def test(dials_regression, tmpdir):
tmpdir.chdir()
from dxtbx.serialize import load
from dials.algorithms import shoebox
from dials.array_family import flex
# Load the sweep and crystal
sweep_filename = os.path.join(dials_regression, 'centroid_test_data', 'sweep.json')
crystal_filename = os.path.join(dials_regression, 'centroid_test_data', 'crystal.json')
sweep = load.imageset(sweep_filename)
crystal = load.crystal(crystal_filename)
# Get models from the sweep
beam = sweep.get_beam()
detector = sweep.get_detector()
gonio = sweep.get_goniometer()
scan = sweep.get_scan()
# Get the reflections and overlaps
reflections, adjacency_list = predict_reflections(sweep, crystal)
reflections['shoebox'] = flex.shoebox(
reflections['panel'],
reflections['bbox'])
reflections['shoebox'].allocate_with_value(shoebox.MaskCode.Valid)
# If the adjacency list is given, then create the reflection mask
assert(len(detector) == 1)
image_size = detector[0].get_image_size()
shoeboxes = reflections['shoebox']
coords = reflections['xyzcal.px']
shoebox_masker = shoebox.MaskOverlapping()
shoebox_masker(shoeboxes, coords, adjacency_list)
# Loop through all edges
overlapping = []
for e in adjacency_list.edges():
v1, v2 = adjacency_list.source(e), adjacency_list.target(e)
overlapping.append(v1)
overlapping.append(v2)
# Ensure elements are unique
overlapping = set(overlapping)
# Ensure we have some overlaps
assert len(overlapping) > 0
# Get all non-overlapping reflections
all_r = set(range(len(reflections)))
non_overlapping = all_r.difference(overlapping)
# Run the tests
tst_non_overlapping(reflections, non_overlapping,
detector[0].get_image_size())
tst_overlapping(reflections, overlapping, adjacency_list,
image_size)
def test(dials_data):
from dxtbx.serialize import load
from dials.algorithms import shoebox
from dials.array_family import flex
# Load the sequence and crystal
sequence = load.imageset(
dials_data("centroid_test_data").join("sweep.json").strpath
)
crystal = load.crystal(
dials_data("centroid_test_data").join("crystal.json").strpath
)
# Get models from the sequence
detector = sequence.get_detector()
# Get the reflections and overlaps
reflections, adjacency_list = predict_reflections(sequence, crystal)
reflections["shoebox"] = flex.shoebox(reflections["panel"], reflections["bbox"])
reflections["shoebox"].allocate_with_value(shoebox.MaskCode.Valid)
# If the adjacency list is given, then create the reflection mask
assert len(detector) == 1
image_size = detector[0].get_image_size()
shoeboxes = reflections["shoebox"]
coords = reflections["xyzcal.px"]
shoebox_masker = shoebox.MaskOverlapping()
shoebox_masker(shoeboxes, coords, adjacency_list)
# Loop through all edges
overlapping = []
for e in adjacency_list.edges():
v1, v2 = adjacency_list.source(e), adjacency_list.target(e)
overlapping.append(v1)
overlapping.append(v2)
# Ensure elements are unique
overlapping = set(overlapping)
# Ensure we have some overlaps
assert len(overlapping) > 0
# Get all non-overlapping reflections
all_r = set(range(len(reflections)))
non_overlapping = all_r.difference(overlapping)
# Run the tests
tst_non_overlapping(reflections, non_overlapping, detector[0].get_image_size())
tst_overlapping(reflections, overlapping, adjacency_list, image_size)
def run(self):
from dials.model.serialize import load
from dials.algorithms import shoebox
from dxtbx.serialize.load import crystal as load_crystal
from dials.array_family import flex
# Load the sweep and crystal
self.sweep = load.sweep(self.sweep_filename)
self.crystal = load_crystal(self.crystal_filename)
# Get the reflections and overlaps
reflections, adjacency_list = self.predict_reflections()
reflections['shoebox'] = flex.shoebox(reflections['panel'],
reflections['bbox'])
reflections['shoebox'].allocate_with_value(shoebox.MaskCode.Valid)
# If the adjacency list is given, then create the reflection mask
assert (len(self.detector) == 1)
image_size = self.detector[0].get_image_size()
shoeboxes = reflections['shoebox']
coords = reflections['xyzcal.px']
shoebox_masker = shoebox.MaskOverlapping()
shoebox_masker(shoeboxes, coords, adjacency_list)
# Loop through all edges
overlapping = []
for e in adjacency_list.edges():
v1, v2 = adjacency_list.source(e), adjacency_list.target(e)
overlapping.append(v1)
overlapping.append(v2)
# Ensure elements are unique
overlapping = set(overlapping)
# Ensure we have some overlaps
assert (len(overlapping) > 0)
# Get all non-overlapping reflections
all_r = set(range(len(reflections)))
non_overlapping = all_r.difference(overlapping)
# Run the tests
self.tst_non_overlapping(reflections, non_overlapping,
self.detector[0].get_image_size())
self.tst_overlapping(reflections, overlapping, adjacency_list,
image_size)