def unrestrained_setting(self):
""" Calculate the basis vectors from N spots using numpy. This is equation 5 in
Brewster et. al 2015.
@return a cctbx crystal_orientation object
"""
from dials.array_family import flex
from scitbx.matrix import sqr
import numpy as np
if len(self.miller_indices) < 3:
return None
N = self.miller_indices.size()
hkl = self.miller_indices.as_double()
hkl.reshape(flex.grid((N,3)))
hkl = hkl.as_numpy_array()
xyz = self.u_vectors.as_double()
xyz.reshape(flex.grid((N,3)))
xyz = xyz.as_numpy_array()
try:
result = np.linalg.lstsq(hkl,xyz)
except Exception,e:
print "Exception while calculating basis vectors: %s"%e.message
return None
def plot_valid(b, s):
from dials.array_family import flex
b = [0.1, 0.2, 0.3, 0.4, 0.5]
s = [0.1, 0.3, 0.5, 0.3, 0.1]
v1 = flex.bool(flex.grid(100, 100))
v2 = flex.bool(flex.grid(100, 100))
v3 = flex.bool(flex.grid(100, 100))
r = [float(ss) / float(bb) for ss, bb in zip(s, b)]
for BB in range(0, 100):
for SS in range(0, 100):
B = -5.0 + BB / 10.0
S = -5.0 + SS / 10.0
V1 = True
V2 = True
V3 = True
for i in range(len(b)):
if B*b[i]+S*s[i] <= 0:
V1 = False
break
for i in range(len(b)):
if B*b[i] <= -S*s[i]:
V2 = False
break
v1[BB,SS] = V1
v2[BB,SS] = V2
from matplotlib import pylab
pylab.imshow(v1.as_numpy_array())
pylab.show()
exit(0)
def plot_prob_for_zero(c, b, s):
from math import log, exp, factorial
from dials.array_family import flex
L = flex.double(flex.grid(100, 100))
MASK = flex.bool(flex.grid(100, 100))
c = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
b = [bb / sum(b) for bb in b]
s = [ss / sum(s) for ss in s]
for BB in range(0, 100):
for SS in range(0, 100):
B = 0 + BB / 10000.0
S = 0 + SS / 40.0
LL = 0
for i in range(len(b)):
if B*b[i] + S*s[i] <= 0:
MASK[BB, SS] = True
LL = -999999
break
else:
LL += c[i]*log(B*b[i]+S*s[i]) - log(factorial(c[i])) - B*b[i] - S*s[i]
L[BB, SS] = LL
index = flex.max_index(L)
i = index % 100
j = index // 100
B = 0 + j / 10000.0
S = 0 + i / 40.0
print flex.max(L), B, S
from matplotlib import pylab
import numpy
im = numpy.ma.masked_array(flex.exp(L).as_numpy_array(), mask=MASK.as_numpy_array())
pylab.imshow(im)
pylab.show()
exit(0)
def plot_scale_vs_x_y(self):
from scitbx.array_family import flex
from math import ceil
print "Getting scale"
points = [(int(xyz[1] / 8), int(xyz[0] / 8)) for xyz in self.xyz]
scale = [x / d for x, d in zip(self.i_xds, self.i_dials)]
print "Creating Grid"
image_size = self.sweep.get_detector()[0].get_image_size()[::-1]
image_size = (int(ceil(image_size[0] / 8)), int(ceil(image_size[1] / 8)))
grid = flex.double(flex.grid(image_size))
count = flex.int(flex.grid(image_size))
for p, s in zip(points, scale):
grid[p] += s
count[p] += 1
for i in range(len(grid)):
if count[i] > 0:
grid[i] /= count[i]
# grid_points = [(j,i) for j in range(image_size[0]) for i in range(image_size[1])]
# grid = griddata(points, scale, grid_points)
# grid.shape = image_size
from matplotlib import pyplot
fig, ax = pyplot.subplots()
pyplot.title("scale vs x/y")
cax = pyplot.imshow(grid.as_numpy_array())
cbar = fig.colorbar(cax)
pyplot.savefig("plot-scale-vs-xy.png")
pyplot.close()
def show_image(c,b,s, BB=None, SS=None):
import numpy.ma
from dials.array_family import flex
N = 100
im = flex.double(flex.grid(N, N))
mask = flex.bool(flex.grid(N, N))
for j in range(N):
for i in range(N):
B = -1.0 + j * 10.0 / N
S = -1.0 + i * 10.0 / N
im[j,i], mask[j,i] = func(c,b,s,B,S)
im[j,i] = -im[j,i]
masked_im = numpy.ma.array(
# im.as_numpy_array(),
flex.exp(im).as_numpy_array(),
mask = mask.as_numpy_array())
mask2 = flex.bool(flex.grid(N, N))
indices = []
for i in range(len(mask)):
if mask[i] == False:
indices.append(i)
indices = flex.size_t(indices)
ind = flex.max_index(im.select(indices))
ind = indices[ind]
maxy = -1.0 + (ind % N) * 10.0 / N
maxx = -1.0 + (ind // N) * 10.0 / N
from matplotlib import pylab
pylab.imshow(masked_im, origin='bottom', extent=[-1.0, 9.0, -1.0, 9.0])
if YY is not None and XX is not None:
pylab.plot(YY, XX)
pylab.scatter([maxy], [maxx])
pylab.show()
def __init__(self, frames, size):
from dials.array_family import flex
self.frames = frames
nframes = frames[1] - frames[0]
self.data = []
self.mask = []
for sz in size:
self.data.append(flex.double(flex.grid(nframes, sz[0], sz[1])))
self.mask.append(flex.bool(flex.grid(nframes, sz[0], sz[1])))
def set_image(self, index, data, mask):
from dials.array_family import flex
for d1, d2 in zip(self.data, data):
h,w = d2.all()
d2.reshape(flex.grid(1,h,w))
d1[index:index+1,:,:] = d2.as_double()
for m1, m2 in zip(self.mask, mask):
h,w = m2.all()
m2.reshape(flex.grid(1,h,w))
m1[index:index+1,:,:] = m2
def build_np_img(nrow=64, ncol=64):
data2d = flex.double(flex.grid(nrow, ncol), 0)
mask2d = flex.int(flex.grid(nrow, ncol), 0)
for x in range(nrow):
for y in range(ncol):
data2d[x, y] += (x * 1.00000000001 + y * 2.5555555555555) * 0.00000000001
#print "number to see(aprox) =", data2d[x, y]
return data2d, mask2d
def generate_shoebox(size, mean, nforeground, ninvalid):
from dials.algorithms.simulation.generate_test_reflections \
import random_background_plane2
from dials.array_family import flex
from random import sample
from dials.algorithms.shoebox import MaskCode
data = flex.double(flex.grid(size), 0.0)
mask = flex.int(flex.grid(size), MaskCode.Valid | MaskCode.Background)
random_background_plane2(data, mean, 0, 0, 0)
