def _match_full_turns(self, reflections):
"""Modify the calculated phi values so that they match the full rotation
from zero taken from the the observations, rather than being modulo 2*pi."""
x_obs, y_obs, phi_obs = reflections["xyzobs.mm.value"].parts()
x_calc, y_calc, phi_calc = reflections["xyzcal.mm"].parts()
resid = phi_calc - (flex.fmod_positive(phi_obs, TWO_PI))
# ensure this is the smaller of two possibilities
resid = flex.fmod_positive((resid + pi), TWO_PI) - pi
phi_calc = phi_obs + resid
reflections["xyzcal.mm"] = flex.vec3_double(x_calc, y_calc, phi_calc)
# Update xyzcal.px with the correct z_px values in keeping with above
for iexp, e in enumerate(self._experiments):
sel = reflections["id"] == iexp
x_px, y_px, z_px = reflections["xyzcal.px"].select(sel).parts()
scan = e.scan
if scan is not None:
z_px = scan.get_array_index_from_angle(phi_calc.select(sel),
deg=False)
else:
# must be a still image, z centroid not meaningful
z_px = phi_calc.select(sel)
xyzcal_px = flex.vec3_double(x_px, y_px, z_px)
reflections["xyzcal.px"].set_selected(sel, xyzcal_px)
return reflections
def _predict_core(self, reflections):
"""perform prediction for the specified reflections"""
# update the reflection_predictor with the scan-independent part of the
# current geometry
self._reflection_predictor.update()
# duck-typing for VaryingCrystalPredictionParameterisation. Only this
# class has a compose(reflections) method. Sets ub_matrix (and caches
# derivatives).
try:
self._prediction_parameterisation.compose(
reflections)
except AttributeError:
pass
# do prediction (updates reflection table in situ). Scan-varying prediction
# is done automatically if the crystal has scan-points (assuming reflections
# have ub_matrix set)
self._reflection_predictor.predict(reflections)
x_obs, y_obs, phi_obs = reflections['xyzobs.mm.value'].parts()
x_calc, y_calc, phi_calc = reflections['xyzcal.mm'].parts()
# do not wrap around multiples of 2*pi; keep the full rotation
# from zero to differentiate repeat observations.
resid = phi_calc - (flex.fmod_positive(phi_obs, TWO_PI))
# ensure this is the smaller of two possibilities
resid = flex.fmod_positive((resid + pi), TWO_PI) - pi
phi_calc = phi_obs + resid
# put back in the reflections
reflections['xyzcal.mm'] = flex.vec3_double(x_calc, y_calc, phi_calc)
# update xyzcal.px with the correct z_px values in keeping with above
experiments = self._reflection_predictor._experiments
for i, expt in enumerate(experiments):
scan = expt.scan
sel = (reflections['id'] == i)
x_px, y_px, z_px = reflections['xyzcal.px'].select(sel).parts()
if scan is not None:
z_px = scan.get_array_index_from_angle(phi_calc.select(sel), deg=False)
else:
# must be a still image, z centroid not meaningful
z_px = phi_calc.select(sel)
xyzcal_px = flex.vec3_double(x_px, y_px, z_px)
reflections['xyzcal.px'].set_selected(sel, xyzcal_px)
# calculate residuals and assign columns
reflections['x_resid'] = x_calc - x_obs
reflections['x_resid2'] = reflections['x_resid']**2
reflections['y_resid'] = y_calc - y_obs
reflections['y_resid2'] = reflections['y_resid']**2
reflections['phi_resid'] = phi_calc - phi_obs
reflections['phi_resid2'] = reflections['phi_resid']**2
return reflections
def _predict_core(self, reflections, skip_derivatives=False):
"""perform prediction for the specified reflections"""
# duck-typing for ScanVaryingPredictionParameterisation. Only this
# class has a compose(reflections) method. Sets ub_matrix (and caches
# derivatives).
try:
self._prediction_parameterisation.compose(
reflections, skip_derivatives)
except AttributeError:
pass
# do prediction (updates reflection table in situ). Scan-varying prediction
# is done automatically if the crystal has scan-points (assuming reflections
# have ub_matrix set)
self._reflection_predictor(reflections)
x_obs, y_obs, phi_obs = reflections['xyzobs.mm.value'].parts()
x_calc, y_calc, phi_calc = reflections['xyzcal.mm'].parts()
# do not wrap around multiples of 2*pi; keep the full rotation
# from zero to differentiate repeat observations.
resid = phi_calc - (flex.fmod_positive(phi_obs, TWO_PI))
# ensure this is the smaller of two possibilities
resid = flex.fmod_positive((resid + pi), TWO_PI) - pi
phi_calc = phi_obs + resid
# put back in the reflections
reflections['xyzcal.mm'] = flex.vec3_double(x_calc, y_calc, phi_calc)
# update xyzcal.px with the correct z_px values in keeping with above
experiments = self._reflection_predictor._experiments
for i, expt in enumerate(experiments):
scan = expt.scan
sel = (reflections['id'] == i)
x_px, y_px, z_px = reflections['xyzcal.px'].select(sel).parts()
if scan is not None:
z_px = scan.get_array_index_from_angle(phi_calc.select(sel), deg=False)
else:
# must be a still image, z centroid not meaningful
z_px = phi_calc.select(sel)
xyzcal_px = flex.vec3_double(x_px, y_px, z_px)
reflections['xyzcal.px'].set_selected(sel, xyzcal_px)
# calculate residuals and assign columns
reflections['x_resid'] = x_calc - x_obs
reflections['x_resid2'] = reflections['x_resid']**2
reflections['y_resid'] = y_calc - y_obs
reflections['y_resid2'] = reflections['y_resid']**2
reflections['phi_resid'] = phi_calc - phi_obs
reflections['phi_resid2'] = reflections['phi_resid']**2
return reflections