def exercise_polygon(): from dials.util import is_inside_polygon from scitbx.array_family import flex poly = flex.vec2_double(((0,0), (1,0), (1,1), (0,1))) assert is_inside_polygon(poly, 0, 0) assert is_inside_polygon(poly, 0.5, 0.5) assert not is_inside_polygon(poly, 1, 1.01) points = flex.vec2_double(((0.3, 0.8), (0.3, 1.5), (-8,9), (0.00001, 0.9999))) assert list(is_inside_polygon(poly, points)) == [True, False, False, True]
def exercise_polygon(): from dials.util import is_inside_polygon from scitbx.array_family import flex poly = flex.vec2_double(((0,0), (1,0), (1,1), (0,1))) assert is_inside_polygon(poly, 0, 0) assert is_inside_polygon(poly, 0.5, 0.5) assert not is_inside_polygon(poly, 1, 1.01) points = flex.vec2_double(((0.3, 0.8), (0.3, 1.5), (-8,9), (0.00001, 0.9999))) assert list(is_inside_polygon(poly, points)) == [True, False, False, True]
def filter_shadowed_reflections(experiments, reflections):
from dials.util import mask_untrusted_polygon
from dials.util import is_inside_polygon
shadowed = flex.bool(reflections.size(), False)
for expt_id in range(len(experiments)):
expt = experiments[expt_id]
imgset = expt.imageset
masker = imgset.reader().get_format().get_goniometer_shadow_masker()
detector = expt.detector
sel = reflections['id'] == expt_id
isel = sel.iselection()
x,y,z = reflections['xyzcal.px'].select(isel).parts()
start, end = expt.scan.get_array_range()
for i in range(start, end):
shadow = masker.project_extrema(
detector, expt.scan.get_angle_from_array_index(i))
img_sel = (z >= i) & (z < (i+1))
img_isel = img_sel.iselection()
for p_id in range(len(detector)):
panel = reflections['panel'].select(img_isel)
if shadow[p_id].size() < 4:
continue
panel_isel = img_isel.select(panel == p_id)
inside = is_inside_polygon(
shadow[p_id],
flex.vec2_double(x.select(isel.select(panel_isel)),
y.select(isel.select(panel_isel))))
shadowed.set_selected(panel_isel, inside)
return shadowed
def project_extrema(self, detector, scan_angle):
from dials.util import is_inside_polygon
coords = self.extrema_at_scan_angle(scan_angle)
shadow_boundary = []
for p_id, p in enumerate(detector):
# project coordinates onto panel plane
a = p.get_D_matrix() * coords
x, y, z = a.parts()
valid = z > 0
x.set_selected(valid, x.select(valid) / z.select(valid))
y.set_selected(valid, y.select(valid) / z.select(valid))
if valid.count(True) < 3:
# no shadow projected onto this panel
shadow_boundary.append(flex.vec2_double())
continue
# Compute convex hull of shadow points
points = flex.vec2_double(x.select(valid), y.select(valid))
shadow = flex.vec2_double(convex_hull(points))
shadow *= 1 / p.get_pixel_size()[0]
shadow_orig = shadow.deep_copy()
for i in (0, p.get_image_size()[0]):
points = flex.vec2_double(
flex.double(p.get_image_size()[1], i),
flex.double_range(0,
p.get_image_size()[1]))
inside = is_inside_polygon(shadow_orig, points)
# only add those points needed to define vertices of shadow
inside_isel = inside.iselection()
outside_isel = (~inside).iselection()
while inside_isel.size():
j = inside_isel[0]
shadow.append(points[j])
outside_isel = outside_isel.select(outside_isel > j)
if outside_isel.size() == 0:
shadow.append(points[inside_isel[-1]])
break
sel = inside_isel >= outside_isel[0]
if sel.count(True) == 0:
shadow.append(points[inside_isel[-1]])
break
inside_isel = inside_isel.select(sel)
for i in (0, p.get_image_size()[1]):
points = flex.vec2_double(
flex.double_range(0,
p.get_image_size()[0]),
flex.double(p.get_image_size()[0], i))
inside = is_inside_polygon(shadow_orig, points)
