def generate_reflections(detector, beam, scan, experiment, num):
from random import randint, seed
from scitbx import matrix
from dials.array_family import flex
from dials.algorithms.shoebox import MaskCode
seed(0)
assert len(detector) == 1
beam_vector = flex.vec3_double(num)
xyzcal_px = flex.vec3_double(num)
xyzcal_mm = flex.vec3_double(num)
panel = flex.size_t(num)
s0_length = matrix.col(beam.get_s0()).length()
for i in range(num):
x = randint(0, 2000)
y = randint(0, 2000)
z = randint(0, 8)
s1 = detector[0].get_pixel_lab_coord((x, y))
s1 = matrix.col(s1).normalize() * s0_length
phi = scan.get_angle_from_array_index(z, deg=False)
beam_vector[i] = s1
xyzcal_px[i] = (x, y, z)
(x, y) = detector[0].pixel_to_millimeter((x, y))
xyzcal_mm[i] = (x, y, phi)
panel[i] = 0
sigma_b = experiment[0].beam.get_sigma_divergence(deg=False)
try:
sigma_m = experiment[0].crystal.get_mosaicity(deg=False)
except AttributeError:
sigma_m = 0
rlist = flex.reflection_table()
rlist["id"] = flex.int(len(beam_vector), 0)
rlist["s1"] = beam_vector
rlist["panel"] = panel
rlist["xyzcal.px"] = xyzcal_px
rlist["xyzcal.mm"] = xyzcal_mm
rlist["bbox"] = rlist.compute_bbox(experiment)
index = []
image_size = experiment[0].detector[0].get_image_size()
array_range = experiment[0].scan.get_array_range()
bbox = rlist["bbox"]
for i in range(len(rlist)):
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)
rlist.del_selected(flex.size_t(index))
rlist["shoebox"] = flex.shoebox(rlist["panel"], rlist["bbox"])
rlist["shoebox"].allocate_with_value(MaskCode.Valid)
return rlist
def generate_reflections(self, num):
from random import randint, seed
from scitbx import matrix
from dials.array_family import flex
from dials.algorithms.shoebox import MaskCode
seed(0)
assert(len(self.detector) == 1)
beam_vector = flex.vec3_double(num)
xyzcal_px = flex.vec3_double(num)
xyzcal_mm = flex.vec3_double(num)
panel = flex.size_t(num)
s0_length = matrix.col(self.beam.get_s0()).length()
for i in range(num):
x = randint(0, 2000)
y = randint(0, 2000)
z = randint(0, 8)
s1 = self.detector[0].get_pixel_lab_coord((x, y))
s1 = matrix.col(s1).normalize() * s0_length
phi = self.scan.get_angle_from_array_index(z, deg=False)
beam_vector[i] = s1
xyzcal_px[i] = (x, y, z)
(x, y) = self.detector[0].pixel_to_millimeter((x, y))
xyzcal_mm[i] = (x, y, phi)
panel[i] = 0
sigma_b = self.experiment[0].beam.get_sigma_divergence(deg=False)
sigma_m = self.experiment[0].crystal.get_mosaicity(deg=False)
rlist = flex.reflection_table()
rlist['id'] = flex.int(len(beam_vector), 0)
rlist['s1'] = beam_vector
rlist['panel'] = panel
rlist['xyzcal.px'] = xyzcal_px
rlist['xyzcal.mm'] = xyzcal_mm
rlist['bbox'] = rlist.compute_bbox(self.experiment)
index = []
image_size = self.experiment[0].detector[0].get_image_size()
array_range = self.experiment[0].scan.get_array_range()
bbox = rlist['bbox']
for i in range(len(rlist)):
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)
rlist.del_selected(flex.size_t(index))
rlist['shoebox'] = flex.shoebox(
