def _compute_bbox(self):
"""
Compute the bounding box
"""
logger.info("Computing the bounding box for %d reflections" %
len(self.reflections))
# Initialise the bounding box calculator
compute_bbox = BBoxCalculator(
self.experiments[0].crystal,
self.experiments[0].beam,
self.experiments[0].detector,
self.experiments[0].goniometer,
self.experiments[0].scan,
self.sigma_d * 6,
0,
)
# Compute the bounding box
bbox = compute_bbox(
self.reflections["s1_obs"],
self.reflections["xyzcal.px"].parts()[2],
self.reflections["panel"],
)
# Set in the reflection table
self.reflections["bbox"] = bbox
def _compute_bbox(self):
"""
Compute the bounding box
"""
print("Computing the bounding box for %d reflections" %
len(self.reflections))
compute_bbox = BBoxCalculator(
self.experiments[0].crystal,
self.experiments[0].beam,
self.experiments[0].detector,
self.experiments[0].goniometer,
self.experiments[0].scan,
self.sigma_d * 6,
0,
)
bbox = compute_bbox(
self.reflections["s1"],
self.reflections["xyzcal.px"].parts()[2],
self.reflections["panel"],
)
self.reflections["bbox_old"] = self.reflections["bbox"]
self.reflections["bbox"] = bbox
def compute_bbox(
self,
reflections,
crystal,
beam,
detector,
goniometer=None,
scan=None,
sigma_b_multiplier=2.0,
**kwargs,
):
"""Given an experiment and list of reflections, compute the
bounding box of the reflections on the detector (and image frames).
:param reflections: The reflection table
:param crystal: The crystal model
:param beam: The beam model
:param detector: The detector model
:param goniometer: The goniometer model
:param scan: The scan model
"""
from dials.algorithms.profile_model.gaussian_rs import BBoxCalculator
# Check the input
assert sigma_b_multiplier >= 1.0
# Compute the size in reciprocal space. Add a sigma_b multiplier to enlarge
# the region of background in the shoebox
delta_b = self._n_sigma * self._sigma_b * sigma_b_multiplier
delta_m = self._n_sigma * self._sigma_m
# Create the bbox calculator
calculate = BBoxCalculator(
crystal, beam, detector, goniometer, scan, delta_b, delta_m
)
# Calculate the bounding boxes of all the reflections
bbox = calculate(
reflections["s1"], reflections["xyzcal.px"].parts()[2], reflections["panel"]
)
# Return the bounding boxes
return bbox
def _compute_bbox(experiment, reflection_table, sigma_d, s1="s1_obs"):
"""Compute the bounding box"""
# Initialise the bounding box calculator
compute_bbox = BBoxCalculator(
experiment.crystal,
experiment.beam,
experiment.detector,
experiment.goniometer,
experiment.scan,
sigma_d * 6,
0,
)
# Compute the bounding box
bbox = compute_bbox(
reflection_table[s1],
reflection_table["xyzcal.px"].parts()[2],
reflection_table["panel"],
)
return bbox
def _compute_bbox_from_sigma_d(self):
"""
Compute the bounding box
"""
logger.info("Computing the bounding box for %d reflections" %
len(self.reflections))
# Initialise the bounding box calculator
compute_bbox = BBoxCalculator(
self.experiments[0].crystal,
self.experiments[0].beam,
self.experiments[0].detector,
self.experiments[0].goniometer,
self.experiments[0].scan,
self.sigma_d * 6,
0,
)
# Compute the bounding box
bbox = compute_bbox(
self.reflections["s1"],
self.reflections["xyzcal.px"].parts()[2],
self.reflections["panel"],
)
# Set in the reflection table
self.reflections["bbox"] = bbox
# Select reflections within detector
x0, x1, y0, y1, _, _ = self.reflections["bbox"].parts()
xsize, ysize = self.experiments[0].detector[0].get_image_size()
selection = (x1 > 0) & (y1 > 0) & (x0 < xsize) & (y0 < ysize)
self.reflections = self.reflections.select(selection)
logger.info("Filtered reflections with bbox outside image range")
logger.info("Kept %d reflections" % len(self.reflections))