def get_projection_matrix(dim_pixel, dim_readout):
"""The get_projection_matrix() function returns the projection
matrices in homogeneous coordinates between readout frame and
fractional row and column indices. The forward transform maps
coordinates in the readout frame, i.e. [x, y, z, 1], to readout
indices, i.e. [i, j, 1], where i and j are the row and column
indices, respectively. The backward transform provides the inverse.
The get_projection_matrix() function assumes that coordinates in the
readout frame are pixel centers. XXX Bad name! Better
readout2metric(), readout_projection_matrices()?
@note If coordinates in the readout frame are the top, left corner
of the pixel, pass dim_readout=(readout_width_in_pixels + 1,
readout_height_in_pixels + 1).
@param dim_pixel Two-tuple of pixel width and height, in meters
@param dim_readout Two-tuple of readout width and height, in pixels
@return Two-tuple of the forward and backward projection
matrices
"""
Pb = matrix.rec(
elems=(0, +dim_pixel[0], dim_pixel[0] * (1 - dim_readout[0]) / 2,
-dim_pixel[1], 0, dim_pixel[1] * (dim_readout[1] - 1) / 2, 0, 0,
0, 0, 0, 1),
n=(4, 3))
Pf = matrix.rec(elems=(0, -1 / dim_pixel[1], 0, (dim_readout[1] - 1) / 2,
+1 / dim_pixel[0], 0, 0, (dim_readout[0] - 1) / 2,
0, 0, 0, 1),
n=(3, 4))
return (Pf, Pb)
def remove_cone_around_axis (array, axis, cone_radius) :
assert (cone_radius < 90) and (cone_radius >= 0)
from scitbx.matrix import rec
unit_cell = array.unit_cell()
indices = array.indices()
rc_vectors = unit_cell.reciprocal_space_vector(indices)
v1 = rec(unit_cell.reciprocal_space_vector(tuple(axis)), (3,1))
n_hkl = indices.size()
data = array.data()
sigmas = array.sigmas()
angle_high = 180 - cone_radius
i = 0
while (i < len(indices)) :
v2 = rec(rc_vectors[i], (3,1))
#print v1, v2
angle = math.degrees(v1.angle(v2))
if (angle <= cone_radius) or (angle >= angle_high) :
del rc_vectors[i]
del indices[i]
del data[i]
if (sigmas is not None) :
del sigmas[i]
else :
i += 1
delta_n_hkl = n_hkl - indices.size()
return (n_hkl, delta_n_hkl)
def remove_cone_around_axis(array, axis, cone_radius):
assert (cone_radius < 90) and (cone_radius >= 0)
from scitbx.matrix import rec
unit_cell = array.unit_cell()
indices = array.indices()
rc_vectors = unit_cell.reciprocal_space_vector(indices)
v1 = rec(unit_cell.reciprocal_space_vector(tuple(axis)), (3, 1))
n_hkl = indices.size()
data = array.data()
sigmas = array.sigmas()
angle_high = 180 - cone_radius
i = 0
while (i < len(indices)):
v2 = rec(rc_vectors[i], (3, 1))
#print v1, v2
angle = math.degrees(v1.angle(v2))
if (angle <= cone_radius) or (angle >= angle_high):
del rc_vectors[i]
del indices[i]
del data[i]
if (sigmas is not None):
del sigmas[i]
else:
i += 1
delta_n_hkl = n_hkl - indices.size()
return (n_hkl, delta_n_hkl)
def hessian_transform(self,
original_hessian,
adp_constraints):
constraint_matrix_tensor = matrix.rec(
adp_constraints.gradient_sum_matrix(),
adp_constraints.gradient_sum_matrix().focus())
hessian_matrix = matrix.rec( original_hessian,
original_hessian.focus())
## now create an expanded matrix
rows=adp_constraints.gradient_sum_matrix().focus()[0]+1
columns=adp_constraints.gradient_sum_matrix().focus()[1]+1
expanded_constraint_array = flex.double(rows*columns,0)
count_new=0
count_old=0
for ii in range(rows):
for jj in range(columns):
if (ii>0):
if (jj>0):
expanded_constraint_array[count_new]=\
constraint_matrix_tensor[count_old]
count_old+=1
count_new+=1
## place the first element please
expanded_constraint_array[0]=1
result=matrix.rec( expanded_constraint_array,
(rows, columns) )
#print result.mathematica_form()
new_hessian = result * hessian_matrix * result.transpose()
result = flex.double(new_hessian)
result.resize(flex.grid( new_hessian.n ) )
return(result)
def hessian_transform(self,
original_hessian,
adp_constraints):
constraint_matrix_tensor = matrix.rec(
adp_constraints.gradient_sum_matrix(),
adp_constraints.gradient_sum_matrix().focus())
hessian_matrix = matrix.rec( original_hessian,
original_hessian.focus())
## now create an expanded matrix
rows=adp_constraints.gradient_sum_matrix().focus()[0]+1
columns=adp_constraints.gradient_sum_matrix().focus()[1]+1
expanded_constraint_array = flex.double(rows*columns,0)
count_new=0
count_old=0
for ii in range(rows):
for jj in range(columns):
if (ii>0):
if (jj>0):
expanded_constraint_array[count_new]=\
constraint_matrix_tensor[count_old]
count_old+=1
count_new+=1
## place the first element please
expanded_constraint_array[0]=1
result=matrix.rec( expanded_constraint_array,
(rows, columns) )
#print result.mathematica_form()
new_hessian = result * hessian_matrix * result.transpose()
result = flex.double(new_hessian)
result.resize(flex.grid( new_hessian.n ) )
return(result)
def run(args):
if (len(args) == 0): args = ["--help"]
from libtbx.option_parser import libtbx_option_parser
import libtbx.load_env
command_line = (libtbx_option_parser(
usage="%s [options] space_group_symbol ..." % libtbx.env.dispatcher_name)
.option(None, "--primitive",
action="store_true",
help="Convert centred space groups to primitive setting.")
.option(None, "--symops",
action="store_true",
help="Show list of symmetry operations.")
).process(args=args)
co = command_line.options
from cctbx import sgtbx
args = command_line.args
if (args == ["all"]):
args = [str(no) for no in xrange(1,230+1)]
for symbol in args:
sgi = sgtbx.space_group_info(symbol=symbol)
if (co.primitive):
sgi = sgi.primitive_setting()
sgi.show_summary()
gr = sgi.group()
print " Crystal system:", gr.crystal_system()
print " Point group type:", gr.point_group_type()
print " Laue group type:", gr.laue_group_type()
print " Number of symmetry operations:", gr.order_z()
print " Lattice centering operations:", gr.n_ltr()
if (gr.n_ltr() != 1):
print " Number of symmetry operations in primitive setting:", \
gr.order_p()
if (gr.is_centric()): s = gr(0, 1, 0)
else: s = None
print " Center of inversion:", s
print " Dimensionality of continuous allowed origin shifts:", \
sgi.number_of_continuous_allowed_origin_shifts()
ssi_vm = sgi.structure_seminvariants().vectors_and_moduli()
print " Structure-seminvariant vectors and moduli:", \
len(ssi_vm)
if (len(ssi_vm) != 0):
for vm in ssi_vm:
print " (%2d, %2d, %2d)" % vm.v, "%2d" % vm.m
print " Direct-space asymmetric unit:"
dau = sgi.direct_space_asu()
print " Number of faces: %d" % len(dau.cuts)
for cut in dau.cuts:
print " " + cut.as_xyz()
print " ADP constraint matrix:"
_ = sgi.group().adp_constraints().gradient_sum_matrix()
from scitbx import matrix
print matrix.rec(tuple(_), _.focus()).mathematica_form(
one_row_per_line=True,
prefix=" ")
if (co.symops):
print " List of symmetry operations:"
for s in sgi.group():
print " %s" % str(s)
print
def get_projection_matrix(dim_pixel, dim_readout):
"""The get_projection_matrix() function returns the projection
matrices in homogeneous coordinates between readout frame and
fractional row and column indices. The forward transform maps
coordinates in the readout frame, i.e. [x, y, z, 1], to readout
indices, i.e. [i, j, 1], where i and j are the row and column
indices, respectively. The backward transform provides the inverse.
The get_projection_matrix() function assumes that coordinates in the
readout frame are pixel centers. XXX Bad name! Better
readout2metric(), readout_projection_matrices()?
@note If coordinates in the readout frame are the top, left corner
of the pixel, pass dim_readout=(readout_width_in_pixels + 1,
readout_height_in_pixels + 1).
@param dim_pixel Two-tuple of pixel width and height, in meters
@param dim_readout Two-tuple of readout width and height, in pixels
@return Two-tuple of the forward and backward projection
matrices
"""
Pb = matrix.rec(
elems=(
0,
+dim_pixel[0],
dim_pixel[0] * (1 - dim_readout[0]) / 2,
-dim_pixel[1],
0,
dim_pixel[1] * (dim_readout[1] - 1) / 2,
0,
0,
0,
0,
0,
1,
),
n=(4, 3),
)
Pf = matrix.rec(
elems=(
0,
-1 / dim_pixel[1],
0,
(dim_readout[1] - 1) / 2,
+1 / dim_pixel[0],
0,
0,
(dim_readout[0] - 1) / 2,
0,
0,
0,
1,
),
n=(3, 4),
)
return (Pf, Pb)
def exercise_rigu():
ins = """
CELL 0.71073 7.772741 8.721603 10.863736 90 102.9832 90
ZERR 2 0.000944 0.001056 0.001068 0 0.0107 0
LATT -1
SYMM -X,0.5+Y,-Z
SFAC C H O
UNIT 24 44 22
RIGU 0.0001 0.0001 O4 C C12
C12 1 -0.12812 0.06329 -0.17592 11.00000 0.01467 0.02689 0.02780 =
-0.00379 0.00441 -0.00377
O4 3 0.08910 0.02721 0.02186 11.00000 0.02001 0.03168 0.03125 =
-0.00504 0.00144 -0.00274
C 1 -0.05545 -0.04221 -0.06528 11.00000 0.01560 0.02699 0.02581 =
-0.00481 0.00597 -0.00068
HKLF 4
END
"""
sio = StringIO(ins)
import iotbx.shelx as shelx
model = shelx.parse_smtbx_refinement_model(file=sio)
sites_cart = model.structure.sites_cart()
u_cart = model.structure.scatterers().extract_u_cart(
model.structure.unit_cell())
arp = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
for rp in model._proxies['rigu']:
rr = adp_restraints.rigu(arp, rp)
U1 = matrix.sym(sym_mat3=u_cart[rp.i_seqs[0]])
U2 = matrix.sym(sym_mat3=u_cart[rp.i_seqs[1]])
vz = matrix.col(sites_cart[rp.i_seqs[1]]) - matrix.col(
sites_cart[rp.i_seqs[0]])
vy = vz.ortho()
vx = vy.cross(vz)
R = matrix.rec(
vx.normalize().elems + vy.normalize().elems + vz.normalize().elems,
(3, 3))
# with this matrix we can only test Z component as X and Y will differ
dU = ((R * U1) * R.transpose() -
(R * U2) * R.transpose()).as_sym_mat3()
assert approx_equal(dU[2], rr.delta_33())
#with the original matrix all components should match
R1 = matrix.rec(rr.RM(), (3, 3))
dU = ((R1 * U1) * R1.transpose() -
(R1 * U2) * R1.transpose()).as_sym_mat3()
assert approx_equal(dU[2], rr.delta_33())
assert approx_equal(dU[4], rr.delta_13())
assert approx_equal(dU[5], rr.delta_23())
# check the raw gradients against the reference implementation
for x, y in zip(rr.reference_gradients(R1), rr.raw_gradients()):
for idx in range(0, 6):
assert approx_equal(x[idx], y[idx])
for x, y in zip(rigu_finite_diff(R1, U1), rr.raw_gradients()):
for idx in range(0, 6):
assert approx_equal(x[idx], y[idx])
def exercise_impl(svd_impl_name, use_fortran):
import scitbx.linalg
svd_impl = getattr(scitbx.linalg, "lapack_%s" % svd_impl_name)
from scitbx.array_family import flex
from scitbx import matrix
from libtbx.test_utils import approx_equal
#
for diag in [0, 1]:
for n in xrange(1, 11):
a = flex.double(flex.grid(n, n), 0)
for i in xrange(n):
a[(i, i)] = diag
a_inp = a.deep_copy()
svd = svd_impl(a=a, use_fortran=use_fortran)
if svd is None:
if not use_fortran:
print "Skipping tests: lapack_%s not available." % svd_impl_name
return
assert svd.info == 0
assert approx_equal(svd.s, [diag] * n)
assert svd.u.all() == (n, n)
assert svd.vt.all() == (n, n)
mt = flex.mersenne_twister(seed=0)
for m in xrange(1, 11):
for n in xrange(1, 11):
a = matrix.rec(elems=tuple(mt.random_double(m * n) * 4 - 2), n=(m, n))
svd = svd_impl(a=a.transpose().as_flex_double_matrix(), use_fortran=use_fortran)
assert svd.info == 0
sigma = matrix.diag(svd.s) # min(m,n) x min(m,n)
# FORTRAN layout, so transpose
u = matrix.rec(svd.u, svd.u.all()).transpose()
vt = matrix.rec(svd.vt, svd.vt.all()).transpose()
assert approx_equal(u * sigma * vt, a)
#
a = matrix.rec(elems=[0.47, 0.10, -0.21, -0.21, -0.03, 0.35], n=(3, 2))
svd = svd_impl(a=a.transpose().as_flex_double_matrix(), use_fortran=use_fortran)
assert svd.info == 0
assert approx_equal(svd.s, [0.55981345199567534, 0.35931726783538481])
# again remember column-major storage
assert approx_equal(
svd.u,
[
0.81402078804155853,
-0.5136261274467826,
0.27121644094748704,
-0.42424674329757839,
-0.20684171439391938,
0.88160717215094342,
],
)
assert approx_equal(svd.vt, [0.8615633693608673, -0.50765003750177129, 0.50765003750177129, 0.8615633693608673])
def exercise_impl(svd_impl_name, use_fortran):
import scitbx.linalg
svd_impl = getattr(scitbx.linalg, "lapack_%s" % svd_impl_name)
from scitbx.array_family import flex
from scitbx import matrix
from libtbx.test_utils import approx_equal
#
for diag in [0, 1]:
for n in range(1, 11):
a = flex.double(flex.grid(n, n), 0)
for i in range(n):
a[(i, i)] = diag
a_inp = a.deep_copy()
svd = svd_impl(a=a, use_fortran=use_fortran)
if (svd is None):
if (not use_fortran):
print("Skipping tests: lapack_%s not available." %
svd_impl_name)
return
assert svd.info == 0
assert approx_equal(svd.s, [diag] * n)
assert svd.u.all() == (n, n)
assert svd.vt.all() == (n, n)
mt = flex.mersenne_twister(seed=0)
for m in range(1, 11):
for n in range(1, 11):
a = matrix.rec(elems=tuple(mt.random_double(m * n) * 4 - 2),
n=(m, n))
svd = svd_impl(a=a.transpose().as_flex_double_matrix(),
use_fortran=use_fortran)
assert svd.info == 0
sigma = matrix.diag(svd.s) # min(m,n) x min(m,n)
# FORTRAN layout, so transpose
u = matrix.rec(svd.u, svd.u.all()).transpose()
vt = matrix.rec(svd.vt, svd.vt.all()).transpose()
assert approx_equal(u * sigma * vt, a)
#
a = matrix.rec(elems=[0.47, 0.10, -0.21, -0.21, -0.03, 0.35], n=(3, 2))
svd = svd_impl(a=a.transpose().as_flex_double_matrix(),
use_fortran=use_fortran)
assert svd.info == 0
assert approx_equal(svd.s, [0.55981345199567534, 0.35931726783538481])
# again remember column-major storage
assert approx_equal(svd.u, [
0.81402078804155853, -0.5136261274467826, 0.27121644094748704,
-0.42424674329757839, -0.20684171439391938, 0.88160717215094342
])
assert approx_equal(svd.vt, [
0.8615633693608673, -0.50765003750177129, 0.50765003750177129,
0.8615633693608673
])
def get_flex_image(self, brightness, **kwargs):