for i in sample(range(len(data)), ninvalid):
mask[i] &= ~MaskCode.Valid
for i in sample(range(len(data)), nforeground):
mask[i] |= MaskCode.Foreground
mask[i] &= ~MaskCode.Background
return data, mask
def generate_image(function, height, width):
from dials.array_family import flex
image = flex.double(flex.grid(height, width))
for j in range(height):
for i in range(width):
image[j,i] = function(j,i)
return image
def build_up(pfh, objective_only=False):
values = pfh.parameterization(pfh.x)
assert 0. < values.G , "G-scale value out of range ( < 0 ) within LevMar build_up"
# XXX revisit these limits. Seems like an ad hoc approach to have to set these limits
# However, the assertions are necessary to avoid floating point exceptions at the C++ level
# Regardless, these tests throw out ~30% of LM14 data, thus search for another approach
assert -150. < values.BFACTOR < 150. ,"B-factor out of range (+/-150) within LevMar build_up"
assert -0.5 < 180.*values.thetax/math.pi < 0.5 , "thetax out of range ( |rotx|>.5 degrees ) within LevMar build_up"
assert -0.5 < 180.*values.thetay/math.pi < 0.5 , "thetay out of range ( |roty|>.5 degrees ) within LevMar build_up"
assert 0.000001 < values.RS , "RLP size out of range (<0.000001) within LevMar build_up"
assert values.RS < 0.001 , "RLP size out of range (>0.001) within LevMar build_up"
residuals = pfh.refinery.fvec_callable(values)
pfh.reset()
if objective_only:
pfh.add_residuals(residuals, weights=pfh.refinery.WEIGHTS)
else:
grad_r = pfh.refinery.jacobian_callable(values)
jacobian = flex.double(
flex.grid(len(pfh.refinery.MILLER), pfh.n_parameters))
for j, der_r in enumerate(grad_r):
jacobian.matrix_paste_column_in_place(der_r,j)
#print >> pfh.out, "COL",j, list(der_r)
pfh.add_equations(residuals, jacobian, weights=pfh.refinery.WEIGHTS)
print >> pfh.out, "rms %10.3f"%math.sqrt(flex.mean(pfh.refinery.WEIGHTS*residuals*residuals)),
values.show(pfh.out)
def __init__(self, parent, refl, orient = "portrait", id = wx.ID_ANY,
title = "", pos = wx.DefaultPosition, size = wx.DefaultSize,
style = wx.DEFAULT_FRAME_STYLE,
name="ShoeboxView"):
super(ShoeboxView, self).__init__(parent, id, title,
pos, size, style, name)
dat_flex = refl['shoebox'].data
n_fr = dat_flex.all()[0]
self.ImgLst = ImageListCtrl(self, orient)
for fr in range(n_fr):
data2d_flex = dat_flex[fr:fr + 1, :, :]
data2d_flex.reshape(flex.grid(dat_flex.all()[1:]))
data2d = data2d_flex.as_numpy_array()
bitmap = GetBitmap_from_np_array(data2d)
self.ImgLst.AppendBitmap(bitmap)
self.top_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.TstButton = wx.Button(self, label="Enbiggen")
self.TstButton.Bind(wx.EVT_BUTTON, self.OnTstBut)
self.top_sizer.Add(self.TstButton)
self.Tst_01_Button = wx.Button(self, label="EnSmallen")
self.Tst_01_Button.Bind(wx.EVT_BUTTON, self.OnTst_01_But)
self.top_sizer.Add(self.Tst_01_Button)
self.bot_sizer = wx.BoxSizer(wx.VERTICAL)
self.bot_sizer.Add(self.top_sizer)
self.bot_sizer.Add(self.ImgLst, 1, wx.EXPAND)
self.SetSizer(self.bot_sizer)
def _create_hot_mask(self, imageset, hot_pixels):
'''
Find hot pixels in images
'''
from dials.array_family import flex
# Write the hot mask
if self.write_hot_mask:
# Create the hot pixel mask
hot_mask = tuple(flex.bool(flex.grid(p.get_image_size()[::-1]), True)
for p in imageset.get_detector())
num_hot = 0
if hot_pixels > 0:
for hp, hm in zip(hot_pixels, hot_mask):
for i in range(len(hp)):
hm[hp[i]] = False
num_hot += len(hp)
logger.info('Found %d possible hot pixel(s)' % num_hot)
else:
hot_mask = None
# Return the hot mask
return hot_mask
def make_dx_dy_ellipse(imageset, phi, l1, l2, centre_xy):
detector = imageset.get_detector()
# Get fast and slow axes from the first panel. These will form the X and Y
# directions for the Cartesian coordinates of the correction map
p0 = detector[0]
f0, s0 = matrix.col(p0.get_fast_axis()), matrix.col(p0.get_slow_axis())
# Get the lab coordinate of the centre of the ellipse
topleft = matrix.col(p0.get_pixel_lab_coord((0, 0)))
mid = topleft + centre_xy[0] * f0 + centre_xy[1] * s0
# Get matrix describing the elliptical distortion
M = ellipse_matrix_form(phi, l1, l2)
distortion_map_x = []
distortion_map_y = []
for panel in detector:
size_x, size_y = panel.get_pixel_size()
nx, ny = panel.get_image_size()
dx = flex.double(flex.grid(nx, ny), 0.0)
dy = flex.double(flex.grid(nx, ny), 0.0)
elt = 0
for j in range(ny):
for i in range(nx):
# Get the X,Y coordinate of this pixel in the frame of the correction
# map, which has its origin at the centre of the ellipse and is aligned
# along fast, slow of the first panel.
lab = matrix.col(panel.get_pixel_lab_coord((i + 0.5, j + 0.5)))
offset = lab - mid
x = offset.dot(f0) # undistorted X coordinate (mm)
y = offset.dot(s0) # undistorted Y coordinate (mm)
distort = M * matrix.col((x, y)) # distorted by ellipse matrix
# store correction in units of the pixel size
dx[elt] = (x - distort[0]) / size_x
dy[elt] = (y - distort[1]) / size_y
elt += 1
# Add results for this panel
distortion_map_x.append(dx)
distortion_map_y.append(dy)
distortion_map_x = tuple(distortion_map_x)
distortion_map_y = tuple(distortion_map_y)
return distortion_map_x, distortion_map_y
def tst_deconvolve_3_with_flat_background(self):
from dials.algorithms.integration.fit import ProfileFitter
from scitbx.array_family import flex
from numpy.random import seed
