def generate_spots(crystal_model,
detector,
beam,
goniometer=None,
scan=None,
sel_fraction=1.0):
import math
experiment = Experiment(beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal_model)
# if we don't set the imageset then from_predictions uses the StillsReflectionPredictor :-(
from dxtbx.imageset import NullReader, ImageSweep
imageset = ImageSweep(NullReader,
indices=range(len(scan.get_epochs())),
beam=beam,
goniometer=goniometer,
detector=detector,
scan=scan)
experiment.imageset = imageset
predicted = flex.reflection_table.from_predictions(experiment)
sel = flex.random_selection(len(predicted),
int(math.floor(sel_fraction * len(predicted))))
predicted = predicted.select(sel)
predicted['imageset_id'] = flex.size_t(len(predicted), 0)
predicted['xyzobs.px.value'] = predicted['xyzcal.px']
predicted['xyzobs.px.variance'] = flex.vec3_double(len(predicted),
(0.5, 0.5, 0.5))
return predicted
def generate_spots(crystal_model,
detector,
beam,
goniometer=None,
scan=None,
sel_fraction=1.0):
experiment = Experiment(beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal_model)
# if we don't set the imageset then from_predictions uses the StillsReflectionPredictor :-(
filenames = [""] * len(scan)
reader = Reader(filenames)
masker = Masker(filenames)
data = ImageSetData(reader, masker)
imageset = ImageSweep(data, beam, detector, goniometer, scan)
experiment.imageset = imageset
predicted = flex.reflection_table.from_predictions(experiment)
sel = flex.random_selection(len(predicted),
int(math.floor(sel_fraction * len(predicted))))
predicted = predicted.select(sel)
predicted['imageset_id'] = flex.size_t(len(predicted), 0)
predicted['xyzobs.px.value'] = predicted['xyzcal.px']
predicted['xyzobs.px.variance'] = flex.vec3_double(len(predicted),
(0.5, 0.5, 0.5))
return predicted
def as_explist(self):
"""
return experiment list for simulated image
"""
exp = Experiment()
exp.crystal = self.crystal
exp.beam = self.beam
exp.detector = self.detector
exp.imageset = self.imageset
explist = ExperimentList()
explist.append(exp)
return explist
def as_explist(self, fname=None, toggle_conventions=False):
"""
return experiment list for simulated image
"""
C = self.crystal
if toggle_conventions:
# switch to DIALS convention before writing CBF
# also change basis of crystal
CURRENT_CONV = self.beamcenter_convention
FSO = sqr(self.fdet_vector + self.sdet_vector +
self.pix0_vector_mm)
self.beamcenter_convention = DIALS
FSO2 = sqr(self.fdet_vector + self.sdet_vector +
self.dials_origin_mm)
xtal_transform = FSO.inverse() * FSO2
# transform the crystal vectors
a, b, c = map(lambda x: xtal_transform * col(x),
C.get_real_space_vectors())
Cdict = C.to_dict()
Cdict['real_space_a'] = a
Cdict['real_space_b'] = b
Cdict['real_space_b'] = c
C = CrystalFactory.from_dict(Cdict)
exp = Experiment()
exp.crystal = C
exp.beam = self.beam
exp.detector = self.detector
exp.imageset = self.imageset
explist = ExperimentList()
explist.append(exp)
if fname is not None:
explist.as_file(fname)
if toggle_conventions:
self.beamcenter_convention = CURRENT_CONV
return explist
# update the background pixel selection with the expanded integration mask
is_bg_pixel[i_panel, j1:j2,
i1:i2] = ~np.logical_or(~bg, expanded_integration_mask)
# <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
# RUN THE TILT PLANE HELPER FUNCTION
# 1. Weighted fit of the background tilt plane
# 2. Updates prediction reflection table with miller indices, and shoeboxes
# 3. Updates prediction reflections with integrations and integration variances
# using Leslie 99
# <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
exper = Experiment()
exper.detector = DET
exper.beam = BEAM
exper.crystal = crystal
exper.imageset = iset # Exper.imageset
if not args.oldway:
refls_predict = TiltPlanes.prep_relfs_for_tiltalization(refls_predict,
exper=exper)
tiltnation = TiltPlanes(panel_imgs=img_data,
panel_bg_masks=is_bg_pixel,
panel_badpix_masks=None)
tiltnation.check_if_refls_are_formatted_for_this_class(refls_predict)
tiltnation.make_quick_bad_pixel_proximity_checker(refls_predict)
tiltnation.sigma_rdout = sigma_readout
tiltnation.adu_per_photon = GAIN
tiltnation.delta_Q = args.deltaq #0.085
tiltnation.zinger_zscore = args.Z
detector_node = DET[
# crystal=cryst_model,
# thresh=0,
# filter=scipy.ndimage.filters.gaussian_filter, sigma=1)
# save the crystal models and other data for later use and debugging
reflsA = refls_strong.select(