rlist['panel'], rlist['bbox'])
rlist['shoebox'].allocate_with_value(MaskCode.Valid)
return rlist
def run(self, flags, sweep=None, shoeboxes=None, **kwargs):
from dials.array_family import flex
from dials.algorithms.shoebox import MaskCode
from dials.algorithms.background.simple import Linear2dModeller
bg_code = MaskCode.Valid | MaskCode.BackgroundUsed
fg_code = MaskCode.Valid | MaskCode.Foreground
strong_code = MaskCode.Valid | MaskCode.Strong
modeller = Linear2dModeller()
expanded_shoeboxes = flex.shoebox()
detector = sweep.get_detector()
zoffset = 0
if sweep.get_scan() is not None:
zoffset = sweep.get_scan().get_array_range()[0]
from libtbx.containers import OrderedDict
class image_data_cache(object):
def __init__(self, imageset, size=10):
self.imageset = imageset
self.size = size
self._image_data = OrderedDict()
def __getitem__(self, i):
image_data = self._image_data.get(i)
if image_data is None:
image_data = self.imageset.get_raw_data(i)
if len(self._image_data) >= self.size:
# remove the oldest entry in the cache
del self._image_data[self._image_data.keys()[0]]
self._image_data[i] = image_data
return image_data
cache = image_data_cache(sweep)
#cache = sweep
# sort shoeboxes by centroid z
frame = shoeboxes.centroid_all().position_frame()
perm = flex.sort_permutation(frame)
shoeboxes = shoeboxes.select(perm)
buffer_size = 1
bg_plus_buffer = self.background_size + buffer_size
import time
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]:
continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
bbox = shoebox.bbox
x1, x2, y1, y2, z1, z2 = bbox
# expand the bbox with a background region around the spotfinder shoebox
# perhaps also should use a buffer zone between the shoebox and the
# background region
expanded_bbox = (max(0, x1-bg_plus_buffer),
min(max_x, x2+bg_plus_buffer),
max(0, y1-bg_plus_buffer),
min(max_y, y2+bg_plus_buffer),
z1, z2)
shoebox.bbox = expanded_bbox
t1 = time.time()
info("Time expand_shoebox: %s" %(t1-t0))
rlist = flex.reflection_table()
rlist['shoebox'] = shoeboxes
rlist['shoebox'].allocate()
rlist['panel'] = shoeboxes.panels()
rlist['bbox'] = shoeboxes.bounding_boxes()
t0 = time.time()
rlist.extract_shoeboxes(sweep)
t1 = time.time()
shoeboxes = rlist['shoebox']
shoeboxes.flatten()
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]: continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
ex1, ex2, ey1, ey2, ez1, ez2 = shoebox.bbox
data = shoebox.data
mask = flex.bool(data.accessor(), False)
for i_y, y in enumerate(range(ey1, ey2)):
for i_x, x in enumerate(range(ex1, ex2)):
value = data[0, i_y, i_x]
if (y >= (ey1+buffer_size) and y < (ey2-buffer_size) and
x >= (ex1+buffer_size) and x < (ex2-buffer_size)):
mask[0, i_y, i_x] = False # foreground
elif (value > trusted_range[0] and value < trusted_range[1]):
mask[0, i_y, i_x] = True # background
model = modeller.create(data.as_double(), mask)
d, a, b = model.params()[:3]
c = -1
if abs(a) > self.gradient_cutoff or abs(b) > self.gradient_cutoff:
