def drizzle_test(sbox, beam_vectors, angles, experiment):
from dials.algorithms.reflection_basis import CoordinateSystem
# from dials.algorithms.image.drizzle import drizzle
beam = experiment.beam
detector = experiment.detector
goniometer = experiment.goniometer
scan = experiment.scan
s0 = beam.get_s0()
m2 = goniometer.get_rotation_axis()
s1 = beam_vectors[0]
phi = angles[0]
cs_target = CoordinateSystem(m2, s0, s1, phi)
from matplotlib import pylab
fig = pylab.figure()
ax = fig.gca()
colour = ["black", "blue", "red", "green", "yellow", "cyan", "magenta"]
output = flex.double(flex.grid(sbox[0].data.all()))
for r in range(len(sbox)):
s1 = beam_vectors[r]
phi = angles[r]
cs = CoordinateSystem(m2, s0, s1, phi)
e = rs_coords(sbox[r].bbox, cs, beam, detector, scan)
e1, e2, e3 = e.parts()
p = px_coords(e, cs_target, detector, scan)
x, y, z = p.parts()
pylab.scatter(x, y, color=colour[r])
input = sbox[r].data.all()
x -= sbox[0].bbox[0]
y -= sbox[0].bbox[2]
z -= sbox[0].bbox[4]
# coords = flex.vec3_double(x, y, z)
# drizzle(output, input, coords)
ax.set_xticks(range(sbox[0].bbox[0], sbox[0].bbox[1] + 1))
ax.set_yticks(range(sbox[0].bbox[2], sbox[0].bbox[3] + 1))
pylab.grid()
pylab.show()
def test_transform(
experiment, shoebox, s1, phi, grid_size, sigma_m, sigma_b, n_sigma, ndiv=5
):
from dials.algorithms.reflection_basis.transform import MapFramesForward
from dials.algorithms.reflection_basis import CoordinateSystem
bbox = shoebox.bbox
data = shoebox.data
mask = shoebox.mask
x0, x1, y0, y1, z0, z1 = bbox
step_size = (
n_sigma * sigma_m / (grid_size + 0.5),
n_sigma * sigma_b / (grid_size + 0.5),
n_sigma * sigma_b / (grid_size + 0.5),
)
grid_range = 2 * grid_size + 1
offset = grid_size + 0.5
grid = flex.double(flex.grid(grid_range, grid_range, grid_range))
m2 = experiment.goniometer.get_rotation_axis()
s0 = experiment.beam.get_s0()
cs = CoordinateSystem(m2, s0, s1, phi)
grid_index = GridIndex(experiment, cs, offset, step_size)
# phi0, dphi = experiment.scan.get_oscillation(deg=False)
# map_frames = MapFramesForward(phi0, dphi, sigma_m, n_sigma, grid_size)
# zfraction = map_frames((z0, z1), phi, cs.zeta())
# for j in range(zfraction.all()[0]):
# print ' '.join(str(zfraction[j,i]) for i in range(zfraction.all()[1]))
# for j in range(zfraction.all()[0]):
# print "Fraction %d: %f" % (j, flex.sum(zfraction[j:j+1,:]))
fraction = 1.0 / (ndiv * ndiv * ndiv)
for k in range(data.all()[0]):
for j in range(data.all()[1]):
for i in range(data.all()[2]):
if mask[k, j, i]:
value = data[k, j, i] * fraction
for kk in range(0, ndiv):
for jj in range(0, ndiv):
for ii in range(0, ndiv):
kkk = z0 + k + 1.0 * (kk + 0.5) / ndiv
jjj = y0 + j + 1.0 * (jj + 0.5) / ndiv
iii = x0 + i + 1.0 * (ii + 0.5) / ndiv
gk, gj, gi = grid_index(kkk, jjj, iii)
if (
gk >= 0
and gk < grid_range
and gj >= 0
and gj < grid_range
and gi >= 0
and gi < grid_range
):
grid[gk, gj, gi] += value
# fraction = 1.0 / (ndiv * ndiv)
# for k in range(data.all()[0]):
# for j in range(data.all()[1]):
# for i in range(data.all()[2]):
# if mask[k,j,i]:
# value = data[k,j,i] * fraction
# for jj in range(0, ndiv):
# for ii in range(0, ndiv):
# jjj = y0 + j + 1.0 * (jj + 0.5) / ndiv
# iii = x0 + i + 1.0 * (ii + 0.5) / ndiv
# gj, gi = grid_index(jjj,iii)
# if (gj >= 0 and gj < grid_range and
# gi >= 0 and gi < grid_range):
# for gk in range(0, 2*grid_size+1):
# grid[gk,gj,gi] += value * zfraction[k,gk]
return grid