# This functionality has migrated to
# rstbx.slip_viewer.tile_generation._get_flex_image_multitile().
# XXX Still used by iotbx/command_line/detector_image_as_png.py
#raise DeprecationWarning(
# "xfel.cftbx.cspad_detector.get_flex_image() is deprecated")
# no kwargs supported at present
from xfel.cftbx.detector.metrology import get_projection_matrix
# E maps picture coordinates onto metric Cartesian coordinates,
# i.e. [row, column, 1 ] -> [x, y, z, 1]. Both frames share the
# same origin, but the first coordinate of the screen coordinate
# system increases downwards, while the second increases towards
# the right. XXX Is this orthographic projection the only one
# that makes any sense?
E = rec(elems=[
0, +self._pixel_size[1], 0, -self._pixel_size[0], 0, 0, 0, 0, 0, 0,
0, 1
],
n=[4, 3])
# P: [x, y, z, 1] -> [row, column, 1]. Note that self._asic_focus
# needs to be flipped.
Pf = get_projection_matrix(
self._pixel_size, (self._asic_focus[1], self._asic_focus[0]))[0]
# XXX Add ASIC:s in order? If a point is contained in two ASIC:s
# simultaneously, it will be assigned to the ASIC defined first.
# XXX Use a Z-buffer instead?
nmemb = 0
for key, asic in six.iteritems(self._tiles):
# Create my_flex_image and rawdata on the first iteration.
if ("rawdata" not in locals()):
rawdata = flex.double(flex.grid(self.size1, self.size2))
my_flex_image = generic_flex_image(
rawdata=rawdata,
binning=1,
size1_readout=self._asic_focus[0],
size2_readout=self._asic_focus[1],
brightness=brightness,
saturation=self._saturation)
rawdata.matrix_paste_block_in_place(block=asic,
i_row=nmemb *
self._asic_padded[0],
i_column=0)
nmemb += 1
# key is guaranteed to exist in self._matrices as per
# readHeader(). Last row of self._matrices[key][0] is always
# [0, 0, 0, 1].
T = Pf * self._matrices[key][0] * E
R = sqr([T(0, 0), T(0, 1), T(1, 0), T(1, 1)])
t = col([T(0, 2), T(1, 2)])
my_flex_image.add_transformation_and_translation(R, t)
my_flex_image.followup_brightness_scale()
return my_flex_image
def __init__(O, type, qE):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.q_size = len(qE)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
#
O.Tps = matrix.rt((O.E, (0,0,0)))
O.Tsp = matrix.rt((O.E.transpose(), (0,0,0)))
O.Xj = T_as_X(O.Tps)
O.S = matrix.rec((
1,0,0,
0,1,0,
0,0,1,
0,0,0,
0,0,0,
0,0,0), n=(6,3))
def glm(x, p=None):
from math import exp, sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
beta0 = 0
if p is None:
p = [1.0] * len(x)
X = matrix.rec([1] * len(x), (len(x), 1))
c = 1.345
while True:
n = beta0
mu = exp(n)
z = [n + (xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
r = [(xx - mu) / sqrt(mu) for xx in x]
w2 = [huber(rr, c) for rr in r]
W = matrix.diag(w)
# W2 = matrix.diag(w2)
Z = matrix.col(z)
beta = (X.transpose() * W * X).inverse() * X.transpose() * W * z
print(beta)
if abs(beta[0] - beta0) < 1e-3:
break
beta0 = beta[0]
# W12 = matrix.diag([sqrt(ww) for ww in w])
# H = W12 * X * (X.transpose() * W * X).inverse() * X.transpose() * W12
mu = exp(n)
return mu
def get_panel_fast_slow(self, serial):
"""Get the average x- and y-coordinates of all the ASIC:s in the
panel with serial @p serial. This is done by back-transforming
the centre's of each ASIC to the screen (sort of) coordinate
system. This is more robust than getting the panel positions
directly.
"""
from xfel.cftbx.detector.metrology import get_projection_matrix
center = col([self._asic_focus[0] / 2, self._asic_focus[1] / 2, 1])
fast, nmemb, slow = 0, 0, 0
# Use the pixel size for the ASIC to construct the final
# projection matrix.
for p in self._metrology_params.detector.panel:
if (p.serial != serial):
continue
for s in p.sensor:
for a in s.asic:
E = rec(elems=[+1 / a.pixel_size[0], 0, 0, 0,
0, -1 / a.pixel_size[1], 0, 0],
n=[2, 4])
Pb = get_projection_matrix(a.pixel_size, a.dimension)[1]
Tb = self._matrices[(0, p.serial, s.serial, a.serial)][1]
t = E * Tb * Pb * center
fast += t(0, 0)
slow += t(1, 0)
nmemb += 1
if (nmemb == 0):
return (0, 0)
return (fast / nmemb, slow / nmemb)
def glm33(X, Y, B, P):
from math import exp, sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
X = matrix.rec(list(X), X.all())
Y = matrix.col(list(Y))
B = matrix.col(list(B))
P = matrix.col(list(P))
while True:
n = X * B
mu = matrix.col([exp(nn) for nn in n])
z = [(yy - mui) / mui for yy, mui in zip(Y, mu)]
w = [pp * mui for pp, mui in zip(P, mu)]
W = matrix.diag(w)
Z = matrix.col(z)
delta = (X.transpose() * W * X).inverse() * X.transpose() * W * z
relE = sqrt(
sum([d * d for d in delta]) / max(1e-10, sum([d * d for d in B])))
B = B + delta
# print relE
if relE < 1e-3:
break
return B
def update_rot_tran(self, x):
"""
Convert the refinable parameters, rotations angles and
scaled translations, back to rotation matrices and translation vectors and
updates the transforms_obj (ncs_restraints_group_list)
!!! IN PLACE !!!
Args:
x : a flex.double of the form (theta_1,psi_1,phi_1,tx_1,ty_1,tz_1,..
theta_n,psi_n,phi_n,tx_n/s,ty_n/s,tz_n/s). where n is the number of
transformations.
Returns:
Nothing
"""
i = 0
for gr in self:
copies = []
for tr in gr.copies:
the, psi, phi = x[i * 6:i * 6 + 3]
rot = scitbx.rigid_body.rb_mat_xyz(the=the,
psi=psi,
phi=phi,
deg=False)
tran = matrix.rec(x[i * 6 + 3:i * 6 + 6], (3, 1))
tr.r = (rot.rot_mat())
tr.t = tran
copies.append(tr)
i += 1
gr.copies = copies
def exercise_derivatives(space_group_info, out):
crystal_symmetry = space_group_info.any_compatible_crystal_symmetry(
volume=1000)
space_group = space_group_info.group()
adp_constraints = space_group.adp_constraints()
m = adp_constraints.row_echelon_form()
print >> out, matrix.rec(m, (m.size()//6, 6)).mathematica_form(
one_row_per_line=True)
print >> out, list(adp_constraints.independent_indices)
u_cart_p1 = adptbx.random_u_cart()
u_star_p1 = adptbx.u_cart_as_u_star(crystal_symmetry.unit_cell(), u_cart_p1)
u_star = space_group.average_u_star(u_star_p1)
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry, d_min=3, anomalous_flag=False)
for h in miller_set.indices():
grads_fin = d_dw_d_u_star_finite(h=h, u_star=u_star)
print >> out, "grads_fin:", list(grads_fin)
grads_ana = d_dw_d_u_star_analytical(h=h, u_star=u_star)
print >> out, "grads_ana:", list(grads_ana)
compare_derivatives(grads_ana, grads_fin)
curvs_fin = d2_dw_d_u_star_d_u_star_finite(h=h, u_star=u_star)
print >> out, "curvs_fin:", list(curvs_fin)
curvs_ana = d2_dw_d_u_star_d_u_star_analytical(h=h, u_star=u_star)
print >> out, "curvs_ana:", list(curvs_ana)
compare_derivatives(curvs_ana, curvs_fin)
#
u_indep = adp_constraints.independent_params(u_star)
grads_indep_fin = d_dw_d_u_indep_finite(
adp_constraints=adp_constraints, h=h, u_indep=u_indep)
print >> out, "grads_indep_fin:", list(grads_indep_fin)
grads_indep_ana = flex.double(adp_constraints.independent_gradients(
all_gradients=list(grads_ana)))
print >> out, "grads_indep_ana:", list(grads_indep_ana)
compare_derivatives(grads_indep_ana, grads_indep_fin)
curvs_indep_fin = d2_dw_d_u_indep_d_u_indep_finite(
adp_constraints=adp_constraints, h=h, u_indep=u_indep)
print >> out, "curvs_indep_fin:", list(curvs_indep_fin)
curvs_indep_ana = adp_constraints.independent_curvatures(
all_curvatures=curvs_ana)
print >> out, "curvs_indep_ana:", list(curvs_indep_ana)
compare_derivatives(curvs_indep_ana, curvs_indep_fin)
#
curvs_indep_mm = None
if (str(space_group_info) == "P 1 2 1"):
assert list(adp_constraints.independent_indices) == [0,1,2,4]
curvs_indep_mm = p2_curv(h, u_star)
elif (str(space_group_info) == "P 4"):
assert list(adp_constraints.independent_indices) == [1,2]
curvs_indep_mm = p4_curv(h, u_star)
elif (str(space_group_info) in ["P 3", "P 6"]):
assert list(adp_constraints.independent_indices) == [2,3]
curvs_indep_mm = p3_curv(h, u_star)
elif (str(space_group_info) == "P 2 3"):
assert list(adp_constraints.independent_indices) == [2]
curvs_indep_mm = p23_curv(h, u_star)
if (curvs_indep_mm is not None):
curvs_indep_mm = flex.double(
curvs_indep_mm).matrix_symmetric_as_packed_u()
print >> out, "curvs_indep_mm:", list(curvs_indep_mm)
compare_derivatives(curvs_indep_ana, curvs_indep_mm)
def glm33(X, Y, B, P):
from math import exp , sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
X = matrix.rec(list(X), X.all())
Y = matrix.col(list(Y))
B = matrix.col(list(B))
P = matrix.col(list(P))
while True:
n = X * B
mu = matrix.col([exp(nn) for nn in n])
z = [(yy - mui) / mui for yy, mui in zip(Y, mu)]
w = [pp * mui for pp, mui in zip(P, mu)]
W = matrix.diag(w)
Z = matrix.col(z)
delta = (X.transpose() * W * X).inverse() * X.transpose()*W*z
relE = sqrt(sum([d*d for d in delta])/max(1e-10, sum([d*d for d in B])))
B = B + delta
# print relE
if relE < 1e-3:
break
return B
def glm(x, p=None):
from math import exp, sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
beta0 = 0
if p is None:
p = [1.0] * len(x)
X = matrix.rec([1] * len(x), (len(x), 1))
c = 1.345
while True:
n = beta0
mu = exp(n)
z = [n + (xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
r = [(xx - mu) / sqrt(mu) for xx in x]
w2 = [huber(rr, c) for rr in r]
W = matrix.diag(w)
# W2 = matrix.diag(w2)
Z = matrix.col(z)
beta = (X.transpose() * W * X).inverse() * X.transpose() * W * z
print beta
if abs(beta[0] - beta0) < 1e-3:
break
beta0 = beta[0]
# W12 = matrix.diag([sqrt(ww) for ww in w])
# H = W12 * X * (X.transpose() * W * X).inverse() * X.transpose() * W12
mu = exp(n)
return mu
def get_flex_image(self, brightness, **kwargs):