seed(0)
I0 = [1000, 2000, 3000]
# Create profile
p = self.generate_3_profiles()
Ical = [[],[],[]]
for it in range(1):
# Copy profile
c = flex.double(flex.grid(40, 9, 9))
for i in range(p.all()[0]):
pp = p[i:i+1,:,:,:]
pp.reshape(c.accessor())
cc = add_poisson_noise(I0[i] * pp)
c += cc
b = flex.double(flex.grid(40, 9, 9), 1)
m = flex.bool(flex.grid(40,9,9), True)
c += add_poisson_noise(b)
# Fit
fit = ProfileFitter(c, b, m, p)
I = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
for i in range(3):
Ical[i].append(I[i])
for i in range(3):
Ical[i] = sum(Ical[i]) / len(Ical[i])
Iknown = [1030.7018033805357, 1948.7152700952695, 2972.983204218213]
Vknown = [4270.701803380534, 5188.715270095279, 6212.983204218214]
# Test intensity is the same
eps = 1e-7
for i in range(3):
assert(abs(I[i] - Iknown[i]) < eps)
assert(abs(V[i] - Vknown[i]) < eps)
print 'OK'
def tst_deconvolve_7_with_no_background(self):
from dials.algorithms.integration.fit import ProfileFitter
from scitbx.array_family import flex
from numpy.random import seed
seed(0)
I0 = [1000, 1500, 2000, 2500, 3000, 3500, 4000]
# Create profile
p = self.generate_7_profiles()
Ical = [[],[],[],[],[],[],[]]
for it in range(1):
# Copy profile
c = flex.double(flex.grid(40, 40, 40))
for i in range(p.all()[0]):
pp = p[i:i+1,:,:,:]
pp.reshape(c.accessor())
cc = add_poisson_noise(I0[i] * pp)
c += cc
b = flex.double(flex.grid(40, 40, 40), 0)
m = flex.bool(flex.grid(40,40,40), True)
# Fit
fit = ProfileFitter(c, b, m, p)
I = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
for i in range(7):
Ical[i].append(I[i])
for i in range(7):
Ical[i] = sum(Ical[i]) / len(Ical[i])
Iknown = [1012.4193633595916, 1472.3322059495797, 2072.136413825826,
2486.4902438469253, 3012.6132119521126, 3409.2053517072773,
3952.803209358826]
# Test intensity is the same
eps = 1e-7
for i in range(7):
assert(abs(I[i] - Iknown[i]) < eps)
assert(abs(V[i] - Iknown[i]) < eps)
print 'OK'
def generate_image(function, height, width):
from dials.array_family import flex
image = flex.double(flex.grid(height, width))
for j in range(height):
for i in range(width):
image[j, i] = function(j, i)
return image
def make_dx_dy_translate(imageset, dx, dy):
images = imageset.indices()
image = imageset[images[0]]
if (len(dx) != len(image)) or (len(dx) != len(image)):
raise Sorry(
"Please provide separate translations for each panel of the detector"
)
distortion_map_x = []
distortion_map_y = []
for block, shift_x, shift_y in zip(image, dx, dy):
distortion_map_x.append(flex.double(flex.grid(block.focus()), shift_x))
distortion_map_y.append(flex.double(flex.grid(block.focus()), shift_y))
return tuple(distortion_map_x), tuple(distortion_map_y)
def compute_profile(experiments, reflection, reference, N):
from dials.array_family import flex
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.modeller import GridSampler
from dials_scratch.jmp.sim import compute_profile_internal
from random import uniform
sbox = reflection["shoebox"]
bbox = sbox.bbox
zs = sbox.zsize()
ys = sbox.ysize()
xs = sbox.xsize()
profile = flex.double(flex.grid(zs, ys, xs))
m2 = experiments[0].goniometer.get_rotation_axis_datum()
s0 = experiments[0].beam.get_s0()
s1 = reflection["s1"]
phi = reflection["xyzcal.mm"][2]
detector = experiments[0].detector
scan = experiments[0].scan
cs = CoordinateSystem(m2, s0, s1, phi)
scan_range = scan.get_array_range()
image_size = detector[0].get_image_size()
grid_size = (3, 3, 40)
assert grid_size[0] * grid_size[1] * grid_size[2] == len(reference[0])
sampler = GridSampler(image_size, scan_range, grid_size)
xyz = reflection["xyzcal.px"]
index = sampler.nearest(0, xyz)
for g in reference[0]:
assert abs(flex.sum(g) - 1.0) < 1e-7
grid = reference[0][index]
sigma_d = experiments[0].profile.sigma_b(deg=False)
sigma_m = experiments[0].profile.sigma_m(deg=False)
delta_d = 3.0 * sigma_d
delta_m = 3.0 * sigma_m
profile = compute_profile_internal(grid, bbox, zs, ys, xs, N, delta_d,
delta_m, detector, scan, cs)
# from dials_scratch.jmp.viewer import show_image_stack_multi_view
# show_image_stack_multi_view(profile.as_numpy_array(), vmax=max(profile))
sum_p = flex.sum(profile)
print("Partiality: %f" % sum_p)
try:
assert sum_p > 0, "sum_p == 0"
except Exception as e:
print(e)
return None
return profile
def tst_deconvolve_3_with_no_background(self):
from dials.algorithms.integration.fit import ProfileFitter
from scitbx.array_family import flex
from numpy.random import seed
seed(0)
I0 = [1000, 2000, 3000]
# Create profile
p = self.generate_3_profiles()
Ical = [[],[],[]]
for it in range(1):
# Copy profile
c = flex.double(flex.grid(40, 9, 9))
for i in range(p.all()[0]):
pp = p[i:i+1,:,:,:]
pp.reshape(c.accessor())
cc = add_poisson_noise(I0[i] * pp)
c += cc
b = flex.double(flex.grid(40, 9, 9), 0)
m = flex.bool(flex.grid(40,9,9), True)
# Fit
fit = ProfileFitter(c, b, m, p)
I = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
for i in range(3):
Ical[i].append(I[i])
for i in range(3):
Ical[i] = sum(Ical[i]) / len(Ical[i])
Iknown = [1048.3221116842406, 1920.9035376774107, 2938.7743506383745]
# Test intensity is the same
eps = 1e-7
for i in range(3):
assert(abs(I[i] - Iknown[i]) < eps)
assert(abs(V[i] - Iknown[i]) < eps)
print 'OK'
def unrestrained_setting(self):
""" Calculate the basis vectors from N spots using numpy. This is equation 5 in
Brewster et. al 2015.
