def get_Eoc_corrected_observations(pickle_filename, iparams):
'''
Read pickle file name and output Eoc corrected original miller array object.
'''
observations_pickle = pickle.load(open(pickle_filename,"rb"))
observations_original = observations_pickle["observations"][0]
wavelength = observations_pickle["wavelength"]
crystal_init_orientation = observations_pickle["current_orientation"][0]
uc_params = observations_original.unit_cell().parameters()
detector_distance_mm = observations_pickle['distance']
mm_predictions = iparams.pixel_size_mm*(observations_pickle['mapped_predictions'][0])
xbeam = observations_pickle["xbeam"]
ybeam = observations_pickle["ybeam"]
alpha_angle = flex.double([math.atan(abs(pred[0]-xbeam)/abs(pred[1]-ybeam)) \
for pred in mm_predictions])
spot_pred_x_mm = flex.double([pred[0]-xbeam for pred in mm_predictions])
spot_pred_y_mm = flex.double([pred[1]-ybeam for pred in mm_predictions])
#filter resolution
i_sel_res = observations_original.resolution_filter_selection(\
d_max=iparams.iotacc.d_max, d_min=iparams.iotacc.d_min)
observations_original = observations_original.customized_copy(\
indices=observations_original.indices().select(i_sel_res), \
data=observations_original.data().select(i_sel_res), \
sigmas=observations_original.sigmas().select(i_sel_res))
alpha_angle = alpha_angle.select(i_sel_res)
spot_pred_x_mm = spot_pred_x_mm.select(i_sel_res)
spot_pred_y_mm = spot_pred_y_mm.select(i_sel_res)
#Filter weak
i_sel = (observations_original.data()/observations_original.sigmas()) > iparams.iotacc.sigma_min
observations_original = observations_original.customized_copy(\
indices=observations_original.indices().select(i_sel),\
data=observations_original.data().select(i_sel),\
sigmas=observations_original.sigmas().select(i_sel))
alpha_angle = alpha_angle.select(i_sel)
spot_pred_x_mm = spot_pred_x_mm.select(i_sel)
spot_pred_y_mm = spot_pred_y_mm.select(i_sel)
#calculate spot radius
from prime.postrefine.mod_leastsqr import calc_spot_radius
spot_radius = calc_spot_radius(sqr(crystal_init_orientation.reciprocal_matrix()),
observations_original.indices(), wavelength)
G = 1
B = 0
from prime.postrefine.mod_leastsqr import calc_partiality_anisotropy_set
two_theta = observations_original.two_theta(wavelength=wavelength).data()
sin_theta_over_lambda_sq = observations_original.two_theta(wavelength=wavelength).sin_theta_over_lambda_sq().data()
ry = 0
rz = 0
re = iparams.gamma_e
rotx = 0
roty = 0
#calc partiality
partiality_init, delta_xy_init, rs_init, rh_init = calc_partiality_anisotropy_set(crystal_init_orientation.unit_cell(), rotx, roty, observations_original.indices(), ry, rz, spot_radius, re, two_theta, alpha_angle, wavelength, crystal_init_orientation, spot_pred_x_mm, spot_pred_y_mm, detector_distance_mm, iparams.partiality_model, iparams.flag_beam_divergence)
from prime.postrefine.mod_leastsqr import calc_full_refl
I_full = calc_full_refl(observations_original.data(), sin_theta_over_lambda_sq,
G, B, partiality_init, rs_init, iparams.flag_volume_correction)
sigI_full = calc_full_refl(observations_original.sigmas(), sin_theta_over_lambda_sq,
G, B, partiality_init, rs_init, iparams.flag_volume_correction)
observations_Eoc_corrected = observations_original.customized_copy(data=I_full, sigmas=sigI_full)
return observations_Eoc_corrected, observations_original
def get_Eoc_corrected_observations(pickle_filename, iparams):
'''
Read pickle file name and output Eoc corrected original miller array object.