# only add those points needed to define vertices of shadow
inside_isel = inside.iselection()
outside_isel = (~inside).iselection()
while inside_isel.size():
j = inside_isel[0]
shadow.append(points[j])
outside_isel = outside_isel.select(outside_isel > j)
if outside_isel.size() == 0:
shadow.append(points[inside_isel[-1]])
break
sel = inside_isel >= outside_isel[0]
if sel.count(True) == 0:
shadow.append(points[inside_isel[-1]])
break
inside_isel = inside_isel.select(sel)
# Select only those vertices that are within the panel dimensions
n_px = p.get_image_size()
x, y = shadow.parts()
valid = (x >= 0) & (x <= n_px[0]) & (y >= 0) & (y <= n_px[1])
shadow = shadow.select(valid)
# sort vertices clockwise from centre of mass
from scitbx.math import principal_axes_of_inertia_2d
com = principal_axes_of_inertia_2d(shadow).center_of_mass()
sx, sy = shadow.parts()
shadow = shadow.select(
flex.sort_permutation(flex.atan2(sy - com[1], sx - com[0])))
shadow_boundary.append(shadow)
return shadow_boundary
def project_extrema(self, detector, scan_angle):
from dials.util import is_inside_polygon
coords = self.extrema_at_scan_angle(scan_angle)
shadow_boundary = []
for p_id, p in enumerate(detector):
# project coordinates onto panel plane
a = p.get_D_matrix() * coords
x, y, z = a.parts()
valid = z > 0
x.set_selected(valid, x.select(valid)/z.select(valid))
y.set_selected(valid, y.select(valid)/z.select(valid))
if valid.count(True) < 3:
# no shadow projected onto this panel
shadow_boundary.append(flex.vec2_double())
continue
# Compute convex hull of shadow points
points = flex.vec2_double(x.select(valid), y.select(valid))
shadow = flex.vec2_double(convex_hull(points))
shadow *= 1/p.get_pixel_size()[0]
shadow_orig = shadow.deep_copy()
for i in (0, p.get_image_size()[0]):
points = flex.vec2_double(flex.double(p.get_image_size()[1], i),
flex.double_range(0, p.get_image_size()[1]))
inside = is_inside_polygon(shadow_orig, points)
# only add those points needed to define vertices of shadow
inside_isel = inside.iselection()
outside_isel = (~inside).iselection()
while inside_isel.size():
j = inside_isel[0]
shadow.append(points[j])
outside_isel = outside_isel.select(outside_isel > j)
if outside_isel.size() == 0:
shadow.append(points[inside_isel[-1]])
break
sel = inside_isel >= outside_isel[0]
if sel.count(True) == 0:
shadow.append(points[inside_isel[-1]])
break
inside_isel = inside_isel.select(sel)
for i in (0, p.get_image_size()[1]):
points = flex.vec2_double(flex.double_range(0, p.get_image_size()[0]),
flex.double(p.get_image_size()[0], i))
inside = is_inside_polygon(shadow_orig, points)
# only add those points needed to define vertices of shadow
inside_isel = inside.iselection()
outside_isel = (~inside).iselection()
while inside_isel.size():
j = inside_isel[0]
shadow.append(points[j])
outside_isel = outside_isel.select(outside_isel > j)
if outside_isel.size() == 0:
shadow.append(points[inside_isel[-1]])
break
sel = inside_isel >= outside_isel[0]
if sel.count(True) == 0:
shadow.append(points[inside_isel[-1]])
break
inside_isel = inside_isel.select(sel)
# Select only those vertices that are within the panel dimensions
n_px = p.get_image_size()
x, y = shadow.parts()
valid = (x >= 0) & (x <= n_px[0]) & (y >= 0) & (y <= n_px[1])
shadow = shadow.select(valid)
# sort vertices clockwise from centre of mass
from scitbx.math import principal_axes_of_inertia_2d
com = principal_axes_of_inertia_2d(shadow).center_of_mass()
sx, sy = shadow.parts()
shadow = shadow.select(
flex.sort_permutation(flex.atan2(sy-com[1],sx-com[0])))
shadow_boundary.append(shadow)
return shadow_boundary