flex.bool(np.logical_and(best == 0, d / .10992 < 5)))
reflsB = refls_strong.select(
flex.bool(np.logical_and(best == 1, d / .10992 < 5)))
eA = Experiment()
eA.beam = beamA
eA.detector = detector
eA.imageset = iset
eA.crystal = cryst_model
eB = Experiment()
eB.beam = beamB
eB.detector = detector
eB.imageset = iset
eB.crystal = cryst_model
EL = ExperimentList()
EL.append(eA)
EL.append(eB)
exp_json = os.path.join(out_dir, "expAB_%d.json" % idx)
reflA_pkl = os.path.join(out_dir, "reflA_%d.pkl" % idx)
reflB_pkl = os.path.join(out_dir, "reflB_%d.pkl" % idx)
def split_for_scan_range(self, experiments, reference, scan_range):
""" Update experiments when scan range is set. """
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
# Only do anything is the scan range is set
if scan_range is not None and len(scan_range) > 0:
# Ensure that all experiments have the same imageset and scan
iset = [e.imageset for e in experiments]
scan = [e.scan for e in experiments]
assert all(x == iset[0] for x in iset)
assert all(x == scan[0] for x in scan)
# Get the imageset and scan
iset = experiments[0].imageset
scan = experiments[0].scan
# Get the array range
if scan is not None:
frames_start, frames_end = scan.get_array_range()
assert scan.get_num_images() == len(iset)
else:
frames_start, frames_end = (0, len(iset))
# Create the new lists
new_experiments = ExperimentList()
new_reference_all = reference.split_by_experiment_id()
new_reference = flex.reflection_table()
for i in range(len(new_reference_all) - len(experiments)):
new_reference_all.append(flex.reflection_table())
assert len(new_reference_all) == len(experiments)
# Loop through all the scan ranges and create a new experiment list with
# the requested scan ranges.
for scan_start, scan_end in scan_range:
# Validate the requested scan range
if scan_end == scan_start:
raise Sorry(
"Scan range end must be higher than start; pass {},{} for single image"
.format(scan_start, scan_start + 1))
if scan_end < scan_start:
raise Sorry("Scan range must be in ascending order")
elif scan_start < frames_start or scan_end > frames_end:
raise Sorry(
"Scan range must be within image range {}..{}".format(
frames_start, frames_end))
assert scan_end > scan_start
assert scan_start >= frames_start
assert scan_end <= frames_end
index_start = scan_start - frames_start
index_end = index_start + (scan_end - scan_start)
assert index_start < index_end
assert index_start >= 0
assert index_end <= len(iset)
new_iset = iset[index_start:index_end]
if scan is None:
new_scan = None
else:
new_scan = scan[index_start:index_end]
for i, e1 in enumerate(experiments):
e2 = Experiment()
e2.beam = e1.beam
e2.detector = e1.detector
e2.goniometer = e1.goniometer
e2.crystal = e1.crystal
e2.profile = e1.profile
e2.imageset = new_iset
e2.scan = new_scan
new_reference_all[i]["id"] = flex.int(
len(new_reference_all[i]), len(new_experiments))
new_reference.extend(new_reference_all[i])
new_experiments.append(e2)
experiments = new_experiments
reference = new_reference
# Print some information
logger.info(
"Modified experiment list to integrate over requested scan range"
)
for scan_start, scan_end in scan_range:
logger.info(" scan_range = %d -> %d" % (scan_start, scan_end))
logger.info("")
# Return the experiments
return experiments, reference
def split_for_scan_range(self, experiments, reference, scan_range):
''' Update experiments when scan range is set. '''
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
from dials.array_family import flex
# Only do anything is the scan range is set
if scan_range is not None and len(scan_range) > 0:
# Ensure that all experiments have the same imageset and scan
iset = [e.imageset for e in experiments]
scan = [e.scan for e in experiments]
assert (all(x == iset[0] for x in iset))
assert (all(x == scan[0] for x in scan))
# Get the imageset and scan
iset = experiments[0].imageset
scan = experiments[0].scan
# Get the array range
if scan is not None:
frame10, frame11 = scan.get_array_range()
assert (scan.get_num_images() == len(iset))
else:
frame10, frame11 = (0, len(iset))
# Create the new lists
new_experiments = ExperimentList()
new_reference_all = reference.split_by_experiment_id()
new_reference = flex.reflection_table()
for i in range(len(new_reference_all) - len(experiments)):
new_reference_all.append(flex.reflection_table())
assert (len(new_reference_all) == len(experiments))