'''
observations_pickle = read_frame(pickle_filename)
observations_original = observations_pickle["observations"][0]
wavelength = observations_pickle["wavelength"]
crystal_init_orientation = observations_pickle["current_orientation"][0]
uc_params = observations_original.unit_cell().parameters()
detector_distance_mm = observations_pickle['distance']
mm_predictions = iparams.pixel_size_mm * (
observations_pickle['mapped_predictions'][0])
xbeam = observations_pickle["xbeam"]
ybeam = observations_pickle["ybeam"]
alpha_angle = flex.double([math.atan(abs(pred[0]-xbeam)/abs(pred[1]-ybeam)) \
for pred in mm_predictions])
spot_pred_x_mm = flex.double([pred[0] - xbeam for pred in mm_predictions])
spot_pred_y_mm = flex.double([pred[1] - ybeam for pred in mm_predictions])
#filter resolution
i_sel_res = observations_original.resolution_filter_selection(\
d_max=iparams.iotacc.d_max, d_min=iparams.iotacc.d_min)
observations_original = observations_original.customized_copy(\
indices=observations_original.indices().select(i_sel_res), \
data=observations_original.data().select(i_sel_res), \
sigmas=observations_original.sigmas().select(i_sel_res))
alpha_angle = alpha_angle.select(i_sel_res)
spot_pred_x_mm = spot_pred_x_mm.select(i_sel_res)
spot_pred_y_mm = spot_pred_y_mm.select(i_sel_res)
#Filter weak
i_sel = (observations_original.data() /
observations_original.sigmas()) > iparams.iotacc.sigma_min
observations_original = observations_original.customized_copy(\
indices=observations_original.indices().select(i_sel),\
data=observations_original.data().select(i_sel),\
sigmas=observations_original.sigmas().select(i_sel))
alpha_angle = alpha_angle.select(i_sel)
spot_pred_x_mm = spot_pred_x_mm.select(i_sel)
spot_pred_y_mm = spot_pred_y_mm.select(i_sel)
#calculate spot radius
from prime.postrefine.mod_leastsqr import calc_spot_radius
spot_radius = calc_spot_radius(
sqr(crystal_init_orientation.reciprocal_matrix()),
observations_original.indices(), wavelength)
G = 1
B = 0
from prime.postrefine.mod_leastsqr import calc_partiality_anisotropy_set
two_theta = observations_original.two_theta(wavelength=wavelength).data()
sin_theta_over_lambda_sq = observations_original.two_theta(
wavelength=wavelength).sin_theta_over_lambda_sq().data()
ry = 0
rz = 0
re = iparams.gamma_e
rotx = 0
roty = 0
#calc partiality
partiality_init, delta_xy_init, rs_init, rh_init = calc_partiality_anisotropy_set(
crystal_init_orientation.unit_cell(), rotx, roty,
observations_original.indices(), ry, rz, spot_radius, re, two_theta,
alpha_angle, wavelength, crystal_init_orientation, spot_pred_x_mm,
spot_pred_y_mm, detector_distance_mm, iparams.partiality_model,
iparams.flag_beam_divergence)
from prime.postrefine.mod_leastsqr import calc_full_refl
I_full = calc_full_refl(observations_original.data(),
sin_theta_over_lambda_sq, G, B, partiality_init,
rs_init, iparams.flag_volume_correction)
sigI_full = calc_full_refl(observations_original.sigmas(),
sin_theta_over_lambda_sq, G, B, partiality_init,
rs_init, iparams.flag_volume_correction)
observations_Eoc_corrected = observations_original.customized_copy(
data=I_full, sigmas=sigI_full)
return observations_Eoc_corrected, observations_original
spot_pred_x_mm = flex.double([pred[0]-xbeam for pred in mm_predictions])
spot_pred_y_mm = flex.double([pred[1]-ybeam for pred in mm_predictions])
#resoultion filter
i_sel_res = observations.resolution_filter_selection(d_min=d_min, d_max=d_max)
observations = observations.select(i_sel_res)
alpha_angle = alpha_angle.select(i_sel_res)
spot_pred_x_mm = spot_pred_x_mm.select(i_sel_res)
spot_pred_y_mm = spot_pred_y_mm.select(i_sel_res)
#sort by resolution
perm = observations.sort_permutation(by_value="resolution", reverse=True)
observations = observations.select(perm)
alpha_angle = alpha_angle.select(perm)
spot_pred_x_mm = spot_pred_x_mm.select(perm)
spot_pred_y_mm = spot_pred_y_mm.select(perm)
from prime.postrefine.mod_leastsqr import calc_spot_radius
r0 = calc_spot_radius(sqr(crystal_init_orientation.reciprocal_matrix()),
observations.indices(), wavelength)
from prime.postrefine.mod_leastsqr import calc_partiality_anisotropy_set
two_theta = observations.two_theta(wavelength=wavelength).data()
sin_theta_over_lambda_sq = observations.two_theta(wavelength=wavelength).sin_theta_over_lambda_sq().data()
ry, rz, re, rotx, roty = (0, 0, 0.003, 0, 0)
flag_beam_divergence = False
partiality_init, delta_xy_init, rs_init, rh_init = calc_partiality_anisotropy_set(crystal_init_orientation.unit_cell(),
rotx, roty, observations.indices(),
ry, rz, r0, re, two_theta, alpha_angle, wavelength,
crystal_init_orientation, spot_pred_x_mm, spot_pred_y_mm,
detector_distance_mm, "Lorentzian",
flag_beam_divergence)
I_full = observations.data()/ partiality_init
sigI_full = observations.sigmas()/ partiality_init
observations_full = observations.customized_copy(data=I_full, sigmas=sigI_full)
#calculate R and cc with reference