def run(i, imp):
from random import randint
from dials.array_family import flex
#building a reflection table
num_ref = 5
ref_table = flex.reflection_table()
shoebox = flex.shoebox(num_ref)
ref_table['shoebox'] = shoebox
intensity = flex.double(num_ref)
ref_table['intensity.sum.value'] = intensity
intensity_var = flex.double(num_ref)
ref_table['intensity.sum.variance'] = intensity_var
iterate = ref_table['shoebox']
i_to_compare = []
# bulding the shoebox with a desired content
# which is a reflection with noise included
n = 0
for arr in iterate:
img = flex.double(flex.grid(3, 3, 3))
bkg = flex.double(flex.grid(3, 3, 3))
msk = flex.int(flex.grid(3, 3, 3))
for row in range(3):
for col in range(3):
for fra in range(3):
img[row, col, fra] = row + col + fra + n * 9 + randint(0, i)
bkg[row, col, fra] = 0.0
msk[row, col, fra] = 3
n += 1
msk[1, 1, 1] = 5
tmp_i = n * n * n * 3
i_to_compare.append(tmp_i)
img[1, 1, 1] += tmp_i
arr.data = img[:, :, :]
arr.background = bkg[:, :, :]
arr.mask = msk[:, :, :]
# calling the functions that we need to test
# first select the algorithm for background calculation
if imp == "inclined":
print "testing inclined_background_subtractor"
from dials.algorithms.background.inclined_background_subtractor \
import layering_and_background_plane
layering_and_background_plane(ref_table)
elif imp == "flat":
print "testing flat_background_subtractor"
from dials.algorithms.background.flat_background_subtractor \
import layering_and_background_avg
layering_and_background_avg(ref_table)
elif imp == "curved":
print "testing curved_background_subtractor"
from dials.algorithms.background.curved_background_subtractor \
import layering_and_background_modl
layering_and_background_modl(ref_table)
# no matter which algorithm was used for background calculation
# the integration summation must remain compatible
from dials.algorithms.integration.summation2d \
import flex_2d_layering_n_integrating
flex_2d_layering_n_integrating(ref_table)
# comparing results
result = "OK"
resl_its = ref_table['intensity.sum.value']
resl_var = ref_table['intensity.sum.variance']
for n_its in range(len(resl_its)):
if resl_its[n_its] <= i_to_compare[n_its] + i and \
resl_its[n_its] >= i_to_compare[n_its] - i and \
resl_var[n_its] > resl_its[n_its]:
print "Ok ", n_its
else:
print "Wrong num", n_its
print "i =", i
print "resl_its[n_its] =", resl_its[n_its]
print "i_to_compare[n_its] =", i_to_compare[n_its]
print "resl_var[n_its] =", resl_var[n_its]
result = "wrong"
raise RuntimeError('wrong result')
return result
def run(i, imp):
from random import randint
from dials.array_family import flex
#building a reflection table
num_ref = 5
ref_table = flex.reflection_table()
shoebox = flex.shoebox(num_ref)
ref_table['shoebox'] = shoebox
intensity = flex.double(num_ref)
ref_table['intensity.sum.value'] = intensity
intensity_var = flex.double(num_ref)
ref_table['intensity.sum.variance'] = intensity_var
iterate = ref_table['shoebox']
i_to_compare = []
# bulding the shoebox with a desired content
# which is a reflection with noise included
n = 0
for arr in iterate:
img = flex.double(flex.grid(3, 3, 3))
bkg = flex.double(flex.grid(3, 3, 3))
msk = flex.int(flex.grid(3, 3, 3))
for row in range(3):
for col in range(3):
for fra in range(3):
img[row, col, fra] = row + col + fra + n * 9 + randint(0, i)
bkg[row, col, fra] = 0.0
msk[row, col, fra] = 3
n += 1
msk[1, 1, 1] = 5
tmp_i = n * n * n * 3
i_to_compare.append(tmp_i)
img[1, 1, 1] += tmp_i
arr.data = img[:, :, :]
arr.background = bkg[:, :, :]
arr.mask = msk[:, :, :]
# calling the functions that we need to test
# first select the algorithm for background calculation
if imp == "inclined":
print("testing inclined_background_subtractor")
from dials.algorithms.background.inclined_background_subtractor \
import layering_and_background_plane
layering_and_background_plane(ref_table)
elif imp == "flat":
print("testing flat_background_subtractor")
from dials.algorithms.background.flat_background_subtractor \
import layering_and_background_avg
layering_and_background_avg(ref_table)
elif imp == "curved":
print("testing curved_background_subtractor")
from dials.algorithms.background.curved_background_subtractor \
import layering_and_background_modl
layering_and_background_modl(ref_table)
# no matter which algorithm was used for background calculation
# the integration summation must remain compatible
from dials.algorithms.integration.summation2d \
import flex_2d_layering_n_integrating
flex_2d_layering_n_integrating(ref_table)
# comparing results
result = "OK"
resl_its = ref_table['intensity.sum.value']
resl_var = ref_table['intensity.sum.variance']
for n_its in range(len(resl_its)):
if resl_its[n_its] <= i_to_compare[n_its] + i and \
resl_its[n_its] >= i_to_compare[n_its] - i and \
resl_var[n_its] > resl_its[n_its]:
print("Ok ", n_its)
else:
print("Wrong num", n_its)
print("i =", i)
print("resl_its[n_its] =", resl_its[n_its])
print("i_to_compare[n_its] =", i_to_compare[n_its])
print("resl_var[n_its] =", resl_var[n_its])
result = "wrong"
raise RuntimeError('wrong result')
return result
#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 dials.algorithms.background.inclined_background_subtractor \ import layering_and_background_plane layering_and_background_plane(rlist) from dials.algorithms.integration.summation2d \ import flex_2d_layering_n_integrating flex_2d_layering_n_integrating(rlist) for r in rlist: matrix_img = r.shoebox.as_numpy_array() print print "shoebox" print matrix_img matrix_bkg = r.shoebox_background.as_numpy_array() print print "background" print matrix_bkg matrix_mask = r.shoebox_mask.as_numpy_array() print print "mask"
# 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 dials.algorithms.background.inclined_background_subtractor import (
layering_and_background_plane, )
layering_and_background_plane(rlist)
from dials.algorithms.integration.summation2d import flex_2d_layering_n_integrating
flex_2d_layering_n_integrating(rlist)
for r in rlist:
matrix_img = r.shoebox.as_numpy_array()
print()
print("shoebox")
print(matrix_img)
matrix_bkg = r.shoebox_background.as_numpy_array()
print()
print("background")
print(matrix_bkg)
matrix_mask = r.shoebox_mask.as_numpy_array()
print()
print("mask")
