def d2_sites(self):
hkl_outer = self.hkl.outer_product()
for js,site in enumerate(self.sites):
d2_site = flex.complex_double(flex.grid(3,3), 0)
for op in self.ops:
op_site = op * site
hkl_op_site = self.hkl.dot(op_site)
d2_op_site = cmath.exp(1j*self.hkl.dot(op_site)) * (-1) * hkl_outer
d2_site += flex.complex_double(op.transpose() * d2_op_site * op)
yield d2_site
def d2_sites(self):
hkl_outer = self.hkl.outer_product()
for js,site in enumerate(self.sites):
d2_site = flex.complex_double(flex.grid(3,3), 0)
for op in self.ops:
op_site = op * site
hkl_op_site = self.hkl.dot(op_site)
d2_op_site = cmath.exp(1j*self.hkl.dot(op_site)) * (-1) * hkl_outer
d2_site += flex.complex_double(op.transpose() * d2_op_site * op)
yield d2_site
def tst():
nmax = 20
max_indx = math.nlm_array(nmax).nlm().size()
a = flex.complex_double(flex.random_double(max_indx),
flex.random_double(max_indx))
b = flex.complex_double(flex.random_double(max_indx),
flex.random_double(max_indx))
c_list = [a]
good_n = good2n(nmax, c_list, b, threshold=0.8)
print good_n
def d_sites(self):
result = []
for site in self.sites:
d_site = flex.complex_double(3, 0)
for op in self.ops:
op_site = op * site
hkl_op_site = self.hkl.dot(op_site)
d_op_site = cmath.exp(1j*self.hkl.dot(op_site)) * 1j * self.hkl
gtmx = op.transpose()
d_site += flex.complex_double(gtmx * d_op_site.transpose())
result.append(d_site)
return result
def d_sites(self):
result = []
for site in self.sites:
d_site = flex.complex_double(3, 0)
for op in self.ops:
op_site = op * site
hkl_op_site = self.hkl.dot(op_site)
d_op_site = cmath.exp(1j*self.hkl.dot(op_site)) * 1j * self.hkl
gtmx = op.transpose()
d_site += flex.complex_double(gtmx * d_op_site.transpose())
result.append(d_site)
return result
def test_real_to_complex(verbose):
fft = fftpack.real_to_complex(6)
vd = flex.double(fft.m_real())
vc = flex.complex_double(fft.n_complex())
for i in xrange(fft.n_real()):
vd[i] = 1.*i
for i in xrange(fft.n_complex()):
vc[i] = complex(vd[2*i], vd[2*i+1])
vdt = fft.forward(vd)
vct = fft.forward(vc)
for t in (vdt, vct):
assert t.origin() == (0,)
assert t.all()[0] == fft.n_complex()
assert t.focus()[0] == fft.n_complex()
if (verbose): show_rseq(vd, fft.m_real())
assert_complex_eq_real(vc, vd)
vdt = fft.backward(vd)
vct = fft.backward(vc)
for t in (vdt, vct):
assert t.origin() == (0,)
assert t.all()[0] == fft.m_real()
assert t.focus()[0] == fft.n_real()
if (verbose): show_rseq(vd, fft.n_real())
assert_complex_eq_real(vc, vd)
""" The backward fft computes
y_k = sum_{n=0}^15 x_n e^{i 2pi n/16 k}
= sum_{n=0}^7 2 Re( x_n e^{i 2pi n/16 k} ) + x_8 cos{i k pi}
because of the assumed Hermitian condition x_{16-i} = x_i^* (=> x_8 real).
Only x_0, ..., x_8 need to be stored.
"""
fft = fftpack.real_to_complex(16)
assert fft.n_complex() == 9
x = flex.complex_double(fft.n_complex(), 0)
x[4] = 1 + 1.j
y = fft.backward(x)
for i in xrange(0, fft.n_real(), 4):
assert tuple(y[i:i+4]) == (2, -2, -2, 2)
x = flex.complex_double(fft.n_complex(), 0)
x[2] = 1 + 1.j
y = fft.backward(x)
for i in xrange(0, fft.n_real(), 8):
assert tuple(y[i:i+3]) == (2, 0, -2)
assert approx_equal(y[i+3], -2*math.sqrt(2))
assert tuple(y[i+4:i+7]) == (-2, 0, 2)
assert approx_equal(y[i+7], 2*math.sqrt(2))
x = flex.complex_double(fft.n_complex(), 0)
x[8] = 1.
y = fft.backward(x)
for i in xrange(0, fft.n_real(), 2):
assert tuple(y[i:i+2]) == (1, -1)
def test_real_to_complex(verbose):
fft = fftpack.real_to_complex(6)
vd = flex.double(fft.m_real())
vc = flex.complex_double(fft.n_complex())
for i in range(fft.n_real()):
vd[i] = 1. * i
for i in range(fft.n_complex()):
vc[i] = complex(vd[2 * i], vd[2 * i + 1])
vdt = fft.forward(vd)
vct = fft.forward(vc)
for t in (vdt, vct):
assert t.origin() == (0, )
assert t.all()[0] == fft.n_complex()
assert t.focus()[0] == fft.n_complex()
if (verbose): show_rseq(vd, fft.m_real())
assert_complex_eq_real(vc, vd)
vdt = fft.backward(vd)
vct = fft.backward(vc)
for t in (vdt, vct):
assert t.origin() == (0, )
assert t.all()[0] == fft.m_real()
assert t.focus()[0] == fft.n_real()
if (verbose): show_rseq(vd, fft.n_real())
assert_complex_eq_real(vc, vd)
""" The backward fft computes
y_k = sum_{n=0}^15 x_n e^{i 2pi n/16 k}
= sum_{n=0}^7 2 Re( x_n e^{i 2pi n/16 k} ) + x_8 cos{i k pi}
because of the assumed Hermitian condition x_{16-i} = x_i^* (=> x_8 real).
Only x_0, ..., x_8 need to be stored.
"""
fft = fftpack.real_to_complex(16)
assert fft.n_complex() == 9
x = flex.complex_double(fft.n_complex(), 0)
x[4] = 1 + 1.j
y = fft.backward(x)
for i in range(0, fft.n_real(), 4):
assert tuple(y[i:i + 4]) == (2, -2, -2, 2)
x = flex.complex_double(fft.n_complex(), 0)
x[2] = 1 + 1.j
y = fft.backward(x)
for i in range(0, fft.n_real(), 8):
assert tuple(y[i:i + 3]) == (2, 0, -2)
assert approx_equal(y[i + 3], -2 * math.sqrt(2))
assert tuple(y[i + 4:i + 7]) == (-2, 0, 2)
assert approx_equal(y[i + 7], 2 * math.sqrt(2))
x = flex.complex_double(fft.n_complex(), 0)
x[8] = 1.
y = fft.backward(x)
for i in range(0, fft.n_real(), 2):
assert tuple(y[i:i + 2]) == (1, -1)
def test_complex_to_complex_2d(verbose):
fft = fftpack.complex_to_complex_2d((6, 10))
n = fft.n()
vc = flex.complex_double(flex.grid(n))
vd = flex.double(flex.grid((n[0], 2 * n[1])))
for i in range(vc.size()):
vc[i] = complex(2 * i, 2 * i + 1)
for i in range(vd.size()):
vd[i] = i
vct = fft.forward(vc)
vdt = fft.forward(vd)
for t in (vct, vdt):
assert t.origin() == (0, 0)
assert t.all() == fft.n()
assert t.focus() == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
vct = fft.backward(vc)
vdt = fft.backward(vd)
for t in (vct, vdt):
assert t.origin() == (0, 0)
assert t.all() == fft.n()
assert t.focus() == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
s = vd.size() // 2
for i in range(vd.size()):
assert approx_equal(vd[i], s * i)
def test_complex_to_complex_3d(verbose):
fft = fftpack.complex_to_complex_3d((3,4,5))
n = fft.n()
vc = flex.complex_double(flex.grid(n))
vd = flex.double(flex.grid((n[0], n[1], 2 * n[2])))
for i in xrange(vc.size()):
vc[i] = complex(2*i, 2*i+1)
for i in xrange(vd.size()):
vd[i] = i
vct = fft.forward(vc)
vdt = fft.forward(vd)
for t in (vct, vdt):
assert t.origin() == (0,0,0)
assert t.all() == fft.n()
assert t.focus() == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
vct = fft.backward(vc)
vdt = fft.backward(vd)
for t in (vct, vdt):
assert t.origin() == (0,0,0)
assert t.all() == fft.n()
assert t.focus() == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
def check_f_calc_derivs():
eps = 1e-6
g_fin = flex.complex_double()
c_fin = flex.vec3_double()
for ih in xrange(f_calc.size()):
c_orig = f_calc[ih]
g_fin_ab = []
c_fin_ab = []
for iab in [0,1]:
fs = []
gs = []
for signed_eps in [eps, -eps]:
if (iab == 0):
f_calc[ih] = complex(c_orig.real + signed_eps, c_orig.imag)
else:
f_calc[ih] = complex(c_orig.real, c_orig.imag + signed_eps)
trg_eps = r1.target(f_obs=f_obs, f_calc=f_calc)
fs.append(trg_eps.t)
gs.append(trg_eps.f_calc_gradients[ih])
g_fin_ab.append((fs[0]-fs[1])/(2*eps))
c_fin_ab.append((gs[0]-gs[1])/(2*eps))
g_fin.append(complex(*g_fin_ab))
assert approx_equal(c_fin_ab[0].imag, c_fin_ab[1].real)
c_fin.append((c_fin_ab[0].real, c_fin_ab[1].imag, c_fin_ab[0].imag))
f_calc[ih] = c_orig
for pn,f,a in zip(
g_fin.part_names(), g_fin.parts(), trg.f_calc_gradients.parts()):
print >> log, "g fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_gradients, g_fin)
for pn,f,a in zip(
["aa", "bb", "ab"], c_fin.parts(), trg.f_calc_hessians.parts()):
print >> log, "c fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_hessians, c_fin)
def check_f_calc_derivs():
eps = 1e-6
g_fin = flex.complex_double()
c_fin = flex.vec3_double()
for ih in xrange(f_calc.size()):
c_orig = f_calc[ih]
g_fin_ab = []
c_fin_ab = []
for iab in [0, 1]:
fs = []
gs = []
for signed_eps in [eps, -eps]:
if iab == 0:
f_calc[ih] = complex(c_orig.real + signed_eps, c_orig.imag)
else:
f_calc[ih] = complex(c_orig.real, c_orig.imag + signed_eps)
trg_eps = r1.target(f_obs=f_obs, f_calc=f_calc)
fs.append(trg_eps.t)
gs.append(trg_eps.f_calc_gradients[ih])
g_fin_ab.append((fs[0] - fs[1]) / (2 * eps))
c_fin_ab.append((gs[0] - gs[1]) / (2 * eps))
g_fin.append(complex(*g_fin_ab))
assert approx_equal(c_fin_ab[0].imag, c_fin_ab[1].real)