@return a cctbx crystal_orientation object
"""
from dials.array_family import flex
from scitbx.matrix import sqr
import numpy as np
if len(self.miller_indices) < 3:
return None
N = self.miller_indices.size()
hkl = self.miller_indices.as_double()
hkl.reshape(flex.grid((N, 3)))
hkl = hkl.as_numpy_array()
xyz = self.u_vectors.as_double()
xyz.reshape(flex.grid((N, 3)))
xyz = xyz.as_numpy_array()
try:
result = np.linalg.lstsq(hkl, xyz)
except Exception as e:
print "Exception while calculating basis vectors: %s" % e.message
return None
solution, self.residuals, rank, singular = result[0], result[
1], result[2], result[3]
if len(self.residuals) == 0:
self.residuals = [0, 0,
0] # happens when only 3 spots in the max clique
#print "Summed squared residuals of x,y,z for %d spots in 1/angstroms: %.7f, %.7f, %.7f"%(N,self.residuals[0],self.residuals[1],self.residuals[2])
Amatrix = sqr(solution.flatten()).transpose()
# Johan believes this can happen if there aren't 3 hkls that aren't co-linear (IIRC)
if Amatrix.determinant() <= 0:
return None
from cctbx import crystal_orientation
ori = crystal_orientation.crystal_orientation(
Amatrix, crystal_orientation.basis_type.reciprocal)
return ori
def __call__ (self, img_flex, palette_in, min_i, max_i):
flex_2d_data = img_flex.as_double()
flex_2d_mask = flex.double(flex.grid(flex_2d_data.all()[0], flex_2d_data.all()[1]), 0)
arr_i = self.arr_img(flex_2d_data, flex_2d_mask, i_min = min_i, i_max = max_i, palette = palette_in)
q_img = QImage(arr_i.data, np.size(arr_i[0:1, :, 0:1]),
np.size(arr_i[:, 0:1, 0:1]), QImage.Format_RGB32)
return q_img
def img_arr_n_cpp(show_nums=True):
n_col = 20
n_row = 10
wx_bmp_arr = rgb_img()
flex_data_in = flex.double(flex.grid(n_row, n_col), 15)
flex_mask_in = flex.double(flex.grid(n_row, n_col), 0)
for col in xrange(n_col):
for row in xrange(n_row):
flex_data_in[row, col] = col + row
err_code = wx_bmp_arr.set_min_max(0.0, 28.0)
palette = "hot ascend"
if palette == "black2white":
palette_num = 1
elif palette == "white2black":
palette_num = 2
elif palette == "hot ascend":
palette_num = 3
else: # assuming "hot descend"
palette_num = 4
print "before c++"
img_array_tmp = wx_bmp_arr.gen_bmp(flex_data_in, flex_mask_in, show_nums,
palette_num)
print "after c++"
np_img_array = img_array_tmp.as_numpy_array()
height = np.size(np_img_array[:, 0:1, 0:1])
width = np.size(np_img_array[0:1, :, 0:1])
img_array = np.zeros([height, width, 4], dtype=np.uint8)
#for some strange reason PyQt4 needs to use RGB as BGR
img_array[:, :, 0:1] = np_img_array[:, :, 2:3]
img_array[:, :, 1:2] = np_img_array[:, :, 1:2]
img_array[:, :, 2:3] = np_img_array[:, :, 0:1]
print "end of np generator"
return img_array
def test_deconvolve_3_with_flat_background():
np.random.seed(0)
I0 = [1000, 2000, 3000]
# Create profile
p = generate_3_profiles()
Ical = [[], [], []]
for it in range(1):
# Copy profile
c = flex.double(flex.grid(40, 9, 9))
for i in range(p.all()[0]):
pp = p[i:i + 1, :, :, :]
pp.reshape(c.accessor())
cc = add_poisson_noise(I0[i] * pp)
c += cc
b = flex.double(flex.grid(40, 9, 9), 1)
m = flex.bool(flex.grid(40, 9, 9), True)
c += add_poisson_noise(b)
# Fit
fit = ProfileFitter(c, b, m, p)
intensity = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
for i in range(3):
Ical[i].append(intensity[i])
for i in range(3):
Ical[i] = sum(Ical[i]) / len(Ical[i])
Iknown = [1030.7018033805357, 1948.7152700952695, 2972.983204218213]
Vknown = [4270.701803380534, 5188.715270095279, 6212.983204218214]
# Test intensity is the same
eps = 1e-7
for i in range(3):
assert intensity[i] == pytest.approx(Iknown[i], abs=eps)
assert V[i] == pytest.approx(Vknown[i], abs=eps)
def refinerdata_testdata(testdata):
experiment = testdata.experiment
reflections = testdata.reflections
panel = experiment.detector[0]
s0_length = matrix.col(experiment.beam.get_s0()).length()
reflections["bbox"] = flex.int6(len(reflections))
reflections["xyzobs.px.value"] = flex.vec3_double(len(reflections))
reflections["s2"] = reflections["s1"].each_normalize() * s0_length
reflections["sp"] = flex.vec3_double(len(reflections))
for i, (x, y, z) in enumerate(reflections["xyzcal.px"]):
x0 = int(x) - 5
x1 = int(x) + 5 + 1
y0 = int(y) - 5
y1 = int(y) + 5 + 1
z0 = int(z)
z1 = z0 + 1
reflections["bbox"][i] = x0, x1, y0, y1, z0, z1
reflections["xyzobs.px.value"][i] = (int(x) + 0.5, int(y) + 0.5,
int(z) + 0.5)
reflections["sp"][i] = (matrix.col(
panel.get_pixel_lab_coord(
reflections["xyzobs.px.value"][i][0:2])).normalize() *
s0_length)
reflections["shoebox"] = flex.shoebox(reflections["panel"],
reflections["bbox"],
allocate=True)
shoebox_data = flex.float(flex.grid(1, 11, 11))
shoebox_mask = flex.int(flex.grid(1, 11, 11))
for j in range(11):
for i in range(11):
shoebox_data[0, j, i] = (100 * exp(-0.5 * (j - 5)**2 / 1**2) *
exp(-0.5 * (i - 5)**2 / 1**2))
shoebox_mask[0, j, i] = 5
for sbox in reflections["shoebox"]:
sbox.data = shoebox_data
sbox.mask = shoebox_mask
return RefinerData.from_reflections(experiment, reflections)
def _build_jacobian(d2theta_dp, nelem=None, nparam=None):
"""construct Jacobian from lists of gradient vectors. This method may be
overridden for the case where these vectors use sparse storage"""
jacobian = flex.double(flex.grid(nelem, nparam))
# loop over parameters
for i in range(nparam):
col = d2theta_dp[i]
jacobian.matrix_paste_column_in_place(col, i)
return jacobian
def set_my_img(self):
tm_start = tm_now()
flex_2d_mask = flex.double(flex.grid(2500, 2400),0)
img_slice = self.img_pos
if( self.block_3d_flex == None ):
q_img = QImage()
else:
flex_2d_data = self.block_3d_flex[img_slice:img_slice + 1, 0:2500, 0:2400]
flex_2d_data.reshape(flex.grid(2500, 2400))
arr_i = self.arr_img(flex_2d_data, flex_2d_mask, i_min = -3.0, i_max = self.imax)
q_img = QImage(arr_i.data, np.size(arr_i[0:1, :, 0:1]),
np.size(arr_i[:, 0:1, 0:1]), QImage.Format_RGB32)
self.img_painter.set_img_pix(q_img)
print "dif_time[set_img_pix(q_img)] =", tm_now() - tm_start
def test_SingleScaler_expand_scales_to_all_reflections(mock_apm):
p, e, r = (generated_param(), generated_exp(), generated_refl())
exp = create_scaling_model(p, e, r)
p.reflection_selection.method = "use_all"
scaler = SingleScaler(p, exp[0], r)
# test expand to all reflections method. First check scales are all 1, then
# update a component to simulate a minimisation result, then check that
# scales are set only in all suitable reflections (as it may not be possible
# to calculate scales for unsuitable reflections!)
# Must also update the scales in the global_Ih_table
assert list(scaler.reflection_table["inverse_scale_factor"]) == [1.0] * 8
scaler.experiment.scaling_model.components[
"scale"].parameters = flex.double([2.0])
scaler.expand_scales_to_all_reflections(calc_cov=False)
assert (list(
scaler.reflection_table["inverse_scale_factor"]) == [2.0] * 5 + [1.0] +
[2.0] * 2)
assert (list(
scaler.global_Ih_table.blocked_data_list[0].inverse_scale_factors) ==
[2.0] * 7)
assert list(
scaler.reflection_table["inverse_scale_factor_variance"]) == [0.0] * 8
# now try again
apm = Mock()
apm.n_active_params = 2
var_list = [1.0, 0.1, 0.1, 0.5]
apm.var_cov_matrix = flex.double(var_list)
apm.var_cov_matrix.reshape(flex.grid(2, 2))
scaler.update_var_cov(apm)
assert scaler.var_cov_matrix[0, 0] == var_list[0]
assert scaler.var_cov_matrix[0, 1] == var_list[1]
assert scaler.var_cov_matrix[1, 0] == var_list[2]
assert scaler.var_cov_matrix[1, 1] == var_list[3]
assert scaler.var_cov_matrix.non_zeroes == 4
scaler.expand_scales_to_all_reflections(calc_cov=True)
assert list(
scaler.reflection_table["inverse_scale_factor_variance"]
) == pytest.approx(
[2.53320, 1.07106, 1.08125, 1.23219, 1.15442, 0.0, 1.0448, 1.0448],
1e-4)
