def find_spots(self, min_spot_size=2, max_spot_size=100):
from dials.algorithms.spot_finding.threshold import XDSThresholdStrategy
from dials.model.data import PixelList
from dials.model.data import PixelListLabeller
image = self.raw_data
mask = self.imageset.get_mask(0)[0]
threshold_image = XDSThresholdStrategy()
threshold_mask = threshold_image(image, mask)
plist = PixelList(0, image, threshold_mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(plist)
creator = flex.PixelListShoeboxCreator(pixel_labeller, 0, 0, True,
min_spot_size, max_spot_size,
False)
shoeboxes = creator.result()
# turns out we need to manually filter the list to get a sensible answer
size = creator.spot_size()
big = size > max_spot_size
small = size < min_spot_size
bad = big | small
shoeboxes = shoeboxes.select(~bad)
centroid = shoeboxes.centroid_valid()
intensity = shoeboxes.summed_intensity()
observed = flex.observation(shoeboxes.panels(), centroid, intensity)
reflections = flex.reflection_table(observed, shoeboxes)
return reflections
def find_spots(image, mask, min_spot_size=1, max_spot_size=1000):
from dials.algorithms.spot_finding.threshold import XDSThresholdStrategy
from dials.model.data import PixelList
from dials.model.data import PixelListLabeller
threshold_image = XDSThresholdStrategy()
threshold_mask = threshold_image(image, mask)
plist = PixelList(0, image, threshold_mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(plist)
creator = flex.PixelListShoeboxCreator(
pixel_labeller,
0, # panel
0, # zrange
True, # twod
min_spot_size, # min_pixels
max_spot_size, # max_pixels
False,
)
shoeboxes = creator.result()
centroid = shoeboxes.centroid_valid()
intensity = shoeboxes.summed_intensity()
observed = flex.observation(shoeboxes.panels(), centroid, intensity)
return flex.reflection_table(observed, shoeboxes)
def find_spots(self, min_spot_size=2, max_spot_size=100):
"""
Find the strong spots on the image
"""
from dials.algorithms.spot_finding.threshold import DispersionThresholdStrategy
from dials.model.data import PixelList
from dials.model.data import PixelListLabeller
from dials.array_family import flex
print("")
print("-" * 80)
print(" Finding strong spots")
print("-" * 80)
print("")
# Instantiate the threshold function
threshold = DispersionThresholdStrategy()
# Get the raw data and image mask
image = self.experiment.imageset.get_raw_data(0)[0]
mask = self.experiment.imageset.get_mask(0)[0]
# Threshold the image and create the pixel labeller
threshold_mask = threshold(image, mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(PixelList(0, image, threshold_mask))
# Create the shoebox list from the pixel list
creator = flex.PixelListShoeboxCreator(
pixel_labeller,
0, # Panel number
0, # Z start
True, # 2D
self.params.spot_finding.min_spot_size, # Min Pixels
self.params.spot_finding.max_spot_size, # Max Pixels
False,
) # Find hot pixels
shoeboxes = creator.result()
# Filter the list to remove large and small spots
size = creator.spot_size()
large = size > self.params.spot_finding.max_spot_size
small = size < self.params.spot_finding.min_spot_size
bad = large | small
shoeboxes = shoeboxes.select(~bad)
print("Discarding %d spots with < %d pixels" %
(small.count(True), self.params.spot_finding.min_spot_size))
print("Discarding %d spots with > %d pixels" %
(large.count(True), self.params.spot_finding.max_spot_size))
# Extract the strong spot information
centroid = shoeboxes.centroid_valid()
intensity = shoeboxes.summed_intensity()
observed = flex.observation(shoeboxes.panels(), centroid, intensity)
# Create the reflection list
self.reflections = flex.reflection_table(observed, shoeboxes)
print("Using %d strong spots" % len(self.reflections))
def __call__(self, imageset, pixel_labeller):
"""
Convert the pixel list to shoeboxes
"""
from dxtbx.imageset import ImageSequence
# 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):
scan = imageset.get_scan()
if scan.is_still():
twod = True
else:
twod = False
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
self.min_spot_size, # min_pixels
self.max_spot_size, # max_pixels
self.write_hot_pixel_mask,
)
shoeboxes.extend(creator.result())
spotsizes.extend(creator.spot_size())
hp.extend(creator.hot_pixels())
logger.info("")
logger.info("Extracted {} spots".format(len(shoeboxes)))
# Get the unallocated spots and print some info
selection = shoeboxes.is_allocated()
shoeboxes = shoeboxes.select(selection)
ntoosmall = (spotsizes < self.min_spot_size).count(True)
ntoolarge = (spotsizes > self.max_spot_size).count(True)
assert ntoosmall + ntoolarge == selection.count(False)
logger.info(
"Removed %d spots with size < %d pixels" % (ntoosmall, self.min_spot_size)
)
logger.info(
"Removed %d spots with size > %d pixels" % (ntoolarge, self.max_spot_size)
)
# Return the shoeboxes
return shoeboxes, hotpixels
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
def find_spots(image):
from dials.algorithms.spot_finding.threshold import DispersionThresholdStrategy
from dials.model.data import PixelList
from dials.model.data import PixelListLabeller
thresholder = DispersionThresholdStrategy(gain=1)
mask = image.as_1d() >= 0 # flex.bool(image.size(), True)
mask.reshape(flex.grid(*image.focus()))
threshold_mask = thresholder(image, mask=mask)
plist = PixelList(0, image, threshold_mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(plist)
creator = flex.PixelListShoeboxCreator(pixel_labeller, 0, 0, True, 2, 100,
False)
shoeboxes = creator.result()
return shoeboxes
def image_to_shoeboxes(image):
"""For a given image, find spots 2 - 100 pixels im size, assuming a gain
of 1, return the list of spot shoeboxes. Also assumes valid intensities in
range 0...N."""
thresholder = DispersionThresholdStrategy(gain=1)
mask = image.as_1d() >= 0
mask.reshape(flex.grid(*image.focus()))
threshold_mask = thresholder(image, mask=mask)
plist = PixelList(0, image, threshold_mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(plist)
creator = flex.PixelListShoeboxCreator(pixel_labeller, 0, 0, True, 2, 100,
False)
shoeboxes = creator.result()
return shoeboxes
def find(greyscale_flex, params, mask=None):
'''Find stars on input greyscale flex image.'''
from dials.algorithms.spot_finding.threshold import \
DispersionThresholdStrategy
from dials.model.data import PixelList
from dials.model.data import PixelListLabeller
from dials.array_family import flex
thresholder = DispersionThresholdStrategy(gain=params.gain)
if not mask:
mask = flex.bool(greyscale_flex.size(), True)
mask.reshape(flex.grid(*greyscale_flex.focus()))
threshold_mask = thresholder(greyscale_flex, mask=mask)
plist = PixelList(0, greyscale_flex, threshold_mask)
pixel_labeller = PixelListLabeller()
pixel_labeller.add(plist)
creator = flex.PixelListShoeboxCreator(pixel_labeller, 0, 0, True,
params.min_size, params.max_size,
False)
shoeboxes = creator.result()
# remove nonsense
size = creator.spot_size()
big = size > params.max_size
small = size < params.min_size
bad = big | small
shoeboxes = shoeboxes.select(~bad)
centroid = shoeboxes.centroid_valid()
intensity = shoeboxes.summed_intensity()
observed = flex.observation(shoeboxes.panels(), centroid, intensity)
stars = flex.reflection_table(observed, shoeboxes)
return stars