c_fin.append((c_fin_ab[0].real, c_fin_ab[1].imag, c_fin_ab[0].imag))
f_calc[ih] = c_orig
for pn, f, a in zip(g_fin.part_names(), g_fin.parts(), trg.f_calc_gradients.parts()):
print >> log, "g fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_gradients, g_fin)
for pn, f, a in zip(["aa", "bb", "ab"], c_fin.parts(), trg.f_calc_hessians.parts()):
print >> log, "c fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_hessians, c_fin)
def get_3D_transform():
#with mrcfile.open("cropout_bin4.mrc") as mrc: # small example
with mrcfile.open("cropout.mrc") as mrc:
imax = 512 #take small subset, optimized for prime factorization
# coerce to double
from scitbx.array_family import flex
realpart = flex.double(mrc.data.astype(np.float64))
# in-place resize to a good multiple of 2
realpart.resize(flex.grid(imax, imax, imax))
complpart = flex.double(flex.grid(imax, imax, imax))
#from IPython import embed; embed()
C3D = flex.complex_double(realpart, complpart)
from matplotlib import pyplot as plt
from scitbx import fftpack
#plt.imshow(S2D)
#plt.show()
#from IPython import embed; embed()
print "C3Dfocus", C3D.focus()
print C3D
FFT = fftpack.complex_to_complex_3d(
(C3D.focus()[0], C3D.focus()[1], C3D.focus()[2]))
c = FFT.forward(C3D)
print c.focus()
print c
return c
def test_real_to_complex_3d(verbose):
for nx in [3,4]:
for ny in [4,5]:
for nz in [7,8]:
fft = fftpack.real_to_complex_3d((nx,ny,nz))
m = fft.m_real()
vd = flex.double(flex.grid(m))
vc = flex.complex_double(flex.grid((m[0], m[1], m[2]//2)))
assert vd.size() == 2 * vc.size()
for i in xrange(vd.size()):
vd[i] = random.random()*2-1
vd_orig = vd.deep_copy()
for i in xrange(vc.size()):
vc[i] = complex(vd[2*i], vd[2*i+1])
vdt = fft.forward(vd)
vct = fft.forward(vc)
for t in (vdt, vct):
assert t.origin() == (0,0,0)
assert t.all() == fft.n_complex()
assert t.focus() == fft.n_complex()
if (verbose): show_rseq_3d(vd, fft.m_real(), fft.m_real())
assert_complex_eq_real(vc, vd)
vdt = fft.backward(vd)
vct = fft.backward(vc)
for t in (vdt, vct):
assert t.origin() == (0,0,0)
assert t.all() == fft.m_real()
assert t.focus() == fft.n_real()
if (verbose): show_rseq_3d(vd, fft.m_real(), fft.n_real())
assert_complex_eq_real(vc, vd)
f = nx*ny*nz
for ix in xrange(nx):
for iy in xrange(ny):
for iz in xrange(nz):
assert approx_equal(vdt[(ix,iy,iz)], vd_orig[(ix,iy,iz)]*f)
def sum_structure_factors_cpu(self):
self.structure_factors = flex.complex_double(len(self.cached_h),
complex(0.0, 0.0))
# sum structure factors
for i_structure in xrange(len(self.structures.species)):
for j_orientation in xrange(
self.structures.species[i_structure].n_copies):
tmp_xyz = self.structures.species[i_structure].xyz.deep_copy()
translation = flex.double(
self.structures.translations[i_structure][j_orientation])
rotation = matrix.sqr(
self.structures.rotations[i_structure][j_orientation])
for i in xrange(len(tmp_xyz)):
xyz = flex.double(rotation * tmp_xyz[i])
tmp_xyz[i] = tuple(xyz + translation)
self.structure_factors += direct_sum_structure_factors\
(self.structures.species[i_structure].
scattering_types,
tmp_xyz,
self.structures.species[i_structure].
boundary_layer_scaling_factors,
self.cached_h,
self.structures.species[i_structure].
scattering_type_registry)
def tst_rotation_fft(args):
filename = args[0]
filename2 = args[1]
beta = float(args[2])
nmax = 20
nlm_array = math.nlm_array(nmax)
coefs = easy_pickle.load(filename)
nlm_array.load_coefs(nlm_array.nlm(), coefs)
this_nlm_array = math.nlm_array(nmax)
coefs = easy_pickle.load(filename2)
this_nlm_array.load_coefs(nlm_array.nlm(), coefs)
beta = smath.pi * beta
cc_obj = correlation(nlm_array, this_nlm_array, nmax, beta)
mm = cc_obj.mm_coef(0)
fft_input = flex.complex_double(flex.grid(2 * nmax + 1, 2 * nmax + 1))
fft_r = tst_rotation(args)
for ii in range(mm.size()):
fft_input[ii] = mm[ii]
# print ii, mm[ii], fft_r[ii]/1681.0
fft = fftpack.complex_to_complex_2d(2 * nmax + 1, 2 * nmax + 1)
result = fft.backward(fft_input)
out = open("fft_" + str(beta) + ".dat", 'w')
for ii in range(2 * nmax + 1):
for jj in range(2 * nmax + 1):
print >> out, ii * 9, jj * 9, abs(result[(ii, jj)])
print >> out
out.close()
def exercise_value(f_c_in_p1, f_o, flags, n_sampled):
""" where we check against the trusted correlation map implemented
in cctbx.translation_search """
crystal_gridding = f_o.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_o.space_group(),
anomalous_flag=f_o.anomalous_flag(),
miller_indices_f_obs=f_o.indices(),
f_obs=f_o.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_c_in_p1.indices(),
p1_f_calc=f_c_in_p1.data()).target_map()
nx, ny, nz = n = crystal_gridding.n_real()
def sampled_indices():
from random import randrange
yield (0, 0, 0)
for i in xrange(n_sampled - 1):
yield randrange(0, n[0]), randrange(0, n[1]), randrange(0, n[2])
f_o_sq = f_o.as_intensity_array()
for i, j, k in sampled_indices():
x = (i / nx, j / ny, k / nz)
if random.random() > 0.5: f_o_or_f_o_sq = f_o
else: f_o_or_f_o_sq = f_o_sq
gos = symmetrised_shifted_structure_factors(f_o_or_f_o_sq, f_c_in_p1,
x).misfit(f_o_or_f_o_sq)
assert approx_equal(gos.correlation, correlation_map[i, j,
k]), (i, j, k)
def exercise_value(f_c_in_p1, f_o, flags, n_sampled):
""" where we check against the trusted correlation map implemented
in cctbx.translation_search """
crystal_gridding = f_o.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_o.space_group(),
anomalous_flag=f_o.anomalous_flag(),
miller_indices_f_obs=f_o.indices(),
f_obs=f_o.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_c_in_p1.indices(),
p1_f_calc=f_c_in_p1.data()).target_map()
nx, ny, nz = n = crystal_gridding.n_real()
def sampled_indices():
from random import randrange
yield (0,0,0)
for i in xrange(n_sampled - 1):
yield randrange(0, n[0]), randrange(0, n[1]), randrange(0, n[2])
f_o_sq = f_o.as_intensity_array()
for i,j,k in sampled_indices():
x = (i/nx, j/ny, k/nz)
if random.random() > 0.5: f_o_or_f_o_sq = f_o
else: f_o_or_f_o_sq = f_o_sq
gos = symmetrised_shifted_structure_factors(
f_o_or_f_o_sq, f_c_in_p1, x).misfit(f_o_or_f_o_sq)
assert approx_equal(gos.correlation, correlation_map[i,j,k]), (i,j,k)
def _fft(self, reciprocal_lattice_vectors, d_min):
reciprocal_space_grid, used_in_indexing = self._map_centroids_to_reciprocal_space_grid(
reciprocal_lattice_vectors, d_min)
logger.info("Number of centroids used: %i" %
((reciprocal_space_grid > 0).count(True)))
# gb_to_bytes = 1073741824
# bytes_to_gb = 1/gb_to_bytes
# (128**3)*8*2*bytes_to_gb
# 0.03125
# (256**3)*8*2*bytes_to_gb
# 0.25
# (512**3)*8*2*bytes_to_gb
# 2.0
fft = fftpack.complex_to_complex_3d(self._gridding)
grid_complex = flex.complex_double(
reals=reciprocal_space_grid,
imags=flex.double(reciprocal_space_grid.size(), 0),
)
grid_transformed = fft.forward(grid_complex)
grid_real = flex.pow2(flex.real(grid_transformed))
del grid_transformed
return grid_real, used_in_indexing
def fs(self):
result = flex.complex_double()
for hkl in self.miller_indices:
result.append(
structure_factor(xray_structure=self.xray_structure,
hkl=hkl).f())
return result
def get_static_fcalcs():
C2_structures = get_C2_structures()
energy = 7070.0
GF_whole7070 = gen_fmodel_with_complex.from_structure(C2_structures[0],energy
).from_parameters(algorithm="fft")
GF_whole7070 = GF_whole7070.as_P1_primitive()
f_container7070 = GF_whole7070.get_fmodel()
Fmodel_whole7070 = f_container7070.f_model
Fmodel_indices = Fmodel_whole7070.indices() # common structure defines the indices
F_bulk = f_container7070.fmodel.arrays.core.data.f_bulk
F_bulk.reshape(flex.grid((Fmodel_indices.size(),1))) # in-place reshape, non-standard
result = flex.complex_double(flex.grid((Fmodel_indices.size(),100)))
# common structure to represent the wavelength-dependent non-Fe diffraction (bulk+atoms)
for incr in range(100):
energy = 7070.5 + incr
GF_non_Fe = gen_fmodel_with_complex.from_structure(C2_structures[1],energy
).from_parameters(algorithm="fft")
GF_non_Fe = GF_non_Fe.as_P1_primitive()
f_container = GF_non_Fe.get_fmodel()
Fcalc_non_Fe = f_container.fmodel.f_calc().data()
Fcalc_non_Fe.reshape(flex.grid((Fmodel_indices.size(),1))) # in-place reshape, non-standard
result.matrix_paste_block_in_place((F_bulk + Fcalc_non_Fe),0,incr)