# This functionality has migrated to
# rstbx.slip_viewer.tile_generation._get_flex_image_multitile().
# XXX Still used by iotbx/command_line/detector_image_as_png.py
#raise DeprecationWarning(
# "xfel.cftbx.cspad_detector.get_flex_image() is deprecated")
# no kwargs supported at present
from xfel.cftbx.detector.metrology import get_projection_matrix
# E maps picture coordinates onto metric Cartesian coordinates,
# i.e. [row, column, 1 ] -> [x, y, z, 1]. Both frames share the
# same origin, but the first coordinate of the screen coordinate
# system increases downwards, while the second increases towards
# the right. XXX Is this orthographic projection the only one
# that makes any sense?
E = rec(elems=[0, +self._pixel_size[1], 0,
-self._pixel_size[0], 0, 0,
0, 0, 0,
0, 0, 1],
n=[4, 3])
# P: [x, y, z, 1] -> [row, column, 1]. Note that self._asic_focus
# needs to be flipped.
Pf = get_projection_matrix(self._pixel_size,
(self._asic_focus[1], self._asic_focus[0]))[0]
# XXX Add ASIC:s in order? If a point is contained in two ASIC:s
# simultaneously, it will be assigned to the ASIC defined first.
# XXX Use a Z-buffer instead?
nmemb = 0
for key, asic in self._tiles.iteritems():
# Create my_flex_image and rawdata on the first iteration.
if ("rawdata" not in locals()):
rawdata = flex.double(flex.grid(self.size1, self.size2))
my_flex_image = generic_flex_image(
rawdata=rawdata,
size1_readout=self._asic_focus[0],
size2_readout=self._asic_focus[1],
brightness=brightness,
saturation=self._saturation)
rawdata.matrix_paste_block_in_place(
block=asic,
i_row=nmemb * self._asic_padded[0],
i_column=0)
nmemb += 1
# key is guaranteed to exist in self._matrices as per
# readHeader(). Last row of self._matrices[key][0] is always
# [0, 0, 0, 1].
T = Pf * self._matrices[key][0] * E
R = sqr([T(0, 0), T(0, 1),
T(1, 0), T(1, 1)])
t = col([T(0, 2), T(1, 2)])
my_flex_image.add_transformation_and_translation(R, t)
my_flex_image.followup_brightness_scale()
return my_flex_image
def RBDA_Eq_4_13(q):
p0, p1, p2, p3 = q
return matrix.rec((
-p1, -p2, -p3,
p0, -p3, p2,
p3, p0, -p1,
-p2, p1, p0), n=(4,3)) * 0.5
def exercise_isotropic_adp():
i_seqs = (0,)
weight = 2
u_cart = ((1,2,3,5,2,8),)
u_iso = (0,)
use_u_aniso = (True,)
p = adp_restraints.isotropic_adp_proxy(
i_seqs=i_seqs,
weight=weight)
assert p.i_seqs == i_seqs
assert approx_equal(p.weight, weight)
i = adp_restraints.isotropic_adp(u_cart=u_cart[0], weight=weight)
expected_deltas = (-1, 0, 1, 5, 2, 8)
expected_gradients = (-4, 0, 4, 40, 16, 64)
assert approx_equal(i.weight, weight)
assert approx_equal(i.deltas(), expected_deltas)
assert approx_equal(i.rms_deltas(), 4.5704364002673632)
assert approx_equal(i.residual(), 376.0)
assert approx_equal(i.gradients(), expected_gradients)
gradients_aniso_cart = flex.sym_mat3_double(1, (0,0,0,0,0,0))
gradients_iso = flex.double(1,0)
proxies = adp_restraints.shared_isotropic_adp_proxy([p,p])
u_cart = flex.sym_mat3_double(u_cart)
u_iso = flex.double(u_iso)
use_u_aniso = flex.bool(use_u_aniso)
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
residuals = adp_restraints.isotropic_adp_residuals(params, proxies=proxies)
assert approx_equal(residuals, (i.residual(),i.residual()))
deltas_rms = adp_restraints.isotropic_adp_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (i.rms_deltas(),i.rms_deltas()))
residual_sum = adp_restraints.isotropic_adp_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart
)
assert approx_equal(residual_sum, 752.0)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.isotropic_adp,
proxy=p,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso
)
for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
assert approx_equal(g, matrix.col(e)*2)
#
# check frame invariance of residual
#
u_cart = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
a = adp_restraints.isotropic_adp(
u_cart=u_cart.as_sym_mat3(), weight=1)
expected_residual = a.residual()
gen = flex.mersenne_twister()
for i in range(20):
R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
u_cart_rot = R * u_cart * R.transpose()
a = adp_restraints.isotropic_adp(
u_cart=u_cart_rot.as_sym_mat3(), weight=1)
assert approx_equal(a.residual(), expected_residual)
def exercise_isotropic_adp():
i_seqs = (0,)
weight = 2
u_cart = ((1,2,3,5,2,8),)
u_iso = (0,)
use_u_aniso = (True,)
p = adp_restraints.isotropic_adp_proxy(
i_seqs=i_seqs,
weight=weight)
assert p.i_seqs == i_seqs
assert approx_equal(p.weight, weight)
i = adp_restraints.isotropic_adp(u_cart=u_cart[0], weight=weight)
expected_deltas = (-1, 0, 1, 5, 2, 8)
expected_gradients = (-4, 0, 4, 40, 16, 64)
assert approx_equal(i.weight, weight)
assert approx_equal(i.deltas(), expected_deltas)
assert approx_equal(i.rms_deltas(), 4.5704364002673632)
assert approx_equal(i.residual(), 376.0)
assert approx_equal(i.gradients(), expected_gradients)
gradients_aniso_cart = flex.sym_mat3_double(1, (0,0,0,0,0,0))
gradients_iso = flex.double(1,0)
proxies = adp_restraints.shared_isotropic_adp_proxy([p,p])
u_cart = flex.sym_mat3_double(u_cart)
u_iso = flex.double(u_iso)
use_u_aniso = flex.bool(use_u_aniso)
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
residuals = adp_restraints.isotropic_adp_residuals(params, proxies=proxies)
assert approx_equal(residuals, (i.residual(),i.residual()))
deltas_rms = adp_restraints.isotropic_adp_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (i.rms_deltas(),i.rms_deltas()))
residual_sum = adp_restraints.isotropic_adp_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart
)
assert approx_equal(residual_sum, 752.0)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.isotropic_adp,
proxy=p,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso
)
for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
assert approx_equal(g, matrix.col(e)*2)
#
# check frame invariance of residual
#
u_cart = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
a = adp_restraints.isotropic_adp(
u_cart=u_cart.as_sym_mat3(), weight=1)
expected_residual = a.residual()
gen = flex.mersenne_twister()
for i in range(20):
R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
u_cart_rot = R * u_cart * R.transpose()
a = adp_restraints.isotropic_adp(
u_cart=u_cart_rot.as_sym_mat3(), weight=1)
assert approx_equal(a.residual(), expected_residual)
def as_4x4_rational(self):
r = self.r().as_rational().elems
t = self.t().as_rational().elems
zero = rational.int(0)
one = rational.int(1)
return matrix.rec((r[0], r[1], r[2], t[0], r[3], r[4], r[5], t[1],
r[6], r[7], r[8], t[2], zero, zero, zero, one),
(4, 4))
def determine_effective_scan_axis(gonio):
x = gonio.rotate_vector(0.0, 1, 0, 0)
y = gonio.rotate_vector(0.0, 0, 1, 0)
z = gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = gonio.rotate_vector(1.0, 1, 0, 0)
y1 = gonio.rotate_vector(1.0, 0, 1, 0)
z1 = gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
return rot.axis, rot.angle(deg = True)
def cbf_gonio_to_effective_axis_fixed_old(cbf_gonio):
'''Given a cbf goniometer handle, first determine the real rotation
axis, then determine the fixed component of rotation which is rotated
about this axis.'''
# First construct the real rotation axis, as the difference in rotating
# the identity matrix at the end of the scan and the beginning.
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
# Then, given this, determine the component of the scan which is fixed -
# which will need to be with respect to the unrotated axis. N.B. this
# will not be unique, but should be correct modulo a free rotation about
# the shifted axis.
start = cbf_gonio.get_rotation_range()[0]
# want positive rotations => if negative invert axis
axis = matrix.col(rot.axis)
angle = rot.angle()
if angle < 0:
axis = -1 * axis
# common sense would suggest in here that if the angle is -ve should
# be made +ve - works OK for omega scans but not phi scans, probably
# incomplete goniometer definition problem...
# start = -start
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
return axis, S.inverse() * R
def setUp(self):
# set_test_matrix
self.rot1 = flex.vec3_double([
(-0.317946, -0.173437, 0.932111),
( 0.760735, -0.633422, 0.141629),
( 0.565855, 0.754120, 0.333333)])
self.rot2 = flex.vec3_double([
(0 , 0 , 1),
(0.784042, -0.620708, 0),
(0.620708, 0.784042, 0)])
self.rot3 = flex.vec3_double([
( 0 , 0 , -1),
( 0.097445, -0.995241, 0),
(-0.995241, -0.097445, 0)])
# Angles for rot, in radians
self.rot_angles1 = flex.double(
(-0.4017753, 1.2001985, 2.6422171))
self.rot_angles2 = flex.double(
(-0.4017753, math.pi/2, 2.6422171))
self.rot_angles3 = flex.double(
(-0.4017753, -math.pi/2, 2.6422171))
self.rot_angles1_deg = flex.double(
(-0.4017753, 1.2001985, 2.6422171)) * 180/math.pi
self.rotation1 = matrix.sqr(self.rot1.as_double())
self.rotation2 = matrix.sqr(self.rot2.as_double())
self.rotation3 = matrix.sqr(self.rot3.as_double())
self.translation1 = matrix.rec((0.5,-0.5,0),(3,1))
self.translation2 = matrix.rec((0,0,0),(3,1))
self.translation3 = matrix.rec((0,1,2),(3,1))
self.r_t = [[self.rotation1, self.translation1],
[self.rotation2, self.translation2],
[self.rotation3, self.translation3]]
self.pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb_str)
self.tr_obj1 = ncs.input(
hierarchy=self.pdb_inp.construct_hierarchy(),
rotations=[self.rotation1,self.rotation2],
translations=[self.translation1,self.translation2])
self.tr_obj2 = ncs.input(
hierarchy=self.pdb_inp.construct_hierarchy(),
rotations=[self.rotation1,self.rotation2,self.rotation3],
translations=[self.translation1,self.translation2,self.translation3])
self.ncs_restraints_group_list = \
self.tr_obj1.get_ncs_restraints_group_list()
def cbf_gonio_to_effective_axis_fixed_old(cbf_gonio):
'''Given a cbf goniometer handle, first determine the real rotation
axis, then determine the fixed component of rotation which is rotated
about this axis.'''
# First construct the real rotation axis, as the difference in rotating
# the identity matrix at the end of the scan and the beginning.
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
# Then, given this, determine the component of the scan which is fixed -
# which will need to be with respect to the unrotated axis. N.B. this
# will not be unique, but should be correct modulo a free rotation about
# the shifted axis.
start = cbf_gonio.get_rotation_range()[0]
# want positive rotations => if negative invert axis
axis = matrix.col(rot.axis)
angle = rot.angle()
if angle < 0:
axis = -1 * axis
# common sense would suggest in here that if the angle is -ve should
# be made +ve - works OK for omega scans but not phi scans, probably
# incomplete goniometer definition problem...
# start = -start
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
return axis, S.inverse() * R
def as_4x4_rational(self):
r = self.r().as_rational().elems
t = self.t().as_rational().elems
zero = rational.int(0)
one = rational.int(1)
return matrix.rec((
r[0], r[1], r[2], t[0],
r[3], r[4], r[5], t[1],
r[6], r[7], r[8], t[2],
zero, zero, zero, one), (4, 4))
def cbf_gonio_to_effective_axis(cbf_gonio): '''Given a cbf goniometer handle, determine the real rotation axis.''' x = cbf_gonio.rotate_vector(0.0, 1, 0, 0) y = cbf_gonio.rotate_vector(0.0, 0, 1, 0) z = cbf_gonio.rotate_vector(0.0, 0, 0, 1) R = matrix.rec(x + y + z, (3, 3)).transpose() x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0) y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0) z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1) R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose() RA = R1 * R.inverse() axis = r3_rotation_axis_and_angle_from_matrix(RA).axis return axis
def cbf_gonio_to_effective_axis(cbf_gonio):
'''Given a cbf goniometer handle, determine the real rotation axis.'''