div = 4
mask1 = flex.bool(flex.grid(int(ysize / div), int(xsize / div)))
mask2 = flex.bool(flex.grid(int(ysize / div), int(xsize / div)))
n = 5
dm = n * 0.157 * pi / 180.0
# dm = n * 1.0 * pi / 180.0
# dm /= pi / 2
print(dm)
xyz = detector.get_pixel_lab_coord((0, 1200))
s1 = matrix.col(xyz).normalize() * s0.length()
phi = 0.0
cs = CoordinateSystem(m2, s0, s1, phi)
print("Limits: ", cs.limits())
# from_angle = FromRotationAngleAccurate(cs)
# phi_list = []
# e3_list = []
# for t in range(-100, 100):
# p = phi - dm * t / 10
# print p, from_angle(p)
# phi_list.append(p)
# e3_list.append(from_angle(p))
# from matplotlib import pylab
# pylab.plot(phi_list, e3_list)
# pylab.axvline(x=phi)
# pylab.show()
from dials.algorithms.reflection_basis import ToRotationAngleAccurate from dials.algorithms.reflection_basis import FromRotationAngleFast # s0 = matrix.col((0.00801639379479156, -3.8514801707506e-14, -1.0208975723528189) ) # m2 = matrix.col((1.0, -1.5919306617286774e-16, -6.904199434387693e-16)) # s1 = matrix.col((0.502248600762, -0.0181543707198, -0.888657908118)) # s0 = matrix.col((0.0, 0.0, -1.0)) # m2 = matrix.col((1.0, 0.0, 0.0)) # s1 = matrix.col((1.0, 0.05, 0.0)).normalize() phi = 0 # c3 = -0.013439 n = 5 c3 = -n * 0.157 * pi / 180.0 cs = CoordinateSystem(m2, s0, s1, phi) print(cs.zeta()) # e1 = matrix.col(cs.e1_axis()) # e3 = matrix.col(cs.e3_axis()) # ps = matrix.col(cs.p_star()) # from math import sqrt # m2e1 = m2.dot(e1) # m2e3 = m2.dot(e3) # m2ps = m2.dot(ps.normalize()) # print tuple(e1) # print tuple(e3) # print tuple(ps) # print "m2.e1", m2e1 # print "m2.e3", m2e3
div = 4 mask1 = flex.bool(flex.grid(int(ysize / div), int(xsize / div))) mask2 = flex.bool(flex.grid(int(ysize / div), int(xsize / div))) n = 5 dm = n * 0.157 * pi / 180.0 #dm = n * 1.0 * pi / 180.0 #dm /= pi / 2 print dm xyz = detector.get_pixel_lab_coord((0, 1200)) s1 = matrix.col(xyz).normalize() * s0.length() phi = 0.0 cs = CoordinateSystem(m2, s0, s1, phi) print "Limits: ", cs.limits() #from_angle = FromRotationAngleAccurate(cs) #phi_list = [] #e3_list = [] #for t in range(-100, 100): # p = phi - dm * t / 10 # print p, from_angle(p) # phi_list.append(p) # e3_list.append(from_angle(p)) #from matplotlib import pylab #pylab.plot(phi_list, e3_list) #pylab.axvline(x=phi) #pylab.show()
from dials.algorithms.reflection_basis import ToRotationAngleAccurate from dials.algorithms.reflection_basis import FromRotationAngleFast #s0 = matrix.col((0.00801639379479156, -3.8514801707506e-14, -1.0208975723528189) ) #m2 = matrix.col((1.0, -1.5919306617286774e-16, -6.904199434387693e-16)) #s1 = matrix.col((0.502248600762, -0.0181543707198, -0.888657908118)) #s0 = matrix.col((0.0, 0.0, -1.0)) #m2 = matrix.col((1.0, 0.0, 0.0)) #s1 = matrix.col((1.0, 0.05, 0.0)).normalize() phi = 0 #c3 = -0.013439 n = 5 c3 = -n * 0.157 * pi / 180.0 cs = CoordinateSystem(m2, s0, s1, phi) print cs.zeta() #e1 = matrix.col(cs.e1_axis()) #e3 = matrix.col(cs.e3_axis()) #ps = matrix.col(cs.p_star()) #from math import sqrt #m2e1 = m2.dot(e1) #m2e3 = m2.dot(e3) #m2ps = m2.dot(ps.normalize()) #print tuple(e1) #print tuple(e3) #print tuple(ps) #print "m2.e1", m2e1 #print "m2.e3", m2e3