# result holds a table of complex double structure factors. Rows are Miller indices H.
# columns are F_H(energy, 100 channels) for F(bulk) + F(non-Fe atoms). Thus this is
# the energy-dependent portion of the calculation that is not dependent on the iron model.
return result
def tst_Inm_array(nmax):
Inm = math.nl_c_array(nmax)
nls = Inm.nl()
moments = flex.double(range(nls.size()))
moments = flex.complex_double(moments, moments)
Inm.load_coefs(nls, moments)
for ii, nl in zip(range(nls.size()), nls):
assert (Inm.get_coef(nl[0], nl[1]).real == ii)
def __init__(self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type=map_type, isotropize=True, fill_missing=False)
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data=flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(fraction=0.3,
n_real=f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s, e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value=0, map_data_to=f_model_map_data, start=s, end=e)
f_model_omit = f_model.structure_factors_from_map(
map=f_model_map_data_omit,
use_scale=True,
anomalous_flag=False,
use_sg=False)
fmodel_ = mmtbx.f_model.manager(f_obs=fmodel.f_obs(),
r_free_flags=fmodel.r_free_flags(),
f_calc=f_model_omit,
f_mask=zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0] - 1, e[1] - 1,
e[2] - 1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(map_data_from=box,
map_data_to=self.map_result,
start=s,
end=e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result / sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map=self.map_result,
use_scale=True,
anomalous_flag=False,
use_sg=False)
def test_flex_loop_nesting():
fo = flex.int(10)
npo = flumpy.to_numpy(fo)
assert fo is flumpy.from_numpy(npo)
# Now try vec
fo = flex.complex_double(5)
npo = flumpy.to_numpy(fo)
assert flumpy.from_numpy(npo) is fo
def tst_2d_zernike_mom(n, l, filename, h5file, flag):
rebuilt = open(filename, 'w')
# image = generate_image()
# image=ImageToDat("/Users/wyf/Desktop/test11.png")
image = preprocess_image(h5file, flag)
# image = ImageToDat('cha.png')
NP = int(smath.sqrt(image.size()))
N = int(NP / 2)
print "=====", NP, N
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
moments = zernike_2d_mom.moments()
coefs = flex.real(moments)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
nl_array.load_coefs(nls, coefs)
lfg = math.log_factorial_generator(nmax)
# print nl_array.get_coef(n,l)*2
for nl, c in zip(nls, moments):
if (abs(c) < 1e-3):
c = 0
print nl, c
reconst = flex.complex_double(NP**2, 0)
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
if (l > 0):
c = c * 2
#rzfa = math.zernike_2d_radial(n,l,lfg)
rap = math.zernike_2d_polynome(n, l) #,rzfa)
i = 0
for x in range(0, NP):
x = x - N
for y in range(0, NP):
y = y - N
rr = smath.sqrt(x * x + y * y) / N
if rr > 1.0:
value = 0.0
else:
tt = smath.atan2(y, x)
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
i = 0
for x in range(0, NP):
for y in range(0, NP):
value = reconst[i].real
print >> rebuilt, x, y, value
i = i + 1
rebuilt.close()
def d2_target_d_params_diag_cpp(self, f_obs, target_type):
da_db = flex.complex_double()
daa_dbb_dab = flex.vec3_double()
for hkl,obs in zip(self.miller_indices, f_obs.data()):
sf = structure_factor(xray_structure=self.xray_structure, hkl=hkl)
target = target_type(obs=obs, calc=sf.f())
da_db.append(complex(target.da(), target.db()))
daa_dbb_dab.append((target.daa(), target.dbb(), target.dab()))
return self.xray_structure.grads_and_curvs_target_simple(
miller_indices=f_obs.indices(), da_db=da_db, daa_dbb_dab=daa_dbb_dab)
def map_calculate_rings(mp):
# set up parameters
mp.structure_generator.random.setstate(mp.random_state)
es = ewald_sphere()
es.set_wavelength(mp.beam_properties.wavelength)
es.set_distance(mp.detector_properties.distance)
ic = image_composer()
ic.set_detector_size(mp.detector_properties.detector_size)
ic.set_beam_center(mp.detector_properties.beam_center)
ic.set_pixel_size(mp.detector_properties.pixel_size)
ic.set_ewald_sphere(es)
im = image_simulator()
im.structures = mp.structure_generator
im.image_composer = ic
im.cached_h = mp.h
# calculate structure factors
for i in xrange(mp.n_images):
im.structures.randomize()
im.sum_structure_factors()
# copy intensities to full image
sf = im.structure_factors
all_sf = flex.complex_double((mp.detector_properties.detector_size[0]+1)*\
(mp.detector_properties.detector_size[1]+1),\
complex(0.0,0.0))
k = 0
for j in xrange(len(mp.use_index)):
if (mp.use_index[j]):
all_sf[j] = sf[k]
k += 1
im.structure_factors = all_sf
image_data = im.build_image(n_photons=bp.flux*bp.t)
if (True):
for q_i in [0.01, 0.1, 0.2]:
print q_i, I_q(ic.get_q(),image_data,q_i,mp.dq)
write_image(file_name='ring.png',
detector_size=mp.detector_properties.detector_size,
image_data=image_data)
if (False):
file_name = './test_rings/' + str(os.getpid()) + '_' + str(i)
f = open(file_name,'wb')
pickle.dump(image_data,f,2)
f.close()
return mp.n_images
def d2_target_d_params_diag_cpp(self, f_obs, target_type):
da_db = flex.complex_double()
daa_dbb_dab = flex.vec3_double()
for hkl, obs in zip(self.miller_indices, f_obs.data()):
sf = structure_factor(xray_structure=self.xray_structure, hkl=hkl)
target = target_type(obs=obs, calc=sf.f())
da_db.append(complex(target.da(), target.db()))
daa_dbb_dab.append((target.daa(), target.dbb(), target.dab()))
return self.xray_structure.grads_and_curvs_target_simple(
miller_indices=f_obs.indices(),
da_db=da_db,
daa_dbb_dab=daa_dbb_dab)
def build_scat_pat(data):
print "DO FFT"
np,np = data.focus()
flex_grid=flex.grid(np,np)
fft_input=flex.complex_double(flex_grid)
for ii in range( fft_input.size() ):
fft_input[ii] = complex( data[ii],0 )
fft_obj = fftpack.complex_to_complex_2d( (np,np) )
result = fft_obj.forward( fft_input )
result = flex.abs( result )
result = result*result
result = reorder_and_cut_data(result,np,np/10)
return result
def kick_fmodel(
fmodel,
map_type,
crystal_gridding,
number_of_kicks,
macro_cycles,
missing = None,
kick_completeness = 0.95):
f_model = fmodel.f_model_no_scales()
zero = fmodel.f_calc().customized_copy(data =
flex.complex_double(fmodel.f_calc().data().size(), 0))
fmodel_dc = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
k_isotropic = fmodel.k_isotropic(),
k_anisotropic = fmodel.k_anisotropic(),
f_calc = fmodel.f_model_no_scales(),
f_part1 = fmodel.f_part1(),
f_part2 = fmodel.f_part2(),
f_mask = zero)
r1 = fmodel.r_work()
r2 = fmodel_dc.r_work()
assert approx_equal(r1, r2, 1.e-4), [r1, r2]
def get_mc(fm):
return fm.electron_density_map().map_coefficients(
map_type = map_type,
isotropize = True,
fill_missing = False)
def recreate_r_free_flags(fmodel):
rc = random.choice([0.05, 0.9])
r_free_flags = flex.random_bool(fmodel.f_obs().indices().size(), rc)
fmodel._r_free_flags._data = r_free_flags
return fmodel
map_data = None
for it in xrange(macro_cycles):
print " %d"%it
f_model_kick = randomize_struture_factors(map_coeffs=f_model,
number_of_kicks=number_of_kicks)
fmodel_dc = recreate_r_free_flags(fmodel = fmodel_dc)
fmodel_dc.update(f_calc = f_model_kick)
mc = get_mc(fm=fmodel_dc)
if(missing is not None):
mc = mc.complete_with(missing, scale=True)
if(kick_completeness):
mc = mc.select(flex.random_bool(mc.size(), kick_completeness))
map_data = compute_map_and_combine(
map_coeffs = mc,
crystal_gridding = crystal_gridding,
map_data = map_data)
return map_data
def generate_image(n, moments, N=100):
# Generate images from the zernike moments, N is the number of points from 0 to 1
nmax = n
image = flex.vec3_double()
NP = 2 * N + 1
reconst = flex.complex_double(NP**2, 0)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
r_theta = flex.vec2_double()
for x in range(0, NP):
x = x - N
for y in range(0, NP):
y = y - N
rr = smath.sqrt(x * x + y * y) / N
if rr > 1.0:
tt = 0.0
else:
tt = smath.atan2(y, x)
r_theta.append([rr, tt])
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
#if(l/2*2 != l): continue
if (l > 0): c = c * 2.0
rap = math.zernike_2d_polynome(n, l)
i = 0
for pt in r_theta:
rr = pt[0]
if rr > 1.0:
value = 0.0
else:
tt = pt[1]
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
return reconst
i = 0
for x in range(0, NP):
for y in range(0, NP):
value = reconst[i].real
image.append([x, y, value])
i = i + 1
return image
def main(filenames,
map_file,
npoints=192,
max_resolution=6,
reverse_phi=False):
rec_range = 1 / max_resolution
image = ImageFactory(filenames[0])
panel = image.get_detector()[0]
beam = image.get_beam()
s0 = beam.get_s0()
pixel_size = panel.get_pixel_size()
xlim, ylim = image.get_raw_data().all()
xy = recviewer.get_target_pixels(panel, s0, xlim, ylim, max_resolution)
s1 = panel.get_lab_coord(xy * pixel_size[0]) # FIXME: assumed square pixel
s1 = s1 / s1.norms() * (1 / beam.get_wavelength()) # / is not supported...
S = s1 - s0
grid = flex.double(flex.grid(npoints, npoints, npoints), 0)
cnts = flex.int(flex.grid(npoints, npoints, npoints), 0)
for filename in filenames:
print "Processing image", filename
try:
fill_voxels(ImageFactory(filename), grid, cnts, S, xy, reverse_phi,
rec_range)
except:
print " Failed to process. Skipped this."
recviewer.normalize_voxels(grid, cnts)
uc = uctbx.unit_cell((npoints, npoints, npoints, 90, 90, 90))
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"), (0, 0, 0),
grid.all(), grid,
flex.std_string(["cctbx.miller.fft_map"]))
return
from scitbx import fftpack
fft = fftpack.complex_to_complex_3d(grid.all())
grid_complex = flex.complex_double(reals=flex.pow2(grid),
imags=flex.double(grid.size(), 0))
grid_transformed = flex.abs(fft.backward(grid_complex))
print flex.max(grid_transformed), flex.min(
grid_transformed), grid_transformed.all()
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"), (0, 0, 0),
grid.all(), grid_transformed,
flex.std_string(["cctbx.miller.fft_map"]))
def kick_fmodel(fmodel,
map_type,
crystal_gridding,
number_of_kicks,
macro_cycles,
missing=None,
kick_completeness=0.95):
f_model = fmodel.f_model_no_scales()
zero = fmodel.f_calc().customized_copy(
data=flex.complex_double(fmodel.f_calc().data().size(), 0))
fmodel_dc = mmtbx.f_model.manager(f_obs=fmodel.f_obs(),
r_free_flags=fmodel.r_free_flags(),
k_isotropic=fmodel.k_isotropic(),
k_anisotropic=fmodel.k_anisotropic(),
f_calc=fmodel.f_model_no_scales(),
f_part1=fmodel.f_part1(),
f_part2=fmodel.f_part2(),
f_mask=zero)
r1 = fmodel.r_work()
r2 = fmodel_dc.r_work()
assert approx_equal(r1, r2, 1.e-4), [r1, r2]
def get_mc(fm):
return fm.electron_density_map().map_coefficients(map_type=map_type,
isotropize=True,
fill_missing=False)
def recreate_r_free_flags(fmodel):
rc = random.choice([0.05, 0.9])
r_free_flags = flex.random_bool(fmodel.f_obs().indices().size(), rc)
fmodel._r_free_flags._data = r_free_flags
return fmodel
map_data = None
for it in xrange(macro_cycles):
print " %d" % it
f_model_kick = randomize_struture_factors(
map_coeffs=f_model, number_of_kicks=number_of_kicks)
fmodel_dc = recreate_r_free_flags(fmodel=fmodel_dc)
fmodel_dc.update(f_calc=f_model_kick)
mc = get_mc(fm=fmodel_dc)
if (missing is not None):
mc = mc.complete_with(missing, scale=True)
if (kick_completeness):
mc = mc.select(flex.random_bool(mc.size(), kick_completeness))
map_data = compute_map_and_combine(map_coeffs=mc,
crystal_gridding=crystal_gridding,
map_data=map_data)
return map_data
def load_fft(filename):
with mrcfile.open(filename) as mrc:
# coerce to double
realpart = flex.double(mrc.data.astype(np.float64))
complpart = flex.double(flex.grid(realpart.focus()))
C3D = flex.complex_double(realpart, complpart)
print "C3Dfocus", C3D.focus()
print C3D
FFT = fftpack.complex_to_complex_3d(
(C3D.focus()[0], C3D.focus()[1], C3D.focus()[2]))
complex_flex = FFT.forward(C3D)
print complex_flex.focus()
print complex_flex
return complex_flex
def main(filenames, map_file, npoints=192, max_resolution=6, reverse_phi=False):
rec_range = 1 / max_resolution
image = ImageFactory(filenames[0])
panel = image.get_detector()[0]
beam = image.get_beam()
s0 = beam.get_s0()
pixel_size = panel.get_pixel_size()
xlim, ylim = image.get_raw_data().all()
xy = recviewer.get_target_pixels(panel, s0, xlim, ylim, max_resolution)
s1 = panel.get_lab_coord(xy * pixel_size[0]) # FIXME: assumed square pixel
s1 = s1 / s1.norms() * (1 / beam.get_wavelength()) # / is not supported...