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
axis = r3_rotation_axis_and_angle_from_matrix(RA).axis
return axis
def run_cplusplus(self):
decomp = decompose_tls_matrices(
T=self.T_M.as_sym_mat3(),
L=self.L_M.as_sym_mat3(),
S=self.S_M.as_mat3(),
l_and_s_in_degrees=False,
verbose=False,
tol=self.
eps, # This is used through the code to determine when something is non-zero
eps=
1e-08, # This is currently hardcoded in the truncate function as a separate value
t_S_formula=(self.find_t_S_using_formula if
self.find_t_S_using_formula is not None else 'Force'),
t_S_value=(self.force_t_S if self.force_t_S is not None else 0.0),
)
# Check result
if not decomp.is_valid():
raise Sorry(decomp.error())
# Unpack results required for finalise object
# Invert the rotation matrices from the c++ implementation as R_ML defined differently
self.R_ML = matrix.sqr(decomp.R_ML).transpose()
self.R_MV = matrix.sqr(decomp.R_MV).transpose()
R_MtoL = self.R_ML.transpose()
# Libration rms around L-axes
self.Lxx = decomp.l_amplitudes[0]**2
self.Lyy = decomp.l_amplitudes[1]**2
self.Lzz = decomp.l_amplitudes[2]**2
# Unit vectors defining three Libration axes
self.l_x = matrix.rec(decomp.l_axis_directions[0], (3, 1))
self.l_y = matrix.rec(decomp.l_axis_directions[1], (3, 1))
self.l_z = matrix.rec(decomp.l_axis_directions[2], (3, 1))
# Rotation axes pass through the points in the L base
self.w = group_args(
w_lx=R_MtoL *
decomp.l_axis_intersections[0], # Transform output to L frame
w_ly=R_MtoL * decomp.l_axis_intersections[1],
w_lz=R_MtoL * decomp.l_axis_intersections[2],
)
# Correlation shifts sx,sy,sz for libration
self.sx = decomp.s_amplitudes[0]
self.sy = decomp.s_amplitudes[1]
self.sz = decomp.s_amplitudes[2]
# Vectors defining three Vibration axes
self.v_x_M = matrix.rec(decomp.v_axis_directions[0], (3, 1))
self.v_y_M = matrix.rec(decomp.v_axis_directions[1], (3, 1))
self.v_z_M = matrix.rec(decomp.v_axis_directions[2], (3, 1))
# Vibrational axes in the M basis
self.v_x = R_MtoL * decomp.v_axis_directions[0]
self.v_y = R_MtoL * decomp.v_axis_directions[1]
self.v_z = R_MtoL * decomp.v_axis_directions[2]
# Vibration rms along V-axes
self.tx = decomp.v_amplitudes[0]
self.ty = decomp.v_amplitudes[1]
self.tz = decomp.v_amplitudes[2]
def setUp(self):
# set_test_matrix
self.rot1 = flex.vec3_double([(-0.317946, -0.173437, 0.932111),
(0.760735, -0.633422, 0.141629),
(0.565855, 0.754120, 0.333333)])
self.rot2 = flex.vec3_double([(0, 0, 1), (0.784042, -0.620708, 0),
(0.620708, 0.784042, 0)])
self.rot3 = flex.vec3_double([(0, 0, -1), (0.097445, -0.995241, 0),
(-0.995241, -0.097445, 0)])
# Angles for rot, in radians
self.rot_angles1 = flex.double((-0.4017753, 1.2001985, 2.6422171))
self.rot_angles2 = flex.double((-0.4017753, math.pi / 2, 2.6422171))
self.rot_angles3 = flex.double((-0.4017753, -math.pi / 2, 2.6422171))
self.rot_angles1_deg = flex.double(
(-0.4017753, 1.2001985, 2.6422171)) * 180 / math.pi
self.rotation1 = matrix.sqr(self.rot1.as_double())
self.rotation2 = matrix.sqr(self.rot2.as_double())
self.rotation3 = matrix.sqr(self.rot3.as_double())
self.translation1 = matrix.rec((0.5, -0.5, 0), (3, 1))
self.translation2 = matrix.rec((0, 0, 0), (3, 1))
self.translation3 = matrix.rec((0, 1, 2), (3, 1))
self.r_t = [[self.rotation1, self.translation1],
[self.rotation2, self.translation2],
[self.rotation3, self.translation3]]
self.pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb_str)
self.tr_obj1 = ncs.input(
hierarchy=self.pdb_inp.construct_hierarchy(),
rotations=[self.rotation1, self.rotation2],
translations=[self.translation1, self.translation2])
self.tr_obj2 = ncs.input(
hierarchy=self.pdb_inp.construct_hierarchy(),
rotations=[self.rotation1, self.rotation2, self.rotation3],
translations=[
self.translation1, self.translation2, self.translation3
])
self.ncs_restraints_group_list = \
self.tr_obj1.get_ncs_restraints_group_list()
def check(a, b, c, expected_free_vars, expected_sol):
m = []
t = []
for i in range(3):
m.append([a[i], b[i]])
t.append(c[i])
m_orig = matrix.rec(flat_list(m), (3,2))
t_orig = list(t)
free_vars = row_echelon.form_rational(m, t)
assert free_vars == expected_free_vars
sol = row_echelon.back_substitution_rational(m, t, free_vars, [3, 11])
assert sol == expected_sol
if (sol is not None):
assert list(m_orig * sol) == t_orig
def check(a, b, c, expected_free_vars, expected_sol):
m = []
t = []
for i in xrange(3):
m.append([a[i], b[i]])
t.append(c[i])
m_orig = matrix.rec(flat_list(m), (3,2))
t_orig = list(t)
free_vars = row_echelon.form_rational(m, t)
assert free_vars == expected_free_vars
sol = row_echelon.back_substitution_rational(m, t, free_vars, [3, 11])
assert sol == expected_sol
if (sol is not None):
assert list(m_orig * sol) == t_orig
def shape_vertices(self):
result = set()
cuts = self.cuts
n_cuts = len(cuts)
for i0 in xrange(0,n_cuts-2):
for i1 in xrange(i0+1,n_cuts-1):
for i2 in xrange(i1+1,n_cuts):
m = matrix.rec(cuts[i0].n+cuts[i1].n+cuts[i2].n,(3,3))
d = m.determinant()
if (d != 0):
m_inv = m.co_factor_matrix_transposed() * (r1/d)
b = matrix.col([-cuts[i0].c,-cuts[i1].c,-cuts[i2].c])
vertex = m_inv * b
if (self.is_inside(vertex, shape_only=True)):
result.add(vertex.elems)
return sorted(result)
def cbf_gonio_to_effective_axis_fixed(cbf_gonio):
axis = matrix.col(cbf_gonio.get_rotation_axis())
start, increment = cbf_gonio.get_rotation_range()
# xia2-56 handle gracefully reverse turning goniometers - this assumes
# that the angles will be correctly inverted in the scan factory
if increment < 0:
start = -start
increment = -increment
axis = -axis
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
fixed = S.inverse() * R
return axis, fixed
def update_rot_tran(x, transforms_obj=None, ncs_restraints_group_list=None):
"""
Convert the refinable parameters, rotations angles and
scaled translations, back to rotation matrices and translation vectors and
updates the transforms_obj (ncs_restraints_group_list)
Args:
x : a flex.double of the form (theta_1,psi_1,phi_1,tx_1,ty_1,tz_1,..
theta_n,psi_n,phi_n,tx_n/s,ty_n/s,tz_n/s). where n is the number of
transformations.
transforms_obj : (ncs_group_object) containing information on Rotation
matrices, Translation vectors and NCS
ncs_restraints_group_list : a list of ncs_restraint_group objects
Returns:
The same type of input object with converted transforms
"""
assert bool(transforms_obj) == (not bool(ncs_restraints_group_list))
if transforms_obj:
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list(
)
if ncs_restraints_group_list:
i = 0
for gr in ncs_restraints_group_list:
copies = []
for tr in gr.copies:
the, psi, phi = x[i * 6:i * 6 + 3]
rot = scitbx.rigid_body.rb_mat_xyz(the=the,
psi=psi,
phi=phi,
deg=False)
tran = matrix.rec(x[i * 6 + 3:i * 6 + 6], (3, 1))
tr.r = (rot.rot_mat())
tr.t = tran
copies.append(tr)
i += 1
gr.copies = copies
if transforms_obj:
transforms_obj.update_using_ncs_restraints_group_list(
ncs_restraints_group_list)
return transforms_obj
else:
return ncs_restraints_group_list
def cbf_gonio_to_effective_axis_fixed(cbf_gonio):
axis = matrix.col(cbf_gonio.get_rotation_axis())
start, increment = cbf_gonio.get_rotation_range()
# xia2-56 handle gracefully reverse turning goniometers - this assumes
# that the angles will be correctly inverted in the scan factory
if increment < 0:
start = -start
increment = -increment
axis = -axis
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
fixed = S.inverse() * R
return axis, fixed
def update_rot_tran(x,transforms_obj=None,ncs_restraints_group_list=None):
"""
Convert the refinable parameters, rotations angles and
scaled translations, back to rotation matrices and translation vectors and
updates the transforms_obj (ncs_restraints_group_list)
Args:
x : a flex.double of the form (theta_1,psi_1,phi_1,tx_1,ty_1,tz_1,..
theta_n,psi_n,phi_n,tx_n/s,ty_n/s,tz_n/s). where n is the number of
transformations.
transforms_obj : (ncs_group_object) containing information on Rotation
matrices, Translation vectors and NCS
ncs_restraints_group_list : a list of ncs_restraint_group objects
Returns:
The same type of input object with converted transforms
"""
assert bool(transforms_obj) == (not bool(ncs_restraints_group_list))
if transforms_obj:
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
if ncs_restraints_group_list:
i = 0
for gr in ncs_restraints_group_list:
copies = []
for tr in gr.copies:
the,psi,phi =x[i*6:i*6+3]
rot = scitbx.rigid_body.rb_mat_xyz(
the=the, psi=psi, phi=phi, deg=False)
tran = matrix.rec(x[i*6+3:i*6+6],(3,1))
tr.r = (rot.rot_mat())
tr.t = tran
copies.append(tr)
i += 1
gr.copies = copies
if transforms_obj:
transforms_obj.update_using_ncs_restraints_group_list(
ncs_restraints_group_list)
return transforms_obj
else:
return ncs_restraints_group_list
def roundoff(val, precision=3, as_string=False):
'''
round off all floats in a list (or tuple) of list (or tuples)
recursively using round2() defined above as in:
>>> math_utils.roundoff( [12.3454, 7.4843, ["foo", (35.3581, -0.3856, [4.2769, 3.2147] )] ])
[12.345, 7.484, ['foo', (35.358, -0.386, [4.277, 3.215])]]
If value is less than 10**-precision or greater than 10**precision then return with scientific notation
'''
if isinstance(val, float):
if math.isnan(val):
return float("nan")
if abs(val) < float("1e-%d" % precision) or abs(val) > float(
"9e%d" % precision):
fstr = "%" + "%d" % precision
fstr += ".%de" % precision
val2str = fstr % val
if as_string:
return val2str
return float(val2str)
return round2(val, precision)
if isinstance(val, list):
for i, v in enumerate(val):
val[i] = roundoff(v, precision)
if isinstance(val, tuple):
val = list(val)
for i, v in enumerate(val):
val[i] = roundoff(v, precision)
val = tuple(val)
if isinstance(val, matrix.sqr):
val = list(val)
for i, v in enumerate(val):
val[i] = roundoff(v, precision)
val = matrix.sqr(val)
if isinstance(val, matrix.rec):
valn = val.n
val = list(val)
for i, v in enumerate(val):
val[i] = roundoff(v, precision)
val = matrix.rec(elems=val, n=valn)
return val
def glm33(x, p):
from math import exp, sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
beta0 = 0
while True:
n = beta0
mu = exp(n)
z = [(xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
W = matrix.diag(w)
Z = matrix.col(z)
X = matrix.rec([1] * len(z), (len(z), 1))
H = X * (X.transpose() * W * X).inverse() * X.transpose() * W
H = [H[i + i * len(z)] for i in range(len(z))]
MSE = sum((xx - mu)**2 for xx in x) / len(x)
r = [xx - mu for xx in x]
D = [rr * rr / (1 * MSE) * (hh / (1 - hh)**2) for rr, hh in zip(r, H)]
N = sum(1 for d in D if d > 4 / len(x))
# print X.transpose()*W*z
# print (W*X)[0]
# print (X.transpose()*W*X).inverse()[0]
delta = (X.transpose() * W * X).inverse() * X.transpose() * W * z
# print delta
relE = sqrt(
sum([d * d
for d in delta]) / max(1e-10, sum([d * d for d in [beta0]])))
beta0 = beta0 + delta[0]
# print relE
if relE < 1e-3:
break
return exp(beta0)
def __init__(O, type, qE):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.q_size = len(qE)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
#
O.Tps = matrix.rt((O.E, (0, 0, 0)))
O.Tsp = matrix.rt((O.E.transpose(), (0, 0, 0)))
O.Xj = T_as_X(O.Tps)
O.S = matrix.rec(
(1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0), n=(6, 3))
def glm33(x, p):
from math import exp , sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
beta0 = 0
while True:
n = beta0
mu = exp(n)
z = [(xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
W = matrix.diag(w)
Z = matrix.col(z)
X = matrix.rec([1]*len(z), (len(z),1))
H = X*(X.transpose() *W* X).inverse() * X.transpose()*W
H = [H[i+i*len(z)] for i in range(len(z))]
MSE = sum((xx-mu)**2 for xx in x) / len(x)
r = [xx - mu for xx in x]
D = [rr*rr / (1 * MSE) * (hh / (1-hh)**2) for rr, hh in zip(r, H)]
N = sum(1 for d in D if d > 4 / len(x))
# print X.transpose()*W*z
# print (W*X)[0]
# print (X.transpose()*W*X).inverse()[0]
delta = (X.transpose() * W * X).inverse() * X.transpose()*W*z
# print delta
relE = sqrt(sum([d*d for d in delta])/max(1e-10, sum([d*d for d in [beta0]])))
beta0 = beta0 + delta[0]
# print relE
if relE < 1e-3:
break
return exp(beta0)
def get_panel_fast_slow(self, serial):
"""Get the average x- and y-coordinates of all the ASIC:s in the
panel with serial @p serial. This is done by back-transforming
the centre's of each ASIC to the screen (sort of) coordinate
system. This is more robust than getting the panel positions
directly.