# Second case - when var_cov_matrix is only part of full matrix.
p, e, r = (generated_param(), generated_exp(), generated_refl())
exp = create_scaling_model(p, e, r)
p.reflection_selection.method = "use_all"
scaler = SingleScaler(p, exp[0], r)
apm = mock_apm
scaler.update_var_cov(apm)
assert scaler.var_cov_matrix.non_zeroes == 1
assert scaler.var_cov_matrix[0, 0] == 2.0
assert scaler.var_cov_matrix.n_cols == 2
assert scaler.var_cov_matrix.n_rows == 2
assert scaler.var_cov_matrix.non_zeroes == 1
def _build_jacobian(d2theta_dp, nelem=None, nparam=None):
"""construct Jacobian from lists of gradient vectors. This method may be
overridden for the case where these vectors use sparse storage"""
jacobian = flex.double(flex.grid(nelem, nparam))
# loop over parameters
for i in range(nparam):
col = d2theta_dp[i]
jacobian.matrix_paste_column_in_place(col, i)
return jacobian
def fisher_information(self):
"""
Compute the fisher information
"""
ctot = self.ctot
# Get info about marginal distribution
S22 = self.S[2, 2]
dS22 = [self.dS[2, 2, i] for i in range(self.dS.shape[2])]
S22_inv = 1 / S22
# Get info about conditional distribution
Sbar = self.conditional.sigma()
dSbar = self.conditional.first_derivatives_of_sigma(
) # list of 2x2 arrays
dmbar = self.conditional.first_derivatives_of_mean(
) # list of 2x1 arrays
Sbar_inv = inv(Sbar)
dmu = self.dmu
# Weights for marginal and conditional components
m_w = ctot
c_w = ctot
# Compute the fisher information wrt parameter i j
I = flex.double(flex.grid(len(dS22), len(dS22)))
for j in range(len(dS22)):
for i in range(len(dS22)):
U = S22_inv * dS22[j] * S22_inv * dS22[i]
V = np.trace(
np.matmul(
np.matmul(
np.matmul(
Sbar_inv,
dSbar[j],
),
Sbar_inv,
),
dSbar[i],
))
W = 2 * np.trace(
np.matmul(
np.matmul(
Sbar_inv,
dmbar[i],
),
dmbar[j].T,
))
X = 2 * dmu[2, i] * S22_inv * dmu[2, j]
I[j, i] = 0.5 * c_w * (V + W) + 0.5 * m_w * (U + X)
return I
def plot_prob_for_zero(c, b, s):
from math import log, exp, factorial
from dials.array_family import flex
L = flex.double(flex.grid(100, 100))
MASK = flex.bool(flex.grid(100, 100))
c = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
b = [bb / sum(b) for bb in b]
s = [ss / sum(s) for ss in s]
for BB in range(0, 100):
for SS in range(0, 100):
B = 0 + BB / 10000.0
S = 0 + SS / 40.0
LL = 0
for i in range(len(b)):
if B * b[i] + S * s[i] <= 0:
MASK[BB, SS] = True
LL = -999999
break
else:
LL += (
c[i] * log(B * b[i] + S * s[i])
- log(factorial(c[i]))
- B * b[i]
- S * s[i]
)
L[BB, SS] = LL
index = flex.max_index(L)
i = index % 100
j = index // 100
B = 0 + j / 10000.0
S = 0 + i / 40.0
print(flex.max(L), B, S)
from matplotlib import pylab
import numpy
im = numpy.ma.masked_array(flex.exp(L).as_numpy_array(), mask=MASK.as_numpy_array())
pylab.imshow(im)
pylab.show()
exit(0)
def __init__(self, experiments):
"""
Do the labelling
"""
from dials.algorithms.spot_prediction import PixelToMillerIndex
from collections import defaultdict
from math import floor, sqrt
from dials.array_family import flex
# Get the experiment
experiment = experiments[0]
# Get the image size
xsize, ysize = experiment.detector[0].get_image_size()
# A class to map pixels to miller indices
transform = PixelToMillerIndex(
experiment.beam, experiment.detector, experiment.crystal
)
# For each pixel, assign to a miller index and also compute the distance
reflections = defaultdict(list)
for j in range(ysize):
for i in range(xsize):
h = transform.h(0, i, j)
h0 = tuple(map(lambda x: int(floor(x + 0.5)), h))
d = sqrt(sum(map(lambda x, y: (x - y) ** 2, h, h0)))
reflections[h0].append((i, j, d))
# Initialise arrays
self._indices = flex.miller_index()
self._distance = flex.double(flex.grid(ysize, xsize))
self._label = flex.int(flex.grid(ysize, xsize))
self._pixels = defaultdict(list)
for index, (h, pixels) in enumerate(reflections.iteritems()):
self._indices.append(h)
for i, j, d in pixels:
self._distance[j, i] = d
self._label[j, i] = index
self._pixels[h].append((i, j))
def radial_average(self, reference=None):
image = LunusDIFFIMAGE()
working_img = self.lunus_data_scitbx.reshape(flex.grid(self.Isizey, self.Isizex))
image.set_image(working_img)
self.radial_avg = image.LunusRadialAvgim(self.beam_center_mm_x, self.beam_center_mm_y, self.pixel_size)
if reference:
np.savez("reference_radial_average", rad=self.radial_avg)
else:
pass
return
def gaussian(size, a, x0, sx):
result = flex.real(flex.grid(size))
index = [0 for i in range(len(size))]
while True:
result[index[::-1]] = evaluate_gaussian(index[::-1], a, x0, sx)
for j in range(len(size)):
index[j] += 1
if index[j] < size[::-1][j]:
break
index[j] = 0
if j == len(size) - 1:
return result
def create_mask(self, size, x0, value):
from scitbx.array_family import flex
from math import sqrt
mask = flex.int(flex.grid(size), 0)
rad = min(s - c for s, c in zip(size, x0))
for k in range(size[0]):
for j in range(size[1]):
for i in range(size[2]):
d = sqrt((j - x0[1])**2 + (i - x0[2])**2)
if d < rad:
mask[k, j, i] = value
return mask
def tst_with_flat_background_partial(self):
from dials.algorithms.integration.fit import ProfileFitter
from scitbx.array_family import flex
from numpy.random import seed
seed(0)
# Create profile
p = gaussian((9, 9, 9), 1, (4, 4, 4), (2, 2, 2))
s = flex.sum(p)
p = p / s
# Copy profile
c0 = add_poisson_noise(100 * p)
b = flex.double(flex.grid(9, 9, 9), 1)
m = flex.bool(flex.grid(9,9,9), True)
c = c0 + add_poisson_noise(b)
# Get the partial profiles
pp = p[0:5,:,:]
mp = m[0:5,:,:]
cp = c[0:5,:,:]
bp = b[0:5,:,:]
c0p = c0[0:5,:,:]
# Fit
fit = ProfileFitter(cp, bp, mp, pp)
I = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
Iknown = 99.06932141277105
Vknown = 504.06932141277105
# Test intensity is the same
eps = 1e-7
assert(abs(I[0] - Iknown) < eps)
assert(abs(V[0] - Vknown) < eps)
print 'OK'
def test_deconvolve_3_with_no_background():
np.random.seed(0)
I0 = [1000, 2000, 3000]
# Create profile
p = generate_3_profiles()
Ical = [[], [], []]
for it in range(1):
# Copy profile
c = flex.double(flex.grid(40, 9, 9))
for i in range(p.all()[0]):
pp = p[i:i + 1, :, :, :]
pp.reshape(c.accessor())
cc = add_poisson_noise(I0[i] * pp)
c += cc
b = flex.double(flex.grid(40, 9, 9), 0)
m = flex.bool(flex.grid(40, 9, 9), True)
# Fit
fit = ProfileFitter(c, b, m, p)
intensity = fit.intensity()
V = fit.variance()
assert fit.niter() < fit.maxiter()
for i in range(3):
Ical[i].append(intensity[i])
for i in range(3):
Ical[i] = sum(Ical[i]) / len(Ical[i])
Iknown = [1048.3221116842406, 1920.9035376774107, 2938.7743506383745]
# Test intensity is the same
eps = 1e-7
for i in range(3):
assert intensity[i] == pytest.approx(Iknown[i], abs=eps)
assert V[i] == pytest.approx(Iknown[i], abs=eps)
def px_coords(e, cs, detector, scan):
xyz = flex.vec3_double(flex.grid(e.all()))
for k in range(e.all()[0]):
for j in range(e.all()[1]):
for i in range(e.all()[2]):
e1, e2, e3 = e[k, j, i]
s1d, phid = to_s1_and_phi(e1, e2, e3, cs)
# s1d = cs.to_beam_vector((e1, e2))
# phid = cs.to_rotation_angle(e3)
x, y = detector[0].get_ray_intersection_px(s1d)
z = scan.get_array_index_from_angle(phid)
xyz[k, j, i] = (x, y, z)
return xyz
def hot(greyscale_flex, params):
'''Find hot pixels in the image (returns flex bool).'''
