def run_spotfinder(O):
_ = O.active_wavelengths
if (_ == 1): px = O.pixels
elif (_ == 2): px = O.pixels_2
else:
if (O.pixels is None or O.pixels_2 is None):
px = None
else:
px = O.pixels + O.pixels_2
px /= 2
if (px is None):
return
if (O.work_params.noise.max == 0):
print
print "WARNING:"
print " noise.max = 0: spotfinder is likely to crash..."
print
sys.stdout.flush()
dpx,dpy = O.work_params.detector.pixels
if (dpx < 100 or dpy < 100):
return
from rstbx.simage import run_spotfinder
O.spots = run_spotfinder.process(
work_params=O.work_params,
pixels=px,
show_spots=False)
O.Refresh()
def run_spotfinder(O):
_ = O.active_wavelengths
if (_ == 1): px = O.pixels
elif (_ == 2): px = O.pixels_2
else:
if (O.pixels is None or O.pixels_2 is None):
px = None
else:
px = O.pixels + O.pixels_2
px /= 2
if (px is None):
return
if (O.work_params.noise.max == 0):
print()
print("WARNING:")
print(" noise.max = 0: spotfinder is likely to crash...")
print()
sys.stdout.flush()
dpx, dpy = O.work_params.detector.pixels
if (dpx < 100 or dpy < 100):
return
from rstbx.simage import run_spotfinder
O.spots = run_spotfinder.process(work_params=O.work_params,
pixels=px,
show_spots=False)
O.Refresh()
def index_and_integrate_one(work_params, image_mdls_miller_indices, pixels):
from rstbx.simage import run_spotfinder
spots = run_spotfinder.process(work_params=work_params,
pixels=pixels,
show_spots=False)
if (spots.size() < work_params.min_number_of_spots_for_indexing):
print "Insufficient number of spots for indexing."
print
sys.stdout.flush()
return (spots.size(), None)
from rstbx.simage import run_labelit_index
ai = run_labelit_index.process(work_params=work_params, spots=spots)
good_i_seqs, miller_indices, co = run_labelit_index.report_uc_cr(ai)
from rstbx.simage import refine_uc_cr
refined = refine_uc_cr.refine(
work_params=work_params,
spots=spots,
good_i_seqs=good_i_seqs,
miller_indices=miller_indices,
unit_cell=co.unit_cell(),
crystal_rotation=co.crystal_rotation_matrix())
from rstbx.simage import integrate_crude
predicted_spot_positions, \
predicted_spot_miller_index_i_seqs = integrate_crude.predict_spot_positions(
work_params=work_params,
miller_indices=image_mdls_miller_indices,
unit_cell=refined.unit_cell,
crystal_rotation=refined.crystal_rotation)
print "Number of predicted spot positions:", predicted_spot_positions.size(
)
print
spot_intensities = integrate_crude.collect_spot_intensities(
pixels=pixels,
spot_positions=predicted_spot_positions,
point_spread_inner=work_params.point_spread,
point_spread_outer=work_params.point_spread + 4)
sel = spot_intensities != 0
return (
spots.size(),
image_model(
spot_positions=predicted_spot_positions.select(sel),
spot_intensities=spot_intensities.select(sel),
miller_index_i_seqs=predicted_spot_miller_index_i_seqs.select(sel),
unit_cell=refined.unit_cell,
crystal_rotation=refined.crystal_rotation))
def index_and_integrate_one(work_params, image_mdls_miller_indices, pixels):
from rstbx.simage import run_spotfinder
spots = run_spotfinder.process(
work_params=work_params, pixels=pixels, show_spots=False)
if (spots.size() < work_params.min_number_of_spots_for_indexing):
print "Insufficient number of spots for indexing."
print
sys.stdout.flush()
return (spots.size(), None)
from rstbx.simage import run_labelit_index
ai = run_labelit_index.process(work_params=work_params, spots=spots)
good_i_seqs, miller_indices, co = run_labelit_index.report_uc_cr(ai)
from rstbx.simage import refine_uc_cr
refined = refine_uc_cr.refine(
work_params=work_params,
spots=spots,
good_i_seqs=good_i_seqs,
miller_indices=miller_indices,
unit_cell=co.unit_cell(),
crystal_rotation=co.crystal_rotation_matrix())
from rstbx.simage import integrate_crude
predicted_spot_positions, \
predicted_spot_miller_index_i_seqs = integrate_crude.predict_spot_positions(
work_params=work_params,
miller_indices=image_mdls_miller_indices,
unit_cell=refined.unit_cell,
crystal_rotation=refined.crystal_rotation)
print "Number of predicted spot positions:", predicted_spot_positions.size()
print
spot_intensities = integrate_crude.collect_spot_intensities(
pixels=pixels,
spot_positions=predicted_spot_positions,
point_spread_inner=work_params.point_spread,
point_spread_outer=work_params.point_spread+4)
sel = spot_intensities != 0
return (
spots.size(), image_model(
spot_positions=predicted_spot_positions.select(sel),
spot_intensities=spot_intensities.select(sel),
miller_index_i_seqs=predicted_spot_miller_index_i_seqs.select(sel),
unit_cell=refined.unit_cell,
crystal_rotation=refined.crystal_rotation))