"""
from xfel.cftbx.detector.metrology import get_projection_matrix
center = col([self._asic_focus[0] / 2, self._asic_focus[1] / 2, 1])
fast, nmemb, slow = 0, 0, 0
# Use the pixel size for the ASIC to construct the final
# projection matrix.
for p in self._metrology_params.detector.panel:
if (p.serial != serial):
continue
for s in p.sensor:
for a in s.asic:
E = rec(elems=[
+1 / a.pixel_size[0], 0, 0, 0, 0, -1 / a.pixel_size[1],
0, 0
],
n=[2, 4])
Pb = get_projection_matrix(a.pixel_size, a.dimension)[1]
Tb = self._matrices[(0, p.serial, s.serial, a.serial)][1]
t = E * Tb * Pb * center
fast += t(0, 0)
slow += t(1, 0)
nmemb += 1
if (nmemb == 0):
return (0, 0)
return (fast / nmemb, slow / nmemb)
def _calc_cell_parameter_sd(self):
from scitbx.math.lefebvre import matrix_inverse_error_propagation
from scitbx.math import angle_derivative_wrt_vectors
from math import pi, acos, sqrt
# self._cov_B is the covariance matrix of elements of the B matrix. We
# need to construct the covariance matrix of elements of the
# transpose of B. The vector of elements of B is related to the
# vector of elements of its transpose by a permutation, P.
P = matrix.sqr((1,0,0,0,0,0,0,0,0,
0,0,0,1,0,0,0,0,0,
0,0,0,0,0,0,1,0,0,
0,1,0,0,0,0,0,0,0,
0,0,0,0,1,0,0,0,0,
0,0,0,0,0,0,0,1,0,
0,0,1,0,0,0,0,0,0,
0,0,0,0,0,1,0,0,0,
0,0,0,0,0,0,0,0,1))
# We can use P to replace var_cov with the covariance matrix of
# elements of the transpose of B.
var_cov = P*self._cov_B*P
# From B = (O^-1)^T we can convert this
# to the covariance matrix of the real space orthogonalisation matrix
Bt = self._B.transpose()
O = Bt.inverse()
cov_O = matrix_inverse_error_propagation(Bt, var_cov)
# The real space unit cell vectors are given by
vec_a = (O * matrix.col((1,0,0)))
vec_b = (O * matrix.col((0,1,0)))
vec_c = (O * matrix.col((0,0,1)))
# So the unit cell parameters are
a, b, c = vec_a.length(), vec_b.length(), vec_c.length()
alpha = acos(vec_b.dot(vec_c) / (b*c))
beta = acos(vec_a.dot(vec_c) / (a*c))
gamma = acos(vec_a.dot(vec_b) / (a*b))
# The estimated errors are calculated by error propagation from cov_O. In
# each case we define a function F(O) that converts the matrix O into the
# unit cell parameter of interest. To do error propagation to get the
# variance of that cell parameter we need the Jacobian of the function.
# This is a 1*9 matrix of derivatives in the order of the elements of O
#
# / dF dF dF dF dF dF dF dF dF \
# J = | ---, ---, ---, ---, ---, ---, ---, ---, --- |
# \ da1 db1 dc1 da2 db2 dc2 da3 db3 dc3 /
#
# For cell length |a|, F = sqrt(a1^2 + a2^2 + a3^2)
jacobian = matrix.rec(
(vec_a[0]/a, 0, 0, vec_a[1]/a, 0, 0, vec_a[2]/a, 0, 0), (1, 9))
var_a = (jacobian * cov_O * jacobian.transpose())[0]
# For cell length |b|, F = sqrt(b1^2 + b2^2 + b3^2)
jacobian = matrix.rec(
(0, vec_b[0]/b, 0, 0, vec_b[1]/b, 0, 0, vec_b[2]/b, 0), (1, 9))
var_b = (jacobian * cov_O * jacobian.transpose())[0]
# For cell length |c|, F = sqrt(c1^2 + c2^2 + c3^2)
jacobian = matrix.rec(
(0, 0, vec_c[0]/c, 0, 0, vec_c[1]/c, 0, 0, vec_c[2]/c), (1, 9))
jacobian_t = jacobian.transpose()
var_c = (jacobian * cov_O * jacobian.transpose())[0]
# For cell volume (a X b).c,
# F = c1(a2*b3 - b2*a3) + c2(a3*b1 - b3*a1) + c3(a1*b2 - b1*a2)
a1, a2, a3 = vec_a
b1, b2, b3 = vec_b
c1, c2, c3 = vec_c
jacobian = matrix.rec((c3*b2 - c2*b3,
c1*b3 - c3*b1,
c2*b1 - c1*b2,
c2*a3 - c3*a2,
c3*a1 - c1*a3,
c1*a2 - c2*a1,
a2*b3 - b2*a3,
a3*b1 - b3*a1,
a1*b2 - b1*a2), (1,9))
jacobian_t = jacobian.transpose()
var_V = (jacobian * cov_O * jacobian.transpose())[0]
self._cell_volume_sd = sqrt(var_V)
# For the unit cell angles we need to calculate derivatives of the angles
# with respect to the elements of O
dalpha_db, dalpha_dc = angle_derivative_wrt_vectors(vec_b, vec_c)
dbeta_da, dbeta_dc = angle_derivative_wrt_vectors(vec_a, vec_c)
dgamma_da, dgamma_db = angle_derivative_wrt_vectors(vec_a, vec_b)
# For angle alpha, F = acos( b.c / |b||c|)
jacobian = matrix.rec(
(0, dalpha_db[0], dalpha_dc[0], 0, dalpha_db[1], dalpha_dc[1], 0,
dalpha_db[2], dalpha_dc[2]), (1, 9))
var_alpha = (jacobian * cov_O * jacobian.transpose())[0]
# For angle beta, F = acos( a.c / |a||c|)
jacobian = matrix.rec(
(dbeta_da[0], 0, dbeta_dc[0], dbeta_da[1], 0, dbeta_dc[1], dbeta_da[2],
0, dbeta_dc[2]), (1, 9))
var_beta = (jacobian * cov_O * jacobian.transpose())[0]
# For angle gamma, F = acos( a.b / |a||b|)
jacobian = matrix.rec(
(dgamma_da[0], dgamma_db[0], 0, dgamma_da[1], dgamma_db[1], 0,
dgamma_da[2], dgamma_db[2], 0), (1, 9))
var_gamma = (jacobian * cov_O * jacobian.transpose())[0]
# Symmetry constraints may mean variances of the angles should be zero.
# Floating point error could lead to negative variances. Ensure these are
# caught before taking their square root!
var_alpha = max(0, var_alpha)
var_beta = max(0, var_beta)
var_gamma = max(0, var_gamma)
from math import pi
rad2deg = 180. / pi
self._cell_sd = (sqrt(var_a),
sqrt(var_b),
sqrt(var_c),
sqrt(var_alpha) * rad2deg,
sqrt(var_beta) * rad2deg,
sqrt(var_gamma) * rad2deg)
return
def __init__(self, ub_beg, ub_end, axis, s0, dmin, margin = 3):
# the source vector and wavelength
self._source = -s0
self._wavelength = 1 / sqrt(s0.dot(s0))
self._wavelength_sq = self._wavelength**2
# the rotation axis
self._axis = axis
# the resolution limit
self._dstarmax = 1 / dmin
self._dstarmax2 = self._dstarmax**2
# Margin by which to expand limits. Mosflm uses 3.
self._margin = int(margin)
# Determine the permutation order of columns of the setting matrix. Use
# the setting from the beginning for this.
# As a side-effect set self._permutation.
col1, col2, col3 = self._permute_axes(ub_beg)
# Thus set the reciprocal lattice axis vectors, in permuted order
# p, q and r for both orientations
rl_vec = [ub_beg.extract_block(start=(0,0), stop=(3,1)),
ub_beg.extract_block(start=(0,1), stop=(3,2)),
ub_beg.extract_block(start=(0,2), stop=(3,3))]
self._rlv_beg = [rl_vec[col1],
rl_vec[col2],
rl_vec[col3]]
rl_vec = [ub_end.extract_block(start=(0,0), stop=(3,1)),
ub_end.extract_block(start=(0,1), stop=(3,2)),
ub_end.extract_block(start=(0,2), stop=(3,3))]
self._rlv_end = [rl_vec[col1],
rl_vec[col2],
rl_vec[col3]]
# Set permuted setting matrices
self._p_beg = matrix.sqr(self._rlv_beg[0].elems +
self._rlv_beg[1].elems +
self._rlv_beg[2].elems).transpose()
self._p_end = matrix.sqr(self._rlv_end[0].elems +
self._rlv_end[1].elems +
self._rlv_end[2].elems).transpose()
