ratio)))
      delta_xy_set = (pred_xy_array - calc_xy_array).norms()
    return partiality_set, delta_xy_set, rs_set, rh_set

from __future__ import division
from cctbx.array_family import flex
from scitbx.matrix import sqr, col
from cctbx.crystal_orientation import crystal_orientation, basis_type
import math
import numpy as np

class partiality_handler(object):
  """
  mod_partiality:
  1. Calculate partiality for given
  miller indices, crystal orientation, unit cell, wavelength.
  2. Cacluate spot centroid delta distance
  """
  def __init__(self):
    """
    Intialitze parameters
    """

  def calc_full_refl(self, I_o_p_set, sin_theta_over_lambda_sq_set,
                   G, B, p_set, rs_set, flag_volume_correction=True):
    I_o_full_set = I_o_p_set/(G * flex.exp(-2*B*sin_theta_over_lambda_sq_set) * p_set)
    return I_o_full_set

  def calc_spot_radius(self, a_star_matrix, miller_indices, wavelength):
    #calculate spot_radius based on rms delta_S for all spots
    S0 = -1*col((0,0,1./wavelength))
    sd_array = a_star_matrix.elems * miller_indices.as_vec3_double() + S0.elems
    rh_set = sd_array.norms() - (1/wavelength)
    return rh_set.standard_deviation_of_the_sample()

  def voigt(self, x, sig, nu):
    if nu < 0:
      nu = 0
    elif nu > 1:
      nu = 1
    f1 = nu * math.sqrt(math.log(2)/math.pi) * flex.exp(-4*math.log(2)*((x/sig)**2)) * (1/abs(sig))
    f2 = (1-nu)/(math.pi*abs(sig)*(1+(4*((x/sig)**2))))
    f3 = ((nu * math.sqrt(math.log(2)/math.pi))/abs(sig)) + ((1-nu)/(math.pi*abs(sig)))
    svx = (f1 + f2)/f3
    return svx

  def lognpdf(self, x, FWHM, zero):
    #find sig from root of this function
    zero = np.abs(zero)
    sig_range = np.arange(50)/100
    t = sig_range * math.sqrt(math.log(4))
    sig_set = np.array([sig_range[np.argmin(np.abs(( fwhm - (zero * (np.exp(t) - np.exp(-1*t))) )))] for fwhm in FWHM])
    #calc x0
    x0 = math.log(zero) + sig_set**2
    g = 1/( sig_set * math.sqrt(2*math.pi) * np.exp(x0-((sig_set**2)/2)) )
    #calc lognpdf
    X = zero - x
    f1 = 1/( X * sig_set * math.sqrt(2*math.pi) )
    f2 = np.exp( -1 * (np.log(X)-x0)**2 / (2*(sig_set**2)) )
    svx = flex.double(f1 * f2 / g)
    return svx

  def calc_partiality_anisotropy_set(self, my_uc, rotx, roty, miller_indices,
      ry, rz, r0, re, nu,
      bragg_angle_set, alpha_angle_set, wavelength, crystal_init_orientation,
      spot_pred_x_mm_set, spot_pred_y_mm_set, detector_distance_mm,
      partiality_model, flag_beam_divergence):
    #use III.4 in Winkler et al 1979 (A35; P901) for set of miller indices
    O = sqr(my_uc.orthogonalization_matrix()).transpose()
    R = sqr(crystal_init_orientation.crystal_rotation_matrix()).transpose()
    CO = crystal_orientation(O*R, basis_type.direct)
    CO_rotate = CO.rotate_thru((1,0,0), rotx
                 ).rotate_thru((0,1,0), roty)
    A_star = sqr(CO_rotate.reciprocal_matrix())
    S0 = -1*col((0,0,1./wavelength))
    #caculate rs
    rs_set = r0 + (re * flex.tan(bragg_angle_set))
    if flag_beam_divergence:
      rs_set += ((ry * flex.cos(alpha_angle_set))**2 + (rz * flex.sin(alpha_angle_set))**2)**(1/2)
    #calculate rh
    x = A_star.elems * miller_indices.as_vec3_double()
    sd_array = x + S0.elems
    rh_set = sd_array.norms() - (1/wavelength)
    #calculate partiality
    if partiality_model == "Lorentzian":
      partiality_set = ((rs_set**2)/((2*(rh_set**2))+(rs_set**2)))
    elif partiality_model == "Voigt":
      partiality_set = self.voigt(rh_set, rs_set, nu)
    elif partiality_model == "Lognormal":
      partiality_set = self.lognpdf(rh_set, rs_set, nu)
    #calculate delta_xy
    if sum(spot_pred_y_mm_set) == 0:
      #hack for dials integration - spot_pred_x_mm_set is s1 * to be fixed *
      delta_xy_set = (spot_pred_x_mm_set - sd_array).norms()
    else:
      d_ratio = -detector_distance_mm/sd_array.parts()[2]
      calc_xy_array = flex.vec3_double(sd_array.parts()[0]*d_ratio, \
          sd_array.parts()[1]*d_ratio, flex.double([0]*len(d_ratio)))
      pred_xy_array = flex.vec3_double(spot_pred_x_mm_set, spot_pred_y_mm_set, flex.double([0]*len(d_ratio)))
      delta_xy_set = (pred_xy_array - calc_xy_array).norms()
    return partiality_set, delta_xy_set, rs_set, rh_set
mod_partiality:   1. Calculate partiality for given   miller indices, crystal orientation, unit cell, wavelength.   2. Cacluate spot centroid delta distance Intialitze parameters #calculate spot_radius based on rms delta_S for all spots #find sig from root of this function #calc x0 #calc lognpdf #use III.4 in Winkler et al 1979 (A35; P901) for set of miller indices #caculate rs #calculate rh #calculate partiality #calculate delta_xy #hack for dials integration - spot_pred_x_mm_set is s1 * to be fixed *