def get_mask(self, detector, scan_angle):
shadow_boundary = self.project_extrema(detector, scan_angle)
from dials.util import mask_untrusted_polygon
mask = [flex.bool(flex.grid(reversed(p.get_image_size())), True) for p in detector]
for panel_id in range(len(detector)):
if shadow_boundary[panel_id].size() > 3:
mask_untrusted_polygon(mask[panel_id], shadow_boundary[panel_id])
return mask
def get_mask(self, detector, scan_angle):
shadow_boundary = self.project_extrema(detector, scan_angle)
from dials.util import mask_untrusted_polygon
mask = [
flex.bool(flex.grid(reversed(p.get_image_size())), True)
for p in detector
]
for panel_id in range(len(detector)):
if shadow_boundary[panel_id].size() > 3:
mask_untrusted_polygon(mask[panel_id],
shadow_boundary[panel_id])
return mask
def generate(self, imageset):
''' Generate the mask. '''
from dials.util import ResolutionMaskGenerator
from dials.util import mask_untrusted_rectangle
from dials.util import mask_untrusted_circle
from dials.util import mask_untrusted_polygon
from dials.util import mask_untrusted_resolution_range
from dials.array_family import flex
from math import floor, ceil
# Get the detector and beam
detector = imageset.get_detector()
beam = imageset.get_beam()
# Get the first image
image = imageset.get_raw_data(0)
assert (len(detector) == len(image))
# Create the mask for each image
masks = []
for index, (im, panel) in enumerate(zip(image, detector)):
# The image width height
height, width = im.all()
# Create the basic mask from the trusted range
if self.params.use_trusted_range:
low, high = panel.get_trusted_range()
imd = im.as_double()
mask = (imd > low) & (imd < high)
else:
mask = flex.bool(flex.grid(im.all()), True)
# Add a border around the image
if self.params.border > 0:
logger.info("Generating border mask:")
logger.info(" border = %d" % self.params.border)
border = self.params.border
height, width = mask.all()
borderx = flex.bool(flex.grid(border, width), False)
bordery = flex.bool(flex.grid(height, border), False)
mask[0:border, :] = borderx
mask[-border:, :] = borderx
mask[:, 0:border] = bordery
mask[:, -border:] = bordery
# Apply the untrusted regions
for region in self.params.untrusted:
if region.panel == index:
if region.circle is not None:
xc, yc, radius = region.circle
logger.info("Generating circle mask:")
logger.info(" panel = %d" % region.panel)
logger.info(" xc = %d" % xc)
logger.info(" yc = %d" % yc)
logger.info(" radius = %d" % radius)
mask_untrusted_circle(mask, xc, yc, radius)
if region.rectangle is not None:
x0, x1, y0, y1 = region.rectangle
logger.info("Generating rectangle mask:")
logger.info(" panel = %d" % region.panel)
logger.info(" x0 = %d" % x0)
logger.info(" y0 = %d" % y0)
logger.info(" x1 = %d" % x1)
logger.info(" y1 = %d" % y1)
mask_untrusted_rectangle(mask, x0, x1, y0, y1)
if region.polygon is not None:
assert len(region.polygon
) % 2 == 0, "Polygon must contain 2D coords"
vertices = []
for i in range(int(len(region.polygon) / 2)):
x = region.polygon[2 * i]
y = region.polygon[2 * i + 1]
vertices.append((x, y))
polygon = flex.vec2_double(vertices)
logger.info("Generating polygon mask:")
logger.info(" panel = %d" % region.panel)
for vertex in vertices:
logger.info(" coord = (%d, %d)" % (vertex))
mask_untrusted_polygon(mask, polygon)
# Create the resolution mask generator
class ResolutionMaskGeneratorGetter(object):
def __init__(self, beam, panel):
self.beam = beam
self.panel = panel
self.result = None
def __call__(self):
if self.result is None:
self.result = ResolutionMaskGenerator(beam, panel)
return self.result
get_resolution_mask_generator = ResolutionMaskGeneratorGetter(
beam, panel)
# Generate high and low resolution masks
if self.params.d_min is not None:
logger.info("Generating high resolution mask:")
logger.info(" d_min = %f" % self.params.d_min)
get_resolution_mask_generator().apply(mask, 0,
self.params.d_min)
if self.params.d_max is not None:
logger.info("Generating low resolution mask:")
logger.info(" d_max = %f" % self.params.d_max)
d_min = self.params.d_max
d_max = max(d_min + 1, 1e9)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Mask out the resolution range
for drange in self.params.resolution_range:
d_min = min(drange)
d_max = max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.info("Generating resolution range mask:")
logger.info(" d_min = %f" % d_min)
logger.info(" d_max = %f" % d_max)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Mask out the resolution ranges for the ice rings