from dials.algorithms.spot_finding.threshold import \
DispersionThresholdStrategy
from dials.array_family import flex
thresholder = DispersionThresholdStrategy(gain=params.gain)
mask = flex.bool(greyscale_flex.size(), True)
mask.reshape(flex.grid(*greyscale_flex.focus()))
threshold_mask = thresholder(greyscale_flex, mask=mask)
return threshold_mask
def correlation(self, x):
"""
The correlation of the Jacobian
"""
J = self.jacobian(x)
C = flex.double(flex.grid(J.all()[1], J.all()[1]))
for j in range(C.all()[0]):
for i in range(C.all()[1]):
a = J[:, i:i + 1].as_1d()
b = J[:, j:j + 1].as_1d()
C[j, i] = flex.linear_correlation(a, b).coefficient()
return C
def read_images(experiments):
from dials.array_family import flex
xsize, ysize = experiments[0].detector[0].get_image_size()
zsize = experiments[0].scan.get_num_images()
data = flex.double(flex.grid(zsize, ysize, xsize))
mask = flex.int(flex.grid(zsize, ysize, xsize))
iset = experiments[0].imageset
for i in range(len(iset)):
print("Reading image %d" % i)
d = iset.get_raw_data(i)[0].as_double()
m = iset.get_mask(i)[0].as_1d().as_int()
m.reshape(flex.grid(ysize, xsize))
d.reshape(flex.grid(1, ysize, xsize))
m.reshape(flex.grid(1, ysize, xsize))
data[i:i + 1, :, :] = d
mask[i:i + 1, :, :] = m
return data, mask
def gaussian(size, a, x0, sx):
result = flex.double(flex.grid(size))
index = [0] * len(size)
while True:
result[index] = evaluate_gaussian(index, a, x0, sx)
for j in range(len(size)):
index[j] += 1
if index[j] < size[j]:
break
index[j] = 0
if j == len(size) - 1:
return result
def second_derivatives(self):
"""
Compute the second derivatives of Sigma w.r.t the parameters
"""
l1 = self.params[0]
d11 = (0, 0, 0, 0, 0, 0, 0, 0, 2)
d2 = flex.mat3_double([d11])
d2.reshape(flex.grid(1, 1))
return d2
def ts2(x):
from numpy import median
from dials.array_family import flex
r = flex.double(flex.grid(len(x), len(x)))
for j in range(len(x)):
for i in range(len(x)):
r[j,i] = (x[i] + x[j]) / 2.0
from matplotlib import pylab
pylab.imshow(r.as_numpy_array())
pylab.show()
return median(r)
def get_lunus_repl(self):
P = Profiler("LUNUS")
# first get the lunus image
from lunus.command_line.filter_peaks import get_image_params
from lunus import LunusDIFFIMAGE
imageset = self.expt.imageset
data = imageset[0]
assert isinstance(
data, tuple) # assume a tuple of flex::double over detector panels
# Instantiate a LUNUS diffraction image
A = LunusDIFFIMAGE(len(data))
# Populate the image with multipanel data
for pidx in range(len(data)):
A.set_image(pidx, data[pidx])
# Define the LUNUS image parameters
deck = '''
#lunus input deck
#punchim_xmin=1203
#punchim_ymin=1250
#punchim_xmax=2459
#punchim_ymax=1314
#windim_xmin=100
#windim_ymin=100
#windim_xmax=2362
#windim_ymax=2426
#thrshim_min=0
#thrshim_max=50
modeim_bin_size=1
modeim_kernel_width=15
'''
image_params = get_image_params(imageset)
# Set the LUNUS image parameters
for pidx in range(len(image_params)):
deck_and_extras = deck + image_params[pidx]
A.LunusSetparamsim(pidx, deck_and_extras)
A.LunusModeim()
# Get the processed image
lunus_filtered_data = flex.double()
assert len(data) == 256 # Jungfrau
for pidx in range(len(data)):
aye_panel = A.get_image_double(pidx)
assert aye_panel.focus() == (254, 254)
lunus_filtered_data.extend(aye_panel.as_1d())
lunus_filtered_data.reshape(flex.grid((256, 254, 254)))
self.lunus_filtered_data = lunus_filtered_data.as_numpy_array()
def make_test_image():
from scitbx import matrix
from dials.array_family import flex
import random
import math
xmin, xmax = 0, 4272
ymin, ymax = 0, 2848
buffer = 100
n = 30
# generate n random positions - well within field of view
x = flex.double(n)
y = flex.double(n)
z = flex.double(n, 0.0)
for j in range(n):
x[j] = random.uniform(xmin + buffer, xmax - buffer)
y[j] = random.uniform(ymin + buffer, ymax - buffer)
r = background(flex.double(flex.grid(ymax, xmax), 0.0), 3)
g = background(flex.double(flex.grid(ymax, xmax), 0.0), 3)
b = background(flex.double(flex.grid(ymax, xmax), 0.0), 3)
# add some stars
for xy in zip(x, y):
star_x, star_y = random_positions(1000, 1).parts()
star_x += xy[0]
star_y += xy[1]
for i, j in zip(star_x.iround(), star_y.iround()):
r[j, i] += 1
g[j, i] += 1
b[j, i] += 1
from astrotbx.input_output.saver import save_image
save_image('example.png', r, g, b)
def profile3d(p, vmin=None, vmax=None):
''' Print a 3D profile. '''
from dials.array_family import flex
if vmin is None:
vmin = flex.min(p)
if vmax is None:
vmax = flex.max(p)
nz, ny, nx = p.all()
text = []
for k in range(nz):
p2 = p[k:k+1,:,:]
p2.reshape(flex.grid(ny, nx))
text.append(profile2d(p2, vmin=vmin, vmax=vmax))
return '\n'.join(text)
def hot_pixel_mask(imageset, reflections):
depth = imageset.get_array_range()[1] - imageset.get_array_range()[0]
xylist = filter_reflections(reflections, depth)
from dials.array_family import flex
mask = flex.bool(flex.grid(reversed(imageset.get_image_size())), True)
for x, y in xylist:
mask[y, x] = False
print 'Found %d hot pixels' % len(xylist)
return (mask,)
def gaussian(size, a, x0, sx):
from dials.array_family import flex
result = flex.real(flex.grid(size))
index = [0 for i in range(len(size))]
while True:
result[index[::-1]] = evaluate_gaussian(index[::-1], a, x0, sx)
for j in range(len(size)):
index[j] += 1
if index[j] < size[::-1][j]:
break
index[j] = 0
if j == len(size) - 1:
return result
def d2f(I):
mask = flex.bool(flex.grid(9,9,9), False)
for k in range(9):
for j in range(9):
for i in range(9):
dx = 5 * (i - 4.5) / 4.5
dy = 5 * (j - 4.5) / 4.5
dz = 5 * (k - 4.5) / 4.5
dd = sqrt(dx**2 + dy**2 + dz**2)
if dd <= 3:
mask[k,j,i] = True
mask = mask.as_1d() & (ref_P.as_1d() > 0)
p = ref_P.as_1d().select(mask)