S = s1 - s0
grid = flex.double(flex.grid(npoints, npoints, npoints), 0)
cnts = flex.int(flex.grid(npoints, npoints, npoints), 0)
for filename in filenames:
print "Processing image", filename
try:
fill_voxels(ImageFactory(filename), grid, cnts, S, xy, reverse_phi, rec_range)
except:
print " Failed to process. Skipped this."
recviewer.normalize_voxels(grid, cnts)
uc = uctbx.unit_cell((npoints, npoints, npoints, 90, 90, 90))
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), grid.all(), grid,
flex.std_string(["cctbx.miller.fft_map"]))
return
from scitbx import fftpack
fft = fftpack.complex_to_complex_3d(grid.all())
grid_complex = flex.complex_double(
reals=flex.pow2(grid),
imags=flex.double(grid.size(), 0))
grid_transformed = flex.abs(fft.backward(grid_complex))
print flex.max(grid_transformed), flex.min(grid_transformed), grid_transformed.all()
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), grid.all(), grid_transformed,
flex.std_string(["cctbx.miller.fft_map"]))
def tst_rotation(args):
filename = args[0]
filename2 = args[1]
beta = float(args[2])
ngrid = 40
nmax = 20
nlm_array = math.nlm_array(nmax)
coefs = easy_pickle.load(filename)
nlm_array.load_coefs(nlm_array.nlm(), coefs)
this_nlm_array = math.nlm_array(nmax)
coefs = easy_pickle.load(filename2)
this_nlm_array.load_coefs(nlm_array.nlm(), coefs)
beta = smath.pi * beta
cc_obj = correlation(nlm_array, this_nlm_array, nmax, beta)
fft_input = flex.complex_double(flex.grid(2 * nmax + 1, 2 * nmax + 1))
count = 0
radian = 180.0 / smath.pi
out = open("scan_" + str(beta) + ".dat", 'w')
for ii in range(ngrid + 1):
for jj in range(ngrid + 1):
alpha = ii * smath.pi * 2.0 / ngrid
gama = jj * smath.pi * 2.0 / ngrid
cc = cc_obj.calc_correlation(alpha, beta, gama)
fft_input[count] = cc
count = count + 1
print >> out, alpha * radian, gama * radian, abs(cc)
print >> out
out.close()
fft = fftpack.complex_to_complex_2d(2 * nmax + 1, 2 * nmax + 1)
result = fft.forward(fft_input)
#return result
result = fft.backward(result)
out = open("fft_fake_" + str(beta) + ".dat", 'w')
for ii in range(2 * nmax + 1):
for jj in range(2 * nmax + 1):
print >> out, ii * 9, jj * 9, abs(result[(jj, ii)])
print >> out
out.close()
def map_random_image(p=None):
result = [None for i in xrange(p.n_images)]
# set random state for current thread
p.structure_generator.random.setstate(p.random_state)
es = ewald_sphere()
es.set_wavelength(p.beam_properties.wavelength)
es.set_distance(p.detector_properties.distance)
ic = image_composer()
ic.set_detector_size(p.detector_properties.detector_size)
ic.set_beam_center(p.detector_properties.beam_center)
ic.set_pixel_size(p.detector_properties.pixel_size)
ic.set_ewald_sphere(es)
im = image_simulator()
im.structures = p.structure_generator
im.image_composer = ic
h = ic.cache_h()
sf_length = (p.detector_properties.detector_size[0] + 1) *\
(p.detector_properties.detector_size[1] + 1)
n_photons = p.beam_properties.flux * p.beam_properties.t
for i in xrange(p.n_images):
sf = flex.complex_double(sf_length, 0.0)
im.structures.species[0].n_copies = p.n_particles[i]
im.structures.randomize()
for j in xrange(p.n_particles[i]):
image_name = p.base_image_directory + im.structures.random.choice(
image_list)
t = im.structures.translations[0][j]
f = open(image_name, 'rb')
sf_tmp = pickle.load(f)
f.close()
sf_tmp = apply_translation(sf_tmp, h, t)
sf += sf_tmp
im.structure_factors = sf
image_data = im.build_image(n_photons=n_photons)
result[i] = image_data.deep_copy()
return result
def generate_image2(n, moments, template_image, np):
nmax = n
image = flex.vec3_double()
np_tot = template_image.size()
reconst = flex.complex_double(np_tot, 0)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
r_theta = flex.vec2_double()
for pt in template_image:
x = pt[0] - np
y = pt[1] - np
rr = smath.sqrt(x * x + y * y) / np
if rr > 1.0:
tt = 0.0
else:
tt = smath.atan2(y, x)
r_theta.append([rr, tt])
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
#if(l/2*2 != l): continue
if (l > 0): c = c * 2.0
rap = math.zernike_2d_polynome(n, l)
i = 0
for pt in r_theta:
rr = pt[0]
if rr > 1.0:
value = 0.0
else:
tt = pt[1]
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
for i in range(np_tot):
x = template_image[i][0]
y = template_image[i][1]
value = reconst[i].real
image.append([x, y, value])
return image
def tst_nlm(): nlm_array = math.nlm_array(10) nlm_array.set_coef(10,2,2, 3.0) a = nlm_array.get_coef(10,2,2) assert ( abs(a-3.0) ) <= 1e-5 nlm_ind = shared.tiny_int_3( [(10,2,2),(8,2,2)] ) nlm_coef = flex.complex_double( [15.0+0j,15.0+0j] ) assert nlm_array.load_coefs( nlm_ind , nlm_coef) a = nlm_array.get_coef(10, 2, 2) b = nlm_array.get_coef(8, 2, 2) assert ( abs(a-15.0) ) <= 1e-5 assert ( abs(b-15.0) ) <= 1e-5 nlm = nlm_array.nlm() cnlm = nlm_array.coefs() sel = nlm_array.select_on_nl(2,2) assert len(sel)==5 assert 5 in sel assert 6 in sel assert 7 in sel assert 8 in sel assert 9 in sel
def tst_nlm(): nlm_array = math.nlm_array(10) nlm_array.set_coef(10,2,2, 3.0) a = nlm_array.get_coef(10,2,2) assert ( abs(a-3.0) ) <= 1e-5 nlm_ind = shared.tiny_int_3( [(10,2,2),(8,2,2)] ) nlm_coef = flex.complex_double( [15.0+0j,15.0+0j] ) assert nlm_array.load_coefs( nlm_ind , nlm_coef) a = nlm_array.get_coef(10, 2, 2) b = nlm_array.get_coef(8, 2, 2) assert ( abs(a-15.0) ) <= 1e-5 assert ( abs(b-15.0) ) <= 1e-5 nlm = nlm_array.nlm() cnlm = nlm_array.coefs() sel = nlm_array.select_on_nl(2,2) assert len(sel)==5 assert 5 in sel assert 6 in sel assert 7 in sel assert 8 in sel assert 9 in sel
def __init__(self,
fmodel,
crystal_gridding,
box_size_as_fraction=0.1,
max_boxes=2000,
neutral_volume_box_cushion_width=2,
full_resolution_map=True,
log=sys.stdout):
adopt_init_args(self, locals())
self.map_type = "mFo-DFc" # using other map types is much worse
self.sd = self.get_p1_map_unscaled(
fmodel=self.fmodel,
map_type=self.map_type).sample_standard_deviation()
xrs_p1 = fmodel.xray_structure.expand_to_p1(sites_mod_positive=True)
self.sgt = fmodel.f_obs().space_group().type()
self.r = flex.double() # for tests only
self.acc_asu = None
# bulk-solvent
mp = mmtbx.masks.mask_master_params.extract()
mp.n_real = crystal_gridding.n_real()
mp.step = None
mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask(xray_structure=xrs_p1,
mask_params=mp)
self.bulk_solvent_mask = mmtbx_masks_asu_mask_obj.mask_data_whole_uc()
self.bulk_solvent_mask_asu = self.to_asu_map(
map_data=self.bulk_solvent_mask)
# atom map
self.atom_map = mmtbx.real_space.sampled_model_density(
xray_structure=xrs_p1, n_real=crystal_gridding.n_real()).data()
self.n_real = self.atom_map.focus()
self.atom_map_asu = self.to_asu_map(map_data=self.atom_map)
# extras
self.zero_cmpl_ma = fmodel.f_calc().customized_copy(
data=flex.complex_double(fmodel.f_calc().size(), 0))
self.r_factor_omit = flex.double() # for regression test only
# result map
self.map_result_asu = flex.double(flex.grid(self.atom_map_asu.focus()))
# iterate over boxes
self.box_iterator()
def load_fft(filename, Tukey):
print "Opening file"
with mrcfile.open(filename) as mrc:
print "Converting to flex"
# coerce to double
if Tukey is True:
mod_vol = apply_tukey_3d(mrc.data.astype(np.float64))
realpart = flex.double(mod_vol)
else:
realpart = flex.double(mrc.data.astype(np.float64))
complpart = flex.double(flex.grid(realpart.focus()))
C3D = flex.complex_double(realpart, complpart)
print "C3Dfocus", C3D.focus()
print C3D
FFT = fftpack.complex_to_complex_3d(
(C3D.focus()[0], C3D.focus()[1], C3D.focus()[2]))
complex_flex = FFT.forward(C3D)
print complex_flex.focus()
print complex_flex
return complex_flex
def __init__(
self,
fmodel,
crystal_gridding,
box_size_as_fraction=0.1,
max_boxes=2000,
neutral_volume_box_cushion_width=2,
full_resolution_map=True,
log=sys.stdout):
adopt_init_args(self, locals())
self.map_type="mFo-DFc" # using other map types is much worse
self.sd = self.get_p1_map_unscaled(fmodel = self.fmodel,
map_type=self.map_type).sample_standard_deviation()
xrs_p1 = fmodel.xray_structure.expand_to_p1(sites_mod_positive=True)
self.sgt = fmodel.f_obs().space_group().type()
self.r = flex.double() # for tests only
self.acc_asu = None
# bulk-solvent
mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask(
xray_structure = xrs_p1,
n_real = crystal_gridding.n_real())
self.bulk_solvent_mask = mmtbx_masks_asu_mask_obj.mask_data_whole_uc()
self.bulk_solvent_mask_asu=self.to_asu_map(map_data=self.bulk_solvent_mask)
# atom map
self.atom_map = mmtbx.real_space.sampled_model_density(
xray_structure = xrs_p1,
n_real = crystal_gridding.n_real()).data()
self.n_real = self.atom_map.focus()
self.atom_map_asu=self.to_asu_map(map_data=self.atom_map)
# extras
self.zero_cmpl_ma = fmodel.f_calc().customized_copy(
data = flex.complex_double(fmodel.f_calc().size(), 0))
self.r_factor_omit = flex.double() # for regression test only
# result map
self.map_result_asu = flex.double(flex.grid(self.atom_map_asu.focus()))
# iterate over boxes
self.box_iterator()
def test_complex_to_complex(verbose):
fft = fftpack.complex_to_complex(5)
vc = flex.complex_double(fft.n())
vd = flex.double(fft.n() * 2)
for i in xrange(fft.n()):
vc[i] = complex(2.*i, 2.*i+1.)