flags[perm[i]] = False
# FIXME should this commented out section be removed?
#if abs(a) < self.gradient_cutoff and abs(b) < self.gradient_cutoff:
#flags[i] = False
#if x2-x1 > 10 or y2-y1 > 10:
#print a, b, d, flags[perm[i]]
#bg = flex.double(data.accessor())
#for x in range(ex2-ex1):
#for y in range(ey2-ey1):
#z = a * x + b * y + d
#bg[0,y,x] = z
#model = modeller.create(data-bg, mask)
#d, a, b = model.params()[:3]
#c = -1
#bg2 = flex.double(data.accessor())
#for x in range(ex2-ex1):
#for y in range(ey2-ey1):
#z = a * x + b * y + d
#bg2[0,y,x] = z
##print a, b, d
#from matplotlib import pyplot
#fig, axes = pyplot.subplots(nrows=1, ncols=5)
#im0 = axes[0].imshow(data.as_numpy_array()[i_z,:,:], interpolation='none')
#im1 = axes[1].imshow(mask.as_numpy_array()[i_z,:,:], interpolation='none')
#im2 = axes[2].imshow(bg.as_numpy_array()[i_z,:,:], interpolation='none')
#im3 = axes[3].imshow((data-bg).as_numpy_array()[i_z,:,:], interpolation='none')
#im4 = axes[4].imshow(bg2.as_numpy_array()[i_z,:,:], interpolation='none')
##pyplot.colorbar(im0)
##pyplot.colorbar(im1)
##pyplot.colorbar(im2)
##pyplot.colorbar(im3)
#pyplot.show()
#from matplotlib import pyplot
#fig, axes = pyplot.subplots(nrows=1, ncols=2)
#im0 = axes[0].imshow(data.as_numpy_array()[i_z,:,:], interpolation='none')
#im1 = axes[1].imshow(bg.as_numpy_array()[i_z,:,:], interpolation='none')
#pyplot.colorbar(im1)
#pyplot.show()
t1 = time.time()
#print "Time fit_bg: %s" %(t1-t0)
return flags
def run(self, flags, sweep=None, shoeboxes=None, **kwargs):
from dials.array_family import flex
from dials.algorithms.shoebox import MaskCode
from dials.algorithms.background.simple import Linear2dModeller
bg_code = MaskCode.Valid | MaskCode.BackgroundUsed
fg_code = MaskCode.Valid | MaskCode.Foreground
strong_code = MaskCode.Valid | MaskCode.Strong
modeller = Linear2dModeller()
expanded_shoeboxes = flex.shoebox()
detector = sweep.get_detector()
zoffset = 0
if sweep.get_scan() is not None:
zoffset = sweep.get_scan().get_array_range()[0]
from libtbx.containers import OrderedDict
class image_data_cache(object):
def __init__(self, imageset, size=10):
self.imageset = imageset
self.size = size
self._image_data = OrderedDict()
def __getitem__(self, i):
image_data = self._image_data.get(i)
if image_data is None:
image_data = self.imageset.get_raw_data(i)
if len(self._image_data) >= self.size:
# remove the oldest entry in the cache
del self._image_data[self._image_data.keys()[0]]
self._image_data[i] = image_data
return image_data
cache = image_data_cache(sweep)
#cache = sweep
# sort shoeboxes by centroid z
frame = shoeboxes.centroid_all().position_frame()
perm = flex.sort_permutation(frame)
shoeboxes = shoeboxes.select(perm)
buffer_size = 1
bg_plus_buffer = self.background_size + buffer_size
import time
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]:
continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
bbox = shoebox.bbox
x1, x2, y1, y2, z1, z2 = bbox
# expand the bbox with a background region around the spotfinder shoebox
# perhaps also should use a buffer zone between the shoebox and the
# background region
expanded_bbox = (max(0, x1 - bg_plus_buffer),
min(max_x, x2 + bg_plus_buffer),
max(0, y1 - bg_plus_buffer),
min(max_y, y2 + bg_plus_buffer), z1, z2)
shoebox.bbox = expanded_bbox
t1 = time.time()
logger.info("Time expand_shoebox: %s" % (t1 - t0))
rlist = flex.reflection_table()
rlist['shoebox'] = shoeboxes
rlist['shoebox'].allocate()
rlist['panel'] = shoeboxes.panels()
rlist['bbox'] = shoeboxes.bounding_boxes()
t0 = time.time()
rlist.extract_shoeboxes(sweep)
t1 = time.time()
shoeboxes = rlist['shoebox']
shoeboxes.flatten()
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]: continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
