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))
def run_labelit_index(O, use_original_uc_cr=False):
if (O.spots is None):
O.run_spotfinder()
if (O.spots is None):
return
if (O.spots.size() < 10):
print "Insufficient number of spotfinder spots."
print
return
else:
if (use_original_uc_cr):
print
print "Using original unit cell and crystal rotation" \
" for spot prediction."
print
uc = O.work_params.unit_cell
cr = O.work_params.crystal_rotation_matrix
else:
from rstbx.simage.run_labelit_index import process
try:
ai = process(work_params=O.work_params, spots=O.spots)
except Exception, e:
print "Indexing exception:", e
print
return
print "Spots indexed: %d of %d" % (
ai.hklobserved().size(),
O.spots.size())
co = ai.getOrientation()
uc = co.unit_cell()
cr = co.crystal_rotation_matrix()
print "labelit index unit cell:", uc
from rstbx.simage import refine_uc_cr
refined = refine_uc_cr.refine(
work_params=O.work_params,
spots=O.spots,
good_i_seqs=ai.get_observed_spot_i_seqs_good_only(),
miller_indices=ai.hklobserved(),
unit_cell=uc,
crystal_rotation=cr)
uc = refined.unit_cell
cr = refined.crystal_rotation
print
import cctbx.crystal
crystal_symmetry = cctbx.crystal.symmetry(
unit_cell=uc,
space_group_symbol="P1")
d_min = O.work_params.d_min
if (d_min is None):
d_min = O.work_params.wavelength
import cctbx.miller
miller_set = cctbx.miller.build_set(
crystal_symmetry=crystal_symmetry,
d_min=d_min,
anomalous_flag=True)
from rstbx.simage import image_simple
O.predicted_spots = image_simple(store_spots=True).compute(
unit_cell=miller_set.unit_cell(),
miller_indices=miller_set.indices(),
spot_intensity_factors=None,
crystal_rotation_matrix=cr,
ewald_radius=1/O.work_params.wavelength,
ewald_proximity=O.work_params.ewald_proximity,
signal_max=O.work_params.signal_max,
detector_distance=O.work_params.detector.distance,
detector_size=O.work_params.detector.size,
detector_pixels=O.work_params.detector.pixels,
point_spread=O.work_params.point_spread,
gaussian_falloff_scale=O.work_params.gaussian_falloff_scale).spots
print "Number of predicted spots:", O.predicted_spots.size()
print
def run_labelit_index(O, use_original_uc_cr=False):
if (O.spots is None):
O.run_spotfinder()
if (O.spots is None):
return
if (O.spots.size() < 10):
print("Insufficient number of spotfinder spots.")
print()
return
else:
if (use_original_uc_cr):
print()
print("Using original unit cell and crystal rotation" \
" for spot prediction.")
print()
uc = O.work_params.unit_cell
cr = O.work_params.crystal_rotation_matrix
else:
from rstbx.simage.run_labelit_index import process
try:
ai = process(work_params=O.work_params, spots=O.spots)
except Exception as e:
print("Indexing exception:", e)
print()
return
print("Spots indexed: %d of %d" %
(ai.hklobserved().size(), O.spots.size()))
co = ai.getOrientation()
uc = co.unit_cell()
cr = co.crystal_rotation_matrix()
print("labelit index unit cell:", uc)
from rstbx.simage import refine_uc_cr
refined = refine_uc_cr.refine(
work_params=O.work_params,
spots=O.spots,
good_i_seqs=ai.get_observed_spot_i_seqs_good_only(),
miller_indices=ai.hklobserved(),
unit_cell=uc,
crystal_rotation=cr)
uc = refined.unit_cell
cr = refined.crystal_rotation
print()
import cctbx.crystal
crystal_symmetry = cctbx.crystal.symmetry(unit_cell=uc,
space_group_symbol="P1")
d_min = O.work_params.d_min
if (d_min is None):
d_min = O.work_params.wavelength
import cctbx.miller
miller_set = cctbx.miller.build_set(
crystal_symmetry=crystal_symmetry,
d_min=d_min,
anomalous_flag=True)
from rstbx.simage import image_simple
O.predicted_spots = image_simple(store_spots=True).compute(
unit_cell=miller_set.unit_cell(),
miller_indices=miller_set.indices(),
spot_intensity_factors=None,
crystal_rotation_matrix=cr,
ewald_radius=1 / O.work_params.wavelength,
ewald_proximity=O.work_params.ewald_proximity,
signal_max=O.work_params.signal_max,
detector_distance=O.work_params.detector.distance,
detector_size=O.work_params.detector.size,
detector_pixels=O.work_params.detector.pixels,
point_spread=O.work_params.point_spread,
gaussian_falloff_scale=O.work_params.gaussian_falloff_scale
).spots
print("Number of predicted spots:", O.predicted_spots.size())
print()
O.Refresh()