for drange in generate_ice_ring_resolution_ranges(
beam, panel, self.params.ice_rings):
d_min = min(drange)
d_max = max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.info("Generating ice ring mask:")
logger.info(" d_min = %f" % d_min)
logger.info(" d_max = %f" % d_max)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Add to the list
masks.append(mask)
# Return the mask
return tuple(masks)
def generate(self, imageset):
''' Generate the mask. '''
from dials.util import ResolutionMaskGenerator
from dials.util import mask_untrusted_rectangle
from dials.util import mask_untrusted_circle
from dials.util import mask_untrusted_polygon
from dials.util import mask_untrusted_resolution_range
from dials.array_family import flex
from math import floor, ceil
# Get the detector and beam
detector = imageset.get_detector()
beam = imageset.get_beam()
# Get the first image
image = imageset.get_raw_data(0)
assert(len(detector) == len(image))
# Create the mask for each image
masks = []
for index, (im, panel) in enumerate(zip(image, detector)):
# The image width height
height, width = im.all()
# Create the basic mask from the trusted range
if self.params.use_trusted_range:
low, high = panel.get_trusted_range()
imd = im.as_double()
mask = (imd > low) & (imd < high)
else:
mask = flex.bool(flex.grid(im.all()), True)
# Add a border around the image
if self.params.border > 0:
logger.info("Generating border mask:")
logger.info(" border = %d" % self.params.border)
border = self.params.border
height, width = mask.all()
borderx = flex.bool(flex.grid(border, width), False)
bordery = flex.bool(flex.grid(height, border), False)
mask[0:border,:] = borderx
mask[-border:,:] = borderx
mask[:,0:border] = bordery
mask[:,-border:] = bordery
# Apply the untrusted regions
for region in self.params.untrusted:
if region.panel == index:
if region.circle is not None:
xc, yc, radius = region.circle
logger.info("Generating circle mask:")
logger.info(" panel = %d" % region.panel)
logger.info(" xc = %d" % xc)
logger.info(" yc = %d" % yc)
logger.info(" radius = %d" % radius)
mask_untrusted_circle(mask, xc, yc, radius)
if region.rectangle is not None:
x0, x1, y0, y1 = region.rectangle
logger.info("Generating rectangle mask:")
logger.info(" panel = %d" % region.panel)
logger.info(" x0 = %d" % x0)
logger.info(" y0 = %d" % y0)
logger.info(" x1 = %d" % x1)
logger.info(" y1 = %d" % y1)
mask_untrusted_rectangle(mask, x0, x1, y0, y1)
if region.polygon is not None:
assert len(region.polygon) % 2 == 0, "Polygon must contain 2D coords"
vertices = []
for i in range(int(len(region.polygon)/2)):
x = region.polygon[2*i]
y = region.polygon[2*i+1]
vertices.append((x,y))
polygon = flex.vec2_double(vertices)
logger.info("Generating polygon mask:")
logger.info(" panel = %d" % region.panel)
for vertex in vertices:
logger.info(" coord = (%d, %d)" % (vertex))
mask_untrusted_polygon(mask, polygon)
# Create the resolution mask generator
class ResolutionMaskGeneratorGetter(object):
def __init__(self, beam, panel):
self.beam = beam
self.panel = panel
self.result = None
def __call__(self):
if self.result is None:
self.result = ResolutionMaskGenerator(beam, panel)
return self.result
get_resolution_mask_generator = ResolutionMaskGeneratorGetter(beam, panel)
# Generate high and low resolution masks
if self.params.d_min is not None:
logger.info("Generating high resolution mask:")
logger.info(" d_min = %f" % self.params.d_min)
get_resolution_mask_generator().apply(mask, 0, self.params.d_min)
if self.params.d_max is not None:
logger.info("Generating low resolution mask:")
logger.info(" d_max = %f" % self.params.d_max)
d_min = self.params.d_max
d_max = max(d_min + 1, 1e9)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Mask out the resolution range
for drange in self.params.resolution_range:
d_min=min(drange)
d_max=max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.info("Generating resolution range mask:")
logger.info(" d_min = %f" % d_min)
logger.info(" d_max = %f" % d_max)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Mask out the resolution ranges for the ice rings
for drange in generate_ice_ring_resolution_ranges(
beam, panel, self.params.ice_rings):
d_min=min(drange)
d_max=max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.info("Generating ice ring mask:")
logger.info(" d_min = %f" % d_min)
logger.info(" d_max = %f" % d_max)
get_resolution_mask_generator().apply(mask, d_min, d_max)
# Add to the list
masks.append(mask)
# Return the mask
return tuple(masks)
