def generate(self, imageset):
"""Generate the mask."""
# 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 panel
masks = []
for index, (im, panel) in enumerate(zip(image, detector)):
# Build a trusted mask by looking for pixels that are always outside
# the trusted range. This identifies bad pixels, but does not include
# pixels that are overloaded on some images.
if self.params.use_trusted_range:
warnings.warn(
"Checking for hot pixels using the trusted_range is"
" deprecated. https://github.com/dials/dials/issues/1156",
FutureWarning,
)
trusted_mask = None
low, high = panel.get_trusted_range()
# Take 10 evenly-spaced images from the imageset. Pixels outside
# the trusted mask on all of these images are considered bad and
# masked. https://github.com/dials/dials/issues/1061
stride = max(int(len(imageset) / 10), 1)
image_indices = range(0, len(imageset), stride)
for image_index in image_indices:
image_data = imageset.get_raw_data(
image_index)[index].as_double()
frame_mask = (image_data > low) & (image_data < high)
if trusted_mask is None:
trusted_mask = frame_mask
else:
trusted_mask = trusted_mask | frame_mask
if trusted_mask.count(False) == 0:
break
mask = trusted_mask
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 is None:
region.panel = 0
if region.panel == index:
if not any([
region.circle, region.rectangle, region.polygon,
region.pixel
]):
mask[:, :] = flex.bool(flex.grid(mask.focus()), False)
continue
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)
if region.pixel is not None:
mask[region.pixel] = False
# 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)
_apply_resolution_mask(mask, beam, panel, 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_max = self.params.d_max
d_inf = max(d_max + 1, 1e9)
_apply_resolution_mask(mask, beam, panel, d_max, d_inf)
try:
# 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)
_apply_resolution_mask(mask, beam, panel, d_min, d_max)
except TypeError:
# Catch the default value None of self.params.resolution_range
if any(self.params.resolution_range):
raise
# 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)
_apply_resolution_mask(mask, beam, panel, d_min, d_max)
# Add to the list
masks.append(mask)
# Return the mask
return tuple(masks)
def generate_mask(imageset: ImageSet,
params: libtbx.phil.scope_extract) -> Tuple[flex.bool]:
"""Generate a mask based on the input parameters.
Args:
imageset (ImageSet): The imageset for which to generate a mask
params (libtbx.phil.scope_extract): The phil parameters for mask generation. This
should be an extract of `dials.util.masking.phil_scope`
"""
# Get the detector and beam
detector = imageset.get_detector()
beam = imageset.get_beam()
# Create the mask for each panel
masks = []
for index, panel in enumerate(detector):
mask = flex.bool(flex.grid(reversed(panel.get_image_size())), True)
# Add a border around the image
if params.border > 0:
logger.debug(f"Generating border mask:\n border = {params.border}")
border = 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 params.untrusted:
if region.panel is None:
region.panel = 0
if region.panel == index:
if not any([
region.circle, region.rectangle, region.polygon,
region.pixel
]):
mask[:, :] = flex.bool(flex.grid(mask.focus()), False)
continue
if region.circle is not None:
xc, yc, radius = region.circle
logger.debug("Generating circle mask:\n" +
f" panel = {region.panel}\n" +
f" xc = {xc}\n" + f" yc = {yc}\n" +
f" radius = {radius}")
mask_untrusted_circle(mask, xc, yc, radius)
if region.rectangle is not None:
x0, x1, y0, y1 = region.rectangle
logger.debug("Generating rectangle mask:\n" +
f" panel = {region.panel}\n" +
f" x0 = {x0}\n" + f" y0 = {y0}\n" +
f" x1 = {x1}\n" + f" y1 = {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.debug(
f"Generating polygon mask:\n panel = {region.panel}\n"
+ "\n".join(f" coord = {vertex}"
for vertex in vertices))
mask_untrusted_polygon(mask, polygon)
if region.pixel is not None:
mask[region.pixel] = False
# Generate high and low resolution masks
if params.d_min is not None:
logger.debug(
f"Generating high resolution mask:\n d_min = {params.d_min}")
_apply_resolution_mask(mask, beam, panel, 0, params.d_min)
if params.d_max is not None:
logger.debug(
f"Generating low resolution mask:\n d_max = {params.d_max}")
d_max = params.d_max
d_inf = max(d_max + 1, 1e9)
_apply_resolution_mask(mask, beam, panel, d_max, d_inf)
try:
# Mask out the resolution range
for drange in params.resolution_range:
d_min = min(drange)
d_max = max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.debug("Generating resolution range mask:\n" +
f" d_min = {d_min}\n" + f" d_max = {d_max}")
_apply_resolution_mask(mask, beam, panel, d_min, d_max)
except TypeError:
# Catch the default value None of params.resolution_range
if any(params.resolution_range):
raise
# Mask out the resolution ranges for the ice rings
for drange in generate_ice_ring_resolution_ranges(
beam, panel, params.ice_rings):
d_min = min(drange)
d_max = max(drange)
assert d_min < d_max, "d_min must be < d_max"
logger.debug("Generating ice ring mask:\n" +
f" d_min = {d_min:.4f}\n" + f" d_max = {d_max:.4f}")
_apply_resolution_mask(mask, beam, panel, d_min, d_max)
# Add to the list
masks.append(mask)
# Return the mask
return tuple(masks)
def generate(self, imageset):
""" Generate the mask. """
# 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)):
# 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)
if region.pixel is not None:
mask[region.pixel] = False
# 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)
try:
# 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)
except TypeError:
# Catch the default value None of self.params.resolution_range
if any(self.params.resolution_range):
raise
else:
pass
# 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)