def generate_predictions(self, N):
"""Generate some reflections."""
from dials.algorithms import filtering
from dials.algorithms.profile_model.gaussian_rs import MaskCalculator3D
from dials.algorithms.profile_model.gaussian_rs import Model as ProfileModel
from dials.algorithms.shoebox import MaskCode
from dials.util.command_line import Command
# Set the profile model
self.experiment.profile = ProfileModel(None, self.n_sigma,
self.sigma_b, self.sigma_m)
# Generate a list of reflections
refl = flex.reflection_table.from_predictions(self.experiment)
refl["id"] = flex.int(len(refl), 0)
# Filter by zeta
zeta = 0.05
Command.start(f"Filtering by zeta >= {zeta:f}")
mask = filtering.by_zeta(self.experiment.goniometer,
self.experiment.beam, refl["s1"], zeta)
refl.del_selected(~mask)
Command.end(f"Filtered {len(refl)} reflections by zeta >= {zeta:f}")
# Compute the bounding box
refl.compute_bbox([self.experiment])
index = []
image_size = self.experiment.detector[0].get_image_size()
array_range = self.experiment.scan.get_array_range()
bbox = refl["bbox"]
for i in range(len(refl)):
x0, x1, y0, y1, z0, z1 = bbox[i]
if (x0 < 0 or x1 > image_size[0] or y0 < 0 or y1 > image_size[1]
or z0 < array_range[0] or z1 > array_range[1]):
index.append(i)
refl.del_selected(flex.size_t(index))
# Sample if specified
index = random.sample(range(len(refl)), N)
refl = refl.select(flex.size_t(index))
# Compute the bounding box
# Create a load of shoeboxes
Command.start(f"Creating shoeboxes for {len(refl)} reflections")
refl["shoebox"] = flex.shoebox(refl["panel"], refl["bbox"])
refl["shoebox"].allocate_with_value(MaskCode.Valid)
Command.end(f"Created shoeboxes for {len(refl)} reflections")
# Get the function object to mask the foreground
Command.start(f"Masking Foreground for {len(refl)} reflections")
mask_foreground = MaskCalculator3D(
self.experiment.beam,
self.experiment.detector,
self.experiment.goniometer,
self.experiment.scan,
self.n_sigma * self.sigma_b,
self.n_sigma * self.sigma_m,
)
# Mask the foreground
mask_foreground(refl["shoebox"], refl["s1"],
refl["xyzcal.px"].parts()[2], refl["panel"])
Command.end(f"Masked foreground for {len(refl)} reflections")
# Return the reflections
return refl
def generate_predictions(self, N):
""" Generate some reflections. """
from dials.algorithms.profile_model.gaussian_rs import MaskCalculator3D
from dials.array_family import flex
from dials.util.command_line import Command
from dials.algorithms import filtering
from dials.algorithms.shoebox import MaskCode
from dials.algorithms.profile_model.gaussian_rs import Model as ProfileModel
import random
# Set the profile model
self.experiment.profile = ProfileModel(None, self.n_sigma, self.sigma_b, self.sigma_m)
# Generate a list of reflections
refl = flex.reflection_table.from_predictions(self.experiment)
refl["id"] = flex.int(len(refl), 0)
# Filter by zeta
zeta = 0.05
Command.start("Filtering by zeta >= %f" % zeta)
mask = filtering.by_zeta(self.experiment.goniometer, self.experiment.beam, refl["s1"], zeta)
refl.del_selected(mask != True)
Command.end("Filtered %d reflections by zeta >= %f" % (len(refl), zeta))
# Compute the bounding box
refl.compute_bbox([self.experiment])
index = []
image_size = self.experiment.detector[0].get_image_size()
array_range = self.experiment.scan.get_array_range()
bbox = refl["bbox"]
for i in range(len(refl)):
x0, x1, y0, y1, z0, z1 = bbox[i]
if (
x0 < 0
or x1 > image_size[0]
or y0 < 0
or y1 > image_size[1]
or z0 < array_range[0]
or z1 > array_range[1]
):
index.append(i)
refl.del_selected(flex.size_t(index))
# Sample if specified
index = random.sample(range(len(refl)), N)
refl = refl.select(flex.size_t(index))
# Compute the bounding box
# Create a load of shoeboxes
Command.start("Creating shoeboxes for %d reflections" % len(refl))
refl["shoebox"] = flex.shoebox(refl["panel"], refl["bbox"])
refl["shoebox"].allocate_with_value(MaskCode.Valid)
Command.end("Created shoeboxes for %d reflections" % len(refl))
# Get the function object to mask the foreground
Command.start("Masking Foreground for %d reflections" % len(refl))
mask_foreground = MaskCalculator3D(
self.experiment.beam,
self.experiment.detector,
self.experiment.goniometer,
self.experiment.scan,
self.n_sigma * self.sigma_b,
self.n_sigma * self.sigma_m,
)
# Mask the foreground
mask_foreground(refl["shoebox"], refl["s1"], refl["xyzcal.px"].parts()[2], refl["panel"])
Command.end("Masked foreground for %d reflections" % len(refl))
# Return the reflections
return refl