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):
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 split_for_scan_range(self, experiments, reference, scan_range):
""" Update experiments when scan range is set. """
from dxtbx.model.experiment.experiment_list import ExperimentList
from dxtbx.model.experiment.experiment_list import Experiment
from logging import info
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
info("Modified experiment list to integrate over requested scan range")
for frame00, frame01 in scan_range:
info(" scan_range = %d -> %d" % (frame00, frame01))
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.experiment_list import ExperimentList
from dxtbx.model.experiment.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