def oneImage(self,framenumber):
self.reporters[framenumber] = []
from dxtbx.format.Registry import Registry
filename = self.phil_params.distl.image[framenumber]
reader = Registry.find(filename)
img = reader(filename)
detector = img.get_detector()
beam = img.get_beam()
S0 = beam.get_s0()
data = img.get_raw_data()
scan = img.get_scan()
print scan
if scan is None:
print "No scan"
RR = (0,1)
else:
print scan.get_oscillation()
RR = scan.get_oscillation_range()
from spotfinder.dxtbx_toolbox import Distl
sfall = Distl(params = self.phil_params, detector = detector, beam = beam, data = data)
resolutions = flex.double()
spotlist = []
from dials.model.data import ReflectionList,Reflection
reflections = ReflectionList()
for ip,panel in enumerate(detector):
for spot in sfall.finderlist[ip].spots:
resolutions.append( panel.get_resolution_at_pixel(S0, (spot.ctr_mass_x(), spot.ctr_mass_y())) )
spotlist.append(spot)
refl = Reflection()
refl.panel_number = ip
refl.centroid_position = (spot.ctr_mass_x(), spot.ctr_mass_y(),0.0)
refl.centroid_variance = (0.5,0.5,0.0)
reflections.append(refl)
selection = (resolutions>0.0)
if self.phil_params.distl.res.outer is not None:
selection = (selection and (resolutions>self.phil_params.distl.res.outer))
if self.phil_params.distl.res.inner is not None:
selection = (selection and (resolutions<self.phil_params.distl.res.inner))
reflections = reflections.select(selection)
return dict(detector=detector, beam=beam, reflections=reflections, scan = scan,
gonio = img.get_goniometer())
def oneImage(self, framenumber):
self.reporters[framenumber] = []
import dxtbx.format.Registry
filename = self.phil_params.distl.image[framenumber]
reader = dxtbx.format.Registry.get_format_class_for_file(filename)
img = reader(filename)
detector = img.get_detector()
beam = img.get_beam()
S0 = beam.get_s0()
data = img.get_raw_data()
scan = img.get_scan()
print(scan)
if scan is None:
print("No scan")
RR = (0, 1)
else:
print(scan.get_oscillation())
RR = scan.get_oscillation_range()
from spotfinder.dxtbx_toolbox import Distl
sfall = Distl(params=self.phil_params,
detector=detector,
beam=beam,
data=data)
resolutions = flex.double()
spotlist = []
from dials.model.data import ReflectionList, Reflection
reflections = ReflectionList()
for ip, panel in enumerate(detector):
for spot in sfall.finderlist[ip].spots:
resolutions.append(
panel.get_resolution_at_pixel(
S0, (spot.ctr_mass_x(), spot.ctr_mass_y())))
spotlist.append(spot)
refl = Reflection()
refl.panel_number = ip
refl.centroid_position = (spot.ctr_mass_x(), spot.ctr_mass_y(),
0.0)
refl.centroid_variance = (0.5, 0.5, 0.0)
reflections.append(refl)
selection = (resolutions > 0.0)
if self.phil_params.distl.res.outer is not None:
selection = (selection
and (resolutions > self.phil_params.distl.res.outer))
if self.phil_params.distl.res.inner is not None:
selection = (selection
and (resolutions < self.phil_params.distl.res.inner))
reflections = reflections.select(selection)
return dict(detector=detector,
beam=beam,
reflections=reflections,
scan=scan,
gonio=img.get_goniometer())
from __future__ import division
from __future__ import print_function
from scitbx.array_family import flex
from dials.model.data import Reflection, ReflectionList
from dials.algorithms import shoebox
rl = ReflectionList()
r1 = Reflection()
r1.shoebox = (10, 20, 10, 20, 10, 20)
r2 = Reflection()
r2.shoebox = (15, 25, 15, 25, 15, 25)
r3 = Reflection()
r3.shoebox = (20, 30, 20, 30, 20, 30)
rl.append(r1)
rl.append(r2)
rl.append(r3)
overlapping = shoebox.find_overlapping(rl)
for e in overlapping.edges():
print("Edge: ", overlapping.edge_vertices(e))
for v in overlapping.vertices():
print("Vertex: ", v, " => ", [a for a in overlapping.adjacent_vertices(v)])
#data2d = numpy.zeros((3, 3), dtype = numpy.float64)
data2d = flex.double(flex.grid(1, 3, 3),15)
data2d[0, 1, 1] = 50
for row in range(3):
for col in range(3):
data2d[0,row, col] += row * 2
data2d[0,row, col] += col * 2
mask2d = flex.int(flex.grid(1, 3, 3),3)
mask2d[0, 1, 1] = 5
background2d = flex.double(flex.grid(1, 3, 3),0)
from dials.model.data import Reflection, ReflectionList
from scitbx.array_family import flex
r = Reflection()
r.shoebox = data2d
r.shoebox_mask = mask2d
r.shoebox_background = background2d
rlist = ReflectionList()
rlist.append(r)
#from dials.algorithms.background.flat_background_subtractor \
# import layering_and_background_avg
#layering_and_background_avg(rlist)
#from dials.algorithms.background.curved_background_subtractor \
# import layering_and_background_modl
#layering_and_background_modl(rlist)
from __future__ import division
from scitbx.array_family import flex
from dials.model.data import Reflection, ReflectionList
from dials.algorithms import shoebox
rl = ReflectionList()
r1 = Reflection()
r1.shoebox = (10, 20, 10, 20, 10, 20)
r2 = Reflection()
r2.shoebox = (15, 25, 15, 25, 15, 25)
r3 = Reflection()
r3.shoebox = (20, 30, 20, 30, 20, 30)
rl.append(r1)
rl.append(r2)
rl.append(r3)
overlapping = shoebox.find_overlapping(rl)
for e in overlapping.edges():
print "Edge: ", overlapping.edge_vertices(e)
for v in overlapping.vertices():
print "Vertex: ", v, " => ", [a for a in overlapping.adjacent_vertices(v)]
data2d = flex.double(flex.grid(1, 3, 3), 15)
data2d[0, 1, 1] = 50
for row in range(3):
for col in range(3):
data2d[0, row, col] += row * 2
data2d[0, row, col] += col * 2
mask2d = flex.int(flex.grid(1, 3, 3), 3)
mask2d[0, 1, 1] = 5
background2d = flex.double(flex.grid(1, 3, 3), 0)
from dials.model.data import Reflection, ReflectionList
from scitbx.array_family import flex
r = Reflection()
r.shoebox = data2d
r.shoebox_mask = mask2d
r.shoebox_background = background2d
rlist = ReflectionList()
rlist.append(r)
# from dials.algorithms.background.flat_background_subtractor \
# import layering_and_background_avg
# layering_and_background_avg(rlist)
# from dials.algorithms.background.curved_background_subtractor \
# import layering_and_background_modl
# layering_and_background_modl(rlist)