c = max_P.as_1d().select(mask)
return flex.sum(2*c*c*p*p / (p*I)**3)
def normalize_profile(self, profile):
from scitbx.array_family import flex
max_profile = flex.max(profile)
threshold = self.threshold * max_profile
sum_profile = 0.0
for i in range(len(profile)):
if profile[i] > threshold:
sum_profile += profile[i]
else:
profile[i] = 0.0
result = flex.double(flex.grid(profile.all()))
for i in range(len(profile)):
result[i] = profile[i] / sum_profile
return result
def __call__(self, img_flex, palette_in, min_i, max_i):
flex_2d_data = img_flex.as_double()
flex_2d_mask = flex.double(
flex.grid(flex_2d_data.all()[0], flex_2d_data.all()[1]), 0
)
arr_i = self.arr_img(
flex_2d_data, flex_2d_mask, i_min=min_i, i_max=max_i, palette=palette_in
)
q_img = QImage(
arr_i.data,
np.size(arr_i[0:1, :, 0:1]),
np.size(arr_i[:, 0:1, 0:1]),
QImage.Format_RGB32,
)
return q_img
def __call__(self, image, mask):
'''
Call the thresholding function
:param image: The image to process
:param mask: The mask to use
:return: The thresholded image
'''
from dials.algorithms.image import threshold
from dials.array_family import flex
# Initialise the algorithm
try:
algorithm = self.algorithm[image.all()]
except Exception:
algorithm = threshold.DispersionThreshold(
image.all(),
self._kernel_size,
self._n_sigma_b,
self._n_sigma_s,
self._threshold,
self._min_count)
self.algorithm[image.all()] = algorithm
# Set the gain
if self._gain is not None:
assert(self._gain > 0)
self._gain_map = flex.double(image.accessor(), self._gain)
self._gain = None
# Compute the threshold
result = flex.bool(flex.grid(image.all()))
if self._gain_map:
algorithm(image, mask, self._gain_map, result)
else:
algorithm(image, mask, result)
# Return the result
return result
def test(counts, background_shape, signal_shape):
S = 1
B = 1
for i in range(20):
S, B = iteration(counts, background_shape, signal_shape, B, S)
print S, B
sigma_b, sigma_s = sigmas(counts, background_shape, signal_shape, B, S)
print sigma_b, sigma_s
from dials.array_family import flex
Fs = sum(signal_shape)
Fb = sum(background_shape)
Rs = flex.double(flex.grid(100, 100))
for B in range(1, 101):
for S in range(1, 101):
Fb2 = sum([b*c/(B*b+S*s) for c, b, s in zip(counts, background_shape, signal_shape)])
Fs2 = sum([s*c/(B*b+S*s) for c, b, s in zip(counts, background_shape, signal_shape)])
R = (Fb2 - Fb)**2 + (Fs2 - Fs)**2
Rs[B-1,S-1] = Fs2 - Fs
from matplotlib import pylab
pylab.imshow(Rs.as_numpy_array())
pylab.show()
def tst_does_bbox_contain_bad_pixels(self):
from dials.array_family import flex
from dials.model.data import Shoebox
from random import randint
mask = flex.bool(flex.grid(100, 100), True)
for j in range(100):
for i in range(40, 60):
mask[j,i] = False
mask[i,j] = False
shoebox = flex.shoebox(1000)
res = flex.bool(1000)
for i in range(1000):
x0 = randint(0, 90)
y0 = randint(0, 90)
z0 = randint(0, 90)
x1 = randint(1, 10) + x0
y1 = randint(1, 10) + y0
z1 = randint(1, 10) + z0
shoebox[i] = Shoebox((x0, x1, y0, y1, z0, z1))
res2 = False
if x0 >= 40 and x0 < 60:
res2 = True
if x1 > 40 and x1 <= 60:
res2 = True
if y0 >= 40 and y0 < 60:
res2 = True
if y1 > 40 and y1 <= 60:
res2 = True
res[i] = res2
assert(shoebox.does_bbox_contain_bad_pixels(mask) == res)
# Test passed
print 'OK'
def tst_consistent(self):
from random import randint
from dials.model.data import Shoebox
from dials.array_family import flex
shoebox = flex.shoebox(10)
for i in range(10):
x0 = randint(0, 1000)
y0 = randint(0, 1000)
z0 = randint(0, 1000)
x1 = randint(1, 10) + x0
y1 = randint(1, 10) + y0
z1 = randint(1, 10) + z0
shoebox[i] = Shoebox((x0, x1, y0, y1, z0, z1))
assert(shoebox.is_consistent() == flex.bool(10, False))
for i in range(10):
shoebox[i].allocate()
assert(shoebox.is_consistent() == flex.bool(10, True))
for i in [0, 2, 4, 6, 8]:
shoebox[i].data.resize(flex.grid(10, 10, 10))
assert(shoebox.is_consistent() == flex.bool([False, True] * 5))
for i in range(10):
shoebox[i].deallocate()
assert(shoebox.is_consistent() == flex.bool(10, False))
# Test passed
print 'OK'
0,
4,
4,
3,
0,
1,
4,
1,
1,
1,
6]
# a[4] = 10
# a[50] = 100
X = flex.double([1] * len(a))
X.reshape(flex.grid(len(a), 1))
Y = flex.double(a)
B = flex.double([0])
result = robust_glm(X, Y, B, family="poisson")
print list(result.parameters())
from matplotlib import pylab
print "MOM1: ", sum(means1) / len(means1)
print "MOM2: ", sum(means2) / len(means2)
pylab.plot(means1, color='black')
pylab.plot(means2, color='blue')
pylab.show()
# Get the imageset
assert len(experiments) == 1
assert len(reflections) == 1
reflections = reflections[0]
imageset = experiments[0].imageset
# Create the reflection lookup
bbox = reflections['bbox']
reflection_lookup = defaultdict(list)
for i in range(len(bbox)):
for j in range(bbox[i][4],bbox[i][5]):
reflection_lookup[j].append(i)
width, height = experiments[0].detector[0].get_image_size()
sum_background = flex.double(flex.grid(height, width), 0)
sum_sq_background = flex.double(flex.grid(height, width), 0)
count = flex.int(flex.grid(height, width), 0)
# Loop through all images
print "START"
for frame in range(len(imageset)):
# Get the subset of reflections on this image and compute the mask
subset = reflections.select(flex.size_t(reflection_lookup[frame]))
subset['shoebox'] = flex.shoebox(
subset['panel'],
subset['bbox'],
allocate=True)
def run(self):
from dials.array_family import flex
import cPickle as pickle
from math import sqrt
from dials.algorithms.shoebox import MaskCode
print self.shoebox_filename
# Read the data
rtable = flex.reflection_table.from_pickle(self.reflection_filename)
shoeboxes, masks = pickle.load(open(self.shoebox_filename, "r"))
assert(len(rtable) == len(shoeboxes))
assert(len(rtable) == len(masks))