# Loop through all the scan ranges and create a new experiment list with
# the requested scan ranges.
for frame00, frame01 in scan_range:
assert (frame01 > frame00)
assert (frame00 >= frame10)
assert (frame01 <= frame11)
index0 = frame00 - frame10
index1 = index0 + (frame01 - frame00)
assert (index0 < index1)
assert (index0 >= 0)
assert (index1 <= len(iset))
new_iset = iset[index0:index1]
if scan is None:
new_scan = None
else:
new_scan = scan[index0:index1]
for i, e1 in enumerate(experiments):
e2 = Experiment()
e2.beam = e1.beam
e2.detector = e1.detector
e2.goniometer = e1.goniometer
e2.crystal = e1.crystal
e2.imageset = new_iset
e2.scan = new_scan
new_reference_all[i]['id'] = flex.int(
len(new_reference_all[i]), len(new_experiments))
new_reference.extend(new_reference_all[i])
new_experiments.append(e2)
experiments = new_experiments
reference = new_reference
# Print some information
logger.info(
'Modified experiment list to integrate over requested scan range'
)
for frame00, frame01 in scan_range:
logger.info(' scan_range = %d -> %d' % (frame00, frame01))
logger.info('')
# Return the experiments
return experiments, reference
is_bg_pixel[i_panel, j1:j2, i1:i2] = ~np.logical_or(~bg, expanded_integration_mask)
# At this point is_bg_pixel returns False for pixels that are inside the expanded strong spot mask
# or the expanded integration mask
# <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
# RUN THE TILT PLANE HELPER FUNCTION
# 1. Weighted fit of the background tilt plane
# 2. Updates prediction reflection table with miller indices, and shoeboxes
# 3. Updates prediction reflections with integrations and integration variances
# using Leslie 99
# <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
exper = Experiment()
exper.detector = DET
exper.beam = BEAM
exper.crystal = crystal
exper.imageset = El[0].imageset
results = tilt_fit(
imgs=img_data, is_bg_pix=is_bg_pixel,
delta_q=args.deltaq, photon_gain=GAIN, sigma_rdout=sigma_readout, zinger_zscore=args.Z,
exper=exper, predicted_refls=refls_predict, sb_pad=args.sbpad)
refls_predict, tilt_abc, error_in_tilt, I_Leslie99, varI_Leslie99 = results
spot_snr = np.array(I_Leslie99) / np.sqrt(varI_Leslie99)
shoeboxes = refls_predict['shoebox']
bboxes = np.vstack([list(sb.bbox)[:4] for sb in shoeboxes])
bbox_panel_ids = np.array(refls_predict['panel'])
Hi = np.vstack(refls_predict['miller_index'])
did_i_index = np.array(refls_predict['id'])
boundary_spot = np.array(refls_predict['boundary'])
# <><><><><><><><><><><><><><><>
except:
pass
continue
print("####\n *_* IndexingWORKED %d *_* \n####" % idx)
n_idx += 1
indexed_shots.append(idx)
try:
np.savetxt(indexed_f, indexed_shots, fmt="%d")
except:
pass
crystalAB = orientAB.refined_experiments.crystals()[0]
E = Experiment()
E.beam = BEAM
E.detector = DET
E.imageset = iset
E.crystal = crystalAB
EL = ExperimentList()
EL.append(E)
exp_json = os.path.join(out_dir, "exp_%d_%s.json" % (idx, tag) )
refl_pkl = os.path.join(out_dir, "refl_%d_%s.pkl" % (idx, tag))
orientAB.export_as_json( EL, exp_json)
utils.save_flex(refls_strong, refl_pkl)
t = loader.times[idx] # event time
sec, nsec, fid = t.seconds(), t.nanoseconds(), t.fiducial()
t_num, _ = utils.make_event_time( sec, nsec, fid)
dump = {"crystalAB": crystalAB,
"event_time": t_num,