def __call__(self, imageset):
'''
Override the parameters
'''
from dxtbx.imageset import ImageSet
from dxtbx.imageset import ImageSweep
from dxtbx.model import BeamFactory
from dxtbx.model import DetectorFactory
from dxtbx.model import GoniometerFactory
from dxtbx.model import ScanFactory
from copy import deepcopy
if self.params.geometry.convert_sweeps_to_stills:
imageset = ImageSet(reader=imageset.reader())
if not isinstance(imageset, ImageSweep):
if self.params.geometry.convert_stills_to_sweeps:
imageset = self.convert_stills_to_sweep(imageset)
if isinstance(imageset, ImageSweep):
beam = BeamFactory.from_phil(
self.params.geometry,
imageset.get_beam())
detector = DetectorFactory.from_phil(
self.params.geometry,
imageset.get_detector(),
beam)
goniometer = GoniometerFactory.from_phil(
self.params.geometry,
imageset.get_goniometer())
scan = ScanFactory.from_phil(
self.params.geometry,
deepcopy(imageset.get_scan()))
i0, i1 = scan.get_array_range()
j0, j1 = imageset.get_scan().get_array_range()
imageset.set_beam(beam)
imageset.set_detector(detector)
imageset.set_goniometer(goniometer)
imageset.set_scan(scan)
else:
for i in range(len(imageset)):
beam = BeamFactory.from_phil(
self.params.geometry,
imageset.get_beam(i))
detector = DetectorFactory.from_phil(
self.params.geometry,
imageset.get_detector(i),
beam)
goniometer = GoniometerFactory.from_phil(
self.params.geometry,
imageset.get_goniometer(i))
scan = ScanFactory.from_phil(
self.params.geometry,
imageset.get_scan(i))
imageset.set_beam(beam, i)
imageset.set_detector(detector, i)
imageset.set_goniometer(goniometer, i)
imageset.set_scan(scan, i)
return imageset
def pixel_list_to_shoeboxes(
imageset: ImageSet,
pixel_labeller: Iterable[PixelListLabeller],
min_spot_size: int,
max_spot_size: int,
write_hot_pixel_mask: bool,
) -> Tuple[flex.shoebox, Tuple[flex.size_t, ...]]:
"""Convert a pixel list to shoeboxes"""
# Extract the pixel lists into a list of reflections
shoeboxes = flex.shoebox()
spotsizes = flex.size_t()
hotpixels = tuple(flex.size_t()
for i in range(len(imageset.get_detector())))
if isinstance(imageset, ImageSequence):
twod = imageset.get_scan().is_still()
else:
twod = True
for i, (p, hp) in enumerate(zip(pixel_labeller, hotpixels)):
if p.num_pixels() > 0:
creator = flex.PixelListShoeboxCreator(
p,
i, # panel
0, # zrange
twod, # twod
min_spot_size, # min_pixels
max_spot_size, # max_pixels
write_hot_pixel_mask,
)
shoeboxes.extend(creator.result())
spotsizes.extend(creator.spot_size())
hp.extend(creator.hot_pixels())
logger.info("\nExtracted %d spots", len(shoeboxes))
# Get the unallocated spots and print some info
selection = shoeboxes.is_allocated()
shoeboxes = shoeboxes.select(selection)
ntoosmall = (spotsizes < min_spot_size).count(True)
ntoolarge = (spotsizes > max_spot_size).count(True)
assert ntoosmall + ntoolarge == selection.count(False)
logger.info("Removed %d spots with size < %d pixels", ntoosmall,
min_spot_size)
logger.info("Removed %d spots with size > %d pixels", ntoolarge,
max_spot_size)
# Return the shoeboxes
return shoeboxes, hotpixels