ex1, ex2, ey1, ey2, ez1, ez2 = shoebox.bbox
data = shoebox.data
mask = flex.bool(data.accessor(), False)
for i_y, y in enumerate(range(ey1, ey2)):
for i_x, x in enumerate(range(ex1, ex2)):
value = data[0, i_y, i_x]
if (y >= (ey1 + buffer_size) and y < (ey2 - buffer_size)
and x >= (ex1 + buffer_size) and x <
(ex2 - buffer_size)):
mask[0, i_y, i_x] = False # foreground
elif value > trusted_range[0] and value < trusted_range[1]:
mask[0, i_y, i_x] = True # background
model = modeller.create(data.as_double(), mask)
d, a, b = model.params()[:3]
c = -1
if abs(a) > self.gradient_cutoff or abs(b) > self.gradient_cutoff:
flags[perm[i]] = False
t1 = time.time()
return flags
def run(self, flags, sweep=None, shoeboxes=None, **kwargs):
from dials.array_family import flex
from dials.algorithms.shoebox import MaskCode
from dials.algorithms.background.simple import Linear2dModeller
bg_code = MaskCode.Valid | MaskCode.BackgroundUsed
fg_code = MaskCode.Valid | MaskCode.Foreground
strong_code = MaskCode.Valid | MaskCode.Strong
modeller = Linear2dModeller()
expanded_shoeboxes = flex.shoebox()
detector = sweep.get_detector()
zoffset = 0
if sweep.get_scan() is not None:
zoffset = sweep.get_scan().get_array_range()[0]
from libtbx.containers import OrderedDict
class image_data_cache(object):
def __init__(self, imageset, size=10):
self.imageset = imageset
self.size = size
self._image_data = OrderedDict()
def __getitem__(self, i):
image_data = self._image_data.get(i)
if image_data is None:
image_data = self.imageset.get_raw_data(i)
if len(self._image_data) >= self.size:
# remove the oldest entry in the cache
del self._image_data[self._image_data.keys()[0]]
self._image_data[i] = image_data
return image_data
cache = image_data_cache(sweep)
#cache = sweep
# sort shoeboxes by centroid z
frame = shoeboxes.centroid_all().position_frame()
perm = flex.sort_permutation(frame)
shoeboxes = shoeboxes.select(perm)
buffer_size = 1
bg_plus_buffer = self.background_size + buffer_size
import time
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]:
continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
bbox = shoebox.bbox
x1, x2, y1, y2, z1, z2 = bbox
# expand the bbox with a background region around the spotfinder shoebox
# perhaps also should use a buffer zone between the shoebox and the
# background region
expanded_bbox = (max(0, x1-bg_plus_buffer),
min(max_x, x2+bg_plus_buffer),
max(0, y1-bg_plus_buffer),
min(max_y, y2+bg_plus_buffer),
z1, z2)
shoebox.bbox = expanded_bbox
t1 = time.time()
logger.info("Time expand_shoebox: %s" %(t1-t0))
rlist = flex.reflection_table()
rlist['shoebox'] = shoeboxes
rlist['shoebox'].allocate()
rlist['panel'] = shoeboxes.panels()
rlist['bbox'] = shoeboxes.bounding_boxes()
t0 = time.time()
rlist.extract_shoeboxes(sweep)
t1 = time.time()
shoeboxes = rlist['shoebox']
shoeboxes.flatten()
t0 = time.time()
for i, shoebox in enumerate(shoeboxes):
if not flags[perm[i]]: continue
panel = detector[shoebox.panel]
trusted_range = panel.get_trusted_range()
max_x, max_y = panel.get_image_size()
ex1, ex2, ey1, ey2, ez1, ez2 = shoebox.bbox
data = shoebox.data
mask = flex.bool(data.accessor(), False)
for i_y, y in enumerate(range(ey1, ey2)):
for i_x, x in enumerate(range(ex1, ex2)):
value = data[0, i_y, i_x]
if (y >= (ey1+buffer_size) and y < (ey2-buffer_size) and
x >= (ex1+buffer_size) and x < (ex2-buffer_size)):
mask[0, i_y, i_x] = False # foreground
elif value > trusted_range[0] and value < trusted_range[1]:
mask[0, i_y, i_x] = True # background
model = modeller.create(data.as_double(), mask)
d, a, b = model.params()[:3]
c = -1
if abs(a) > self.gradient_cutoff or abs(b) > self.gradient_cutoff:
flags[perm[i]] = False
t1 = time.time()
return flags