Beispiel #1
0
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))
Beispiel #2
0
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))
Beispiel #3
0
 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
Beispiel #4
0
 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()