## Define a new coordinate system concentric with the Ewald sphere.
##
## X' = X - source_x
## Y' = Y - source_y
## Z' = Z - source_z
##
## X = P' h'
## - = -
## / p11 p12 p13 -source_X \
## where h' = (p, q, r, 1)^T and P' = | p21 p22 p23 -source_y |
## - = \ p31 p32 p33 -source_z /
##
# Calculate P' matrices for the beginning and end settings
pp_beg = matrix.rec(self._p_beg.elems[0:3] + (-1.*self._source[0],) +
self._p_beg.elems[3:6] + (-1.*self._source[1],) +
self._p_beg.elems[6:9] + (-1.*self._source[2],),
n=(3, 4))
pp_end = matrix.rec(self._p_end.elems[0:3] + (-1.*self._source[0],) +
self._p_end.elems[3:6] + (-1.*self._source[1],) +
self._p_end.elems[6:9] + (-1.*self._source[2],),
n=(3, 4))
# Various quantities of interest are obtained from the reciprocal metric
# tensor T of P'. These quantities are to be used (later) for solving
# the intersection of a line of constant p, q index with the Ewald
# sphere. It is efficient to calculate these before the outer loop. So,
# calculate T for both beginning and end settings
t_beg = (pp_beg.transpose() * pp_beg).as_list_of_lists()
t_end = (pp_end.transpose() * pp_end).as_list_of_lists()
# quantities that are constant with p, beginning orientation
self._cp_beg = [t_beg[2][2],
t_beg[2][3]**2,
t_beg[0][2] * t_beg[2][3] - t_beg[0][3] * t_beg[2][2],
t_beg[0][2]**2 - t_beg[0][0] * t_beg[2][2],
t_beg[1][2] * t_beg[2][3] - t_beg[1][3] * t_beg[2][2],
t_beg[0][2] * t_beg[1][2] - t_beg[0][1] * t_beg[2][2],
t_beg[1][2]**2 - t_beg[1][1] * t_beg[2][2],
2.0 * t_beg[0][2],
2.0 * t_beg[1][2],
t_beg[0][0],
t_beg[1][1],
2.0 * t_beg[0][1],
2.0 * t_beg[2][3],
2.0 * t_beg[1][3],
2.0 * t_beg[0][3]]
# quantities that are constant with p, end orientation
self._cp_end = [t_end[2][2],
t_end[2][3]**2,
t_end[0][2] * t_end[2][3] - t_end[0][3] * t_end[2][2],
t_end[0][2]**2 - t_end[0][0] * t_end[2][2],
t_end[1][2] * t_end[2][3] - t_end[1][3] * t_end[2][2],
t_end[0][2] * t_end[1][2] - t_end[0][1] * t_end[2][2],
t_end[1][2]**2 - t_end[1][1] * t_end[2][2],
2.0 * t_end[0][2],
2.0 * t_end[1][2],
t_end[0][0],
t_end[1][1],
2.0 * t_end[0][1],
2.0 * t_end[2][3],
2.0 * t_end[1][3],
2.0 * t_end[0][3]]
## The following are set during the generation of indices
# planes of constant p tangential to the Ewald sphere
self._ewald_p_lim_beg = None
self._ewald_p_lim_end = None
# planes of constant p touching the circle of intersection between the
# Ewald and resolution limiting spheres
self._res_p_lim_beg = None
self._res_p_lim_end = None
# looping p limits
self._p_lim = None
return
def exercise_rational():
from scitbx.matrix import row_echelon
from scitbx import matrix
from libtbx.utils import flat_list
from boost_adaptbx.boost import rational
import random
rng = random.Random(0)
#
m = [[0]]
t = [0]
free_vars = row_echelon.form_rational(m, t)
assert m == [[0]]
assert t == [0]
assert free_vars == [0]
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol == [1]
sol = row_echelon.back_substitution_rational(m, None, free_vars, [2])
assert sol == [2]
#
m = [[0]]
t = [1]
free_vars = row_echelon.form_rational(m, t)
assert m == [[0]]
assert t == [1]
assert free_vars == [0]
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol is None
#
m = [[1]]
t = [2]
free_vars = row_echelon.form_rational(m, t)
assert m == [[1]]
assert t == [2]
assert free_vars == []
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol == [2]
#
def rr():
return rational.int(rng.randrange(-5,6), rng.randrange(1,10))
#
for i_trial in range(10):
for nr in [1,2,3]:
for nc in [1,2,3]:
m = []
for ir in range(nr):
m.append([rr() for ic in range(nc)])
m_orig = matrix.rec(flat_list(m), (nr,nc))
sol_orig = [rr() for ic in range(nc)]
t_orig = list(m_orig * matrix.col(sol_orig))
t = list(t_orig)
free_vars = row_echelon.form_rational(m, t)
sol = [None] * nc
for ic in free_vars:
sol[ic] = sol_orig[ic]
sol = row_echelon.back_substitution_rational(m, t, free_vars, sol)
assert sol is not None
assert sol.count(None) == 0
assert sol == sol_orig
sol = [1] * nc
sol = row_echelon.back_substitution_rational(m, None, free_vars, sol)
assert sol is not None
assert (m_orig * matrix.col(sol)).dot() == 0
#
for i_trial in range(10):
from itertools import count
for i in count(10):
a = matrix.col([rr(), rr(), rr()])
b = matrix.col([rr(), rr(), rr()])
if (a.cross(b).dot() != 0):
break
else:
raise RuntimeError
p = rng.randrange(-5,6)
q = rng.randrange(-5,6)
def check(a, b, c, expected_free_vars, expected_sol):
m = []
t = []
for i in range(3):
m.append([a[i], b[i]])
t.append(c[i])
m_orig = matrix.rec(flat_list(m), (3,2))
t_orig = list(t)
free_vars = row_echelon.form_rational(m, t)
assert free_vars == expected_free_vars
sol = row_echelon.back_substitution_rational(m, t, free_vars, [3, 11])
assert sol == expected_sol
if (sol is not None):
assert list(m_orig * sol) == t_orig
check(a, b, p*a+q*b, [], [p,q])
check(a, b, a.cross(b), [], None)
check(a, 5*a, -7*a, [1], [-62,11])
check(a, 5*a, b, [1], None)
check([0,0,0], [0,0,0], [0,0,0], [0,1], [3,11])
def __init__(self, xray_structure, name='??',
**kwds):
super(xray_structure_viewer, self).__init__(
unit_cell=xray_structure.unit_cell(),
orthographic=True,
light_position=(-1, 1, 1, 0),
**kwds)
assert self.bonding in ("covalent", "all")
assert self.bonding != "all" or self.distance_cutoff is not None
self.xray_structure = xs = xray_structure
self.setWindowTitle("%s in %s" % (name,
xs.space_group().type().hall_symbol()))
sites_frac = xs.sites_frac()
self.set_extent(sites_frac.min(), sites_frac.max())
self.is_unit_cell_shown = False
sites_cart = self.sites_cart = xs.sites_cart()
thermal_tensors = xs.extract_u_cart_plus_u_iso()
self.ellipsoid_to_sphere_transforms = {}
self.scatterer_indices = flex.std_string()
self.scatterer_labels = flex.std_string()
for i, (sc, site, u_cart) in enumerate(itertools.izip(xs.scatterers(),
sites_cart,
thermal_tensors)):
t = quadrics.ellipsoid_to_sphere_transform(site, u_cart)
self.ellipsoid_to_sphere_transforms.setdefault(
sc.element_symbol(),
quadrics.shared_ellipsoid_to_sphere_transforms()).append(t)
self.scatterer_indices.append("# %i" % i)
self.scatterer_labels.append(sc.label)
self.labels = None
self.label_font = QtGui.QFont("Arial Black", pointSize=18)
if self.bonding == "covalent":
radii = [
covalent_radii.table(elt).radius()
for elt in xs.scattering_type_registry().type_index_pairs_as_dict() ]
buffer_thickness = 2*max(radii) + self.covalent_bond_tolerance
asu_mappings = xs.asu_mappings(buffer_thickness=buffer_thickness)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_covalent_pairs(xs.scattering_types(),
tolerance=self.covalent_bond_tolerance)
elif self.bonding == "all":
asu_mappings = xs.asu_mappings(buffer_thickness=self.distance_cutoff)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_all_pairs(self.distance_cutoff)
pair_sym_table = bond_table.extract_pair_sym_table(
all_interactions_from_inside_asu=True)
self.bonds = flex.vec3_double()
self.bonds.reserve(len(xs.scatterers()))
uc = self.xray_structure.unit_cell()
frac = mat.rec(uc.fractionalization_matrix(), (3,3))
inv_frac = frac.inverse()
site_symms = xs.site_symmetry_table()
scatt = self.xray_structure.scatterers()
for i, neighbours in enumerate(pair_sym_table):
x0 = sites_cart[i]
sc0 = scatt[i]
for j, ops in neighbours.items():
sc1 = scatt[j]
if sc0.scattering_type == 'H' and sc1.scattering_type == 'H':
continue
for op in ops:
if op.is_unit_mx():
x1 = sites_cart[j]
else:
x1 = uc.orthogonalize(op*sites_frac[j])
op_cart = inv_frac*mat.rec(op.r().as_double(), (3,3))*frac
u1 = (op_cart
*mat.sym(sym_mat3=thermal_tensors[j])
*op_cart.transpose())
t = quadrics.ellipsoid_to_sphere_transform(x1, u1.as_sym_mat3())
self.ellipsoid_to_sphere_transforms[sc1.element_symbol()].append(t)
self.sites_cart.append(x1)
op_lbl = (" [%s]" % op).lower()
self.scatterer_indices.append("# %i%s" % (j, op_lbl))
self.scatterer_labels.append("%s%s" % (sc1.label, op_lbl))
self.bonds.append(x0)
self.bonds.append(x1)
def glm2(y):
from math import sqrt, exp, floor, log
from scipy.stats import poisson
from scitbx import matrix
from dials.array_family import flex
y = flex.double(y)
x = flex.double([1.0 for yy in y])
w = flex.double([1.0 for yy in y])
X = matrix.rec(x, (len(x), 1))
c = 1.345
beta = matrix.col([0])
maxiter = 10
accuracy = 1e-3
for iter in range(maxiter):
ni = flex.double([1.0 for xx in x])
sni = flex.sqrt(ni)
eta = flex.double(X * beta)
mu = flex.exp(eta)
dmu_deta = flex.exp(eta)
Vmu = mu
sVF = flex.sqrt(Vmu)
residP = (y - mu) * sni / sVF
phi = 1
sV = sVF * sqrt(phi)
residPS = residP / sqrt(phi)
H = flex.floor(mu * ni - c * sni * sV)
K = flex.floor(mu * ni + c * sni * sV)
# print min(H)
dpH = flex.double([poisson(mui).pmf(Hi) for mui, Hi in zip(mu, H)])
dpH1 = flex.double([poisson(mui).pmf(Hi - 1) for mui, Hi in zip(mu, H)])
dpK = flex.double([poisson(mui).pmf(Ki) for mui, Ki in zip(mu, K)])
dpK1 = flex.double([poisson(mui).pmf(Ki - 1) for mui, Ki in zip(mu, K)])
pHm1 = flex.double([poisson(mui).cdf(Hi - 1) for mui, Hi in zip(mu, H)])
pKm1 = flex.double([poisson(mui).cdf(Ki - 1) for mui, Ki in zip(mu, K)])
pH = pHm1 + dpH # = ppois(H,*)
pK = pKm1 + dpK # = ppois(K,*)
E2f = mu * (dpH1 - dpH - dpK1 + dpK) + pKm1 - pHm1
Epsi = c * (1.0 - pK - pH) + (mu / sV) * (dpH - dpK)
Epsi2 = c * c * (pH + 1.0 - pK) + E2f
EpsiS = c * (dpH + dpK) + E2f / sV
psi = flex.double([huber(rr, c) for rr in residPS])
cpsi = psi - Epsi
temp = cpsi * w * sni / sV * dmu_deta
EEqMat = [0] * len(X)
for j in range(X.n_rows()):
for i in range(X.n_columns()):
k = i + j * X.n_columns()
EEqMat[k] = X[k] * temp[j]
EEqMat = matrix.rec(EEqMat, (X.n_rows(), X.n_columns()))
EEq = []
for i in range(EEqMat.n_columns()):
col = []
for j in range(EEqMat.n_rows()):
k = i + j * EEqMat.n_columns()
col.append(EEqMat[k])
EEq.append(sum(col) / len(col))
EEq = matrix.col(EEq)
DiagB = EpsiS / (sni * sV) * w * (ni * dmu_deta) ** 2
B = matrix.diag(DiagB)
H = (X.transpose() * B * X) / len(y)
dbeta = H.inverse() * EEq
beta_new = beta + dbeta
relE = sqrt(sum([d * d for d in dbeta]) / max(1e-10, sum([d * d for d in beta])))
beta = beta_new
# print relE
if relE < accuracy:
break
weights = [min(1, c / abs(r)) for r in residPS]
eta = flex.double(X * beta)
mu = flex.exp(eta)
return beta
from scipy.stats import linregress from scipy.spatial.transform import Rotation from simtbx.nanoBragg import sim_data from scitbx.matrix import sqr, rec from cctbx import uctbx from dxtbx.model import Crystal ucell = (70, 60, 50, 90.0, 110, 90.0) symbol = "C121" a_real, b_real, c_real = sqr(uctbx.unit_cell(ucell).orthogonalization_matrix()).transpose().as_list_of_lists() C = Crystal(a_real, b_real, c_real, symbol) # random raotation rotation = Rotation.random(num=1, random_state=101)[0] Q = rec(rotation.as_quat(), n=(4, 1)) rot_ang, rot_axis = Q.unit_quaternion_as_axis_and_angle() C.rotate_around_origin(rot_axis, rot_ang) S = sim_data.SimData(use_default_crystal=True) S.crystal.dxtbx_crystal = C spectrum = S.beam.spectrum wave, flux = spectrum[0] Nwave = 5 waves = np.linspace(wave-wave*0.002, wave+wave*0.002, Nwave) fluxes = np.ones(Nwave) * flux / Nwave lambda0_GT = 0 lambda1_GT = 1 S.beam.spectrum = list(zip(waves, fluxes))
def exercise_rational():
from scitbx.matrix import row_echelon
from scitbx import matrix
from libtbx.utils import flat_list
from boost import rational
import random
rng = random.Random(0)
#
m = [[0]]
t = [0]
free_vars = row_echelon.form_rational(m, t)
assert m == [[0]]
assert t == [0]
assert free_vars == [0]
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol == [1]
sol = row_echelon.back_substitution_rational(m, None, free_vars, [2])
assert sol == [2]
#
m = [[0]]
t = [1]
free_vars = row_echelon.form_rational(m, t)
assert m == [[0]]
assert t == [1]
assert free_vars == [0]
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol is None
#
m = [[1]]
t = [2]
free_vars = row_echelon.form_rational(m, t)
assert m == [[1]]
assert t == [2]
assert free_vars == []
sol = row_echelon.back_substitution_rational(m, t, free_vars, [1])
assert sol == [2]
#
def rr():
return rational.int(rng.randrange(-5,6), rng.randrange(1,10))
#
for i_trial in xrange(10):
for nr in [1,2,3]:
for nc in [1,2,3]:
m = []
for ir in xrange(nr):
m.append([rr() for ic in xrange(nc)])
m_orig = matrix.rec(flat_list(m), (nr,nc))
sol_orig = [rr() for ic in xrange(nc)]
t_orig = list(m_orig * matrix.col(sol_orig))
t = list(t_orig)
free_vars = row_echelon.form_rational(m, t)
sol = [None] * nc
for ic in free_vars:
sol[ic] = sol_orig[ic]
sol = row_echelon.back_substitution_rational(m, t, free_vars, sol)
assert sol is not None
assert sol.count(None) == 0
assert sol == sol_orig
sol = [1] * nc
sol = row_echelon.back_substitution_rational(m, None, free_vars, sol)
assert sol is not None
assert (m_orig * matrix.col(sol)).dot() == 0
#
for i_trial in xrange(10):
from itertools import count
for i in count(10):
a = matrix.col([rr(), rr(), rr()])
b = matrix.col([rr(), rr(), rr()])
if (a.cross(b).dot() != 0):
break
else:
raise RuntimeError
p = rng.randrange(-5,6)
q = rng.randrange(-5,6)
def check(a, b, c, expected_free_vars, expected_sol):
m = []
t = []
for i in xrange(3):
m.append([a[i], b[i]])
t.append(c[i])
m_orig = matrix.rec(flat_list(m), (3,2))
t_orig = list(t)
free_vars = row_echelon.form_rational(m, t)
assert free_vars == expected_free_vars
sol = row_echelon.back_substitution_rational(m, t, free_vars, [3, 11])
assert sol == expected_sol
if (sol is not None):
assert list(m_orig * sol) == t_orig
check(a, b, p*a+q*b, [], [p,q])
check(a, b, a.cross(b), [], None)
check(a, 5*a, -7*a, [1], [-62,11])
check(a, 5*a, b, [1], None)
check([0,0,0], [0,0,0], [0,0,0], [0,1], [3,11])
def df_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
h, k, l = self.hkl
d_exp_huh_d_u_star = matrix.col(
[h**2, k**2, l**2, 2 * h * k, 2 * h * l, 2 * k * l])
for i_scatterer, scatterer in enumerate(self.scatterers):
site_symmetry_ops = None
if (self.site_symmetry_table.is_special_position(i_scatterer)):
site_symmetry_ops = self.site_symmetry_table.get(i_scatterer)
site_constraints = site_symmetry_ops.site_constraints()
if (scatterer.flags.use_u_aniso()):
adp_constraints = site_symmetry_ops.adp_constraints()
w = scatterer.weight()
wwo = scatterer.weight_without_occupancy()
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
gaussian = self.scattering_type_registry.gaussian_not_optional(
scattering_type=scatterer.scattering_type)
f0 = gaussian.at_d_star_sq(self.d_star_sq)
ffp = f0 + scatterer.fp
fdp = scatterer.fdp
ff = ffp + 1j * fdp
d_site = matrix.col([0, 0, 0])
if (not scatterer.flags.use_u_aniso()):
d_u_iso = 0
d_u_star = None
else:
d_u_iso = None
d_u_star = matrix.col([0, 0, 0, 0, 0, 0])
d_occ = 0j
d_fp = 0j
d_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = matrix.col(s_site).dot(tphkl)
if (scatterer.flags.use_u_aniso()):
s_u_star_s = r * matrix.sym(
sym_mat3=scatterer.u_star) * r.transpose()
huh = (matrix.row(self.hkl) * s_u_star_s).dot(
matrix.col(self.hkl))
dw = math.exp(mtps * huh)
e = cmath.exp(1j * alpha)
site_gtmx = r.transpose()
d_site += site_gtmx * (w * dw * ff * e * 1j * tphkl)
if (not scatterer.flags.use_u_aniso()):
d_u_iso += w * dw * ff * e * mtps * self.d_star_sq
else:
u_star_gtmx = matrix.sqr(
tensor_rank_2_gradient_transform_matrix(r))
d_u_star += u_star_gtmx * (w * dw * ff * e * mtps *
d_exp_huh_d_u_star)
d_occ += wwo * dw * ff * e
d_fp += w * dw * e
d_fdp += w * dw * e * 1j
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_site = gsm * d_site
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
gsm = matrix.rec(elems=gsm, n=gsm.focus())
d_u_star = gsm * d_u_star
result = flex.complex_double(d_site)
if (not scatterer.flags.use_u_aniso()):
result.append(d_u_iso)
else:
result.extend(flex.complex_double(d_u_star))
result.extend(flex.complex_double([d_occ, d_fp, d_fdp]))
yield result
def _get_flex_image_multipanel(panels, raw_data, brightness=1.0, show_untrusted=False):