vd[2*i] = 2.*i
vd[2*i+1] = 2.*i+1.
vct = fft.forward(vc)
vdt = fft.forward(vd)
for t in (vct, vdt):
assert t.origin() == (0,)
assert t.all()[0] == fft.n()
assert t.focus()[0] == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
vct = fft.backward(vc)
vdt = fft.backward(vd)
for t in (vct, vdt):
assert t.origin() == (0,)
assert t.all()[0] == fft.n()
assert t.focus()[0] == fft.n()
if (verbose): show_cseq(vc)
assert_complex_eq_real(vc, vd)
def structure_factors(self, d_min):
print "WARNING: RESULTS NOT VERIFIED" # XXX
miller_set = miller.build_set(
crystal_symmetry=self,
anomalous_flag=True, # XXX always True?
d_min=d_min)
f_calc = flex.complex_double()
for h in miller_set.indices():
fc = 0j
for scatterer in self.scatterers():
site_symmetry = self.site_symmetry(scatterer.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
sum_exp_j_two_pi_hx = 0j
for i_symop,x in enumerate(equiv_sites.coordinates()):
sum_hx = 0
for i in xrange(3):
sum_hx += h[i] * x[i]
phase = 2 * math.pi * sum_hx
exp_j_two_pi_hx = complex(math.cos(phase), math.sin(phase))
if (scatterer.anisotropic_flag):
r = self.space_group()(i_symop).r()
hr = h
dw = adptbx.debye_waller_factor_u_star(hr, scatterer.u_star)
exp_j_two_pi_hx *= dw
sum_exp_j_two_pi_hx += exp_j_two_pi_hx
b_j = scatterer.scattering_info.bound_coh_scatt_length()
fc_site = scatterer.weight() * b_j * sum_exp_j_two_pi_hx
if (not scatterer.anisotropic_flag):
d_star_sq = self.unit_cell().d_star_sq(h)
dw = adptbx.debye_waller_factor_u_iso(d_star_sq/4, scatterer.u_iso)
fc_site *= dw
fc += fc_site
f_calc.append(fc)
return miller.array(
miller_set=miller_set,
data=f_calc)
def __init__(
self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type = map_type,
isotropize = True,
fill_missing = False)
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data = flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(
fraction = 0.3,
n_real = f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s,e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value = 0,
map_data_to = f_model_map_data,
start = s,
end = e)
f_model_omit = f_model.structure_factors_from_map(
map = f_model_map_data_omit,
use_scale = True,
anomalous_flag = False,
use_sg = False)
fmodel_ = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
f_calc = f_model_omit,
f_mask = zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0]-1, e[1]-1, e[2]-1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(
map_data_from = box,
map_data_to = self.map_result,
start = s,
end = e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result/sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map = self.map_result,
use_scale = True,
anomalous_flag = False,
use_sg = False)
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 __init__(self,instance,algorithm,verbose=False):
"""Initializes a direct parallel worker
:param instance: an instance of class from_scatterers_direct(\
cctbx.xray.structure_factors.manager.managed_calculation_base)
:type instance: cctbx.xray.structure_factors.from_scatterers_direct
:param algorithm: an instance of class direct_summation_cuda_platform(\
direct_summation_simple) with algorithm set to "simple" or "pycuda"
:type algorithm: cctbx.xray.structure_factors.direct_summation_cuda_platform
"""
self.scatterers = instance._xray_structure.scatterers()
self.registry = instance._xray_structure.scattering_type_registry()
self.miller_indices = instance._miller_set.indices()
self.unit_cell = instance._miller_set.unit_cell()
self.space_group = instance._miller_set.space_group().make_tidy()
if verbose: self.print_diagnostics() # some diagnostics used for development
if hasattr(algorithm,"simple"):
instance._results = ext.structure_factors_simple(
self.unit_cell,
instance._miller_set.space_group(),
self.miller_indices,
self.scatterers,
self.registry); return
if hasattr(algorithm,"pycuda"):
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
self.validate_the_inputs(instance,cuda,algorithm)
self.prepare_miller_arrays_for_cuda(algorithm)
self.prepare_scattering_sites_for_cuda(algorithm)
self.prepare_gaussians_symmetries_cell(algorithm)
assert cuda.Device.count() >= 1
device = cuda.Device(0)
WARPSIZE=device.get_attribute(cuda.device_attribute.WARP_SIZE) # 32
MULTIPROCESSOR_COUNT=device.get_attribute(cuda.device_attribute.MULTIPROCESSOR_COUNT)
sort_mod = SourceModule((mod_fhkl_sorted%(self.gaussians.shape[0],
self.symmetry.shape[0],
self.sym_stride,
self.g_stride,
int(self.use_debye_waller),
self.order_z,self.order_p)).replace("floating_point_t",algorithm.float_t)
)
r_m_m_address = sort_mod.get_global("reciprocal_metrical_matrix")[0]
cuda.memcpy_htod(r_m_m_address, self.reciprocal_metrical_matrix)
gaussian_address = sort_mod.get_global("gaussians")[0]
cuda.memcpy_htod(gaussian_address, self.gaussians)
symmetry_address = sort_mod.get_global("symmetry")[0]
cuda.memcpy_htod(symmetry_address, self.symmetry)
CUDA_fhkl = sort_mod.get_function("CUDA_fhkl")
intermediate_real = algorithm.numpy.zeros((self.n_flat_hkl,),algorithm.numpy_t)
intermediate_imag = algorithm.numpy.zeros((self.n_flat_hkl,),algorithm.numpy_t)
for x in xrange(self.scatterers.number_of_types):
fhkl_real = algorithm.numpy.zeros((self.n_flat_hkl,),algorithm.numpy_t)
fhkl_imag = algorithm.numpy.zeros((self.n_flat_hkl,),algorithm.numpy_t)
CUDA_fhkl(cuda.InOut(fhkl_real),
cuda.InOut(fhkl_imag),
cuda.In(self.flat_sites),
cuda.In(self.weights),
cuda.In(self.u_iso),
algorithm.numpy.uint32(self.scatterers.increasing_order[x]),
algorithm.numpy.uint32(self.scatterers.sorted_ranges[x][0]),
algorithm.numpy.uint32(self.scatterers.sorted_ranges[x][1]),
cuda.In(self.flat_mix),
block=(FHKL_BLOCKSIZE,1,1),
grid=((self.n_flat_hkl//FHKL_BLOCKSIZE,1)))
intermediate_real += fhkl_real
intermediate_imag += fhkl_imag
flex_fhkl_real = flex.double(intermediate_real[0:len(self.miller_indices)].astype(algorithm.numpy.float64))
flex_fhkl_imag = flex.double(intermediate_imag[0:len(self.miller_indices)].astype(algorithm.numpy.float64))
instance._results = fcalc_container(flex.complex_double(flex_fhkl_real,flex_fhkl_imag))
return
def build_up(self, objective_only=False):
if self.f_mask is not None:
f_mask = self.f_mask.data()
else:
f_mask = flex.complex_double()
extinction_correction = self.reparametrisation.extinction
if extinction_correction is None:
extinction_correction = xray.dummy_extinction_correction()
def args(scale_factor, weighting_scheme, objective_only):
args = (self,
self.observations,
f_mask,
weighting_scheme,
scale_factor,
self.one_h_linearisation,
self.reparametrisation.jacobian_transpose_matching_grad_fc(),
extinction_correction
)
if objective_only:
args += (True,)
return args
if not self.finalised: #i.e. never been called
self.reparametrisation.linearise()
self.reparametrisation.store()
scale_factor = self.initial_scale_factor
if scale_factor is None: # we haven't got one from previous refinement
result = ext.build_normal_equations(
*args(scale_factor=None, weighting_scheme=sigma_weighting(),
objective_only=True))
scale_factor = self.scale_factor()
else: # use scale factor from the previous step
scale_factor = self.scale_factor()
self.reset()
result = ext.build_normal_equations(*args(scale_factor,
self.weighting_scheme,
objective_only))
self.f_calc = self.observations.fo_sq.array(
data=result.f_calc(), sigmas=None)
self.fc_sq = self.observations.fo_sq.array(
data=result.observables(), sigmas=None)\
.set_observation_type_xray_intensity()
self.weights = result.weights()
self.objective_data_only = self.objective()
self.chi_sq_data_only = self.chi_sq()
if self.restraints_manager is not None:
# Here we determine a normalisation factor to place the restraints on the
# same scale as the average residual. This is the normalisation
# factor suggested in Giacovazzo and similar to that used by shelxl.
# (shelx manual, page 5-1).
# The factor 2 comes from the fact that we minimize 1/2 sum w delta^2
if self.restraints_normalisation_factor is None:
self.restraints_normalisation_factor \
= 2 * self.objective_data_only/(self.n_equations-self.n_parameters)
linearised_eqns = self.restraints_manager.build_linearised_eqns(
self.xray_structure, self.reparametrisation.parameter_map())
jacobian = \
self.reparametrisation.jacobian_transpose_matching(
self.reparametrisation.mapping_to_grad_fc_all).transpose()
self.reduced_problem().add_equations(
linearised_eqns.deltas,
linearised_eqns.design_matrix * jacobian,
linearised_eqns.weights * self.restraints_normalisation_factor)
self.n_restraints = linearised_eqns.n_restraints()
self.chi_sq_data_and_restraints = self.chi_sq()
if not objective_only:
self.origin_fixing_restraint.add_to(
self.step_equations(),
self.reparametrisation.jacobian_transpose_matching_grad_fc(),
self.reparametrisation.asu_scatterer_parameters)
def tst_2d_zernike_mom(n,l, N=100, filename=None):
nmax = max(20,n)
rebuilt=open('rebuilt.dat','w')
tt1=time.time()
if(filename is not None):
image=read_data(filename)
else:
image=generate_image(n,l)
NP=int(smath.sqrt( image.size() ))
N=NP/2
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space( image )
grid_2d.construct_space_sum()
tt2=time.time()
print "time used: ", tt2-tt1
zernike_2d_mom = math.two_d_zernike_moments( grid_2d, nmax )
moments = zernike_2d_mom.moments()
tt2=time.time()
print "time used: ", tt2-tt1
coefs = flex.real( moments )
nl_array = math.nl_array( nmax )
nls = nl_array.nl()
nl_array.load_coefs( nls, coefs )
lfg = math.log_factorial_generator(nmax)
print nl_array.get_coef(n,l)*2
for nl, c in zip( nls, moments):
if(abs(c)<1e-3):
c=0
print nl, c
print
reconst=flex.complex_double(NP**2, 0)
for nl,c in zip( nls, moments):
n=nl[0]
l=nl[1]
if(l>0):
c=c*2
#rzfa = math.zernike_2d_radial(n,l,lfg)
rap = math.zernike_2d_polynome(n,l) #,rzfa)
i=0
for x in range(0,NP):
x=x-N
for y in range(0,NP):
y=y-N
rr = smath.sqrt(x*x+y*y)/N
if rr>1.0:
value=0.0
else:
tt = smath.atan2(y,x)
value = rap.f(rr,tt)
reconst[i]=reconst[i]+value*c
i=i+1
i = 0
for x in range(0,NP):
for y in range(0,NP):
value=reconst[i].real
if(value>0):
print>>rebuilt, x,y,image[i][2],value
i=i+1
rebuilt.close()
def fs(self):
result = flex.complex_double()
for hkl in self.miller_indices:
result.append(structure_factor(
xray_structure=self.xray_structure, hkl=hkl).f())
return result
def d2f_d_params(self):
tphkl = 2 * math.pi * matrix.col(self.hkl)
tphkl_outer = tphkl.outer_product()
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])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.outer_product()
for scatterer in self.scatterers:
assert scatterer.scattering_type == "const"
w = scatterer.occupancy
if (not scatterer.flags.use_u_aniso()):
huh = scatterer.u_iso * self.d_star_sq
dw = math.exp(mtps * huh)
ffp = 1 + scatterer.fp
fdp = scatterer.fdp
ff = (ffp + 1j * fdp)
d2_site_site = flex.complex_double(flex.grid(3,3), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3,1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3,6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3,1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(flex.grid(6,6), 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6,1), 0j)
d2_occ_fp = 0j
d2_occ_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()
d2_site_site += flex.complex_double(
site_gtmx *
(w * dw * ff * e * (-1) * tphkl_outer)
* site_gtmx.transpose())
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += flex.complex_double(site_gtmx * (
w * dw * ff * e * 1j * mtps * self.d_star_sq * tphkl))
else:
u_star_gtmx = matrix.sqr(tensor_rank_2_gradient_transform_matrix(r))
d2_site_u_star += flex.complex_double(
site_gtmx
* ((w * dw * ff * e * 1j * tphkl).outer_product(
mtps * d_exp_huh_d_u_star))
* u_star_gtmx.transpose())
d2_site_occ += flex.complex_double(site_gtmx * (
dw * ff * e * 1j * tphkl))
d2_site_fp += flex.complex_double(site_gtmx * (
w * dw * e * 1j * tphkl))
d2_site_fdp += flex.complex_double(site_gtmx * (
w * dw * e * (-1) * tphkl))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
d2_u_iso_occ += dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star += flex.complex_double(
u_star_gtmx
* (w * dw * ff * e * mtps**2 * d2_exp_huh_d_u_star_u_star)
* u_star_gtmx.transpose())
d2_u_star_occ += flex.complex_double(u_star_gtmx * (
dw * ff * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fp += flex.complex_double(u_star_gtmx * (
w * dw * e * mtps * d_exp_huh_d_u_star))
d2_u_star_fdp += flex.complex_double(u_star_gtmx * (
w * dw * 1j * e * mtps * d_exp_huh_d_u_star))
d2_occ_fp += dw * e
d2_occ_fdp += dw * e * 1j
if (not scatterer.flags.use_u_aniso()):
i_occ, i_fp, i_fdp, np = 4, 5, 6, 7
else:
i_occ, i_fp, i_fdp, np = 9, 10, 11, 12
dp = flex.complex_double(flex.grid(np,np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site, 0,0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0,3)
paste(d2_site_u_iso.matrix_transpose(), 3,0)
else:
paste(d2_site_u_star, 0,3)
paste(d2_site_u_star.matrix_transpose(), 3,0)
paste(d2_site_occ, 0,i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ,0)
paste(d2_site_fp, 0,i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp,0)
paste(d2_site_fdp, 0,i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp,0)
if (not scatterer.flags.use_u_aniso()):
dp[3*7+3] = d2_u_iso_u_iso
dp[3*7+4] = d2_u_iso_occ
dp[4*7+3] = d2_u_iso_occ
dp[3*7+5] = d2_u_iso_fp
dp[5*7+3] = d2_u_iso_fp
dp[3*7+6] = d2_u_iso_fdp
dp[6*7+3] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star, 3,3)
paste(d2_u_star_occ, 3, 9)
paste(d2_u_star_occ.matrix_transpose(), 9, 3)
paste(d2_u_star_fp, 3, 10)
paste(d2_u_star_fp.matrix_transpose(), 10, 3)
paste(d2_u_star_fdp, 3, 11)
paste(d2_u_star_fdp.matrix_transpose(), 11, 3)
dp[i_occ*np+i_fp] = d2_occ_fp
dp[i_fp*np+i_occ] = d2_occ_fp
dp[i_occ*np+i_fdp] = d2_occ_fdp
dp[i_fdp*np+i_occ] = d2_occ_fdp
yield dp
def __init__(
self,
crystal_gridding,
fmodel,
map_type,
box_size_as_fraction=0.03,
max_boxes=100,
n_debias_cycles=2,
neutral_volume_box_cushion_width=1,
full_resolution_map=True,
log=sys.stdout):
self.crystal_gridding = crystal_gridding
# assert compatibility of symops with griding
assert self.crystal_gridding._symmetry_flags is not None
self.sgt = fmodel.f_obs().space_group().type()
self.zero_cmpl_ma = fmodel.f_calc().customized_copy(
data = flex.complex_double(fmodel.f_calc().size(), 0))
# embedded utility functions
def get_map(fmodel, map_type, crystal_gridding, asu=True):
f_map = fmodel.electron_density_map().map_coefficients(
map_type = map_type,
isotropize = True,
exclude_free_r_reflections = True,
fill_missing = False)
fft_map = cctbx.miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_map)
if(asu): return asu_map_ext.asymmetric_map(self.sgt,
fft_map.real_map_unpadded()).data()
else:
return fft_map.real_map_unpadded()
# f_model map
f_model_map_data = fmodel.f_model_scaled_with_k1().fft_map(
symmetry_flags = maptbx.use_space_group_symmetry,
crystal_gridding = self.crystal_gridding).real_map_unpadded()
self.n_real = f_model_map_data.focus()
# extract asu map from full P1
f_model_map_data_asu=asu_map_ext.asymmetric_map(
self.sgt, f_model_map_data).data()
self.acc = f_model_map_data_asu.accessor()
f_model_map_data_asu = f_model_map_data_asu.shift_origin()
# set up boxes
b = maptbx.boxes(
n_real = f_model_map_data_asu.focus(),
fraction = box_size_as_fraction,
max_boxes= max_boxes,
log = log)
self.map_result_asu = flex.double(flex.grid(b.n_real))
assert f_model_map_data_asu.focus()==b.n_real
assert b.n_real==self.map_result_asu.focus()
n_real_asu = b.n_real
self.r = flex.double() # for regression test only
n_boxes = len(b.starts)
i_box = 0
for s,e in zip(b.starts, b.ends):
i_box+=1
# define wide box: neutral + phased volumes
if(neutral_volume_box_cushion_width>0):
sh = neutral_volume_box_cushion_width
ss = [max(s[i]-sh,0) for i in [0,1,2]]
ee = [min(e[i]+sh,n_real_asu[i]) for i in [0,1,2]]
else: ss,ee = s,e
# omit wide box from f_model map, repeat n_debias_cycles times
f_model_map_data_asu_ = f_model_map_data_asu.deep_copy()
for i in xrange(n_debias_cycles):
f_model_omit, f_model_map_data_asu_ = self.omit_box(s=ss, e=ee,
md_asu=f_model_map_data_asu_)
# get fmodel for omit map calculation
fmodel_ = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
f_calc = f_model_omit,
f_mask = self.zero_cmpl_ma)
rw = fmodel_.r_work()
self.r.append(rw) # for regression test only
f_map_data_asu = get_map(fmodel=fmodel_, map_type=map_type,
crystal_gridding=self.crystal_gridding)
f_map_data_asu = f_map_data_asu.shift_origin()
if(log):
print >> log, "box %2d of %2d:"%(i_box, n_boxes), s, e, "%6.4f"%rw
assert f_map_data_asu.focus() == self.map_result_asu.focus()
maptbx.copy_box(
map_data_from = f_map_data_asu,
map_data_to = self.map_result_asu,
start = s,
end = e)
# result
self.map_result_asu.reshape(self.acc)
self.asu_map_omit = asu_map_ext.asymmetric_map(
self.sgt, self.map_result_asu, self.n_real)
self.map_coefficients = self.zero_cmpl_ma.customized_copy(
indices = self.zero_cmpl_ma.indices(),
data = self.asu_map_omit.structure_factors(self.zero_cmpl_ma.indices()))
# full resolution map (reflections in sphere, not in box!)
if(full_resolution_map):
cs = self.zero_cmpl_ma.complete_set(d_min=self.zero_cmpl_ma.d_min())
asu_map_omit = asu_map_ext.asymmetric_map(
self.sgt,self.map_result_asu,self.n_real)
fill = self.zero_cmpl_ma.customized_copy(
indices = cs.indices(),
data = asu_map_omit.structure_factors(cs.indices()))
self.map_coefficients = self.map_coefficients.complete_with(
other=fill, scale=True)
def lewis(template, img):
"""The lewis() function computes the normalised cross-correlation
(NCC) of an image, @p img, and a template, @p template. Both image
and template must be two-dimensional, real, and finite. The image
must be larger than the template, which in turn should contain more
than one pixel, and the template must have positive variance. The
function returns the correlation coefficients in the range [-1, +1].
See Lewis, J. P. (1995) "Fast Template Matching", Vision Interface,
120-123.
@note This function should be equivalent to MATLAB's normxcorr2()
function.