# Compute the background for each reflection and check against the values
# read from the mosflm.lp file. Currently this fails for 1 strange
# reflection whose pixel values in the mosflm file do not match those
# extracted from the images.
count = 0
VAR1 = []
VAR2 = []
DIFF = []
for i in range(len(rtable)):
xdet, ydet = rtable[i]["xy"]
nx = rtable[i]['nx']
ny = rtable[i]['ny']
nc = rtable[i]['nc']
nrx = rtable[i]['nrx']
nry = rtable[i]['nry']
bbox = rtable[i]['bbox']
I = rtable[i]['intensity.sum.value']
Ivar = rtable[i]['intensity.sum.variance']
lp = rtable[i]['lp']
data = shoeboxes[i].as_double()
mask = masks[i]
fraction = 1.0
nsigma = 4
try:
# model = PlaneModel(data, mask, fraction, nsigma)
assert(len(data.all()) == 2)
assert(len(mask.all()) == 2)
data.reshape(flex.grid(1, *data.all()))
mask.reshape(flex.grid(1, *mask.all()))
self.outlier_rejector(data, mask)
mask2 = (mask.as_1d() & int(MaskCode.BackgroundUsed)) != 0
mask2.reshape(flex.grid(*mask.all()))
model = self.linear_modeller.create(data, mask2)
except Exception:
count += 1
raise
continue
# n = model.noutlier()
assert(len(model.params()) == 3)
hy = data.all()[1] // 2
hx = data.all()[2] // 2
c1 = model.params()[0]
a1 = model.params()[1]
b1 = model.params()[2]
c3 = c1 + a1*(0.5 + hx) + b1*(0.5 + hy)
# a1 = model.a()
# b1 = model.b()
# c1 = model.c()
a2 = rtable[i]['background'][0]
b2 = rtable[i]['background'][1]
c2 = rtable[i]['background'][2]
try:
assert(abs(a1 - b2) < 0.01)
assert(abs(b1 + a2) < 0.01)
assert(abs(c3 - c2) < 0.1)
except Exception:
count += 1
continue
#print "BG %d:(%.2f, %.2f, %.1f), (%.2f, %.2f, %.1f): %d" % \
#(i, a1, b1, c1, a2, b2, c2, n)
#print "X, Y: ", xdet, ydet
#print "NX, NY: ", nx, ny
#print "NRX, NRY, NC", nrx, nry, nc
#print int(floor(xdet + 0.5)) - nx // 2, int(floor(ydet + 0.5)) - ny // 2
#print "BBOX: ", bbox
#print "N Outliers: ", model.noutlier()
#print "N Background: ", model.nbackground()
#print "Max DIff: ", model.maxdiff()
#print data.as_numpy_array().transpose()[::-1,::-1]
#print mask.as_numpy_array().transpose()[::-1,::-1]
#raise
background = data.as_double()
# hy = background.all()[1] // 2
# hx = background.all()[2] // 2
for jj in range(background.all()[1]):
for ii in range(background.all()[2]):
# x = ii - hx
# y = jj - hy
x = ii + 0.5
y = jj + 0.5
background[0, jj,ii] = a1 * x + b1 * y + c1
# Test the summation results. Edge reflections use profile fitted
# intensity in MOSFLM. Therefore ignore these. There also appears to be a
# some discrepancy with very low <= 0 reflections where an extra 0.5 is
# added. Not sure why this is so ignore these reflections as well.
from dials.algorithms.integration.sum import integrate_by_summation
intensity = integrate_by_summation(data.as_double(), background, mask)
I2 = intensity.intensity()
Ivar2 = intensity.variance()
I1 = I
Ivar1 = Ivar
if mask.count(0) == 0 and mask.count(2) == 0 and I1 > 0:
VAR1.append(sqrt(Ivar1))
VAR2.append(sqrt(Ivar2))
DIFF.append(sqrt(Ivar1) - sqrt(Ivar2))
try:
assert(abs(I1 - I2) < 1.0)
assert(abs(sqrt(Ivar1) - sqrt(Ivar2)) < 1.0)
except Exception:
count += 1
#import numpy
#numpy.set_printoptions(precision=4, linewidth=200)
#print "# %d" % i
#print "I: %f, %f, %f" % (I2, I1, lp)
#print "DEBUG: ", c1 * 25
#print "PF: %f" % rtable[i]['intensity.prf.value']
#print "BG (%.4f, %.4f, %.4f), (%.2f, %.2f, %.1f): %d" % \
#(a1, b1, c1, a2, b2, c2, n)
#print "X, Y: ", xdet, ydet
#print "NX, NY: ", nx, ny
#print "NRX, NRY, NC", nrx, nry, nc
#print int(floor(xdet + 0.5)) - nx // 2, int(floor(ydet + 0.5)) - ny // 2
#print "BBOX: ", bbox
#print "N Outliers: ", model.noutlier()
#print "N Background: ", model.nbackground()
#print "Max DIff: ", model.maxdiff()
#temp = (mask == MaskCode.Valid | MaskCode.Foreground).as_1d().as_int()
#temp.resize(flex.grid(*data.all()))
#temp = temp.as_double()
#print data.as_numpy_array().transpose()[::-1,::-1]
#print (background * temp).as_numpy_array().transpose()[::-1,::-1]
#print mask.as_numpy_array().transpose()[::-1,::-1]
#print ((data.as_double() - background) * temp).as_numpy_array().transpose()[::-1,::-1]
#raise
continue
# Only 1 should fail
assert(count == 1)
print 'OK'
#
# Author: Luis Fuentes-Montero (Luiso)
#
# This code is distributed under the BSD license, a copy of which is
# included in the root directory of this package.
from __future__ import division
from dials.array_family import flex
import boost.python
from dials_viewer_ext import gen_font_img
if(__name__ == "__main__"):
lst_flex = []
lst_flex_norm = []
size_xyz = 7
arr_2d = flex.double(flex.grid(size_xyz, size_xyz), 00)
tot = 0.0
for row in range(size_xyz):
for col in range(size_xyz):
arr_2d[row, col] += (row * 2 + col * 2)
tot += arr_2d[row, col]
print "arr_2d.as_numpy_array() = \n", arr_2d.as_numpy_array()
print "gen_font_img(arr_2d).as_numpy_array() = \n", gen_font_img(arr_2d).as_numpy_array()