# From xfel.cftbx.cspad_detector.readHeader() and
# xfel.cftbx.cspad_detector.get_flex_image(). XXX Is it possible to
# merge this with _get_flex_image() above? XXX Move to dxtbx Format
# class (or a superclass for multipanel images)?
from math import ceil
from iotbx.detectors import generic_flex_image
from libtbx.test_utils import approx_equal
from scitbx.array_family import flex
from scitbx.matrix import col, rec, sqr
from xfel.cftbx.detector.metrology import get_projection_matrix
assert len(panels) == len(raw_data)
# Determine next multiple of eight of the largest panel size.
for data in raw_data:
if 'data_max_focus' not in locals():
data_max_focus = data.focus()
else:
data_max_focus = (max(data_max_focus[0], data.focus()[0]),
max(data_max_focus[1], data.focus()[1]))
data_padded = (8 * int(ceil(data_max_focus[0] / 8)),
8 * int(ceil(data_max_focus[1] / 8)))
# Assert that all saturated values are equal and not None. While
# dxtbx records a separated trusted_range for each panel,
# generic_flex_image supports only accepts a single common value for
# the saturation.
for panel in panels:
if 'saturation' not in locals():
saturation = panel.get_trusted_range()[1]
else:
assert approx_equal(saturation, panel.get_trusted_range()[1])
assert 'saturation' in locals() and saturation is not None
# Create rawdata and my_flex_image before populating it.
rawdata = flex.double(
flex.grid(len(panels) * data_padded[0], data_padded[1]))
my_flex_image = generic_flex_image(
rawdata=rawdata,
size1_readout=data_max_focus[0],
size2_readout=data_max_focus[1],
brightness=brightness,
saturation=saturation,
show_untrusted=show_untrusted
)
# XXX If a point is contained in two panels simultaneously, it will
# be assigned to the panel defined first. XXX Use a Z-buffer
# instead?
for i in range(len(panels)):
# Determine the pixel size for the panel (in meters), as pixel
# sizes need not be identical.
data = raw_data[i]
panel = panels[i]
pixel_size = (panel.get_pixel_size()[0] * 1e-3,
panel.get_pixel_size()[1] * 1e-3)
if len(panels) == 24 and panels[0].get_image_size() == (2463,195):
#print "DLS I23 12M"
rawdata.matrix_paste_block_in_place(
block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# XXX hardcoded panel height and row gap
my_flex_image.add_transformation_and_translation((1,0,0,1), (-i*(195+17),0))
continue
elif len(panels) == 120 and panels[0].get_image_size() == (487,195):
i_row = i // 5
i_col = i % 5
#print i_row, i_col
#print data_padded
#print "DLS I23 12M"
rawdata.matrix_paste_block_in_place(
block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# XXX hardcoded panel height and row gap
my_flex_image.add_transformation_and_translation(
(1,0,0,1), (-i_row*(195+17),-i_col*(487+7)))
continue
# Get unit vectors in the fast and slow directions, as well as the
# the locations of the origin and the center of the panel, in
# meters.
fast = col(panel.get_fast_axis())
slow = col(panel.get_slow_axis())
origin = col(panel.get_origin()) * 1e-3
# Viewer will show an orthographic projection of the data onto a plane perpendicular to 0 0 1
projection_normal = col((0.,0.,1.))
beam_to_origin_proj = origin.dot(projection_normal)*projection_normal
projected_origin = origin - beam_to_origin_proj
center = projected_origin \
+ (data.focus()[0] - 1) / 2 * pixel_size[1] * slow \
+ (data.focus()[1] - 1) / 2 * pixel_size[0] * fast
normal = slow.cross(fast).normalize()
# Determine rotational and translational components of the
# homogeneous transformation that maps the readout indices to the
# three-dimensional laboratory frame.
Rf = sqr(( fast(0, 0), fast(1, 0), fast(2, 0),
-slow(0, 0), -slow(1, 0), -slow(2, 0),
normal(0, 0), normal(1, 0), normal(2, 0)))
tf = -Rf * center
Tf = sqr((Rf(0, 0), Rf(0, 1), Rf(0, 2), tf(0, 0),
Rf(1, 0), Rf(1, 1), Rf(1, 2), tf(1, 0),
Rf(2, 0), Rf(2, 1), Rf(2, 2), tf(2, 0),
0, 0, 0, 1))
# E maps picture coordinates onto metric Cartesian coordinates,
# i.e. [row, column, 1 ] -> [x, y, z, 1]. Both frames share the
# same origin, but the first coordinate of the screen coordinate
# system increases downwards, while the second increases towards
# the right. XXX Is this orthographic projection the only one
# that makes any sense?
E = rec(elems=[0, +pixel_size[1], 0,
-pixel_size[0], 0, 0,
0, 0, 0,
0, 0, 1],
n=[4, 3])
# P: [x, y, z, 1] -> [row, column, 1]. Note that data.focus()
# needs to be flipped to give (horizontal, vertical) size,
# i.e. (width, height).
Pf = get_projection_matrix(
pixel_size, (data.focus()[1], data.focus()[0]))[0]
rawdata.matrix_paste_block_in_place(
block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# Last row of T is always [0, 0, 0, 1].
T = Pf * Tf * E
R = sqr((T(0, 0), T(0, 1),
T(1, 0), T(1, 1)))
t = col((T(0, 2), T(1, 2)))
#print i,R[0],R[1],R[2],R[3],t[0],t[1]
my_flex_image.add_transformation_and_translation(R, t)
my_flex_image.followup_brightness_scale()
return my_flex_image
def glm(x, p = None):
from math import exp , sqrt, log, factorial, lgamma
from scitbx import matrix
from scipy.stats import poisson
beta0 = 0
if p is None:
p = [1.0] * len(x)
while True:
n = beta0
mu = exp(n)
z = [n + (xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
W = matrix.diag(w)
Z = matrix.col(z)
X = matrix.rec([1]*len(z), (len(z),1))
beta = (X.transpose() * W * X).inverse() * X.transpose()*W*z
if abs(beta[0] - beta0) < 1e-3:
break
beta0 = beta[0]
n = beta[0]
mu = exp(n)
z = [n + (xx - mu) / mu for xx in x]
w = [pp * mu for pp in p]
W = matrix.diag(w)
Z = matrix.col(z)
X = matrix.rec([1]*len(z), (len(z),1))
W12 = matrix.diag([sqrt(ww) for ww in w])
H = X * (X.transpose()*W*X).inverse() * X.transpose()
r = [(xx - mu) / mu for xx in x]
sum1 = 0
sum2 = 0
sum3 = 0
D = []
for xx in x:
d = 0
if xx != 0:
d += xx * log(xx)
d -= xx * log(mu)
d -= (xx - mu)
D.append(2*d)
# r = []
# for xx in x:
# if xx == 0:
# r.append(0)
# else:
# r.append(2*(log(xx) - log(mu)))
# D = []
# for i in range(len(r)):
# h = H[i+i*H.n[0]]
# d = (r[i]/(1 - h))**2 * h/1.0
# D.append(d)
# print min(x), max(x)
print min(D), max(D), F(1, len(x))
return exp(beta[0]), max(D) > F(1, len(x))
def _get_flex_image_multipanel(
panels,
raw_data,
beam,
brightness=1.0,
binning=1,
show_untrusted=False,
color_scheme=0,
):
# From xfel.cftbx.cspad_detector.readHeader() and
# xfel.cftbx.cspad_detector.get_flex_image(). XXX Is it possible to
# merge this with _get_flex_image() above? XXX Move to dxtbx Format
# class (or a superclass for multipanel images)?
from math import ceil
from iotbx.detectors import generic_flex_image
from libtbx.test_utils import approx_equal
from scitbx.array_family import flex
from scitbx.matrix import col, rec, sqr
from xfel.cftbx.detector.metrology import get_projection_matrix
assert len(panels) == len(raw_data), (len(panels), len(raw_data))
# Determine next multiple of eight of the largest panel size.
for data in raw_data:
if "data_max_focus" not in locals():
data_max_focus = data.focus()
else:
data_max_focus = (
max(data_max_focus[0],
data.focus()[0]),
max(data_max_focus[1],
data.focus()[1]),
)
data_padded = (
8 * int(ceil(data_max_focus[0] / 8)),
8 * int(ceil(data_max_focus[1] / 8)),
)
# Assert that all saturated values are equal and not None. While
# dxtbx records a separated trusted_range for each panel,
# generic_flex_image supports only accepts a single common value for
# the saturation.
for panel in panels:
if "saturation" not in locals():
saturation = panel.get_trusted_range()[1]
else:
assert approx_equal(saturation, panel.get_trusted_range()[1])
assert "saturation" in locals() and saturation is not None
# Create rawdata and my_flex_image before populating it.
rawdata = flex.double(
flex.grid(len(panels) * data_padded[0], data_padded[1]))
my_flex_image = generic_flex_image(
rawdata=rawdata,
binning=binning,
size1_readout=data_max_focus[0],
size2_readout=data_max_focus[1],
brightness=brightness,
saturation=saturation,
show_untrusted=show_untrusted,
color_scheme=color_scheme,
)
# Calculate the average beam center across all panels, in meters
# not sure this makes sense for detector which is not on a plane?
beam_center = col((0, 0, 0))
npanels = 0
for panel in panels:
try:
beam_center += col(panel.get_beam_centre_lab(beam.get_s0()))
npanels += 1
except RuntimeError: # catch DXTBX_ASSERT for no intersection
pass
beam_center /= npanels / 1e-3
# XXX If a point is contained in two panels simultaneously, it will
# be assigned to the panel defined first. XXX Use a Z-buffer
# instead?
for i, panel in enumerate(panels):
# Determine the pixel size for the panel (in meters), as pixel
# sizes need not be identical.
data = raw_data[i]
pixel_size = (
panel.get_pixel_size()[0] * 1e-3,
panel.get_pixel_size()[1] * 1e-3,
)
if len(panels) == 24 and panels[0].get_image_size() == (2463, 195):
rawdata.matrix_paste_block_in_place(block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# XXX hardcoded panel height and row gap
my_flex_image.add_transformation_and_translation(
(1, 0, 0, 1), (-i * (195 + 17), 0))
continue
elif len(panels) == 120 and panels[0].get_image_size() == (487, 195):
i_row = i // 5
i_col = i % 5
rawdata.matrix_paste_block_in_place(block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# XXX hardcoded panel height and row gap
my_flex_image.add_transformation_and_translation(
(1, 0, 0, 1), (-i_row * (195 + 17), -i_col * (487 + 7)))
continue
# Get unit vectors in the fast and slow directions, as well as the
# the locations of the origin and the center of the panel, in
# meters. The origin is taken w.r.t. to average beam center of all
# panels. This avoids excessive translations that can result from
# rotations around the laboratory origin. Related to beam centre above
# and dials#380 not sure this is right for detectors which are not
# coplanar since system derived from first panel...
fast = col(panel.get_fast_axis())
slow = col(panel.get_slow_axis())
origin = col(panel.get_origin()) * 1e-3 - beam_center
center = (origin + (data.focus()[0] - 1) / 2 * pixel_size[1] * slow +
(data.focus()[1] - 1) / 2 * pixel_size[0] * fast)
normal = slow.cross(fast).normalize()