@param img Two-dimensional intensity image
@param template Two-dimensional intensity template
@return Correlation coefficients
"""
import math
import numpy
from sys import float_info
from scitbx import fftpack
from scitbx.array_family import flex
# Assert that image and template are two-dimensional arrays, and
# that the template is no larger than image. Assert that template
# is not flat. XXX Check for real and finite, too?
assert len(img.focus()) == 2 and len(template.focus()) == 2
assert img.focus()[0] >= template.focus()[0] and img.focus()[1] >= template.focus()[1]
assert template.sample_standard_deviation() > 0
# For conformance with MATLAB's normxcorr2() and geck 342320: for
# numerical robustness, ensure that both image and template are
# always non-negative.
img_nn = img - min(0, flex.min(img))
template_nn = template - min(0, flex.min(template))
# Calculate the terms of the denominator of gamma. Must guard
# against negative variance of the image due to inaccuracies in the
# one-pass formula.
img_sum = _summed_area_table(img_nn, template_nn.focus()[0], template_nn.focus()[1])
img_ssq = _summed_area_table(flex.pow2(img_nn), template_nn.focus()[0], template_nn.focus()[1])
f_sigma = img_ssq - img_sum * img_sum / (template_nn.focus()[0] * template_nn.focus()[1])
f_sigma.set_selected(f_sigma < 0, 0)
f_sigma = flex.sqrt(f_sigma)
t_sigma = (template_nn - flex.mean(template_nn)).norm()
gamma_denominator = f_sigma * t_sigma
# Zero-pad the image to permit partial overlap of template and
# image, and embed the time-reversed template in a zero-padded array
# of the same size. Zero-padding means the entire template is
# always overlapping the image, and terms involving the template
# mean cancel in the expansion of the numerator of gamma.
#
# Note: the NCC demands the template to be time-reversed, which can
# be accomplished by conjugation in the frequency domain. An
# implementation following that approach would however require
# special care to be taken for the first rows and columns:
#
# from numpy import roll
# t_embed.matrix_paste_block_in_place(
# block=template_nn,
# i_row=full[0] - template_nn.focus()[0],
# i_column=full[1] - template_nn.focus()[1])
# t_embed = flex.double(roll(
# roll(t_embed.as_numpy_array(), 1, axis=0), 1, axis=1))
#
# Calculate correlation in frequency domain. XXX Could use spatial
# domain calculation in cases where it's faster (see MATLAB's
# implementation).
full = (img_nn.focus()[0] + template_nn.focus()[0] - 1, img_nn.focus()[1] + template_nn.focus()[1] - 1)
f_embed = flex.double(flex.grid(full))
f_embed.matrix_paste_block_in_place(block=img_nn, i_row=0, i_column=0)
f_prime = flex.complex_double(reals=f_embed, imags=flex.double(flex.grid(full)))
t_embed = flex.double(flex.grid(full))
t_embed.matrix_paste_block_in_place(block=template_nn.matrix_rot90(2), i_row=0, i_column=0)
t_prime = flex.complex_double(reals=t_embed, imags=flex.double(flex.grid(full)))
fft = fftpack.complex_to_complex_2d(full)
fft.forward(f_prime)
fft.forward(t_prime)
gamma_numerator = f_prime * t_prime
fft.backward(gamma_numerator)
gamma_numerator = flex.real(gamma_numerator) / (fft.n()[0] * fft.n()[1]) - img_sum * flex.mean(template_nn)
# For conformance with MATLAB: set the NCC to zero in regions where
# the image has zero variance over the extent of the template. If,
# due to small variances in the image or the template, a correlation
# coefficient falls outside the range [-1, 1], set it to zero to
# reflect the undefined 0/0 condition.
tol = math.sqrt(math.ldexp(float_info.epsilon, math.frexp(flex.max(flex.abs(gamma_denominator)))[1] - 1))
sel = gamma_denominator <= tol
gamma = gamma_numerator.set_selected(sel, 0) / gamma_denominator.set_selected(sel, 1)
gamma.set_selected(flex.abs(gamma) > 1 + math.sqrt(float_info.epsilon), 0)
return gamma
output_labels = F-obs(+) SIGF-obs(+) F-obs(-) SIGF-obs(-)
}
miller_array {
file_name = tst_data9.mtz
labels = R-free-flags
output_labels = R-free-flags
}
}""")
params = master_phil.fetch(source=new_phil).extract()
miller_arrays = run_and_reload(params, "tst9.mtz")
assert approx_equal(miller_arrays[0].info().wavelength, 1.54)
# map coefficients
n_refl = len(array2.indices())
d1 = flex.random_double(n_refl)
d2 = flex.random_double(n_refl)
coeffs_data = flex.complex_double(d1, d2)
map_coeffs = array2.customized_copy(data=coeffs_data,
sigmas=None).average_bijvoet_mates()
map_coeffs.as_mtz_dataset(column_root_label="2FOFCWT").mtz_object().write(
"tst_data10.mtz")
new_phil = libtbx.phil.parse("""
mtz_file {
output_file = tst10.mtz
crystal_symmetry.space_group = P212121
crystal_symmetry.unit_cell = 6,7,8,90,90,90
miller_array {
file_name = tst_data10.mtz
labels = 2FOFCWT,PHI2FOFCWT
output_labels = 2FOFCWT PHI2FOFCWT
}
}""")
def d2f_d_params_diag(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h,k,l = self.hkl
d_exp_huh_d_u_star = flex.double([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
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()
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)
d2_site_site = flex.complex_double(3*(3+1)//2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
else:
d2_u_star_u_star = flex.complex_double(6*(6+1)//2, 0j)
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
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 = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3,3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
np = i_occ+3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
#
dpd = flex.complex_double(flex.grid(np,1), 0j)
def paste(d, i):
d.reshape(flex.grid(d.size(),1))
dpd.matrix_paste_block_in_place(d, i,0)
paste(d2_site_site.matrix_packed_u_diagonal(), 0)
if (not scatterer.flags.use_u_aniso()):
dpd[i_u] = d2_u_iso_u_iso
else:
paste(d2_u_star_u_star.matrix_packed_u_diagonal(), i_u)
yield dpd
def exercise(mt, n_refl, log):
f_obs = mt.random_double(size=n_refl)
f_calc = flex.complex_double(mt.random_double(size=f_obs.size()), mt.random_double(size=f_obs.size()))
f_calc_abs = flex.abs(f_calc)
trg = r1.target(f_obs=f_obs, f_calc=f_calc)
def check_f_calc_abs_derivs():
eps = 1e-6
g_fin = flex.double()
c_fin = flex.double()
for ih in xrange(f_calc_abs.size()):
fs = []
gs = []
c_orig = f_calc_abs[ih]
for signed_eps in [eps, -eps]:
f_calc_abs[ih] = c_orig + signed_eps
trg_eps = r1.target(f_obs=f_obs, f_calc_abs=f_calc_abs)
fs.append(trg_eps.t)
gs.append(trg_eps.g[ih])
g_fin.append((fs[0] - fs[1]) / (2 * eps))
c_fin.append((gs[0] - gs[1]) / (2 * eps))
f_calc_abs[ih] = c_orig
print >> log, "g fin:", numstr(g_fin)
print >> log, " ana:", numstr(trg.g)
assert approx_equal(trg.g, g_fin)
print >> log, "c fin:", numstr(c_fin)
print >> log, " ana:", numstr(trg.c)
assert approx_equal(trg.c, c_fin)
def check_f_calc_derivs():
eps = 1e-6
g_fin = flex.complex_double()
c_fin = flex.vec3_double()
for ih in xrange(f_calc.size()):
c_orig = f_calc[ih]
g_fin_ab = []
c_fin_ab = []
for iab in [0, 1]:
fs = []
gs = []
for signed_eps in [eps, -eps]:
if iab == 0:
f_calc[ih] = complex(c_orig.real + signed_eps, c_orig.imag)
else:
f_calc[ih] = complex(c_orig.real, c_orig.imag + signed_eps)
trg_eps = r1.target(f_obs=f_obs, f_calc=f_calc)
fs.append(trg_eps.t)
gs.append(trg_eps.f_calc_gradients[ih])
g_fin_ab.append((fs[0] - fs[1]) / (2 * eps))
c_fin_ab.append((gs[0] - gs[1]) / (2 * eps))
g_fin.append(complex(*g_fin_ab))
assert approx_equal(c_fin_ab[0].imag, c_fin_ab[1].real)
c_fin.append((c_fin_ab[0].real, c_fin_ab[1].imag, c_fin_ab[0].imag))
f_calc[ih] = c_orig
for pn, f, a in zip(g_fin.part_names(), g_fin.parts(), trg.f_calc_gradients.parts()):
print >> log, "g fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_gradients, g_fin)
for pn, f, a in zip(["aa", "bb", "ab"], c_fin.parts(), trg.f_calc_hessians.parts()):
print >> log, "c fin %s:" % pn, numstr(f)
print >> log, " ana %s:" % pn, numstr(a)
assert approx_equal(trg.f_calc_hessians, c_fin)
check_f_calc_abs_derivs()
check_f_calc_derivs()
#
f_calc[0] = 0j
f_calc_abs = flex.abs(f_calc)
trg = r1.target(f_obs=f_obs, f_calc=f_calc)
assert trg.gradients_work()[0] == 0j
assert trg.hessians_work()[0] == (0, 0, 0)
def __init__(self,
f_calc,
f_masks=None,
f_part1=None,
f_part2=None,
k_masks=None,
k_isotropic_exp=None,
k_isotropic=None,
k_anisotropic=None):
adopt_init_args(self, locals())
if(self.f_masks is None):
self.f_masks = [self.f_calc.customized_copy(
data=flex.complex_double(f_calc.data().size(), 0))]
else:
if(not (type(self.f_masks) in [list, tuple])):
self.f_masks = [self.f_masks]
for fm in self.f_masks:
assert self.f_calc.indices().all_eq(fm.indices())
if(self.k_isotropic_exp is not None):
assert self.k_isotropic_exp.size() == self.f_calc.indices().size()
else: self.k_isotropic_exp = flex.double(f_calc.data().size(), 1)
if(self.k_isotropic is not None):
assert self.k_isotropic.size() == self.f_calc.indices().size()
else: self.k_isotropic = flex.double(f_calc.data().size(), 1)
if(self.k_anisotropic is not None):
assert self.k_anisotropic.size() == self.f_calc.indices().size()
else: self.k_anisotropic = flex.double(f_calc.data().size(), 1)
if(self.k_masks is None):
n=len(self.f_masks)
self.k_masks = [flex.double(f_calc.data().size(), 0)]*n
else:
if(not (type(self.k_masks) in [list, tuple])):
self.k_masks = [self.k_masks]
if(self.f_part1 is not None):
assert self.f_calc.indices().all_eq(self.f_part1.indices())
else:
self.f_part1 = self.f_calc.customized_copy(
data=flex.complex_double(f_calc.data().size(), 0))
if(self.f_part2 is not None):
assert self.f_calc.indices().all_eq(self.f_part2.indices())
else:
self.f_part2 = self.f_calc.customized_copy(
data=flex.complex_double(f_calc.data().size(), 0))
# assemble f_bulk
f_bulk_data = flex.complex_double(f_calc.data().size(), 0)
assert len(self.k_masks) == len(self.f_masks)
for i in xrange(len(self.k_masks)):
f_bulk_data += self.k_masks[i]*self.f_masks[i].data()
#
self.data = ext.data(
f_calc = self.f_calc.data(),
f_bulk = f_bulk_data,
k_isotropic_exp = self.k_isotropic_exp,
k_isotropic = self.k_isotropic,
k_anisotropic = self.k_anisotropic,
f_part1 = self.f_part1.data(),
f_part2 = self.f_part2.data())
self.f_model = miller.array(miller_set=self.f_calc, data=self.data.f_model)
self.f_model_no_aniso_scale = miller.array(
miller_set=self.f_calc,
data =self.data.f_model_no_aniso_scale)
def d2f_d_params(self):
tphkl = 2 * math.pi * flex.double(self.hkl)
tphkl_outer = tphkl.matrix_outer_product(tphkl) \
.matrix_symmetric_as_packed_u()
h,k,l = self.hkl
d_exp_huh_d_u_star = flex.double([h**2, k**2, l**2, 2*h*k, 2*h*l, 2*k*l])
d2_exp_huh_d_u_star_u_star = d_exp_huh_d_u_star.matrix_outer_product(
d_exp_huh_d_u_star).matrix_symmetric_as_packed_u()
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)
d2_site_site = flex.complex_double(3*(3+1)//2, 0j)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = flex.complex_double(flex.grid(3,1), 0j)
d2_site_u_star = None
else:
d2_site_u_iso = None
d2_site_u_star = flex.complex_double(flex.grid(3,6), 0j)
d2_site_occ = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fp = flex.complex_double(flex.grid(3,1), 0j)
d2_site_fdp = flex.complex_double(flex.grid(3,1), 0j)
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso = 0j
d2_u_iso_occ = 0j
d2_u_iso_fp = 0j
d2_u_iso_fdp = 0j
else:
d2_u_star_u_star = flex.complex_double(6*(6+1)//2, 0j)
d2_u_star_occ = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fp = flex.complex_double(flex.grid(6,1), 0j)
d2_u_star_fdp = flex.complex_double(flex.grid(6,1), 0j)
d2_occ_fp = 0j
d2_occ_fdp = 0j
for s in self.space_group:
r = s.r().as_rational().as_float()
s_site = s * scatterer.site
alpha = tphkl.dot(flex.double(s_site))
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 = flex.double(r.transpose())
site_gtmx.reshape(flex.grid(3,3))
d2_site_site += (w * dw * ff * e * (-1)) * (
site_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
tphkl_outer))
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso += (w * dw * ff * e * 1j * mtps * self.d_star_sq) \
* site_gtmx.matrix_multiply(tphkl)
else:
u_star_gtmx = tensor_rank_2_gradient_transform_matrix(r)
d2_site_u_star += (w * dw * ff * e * 1j * mtps) \
* site_gtmx.matrix_multiply(
tphkl.matrix_outer_product(d_exp_huh_d_u_star)) \
.matrix_multiply(u_star_gtmx.matrix_transpose())
site_gtmx_tphkl = site_gtmx.matrix_multiply(tphkl)
d2_site_occ += (wwo * dw * ff * e * 1j) * site_gtmx_tphkl
d2_site_fp += (w * dw * e * 1j) * site_gtmx_tphkl
d2_site_fdp += (w * dw * e * (-1)) * site_gtmx_tphkl
if (not scatterer.flags.use_u_aniso()):
d2_u_iso_u_iso += w * dw * ff * e * (mtps * self.d_star_sq)**2
d2_u_iso_occ += wwo * dw * ff * e * mtps * self.d_star_sq
d2_u_iso_fp += w * dw * e * mtps * self.d_star_sq
d2_u_iso_fdp += 1j * w * dw * e * mtps * self.d_star_sq
else:
d2_u_star_u_star +=(w * dw * ff * e * mtps**2) \
* u_star_gtmx.matrix_multiply_packed_u_multiply_lhs_transpose(
d2_exp_huh_d_u_star_u_star)
u_star_gtmx_d_exp_huh_d_u_star = u_star_gtmx.matrix_multiply(
d_exp_huh_d_u_star)
d2_u_star_occ += (wwo * dw * ff * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fp += (w * dw * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_u_star_fdp += (w * dw * 1j * e * mtps) \
* u_star_gtmx_d_exp_huh_d_u_star
d2_occ_fp += wwo * dw * e
d2_occ_fdp += wwo * dw * e * 1j
if (site_symmetry_ops is None):
i_u = 3
else:
i_u = site_constraints.n_independent_params()
if (not scatterer.flags.use_u_aniso()):
i_occ = i_u + 1
elif (site_symmetry_ops is None):
i_occ = i_u + 6
else:
i_occ = i_u + adp_constraints.n_independent_params()
i_fp, i_fdp, np = i_occ+1, i_occ+2, i_occ+3
if (site_symmetry_ops is not None):
gsm = site_constraints.gradient_sum_matrix()
d2_site_site = gsm.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_site_site)
if (not scatterer.flags.use_u_aniso()):
d2_site_u_iso = gsm.matrix_multiply(d2_site_u_iso)
else:
d2_site_u_star = gsm.matrix_multiply(d2_site_u_star)
d2_site_occ = gsm.matrix_multiply(d2_site_occ)
d2_site_fp = gsm.matrix_multiply(d2_site_fp)
d2_site_fdp = gsm.matrix_multiply(d2_site_fdp)
if (scatterer.flags.use_u_aniso()):
gsm = adp_constraints.gradient_sum_matrix()
d2_site_u_star = d2_site_u_star.matrix_multiply(
gsm.matrix_transpose())
d2_u_star_u_star = gsm \
.matrix_multiply_packed_u_multiply_lhs_transpose(
packed_u=d2_u_star_u_star)
d2_u_star_occ = gsm.matrix_multiply(d2_u_star_occ)
d2_u_star_fp = gsm.matrix_multiply(d2_u_star_fp)
d2_u_star_fdp = gsm.matrix_multiply(d2_u_star_fdp)
dp = flex.complex_double(flex.grid(np,np), 0j)
paste = dp.matrix_paste_block_in_place
paste(d2_site_site.matrix_packed_u_as_symmetric(), 0,0)
if (not scatterer.flags.use_u_aniso()):
paste(d2_site_u_iso, 0,i_u)
paste(d2_site_u_iso.matrix_transpose(), i_u,0)
else:
paste(d2_site_u_star, 0,i_u)
paste(d2_site_u_star.matrix_transpose(), i_u,0)
paste(d2_site_occ, 0,i_occ)
paste(d2_site_occ.matrix_transpose(), i_occ,0)
paste(d2_site_fp, 0,i_fp)
paste(d2_site_fp.matrix_transpose(), i_fp,0)
paste(d2_site_fdp, 0,i_fdp)
paste(d2_site_fdp.matrix_transpose(), i_fdp,0)
if (not scatterer.flags.use_u_aniso()):
dp[i_u*np+i_u] = d2_u_iso_u_iso
dp[i_u*np+i_occ] = d2_u_iso_occ
dp[i_occ*np+i_u] = d2_u_iso_occ
dp[i_u*np+i_fp] = d2_u_iso_fp
dp[i_fp*np+i_u] = d2_u_iso_fp
dp[i_u*np+i_fdp] = d2_u_iso_fdp
dp[i_fdp*np+i_u] = d2_u_iso_fdp
else:
paste(d2_u_star_u_star.matrix_packed_u_as_symmetric(), i_u, i_u)
paste(d2_u_star_occ, i_u, i_occ)
paste(d2_u_star_occ.matrix_transpose(), i_occ, i_u)
paste(d2_u_star_fp, i_u, i_fp)
paste(d2_u_star_fp.matrix_transpose(), i_fp, i_u)
paste(d2_u_star_fdp, i_u, i_fdp)
paste(d2_u_star_fdp.matrix_transpose(), i_fdp, i_u)
dp[i_occ*np+i_fp] = d2_occ_fp
dp[i_fp*np+i_occ] = d2_occ_fp
dp[i_occ*np+i_fdp] = d2_occ_fdp
dp[i_fdp*np+i_occ] = d2_occ_fdp
yield dp
def anisotropic_scaling(self, r_start):
r_expanal, r_poly, r_expmin = None,None,None
k_anisotropic_expanal, k_anisotropic_poly, \
k_anisotropic_expmin = None, None, None
scale_matrix_expanal, scale_matrix_poly, scale_matrix_expmin= None,None,None
sel = self.selection_work.data()
f_model_abs = flex.abs(self.core.f_model_no_aniso_scale.data().select(sel))
f_obs = self.f_obs.data().select(sel)
mi = self.f_obs.indices().select(sel)
uc = self.f_obs.unit_cell()
mi_all = self.f_obs.indices()
# try exp_anal
if(self.try_expanal):
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = f_model_abs,
f_obs = f_obs,
miller_indices = mi,
adp_constraint_matrix = self.adp_constraints.gradient_sum_matrix())
u_star = self.adp_constraints.all_params(tuple(obj.u_star_independent))
scale_matrix_expanal = adptbx.u_as_b(adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expanal = ext.k_anisotropic(mi_all, u_star)
r_expanal = self.try_scale(k_anisotropic = k_anisotropic_expanal)
if(self.verbose):
print >> self.log, " r_expanal: %6.4f"%r_expanal
# try poly
if(self.try_poly):
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = f_model_abs,
f_obs = f_obs,
miller_indices = mi,
unit_cell = uc)
scale_matrix_poly = obj.a
k_anisotropic_poly = ext.k_anisotropic(mi_all, obj.a, uc)
r_poly = self.try_scale(k_anisotropic = k_anisotropic_poly)
if(self.verbose):
print >> self.log, " r_poly : %6.4f"%r_poly
# pre-analyze
force_to_use_expmin=False
if(k_anisotropic_poly is not None and self.auto and r_poly<r_expanal and
(k_anisotropic_poly<=0).count(True)>0):
force_to_use_expmin = True
self.try_expmin = True
# try expmin
if(self.try_expmin):
zero = self.f_obs.select(sel).customized_copy(data =
flex.complex_double(f_obs.size(), 0))
fm = mmtbx.f_model.manager_kbu(
f_obs = self.f_obs.select(sel),
f_calc = self.core.f_model_no_aniso_scale.select(sel),
f_masks = [zero],
f_part1 = zero,
f_part2 = zero,
ss = self.ss)
obj = kbu_refinery.tgc(
f_obs = self.f_obs.select(sel),
f_calc = self.core.f_model_no_aniso_scale.select(sel),
f_masks = [zero],
ss = self.ss,
k_sols = [0,],
b_sols = [0,],
u_star = [0,0,0,0,0,0])
obj.minimize_u()
u_star = obj.kbu.u_star()
scale_matrix_expmin = adptbx.u_as_b(adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expmin = ext.k_anisotropic(mi_all, u_star)
r_expmin = self.try_scale(k_anisotropic = k_anisotropic_expmin)
if(self.verbose): print >> self.log, " r_expmin : %6.4f"%r_expmin
if(force_to_use_expmin):
self.core = self.core.update(k_anisotropic = k_anisotropic_expmin)
if(self.verbose):
self.format_scale_matrix(m=scale_matrix_expmin)
return
# select best
r = [(r_expanal, k_anisotropic_expanal, scale_matrix_expanal),
(r_poly, k_anisotropic_poly, scale_matrix_poly),
(r_expmin, k_anisotropic_expmin, scale_matrix_expmin)]
r_best = r_start
k_anisotropic_best = None
scale_matrix_best = None
for result in r:
r_factor, k_anisotropic, scale_matrix = result
if(r_factor is not None and r_factor < r_best):
r_best = r_factor
k_anisotropic_best = k_anisotropic.deep_copy()
scale_matrix_best = scale_matrix[:]
if(scale_matrix_best is None):
if(self.verbose):
print >> self.log, " result rejected due to r-factor increase"
else:
self.scale_matrices = scale_matrix_best
self.core = self.core.update(k_anisotropic = k_anisotropic_best)
r_aniso = self.r_factor()
if(self.verbose):
self.format_scale_matrix()
print >> self.log, " r_final : %6.4f"%r_aniso
