def test_single_panel():
from dials.array_family import flex
nrefl = 1000
# Generate bboxes
bbox = flex.int6(nrefl)
for i in range(nrefl):
x0 = random.randint(0, 500)
y0 = random.randint(0, 500)
z0 = random.randint(0, 10)
x1 = x0 + random.randint(2, 10)
y1 = y0 + random.randint(2, 10)
z1 = z0 + random.randint(2, 10)
bbox[i] = (x0, x1, y0, y1, z0, z1)
# Find the overlaps
overlaps = find_overlapping(bbox)
assert overlaps.num_vertices() == nrefl
overlaps2 = brute_force(bbox)
assert overlaps.num_edges() == len(overlaps2)
edges = {}
for edge in overlaps2:
edge = (min(edge), max(edge))
edges[edge] = None
for edge in overlaps.edges():
edge = overlaps.source(edge), overlaps.target(edge)
edge = (min(edge), max(edge))
assert edge in edges
def predict_reflections(self):
from dials.algorithms import shoebox
from dials.array_family import flex
from dxtbx.model.experiment_list import ExperimentList
from dxtbx.model.experiment_list import Experiment
from dials.algorithms.profile_model.gaussian_rs import Model
# Get models from the sweep
self.beam = self.sweep.get_beam()
self.detector = self.sweep.get_detector()
self.gonio = self.sweep.get_goniometer()
self.scan = self.sweep.get_scan()
sigma_b = self.beam.get_sigma_divergence(deg=True)
sigma_m = self.crystal.get_mosaicity(deg=True)
exlist = ExperimentList()
exlist.append(
Experiment(imageset=self.sweep,
beam=self.beam,
detector=self.detector,
goniometer=self.gonio,
scan=self.scan,
crystal=self.crystal,
profile=Model(None, 3, sigma_b, sigma_m, deg=True)))
predicted = flex.reflection_table.from_predictions(exlist[0])
predicted['id'] = flex.int(len(predicted), 0)
predicted.compute_bbox(exlist)
# Find overlapping reflections
overlaps = shoebox.find_overlapping(predicted['bbox'])
# Return the reflections and overlaps
return predicted, overlaps
def tst_multiple_panels(self):
from dials.array_family import flex
from random import randint
nrefl = 1000
# Generate bboxes
bbox = flex.int6(nrefl)
panel = flex.size_t(nrefl)
for i in range(nrefl):
x0 = randint(0, 500)
y0 = randint(0, 500)
z0 = randint(0, 10)
x1 = x0 + randint(2, 10)
y1 = y0 + randint(2, 10)
z1 = z0 + randint(2, 10)
bbox[i] = (x0, x1, y0, y1, z0, z1)
panel[i] = randint(0,2)
# Find the overlaps
overlaps = find_overlapping(bbox, panel)
assert(overlaps.num_vertices() == nrefl)
overlaps2 = self.brute_force(bbox, panel)
assert(overlaps.num_edges() == len(overlaps2))
edges = {}
for edge in overlaps2:
edge = (min(edge), max(edge))
edges[edge] = None
for edge in overlaps.edges():
edge = (overlaps.source(edge), overlaps.target(edge))
edge = (min(edge), max(edge))
assert(edge in edges)
print 'OK'
def tst_multiple_panels(self):
from dials.array_family import flex
from random import randint
nrefl = 1000
# Generate bboxes
bbox = flex.int6(nrefl)
panel = flex.size_t(nrefl)
for i in range(nrefl):
x0 = randint(0, 500)
y0 = randint(0, 500)
z0 = randint(0, 10)
x1 = x0 + randint(2, 10)
y1 = y0 + randint(2, 10)
z1 = z0 + randint(2, 10)
bbox[i] = (x0, x1, y0, y1, z0, z1)
panel[i] = randint(0,2)
# Find the overlaps
overlaps = find_overlapping(bbox, panel)
assert(overlaps.num_vertices() == nrefl)
overlaps2 = self.brute_force(bbox, panel)
assert(overlaps.num_edges() == len(overlaps2))
edges = {}
for edge in overlaps2:
edge = (min(edge), max(edge))
edges[edge] = None
for edge in overlaps.edges():
edge = (overlaps.source(edge), overlaps.target(edge))
edge = (min(edge), max(edge))
assert(edge in edges)
print 'OK'
def predict_reflections(self):
from dials.algorithms import shoebox
from dials.array_family import flex
from dxtbx.model.experiment.experiment_list import ExperimentList
from dxtbx.model.experiment.experiment_list import Experiment
from dials.algorithms.profile_model.gaussian_rs import Model
# Get models from the sweep
self.beam = self.sweep.get_beam()
self.detector = self.sweep.get_detector()
self.gonio = self.sweep.get_goniometer()
self.scan = self.sweep.get_scan()
sigma_b = self.beam.get_sigma_divergence(deg=True)
sigma_m = self.crystal.get_mosaicity(deg=True)
exlist = ExperimentList()
exlist.append(Experiment(
imageset=self.sweep,
beam=self.beam,
detector=self.detector,
goniometer=self.gonio,
scan=self.scan,
crystal=self.crystal,
profile=Model(
None, 3, sigma_b, sigma_m, deg=True)))
predicted = flex.reflection_table.from_predictions(exlist[0])
predicted['id'] = flex.int(len(predicted), 0)
predicted.compute_bbox(exlist)
# Find overlapping reflections
overlaps = shoebox.find_overlapping(predicted['bbox'])
# Return the reflections and overlaps
return predicted, overlaps
from __future__ import division
from __future__ import print_function
from scitbx.array_family import flex
from dials.model.data import Reflection, ReflectionList
from dials.algorithms import shoebox
rl = ReflectionList()
r1 = Reflection()
r1.shoebox = (10, 20, 10, 20, 10, 20)
r2 = Reflection()
r2.shoebox = (15, 25, 15, 25, 15, 25)
r3 = Reflection()
r3.shoebox = (20, 30, 20, 30, 20, 30)
rl.append(r1)
rl.append(r2)
rl.append(r3)
overlapping = shoebox.find_overlapping(rl)
for e in overlapping.edges():
print("Edge: ", overlapping.edge_vertices(e))
for v in overlapping.vertices():
print("Vertex: ", v, " => ", [a for a in overlapping.adjacent_vertices(v)])
from __future__ import division
from scitbx.array_family import flex
from dials.model.data import Reflection, ReflectionList
from dials.algorithms import shoebox
rl = ReflectionList()
r1 = Reflection()
r1.shoebox = (10, 20, 10, 20, 10, 20)
r2 = Reflection()
r2.shoebox = (15, 25, 15, 25, 15, 25)
r3 = Reflection()
r3.shoebox = (20, 30, 20, 30, 20, 30)
rl.append(r1)
rl.append(r2)
rl.append(r3)
overlapping = shoebox.find_overlapping(rl)
for e in overlapping.edges():
print "Edge: ", overlapping.edge_vertices(e)
for v in overlapping.vertices():
print "Vertex: ", v, " => ", [a for a in overlapping.adjacent_vertices(v)]