# Determine rotational and translational components of the
# homogeneous transformation that maps the readout indices to the
# three-dimensional laboratory frame.
Rf = sqr((
fast(0, 0),
fast(1, 0),
fast(2, 0),
-slow(0, 0),
-slow(1, 0),
-slow(2, 0),
normal(0, 0),
normal(1, 0),
normal(2, 0),
))
tf = -Rf * center
Tf = sqr((
Rf(0, 0),
Rf(0, 1),
Rf(0, 2),
tf(0, 0),
Rf(1, 0),
Rf(1, 1),
Rf(1, 2),
tf(1, 0),
Rf(2, 0),
Rf(2, 1),
Rf(2, 2),
tf(2, 0),
0,
0,
0,
1,
))
# E maps picture coordinates onto metric Cartesian coordinates,
# i.e. [row, column, 1 ] -> [x, y, z, 1]. Both frames share the
# same origin, but the first coordinate of the screen coordinate
# system increases downwards, while the second increases towards
# the right. XXX Is this orthographic projection the only one
# that makes any sense?
E = rec(
elems=[
0, +pixel_size[1], 0, -pixel_size[0], 0, 0, 0, 0, 0, 0, 0, 1
],
n=[4, 3],
)
# P: [x, y, z, 1] -> [row, column, 1]. Note that data.focus()
# needs to be flipped to give (horizontal, vertical) size,
# i.e. (width, height).
Pf = get_projection_matrix(pixel_size,
(data.focus()[1], data.focus()[0]))[0]
rawdata.matrix_paste_block_in_place(block=data.as_double(),
i_row=i * data_padded[0],
i_column=0)
# Last row of T is always [0, 0, 0, 1].
T = Pf * Tf * E
R = sqr((T(0, 0), T(0, 1), T(1, 0), T(1, 1)))
t = col((T(0, 2), T(1, 2)))
my_flex_image.add_transformation_and_translation(R, t)
my_flex_image.followup_brightness_scale()
return my_flex_image
def __init__(self, ub_beg, ub_end, axis, s0, dmin, margin=3):
# the source vector and wavelength
self._source = -s0
self._wavelength = 1 / sqrt(s0.dot(s0))
self._wavelength_sq = self._wavelength**2
# the rotation axis
self._axis = axis
# the resolution limit
self._dstarmax = 1 / dmin
self._dstarmax2 = self._dstarmax**2
# Margin by which to expand limits. Mosflm uses 3.
self._margin = int(margin)
# Determine the permutation order of columns of the setting matrix. Use
# the setting from the beginning for this.
# As a side-effect set self._permutation.
col1, col2, col3 = self._permute_axes(ub_beg)
# Thus set the reciprocal lattice axis vectors, in permuted order
# p, q and r for both orientations
rl_vec = [
ub_beg.extract_block(start=(0, 0), stop=(3, 1)),
ub_beg.extract_block(start=(0, 1), stop=(3, 2)),
ub_beg.extract_block(start=(0, 2), stop=(3, 3))
]
self._rlv_beg = [rl_vec[col1], rl_vec[col2], rl_vec[col3]]
rl_vec = [
ub_end.extract_block(start=(0, 0), stop=(3, 1)),
ub_end.extract_block(start=(0, 1), stop=(3, 2)),
ub_end.extract_block(start=(0, 2), stop=(3, 3))
]
self._rlv_end = [rl_vec[col1], rl_vec[col2], rl_vec[col3]]
# Set permuted setting matrices
self._p_beg = matrix.sqr(self._rlv_beg[0].elems +
self._rlv_beg[1].elems +
self._rlv_beg[2].elems).transpose()
self._p_end = matrix.sqr(self._rlv_end[0].elems +
self._rlv_end[1].elems +
self._rlv_end[2].elems).transpose()
## Define a new coordinate system concentric with the Ewald sphere.
##
## X' = X - source_x
## Y' = Y - source_y
## Z' = Z - source_z
##
## X = P' h'
## - = -
## / p11 p12 p13 -source_X \
## where h' = (p, q, r, 1)^T and P' = | p21 p22 p23 -source_y |
## - = \ p31 p32 p33 -source_z /
##
# Calculate P' matrices for the beginning and end settings
pp_beg = matrix.rec(
self._p_beg.elems[0:3] + (-1. * self._source[0], ) +
self._p_beg.elems[3:6] + (-1. * self._source[1], ) +
self._p_beg.elems[6:9] + (-1. * self._source[2], ),
n=(3, 4))
pp_end = matrix.rec(
self._p_end.elems[0:3] + (-1. * self._source[0], ) +
self._p_end.elems[3:6] + (-1. * self._source[1], ) +
self._p_end.elems[6:9] + (-1. * self._source[2], ),
n=(3, 4))
# Various quantities of interest are obtained from the reciprocal metric
# tensor T of P'. These quantities are to be used (later) for solving
# the intersection of a line of constant p, q index with the Ewald
# sphere. It is efficient to calculate these before the outer loop. So,
# calculate T for both beginning and end settings
t_beg = (pp_beg.transpose() * pp_beg).as_list_of_lists()
t_end = (pp_end.transpose() * pp_end).as_list_of_lists()
# quantities that are constant with p, beginning orientation
self._cp_beg = [
t_beg[2][2], t_beg[2][3]**2,
t_beg[0][2] * t_beg[2][3] - t_beg[0][3] * t_beg[2][2],
t_beg[0][2]**2 - t_beg[0][0] * t_beg[2][2],
t_beg[1][2] * t_beg[2][3] - t_beg[1][3] * t_beg[2][2],
t_beg[0][2] * t_beg[1][2] - t_beg[0][1] * t_beg[2][2],
t_beg[1][2]**2 - t_beg[1][1] * t_beg[2][2], 2.0 * t_beg[0][2],
2.0 * t_beg[1][2], t_beg[0][0], t_beg[1][1], 2.0 * t_beg[0][1],
2.0 * t_beg[2][3], 2.0 * t_beg[1][3], 2.0 * t_beg[0][3]
]
# quantities that are constant with p, end orientation
self._cp_end = [
t_end[2][2], t_end[2][3]**2,
t_end[0][2] * t_end[2][3] - t_end[0][3] * t_end[2][2],
t_end[0][2]**2 - t_end[0][0] * t_end[2][2],
t_end[1][2] * t_end[2][3] - t_end[1][3] * t_end[2][2],
t_end[0][2] * t_end[1][2] - t_end[0][1] * t_end[2][2],
t_end[1][2]**2 - t_end[1][1] * t_end[2][2], 2.0 * t_end[0][2],
2.0 * t_end[1][2], t_end[0][0], t_end[1][1], 2.0 * t_end[0][1],
2.0 * t_end[2][3], 2.0 * t_end[1][3], 2.0 * t_end[0][3]
]
## The following are set during the generation of indices
# planes of constant p tangential to the Ewald sphere
self._ewald_p_lim_beg = None
self._ewald_p_lim_end = None
# planes of constant p touching the circle of intersection between the
# Ewald and resolution limiting spheres
self._res_p_lim_beg = None
self._res_p_lim_end = None
# looping p limits
self._p_lim = None
return
def _calc_cell_parameter_sd(self):
# self._cov_B is the covariance matrix of elements of the B matrix. We
# need to construct the covariance matrix of elements of the
# transpose of B. The vector of elements of B is related to the
# vector of elements of its transpose by a permutation, P.
P = matrix.sqr((
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
))
# We can use P to replace var_cov with the covariance matrix of
# elements of the transpose of B.
var_cov = P * self._cov_B * P
# From B = (O^-1)^T we can convert this
# to the covariance matrix of the real space orthogonalisation matrix
Bt = self._B.transpose()
O = Bt.inverse() # noqa: E741, is name of the matrix
cov_O = matrix_inverse_error_propagation(Bt, var_cov)
# The real space unit cell vectors are given by
vec_a = O * matrix.col((1, 0, 0))
vec_b = O * matrix.col((0, 1, 0))
vec_c = O * matrix.col((0, 0, 1))
# So the unit cell parameters are
a, b, c = vec_a.length(), vec_b.length(), vec_c.length()
# alpha = acos(vec_b.dot(vec_c) / (b * c))
# beta = acos(vec_a.dot(vec_c) / (a * c))
# gamma = acos(vec_a.dot(vec_b) / (a * b))
# The estimated errors are calculated by error propagation from cov_O. In
# each case we define a function F(O) that converts the matrix O into the
# unit cell parameter of interest. To do error propagation to get the
# variance of that cell parameter we need the Jacobian of the function.
# This is a 1*9 matrix of derivatives in the order of the elements of O
#
# / dF dF dF dF dF dF dF dF dF \
# J = | ---, ---, ---, ---, ---, ---, ---, ---, --- |
# \ da1 db1 dc1 da2 db2 dc2 da3 db3 dc3 /
#
# For cell length |a|, F = sqrt(a1^2 + a2^2 + a3^2)
jacobian = matrix.rec(
(vec_a[0] / a, 0, 0, vec_a[1] / a, 0, 0, vec_a[2] / a, 0, 0),
(1, 9))
var_a = (jacobian * cov_O * jacobian.transpose())[0]
# For cell length |b|, F = sqrt(b1^2 + b2^2 + b3^2)
jacobian = matrix.rec(
(0, vec_b[0] / b, 0, 0, vec_b[1] / b, 0, 0, vec_b[2] / b, 0),
(1, 9))
var_b = (jacobian * cov_O * jacobian.transpose())[0]
# For cell length |c|, F = sqrt(c1^2 + c2^2 + c3^2)
jacobian = matrix.rec(
(0, 0, vec_c[0] / c, 0, 0, vec_c[1] / c, 0, 0, vec_c[2] / c),
(1, 9))
var_c = (jacobian * cov_O * jacobian.transpose())[0]
# For cell volume (a X b).c,
# F = c1(a2*b3 - b2*a3) + c2(a3*b1 - b3*a1) + c3(a1*b2 - b1*a2)
a1, a2, a3 = vec_a
b1, b2, b3 = vec_b
c1, c2, c3 = vec_c
jacobian = matrix.rec(
(
c3 * b2 - c2 * b3,
c1 * b3 - c3 * b1,
c2 * b1 - c1 * b2,
c2 * a3 - c3 * a2,
c3 * a1 - c1 * a3,
c1 * a2 - c2 * a1,
a2 * b3 - b2 * a3,
a3 * b1 - b3 * a1,
a1 * b2 - b1 * a2,
),
(1, 9),
)
var_V = (jacobian * cov_O * jacobian.transpose())[0]
self._cell_volume_sd = sqrt(var_V)
# For the unit cell angles we need to calculate derivatives of the angles
# with respect to the elements of O
dalpha_db, dalpha_dc = angle_derivative_wrt_vectors(vec_b, vec_c)
dbeta_da, dbeta_dc = angle_derivative_wrt_vectors(vec_a, vec_c)
dgamma_da, dgamma_db = angle_derivative_wrt_vectors(vec_a, vec_b)
# For angle alpha, F = acos( b.c / |b||c|)
jacobian = matrix.rec(
(
0,
dalpha_db[0],
dalpha_dc[0],
0,
dalpha_db[1],
dalpha_dc[1],
0,
dalpha_db[2],
dalpha_dc[2],
),
(1, 9),
)
var_alpha = (jacobian * cov_O * jacobian.transpose())[0]
# For angle beta, F = acos( a.c / |a||c|)
jacobian = matrix.rec(
(
dbeta_da[0],
0,
dbeta_dc[0],
dbeta_da[1],
0,
dbeta_dc[1],
dbeta_da[2],
0,
dbeta_dc[2],
),
(1, 9),
)
var_beta = (jacobian * cov_O * jacobian.transpose())[0]
# For angle gamma, F = acos( a.b / |a||b|)
jacobian = matrix.rec(
(
dgamma_da[0],
dgamma_db[0],
0,
dgamma_da[1],
dgamma_db[1],
0,
dgamma_da[2],
dgamma_db[2],
0,
),
(1, 9),
)
var_gamma = (jacobian * cov_O * jacobian.transpose())[0]
# Symmetry constraints may mean variances of the angles should be zero.
# Floating point error could lead to negative variances. Ensure these are
# caught before taking their square root!
var_alpha = max(0, var_alpha)
var_beta = max(0, var_beta)
var_gamma = max(0, var_gamma)
rad2deg = 180.0 / pi
self._cell_sd = (
sqrt(var_a),
sqrt(var_b),
sqrt(var_c),
sqrt(var_alpha) * rad2deg,
sqrt(var_beta) * rad2deg,
sqrt(var_gamma) * rad2deg,
)